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Chem & Bio Draw 12.0 for Windows and Macintosh

1. e En 6 ChemDrow Uira WwinMa 8 e amp Fri Win Wan ChemDraw Sid n Mac LI L L ChenDeaw E E i E ChemBic3D Uro Wa ChemBiesD ActiveX Pro We E Li L ChimBiisl Pus Wee Chief Skl Win L 0 Chemffinder Pro LEE Chenfinder Std We Li tiros 19 BioAssay Pro We a L Ive l dE OE d d del E ded Yhynnkey Free We a ma LNokback BE CNetcbook Pro We LI L Li E ChemDraw Excel We a E Cli NAAR amp Chop Winn a P Hollis tink Winn a Strudure Clean Up a a jajajaja 8 Stokhiomery Grid a s Mose Tool Win Mac s a E Polymer Draw Win Mac m 2 E Sepan lind Wins L Clase sipil Wie LI GAMESS We LI Gaussan Infertacc We a E Jaguor Interface We a a Interface We Ei s a 8 1 Win Mac m E ChemINDEX Ultra We a a E Chesf XN NCI amp AIDS We a 4xadcble Sepcrately zpacihicatare subject to change without notice US 1 800 315 7300 INT L 1617 588 9300 FAX 1617 588 9390 EMAIL info cambridgesoft com EU
2. 7 4a Gcr E Wi vum a PowerPoint Integration EMAIL info cambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com MANAGEMENT Biology DMPK Screening Biology Microscopy Discovery Biology These scientists are involved at the very start of the drug discovery process as genomics and genetics are essential disciplines used when identifying a disease target This work is methodical but unscripted and so requires an electronic note book pallet that is as free form as its paper predecessor This is where the benefit of E Notebook s flexibility is unmistakable While the system can be set up with rigid form based data entry appropriate for later stage research and development discovery biology configurations are typically open and boundless Genomic map and DNA RNA and protein sequence files can be dragged and dropped into E Notebook sequencing results can be sent directly from instruments to electronic experiments and protocols and data can be managed with familiar tools such as Microsoft Word and Excel The beauty of capturing data in E Votebook is that information can be compiled and viewed in a meaningful way For example the creation of a new biological strain entails many steps potentially involving nonconsecutive workdays of va
3. Examples In cell CHEMPROPPRO MOL REFRACTIVITY A2 Result 53 305 In cell CLOGP DRIVER MOL REFRACTIVITY A2 Result 5 3297 Water solubility Prediction of the water solubility of the struc ture at 25 C Units mg L Function CHEMPROPPRO WATER SOLUBILITY cell ref Example In cell CHEMPROPPRO WATER SOLUBILITY A2 Result 0 Connolly Solvent Accessible Surface Area The locus of the center of a spherical probe representing the solvent as it is rolled over the molecular model Units Angstroms 114 ChemDraw Excel Chapter 9 Function CHEMPROPSTD CONNOLLY ACCESSIBLE AR EA cell ref Example In cell CHEMPROPSTD CONNOLLY ACCESSIBLE A REA A2 Result 428 557 NOTE The default probe radius used in the calculations is 1 4 angstroms Connolly Molecular Surface Area The contact surface created when a spherical probe representing the solvent is rolled over the molecular model Units Angstroms Function CHEMPROPSTD CONNOLLY MOLECULAR ARE A cell ref Example In cell CHEMPROPSTD CONNOLLY MOLECULAR AR EA A2 Result 212 294 NOTE The default probe radius used in the calculations is 1 4 angstroms Connolly Solvent Excluded Volume The volume contained within the contact molecular surface Units Angstroms Function CHEMPROPSTD CONNOLL
4. ES ss pos LN oo Caner a E f che PATI Assay Procedure o atest S i SETET Coney Sie 4 Manage your Inventory Properties Rhombohedeal platelets from 95 alchol mp 220 224 some decompa when heated evac capillary gs 209 c 1 2 in 98 alcoho af 0 125 in benzene f 2488 c 0 1 t0 ibid 291 Baily vo much les sol in ether benzen water 28 mg 100 ml at 25 Us 1800 315 7300 INT L EU 0080087520000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA DocManager parses Word Excel and PowerPoint documents including free text and structures e ChemfFinder is tightly integrated with BioSAR BioViz and Oracle Support for advanced form layout and design DocManager Enterprise DocManager parses Microsoft Word Excel and PowerPoint documents including free text and structures DocManager has a web based interface and a file drop folder for quick submissions Oracle Cartridge is compatible with Linux Solaris AIX and Windows and includes structure searching property predictions and nomenclature Web browser based DocManager Enterprise ex
5. esses 20 Setting Preferences 20 RTGS saa 21 Spiro and sprout rings esses 21 Aromatic Structures ossessi 22 Acyclie C Das aset potui boda 22 Arrows and Shapes 23 PII 23 Drawing Elements sss 25 The Bracket Tools palette 26 Framing Objects sss 27 Pen 10015 eie ti sas 27 Selecting Objects sss 27 Resizing Objects sss 29 Rotating Objects 29 Moving Objects cecene 30 Copying Objects 30 Deleting Objects sss 30 Joining Objects 3l Grouping Objects esses 3l Scaling Objects sss 32 Chem amp Bio Draw 12 0 1 User Guide Centering Objects esses 32 Aligning Objects sss 32 Distributing Objects sss 32 Check fo nel Con iila PP E 32 Checking copied structures 33 Chemical secet odas isis 33 Disabling chemical warnings 33 Warning 33 Chapter 4 BioDraw pe C n 35 BioDraw Tools esses 33 BioDraw Templates sess 35 Customizable Objects esses 36 Drawing sequences 40 Nonlinear sequences 41 Bonding from sequences sss 42 T
6. CHEMICAL INFORMATICS Managing huge data streams is a key challenge Registration Enterprise organizes information about new compounds according to an organization s business rules SOLUTIONS to Enterprise Solutions LABORATORY amp MANUFACTURING A 2 Inventory Enterprise ChemACX Database SCIENTIFIC DATABASES moe The Merck Index Registration Enterprise GxP Validation MANUFACTURING INFORMATICS CambridgeSoft s chemical chemical and pharmaceutical laboratories Inventory Enterprise is an Oracle based ChemOffice Enterprise product that container types racks and multi well plate formats Inventory Enterprise Materials Management Compliance Management ChemDraw amp Chem3D Compliant SDMS Gateway Inventory Enterprise reagent sample and designed needs of application is compound tracking to manage the large multi site is designed for multiple users with diverse DESKTOP SOFTWARE ChemFinder amp Chemlnfo Success begins at the desktop where scientists use ChemOffice ChemDraw BioOffice and BioDraw to pursue ideas and communicate with the natural language of chemical structures BioDraw BioAssay amp biological pathways and models Scientists organize information and manage data with BioViz 5 Notebook and nvenfory ChemBio3D provides modeling ChemBioFinder aids searching while BioOffice adds BioDraw BioAssay
7. Cross arrows used to enlarge a spot Horizontal arrow used to widen a spot Vertical arrow used to elongate a spot or cre ate a crescent Rr Display Right click a spot and select Show Ry to indi cate the spot s retention value By default the value is set to Rp to two decimal places To move the tag Either click and drag the tag using a selection tool or Right click or Control click the tag and choose Position Then edit the values in the Position Indicators box Editing the Rf value Select the tag with the Text tool and edit the value If you change the R the spot will move to the new position indicated If you edit the R to have different precision that precision will be preserved Resizing Spots You can resize spots by holding down the Shift key while pointing at an edge of the spot Drag the left or right sides of the spot to adjust the width only Drag from the top to adjust the height Drag from the bottom to adjust the tail Dragging from any of the other four corners will scale all three values Custom Spots The TLC tool can create the most common spot shapes Other types of spots such as smears can be reproduced as custom spots The Set Custom Spot command lets you insert a graphic file for a spot Typically these files would be produced by scanning a TLC plate and saving the spots in a library of spot shapes ChemNMR ChemBioDraw Ultra and ChemDraw Ultra include ChemNMR
8. OH OH glucose Chemical Formula C6H1206 Exact Mass 180 06 Molecular Weight 180 16 m z 180 06 100 0 181 07 6 9 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 53 29 Figure 8 1 Structural analysis The information updates as you edit the struc ture You can show or hide the information 1 Using any tool right click the caption 2 Point to Analysis and select or deselect the item to show hide ChemBioFinder HotLink CambridgeSoft maintains a vast database of compounds and their properties ChemBio Draw 12 0 and ChemDraw Ultra 12 0 provide a live Internet connection to the database which includes a variety of valuable informa tion such as Links to available data resources such as the CambridgeSoft ChemIndex Basic properties such as molecular weight and formulae Names and synonyms Chemical identifiers such as CAS Registry Numbers and ChemACX IDs 86 Chemistry Features Chapter 8 The HotLink information and the data itself are continually updated Using the ChemBioFinder HotLink The HotLink displays information for any structure that is shown in the document win dow If you have more than one structure the HotLink displays information for the structure you select If none of the structures are selected no HotLink information appears To open the ChemBioFinder HotLink 1 Select a structure of interest 2 Go to View gt Show ChemBioFinder HotLink Window Stere
9. BioDraw provides support for biological pathway drawing and annotation A wide variety of customizable drawing tools are available including membranes DNA enzymes receptors tRNA ribosomes and a plasmid map tool BioAssay manages both high and low throughput biological screening data Designed for complex lead optimization experiments the software supports the quick set up of biological models BioViz offers automated statistical analysis curve fitting and customized structure activity reports including a user friendly interface for importing viewing validating and plotting chemical and biological data Handle reagent Inventory manages your reagent and biological tracking needs Using MSDE as the desktop database you organize store racking and search over your inventory Inventory integrates with the ChemACX database of available chemicals and ChemMSDX safety data providing chemical sourcing and purchasing Efficient notebook E Notebook is an efficient accurate way to write notebooks It stores Microsoft Office documents ChemDraw keeping structures and reaction drawings and related data in a notebook searchable by text or chemical structure Organize pages by project experiment or in your own style Use CombiChem Excel to build libraries Access info Databases include ChemINDEX including the NCI and AIDS databases The ChemACX database contains nearly 400 with ease catalogs from leading suppliers and ChemMSDX Database contains ov
10. To insert a ChemDraw Excel function into your worksheet 1 Select an empty cell 2 Goto Insert gt Function The Insert Functions dialog box appears 3 In the Category dropdown list select ChemDraw Functions 4 Select the function to insert from the list and click OK A dialog box appears 5 Enter the structure cell reference for which you want to calculate properties in the Structure box 6 Ifthe function takes a second argument enter it in the Element type box Element type arguments are optional 7 Click OK Each property is calculated using the best available method If the cell reference argu ment does not point to a valid structure cell N A appears in the cell All ChemDraw Excel functions are described below Chemical name Displays systematic names for chemical struc tures with support for the Cahn Ingold Prelog rules for stereochemistry Function CFW CHEMICAL NAME cell ref Example In cell CFW CHEMICAL NAME A2 Result 1 2 3 dihydro 1H inden 2 yl propan 2 one NOTE Some CambridgeSoft product pack ages and levels allow unlimited structure to name conversions while others impose a daily limit on conversions Chemical composition When this function is called with just a cell ref erence it displays the elemental percent by weight for all elements in the structure When this function is called with a cell reference and an atomic symbol it displays the fr
11. 100 180 Preferences and Settings Appendix A Wiley Document HO Fixed Length 17 pt Bold Width 2 6 pt Line Width 0 75 pt Margin Width 2 pt Hash Spacing 2 6 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Atom Label Size 12 pt Caption Font Win Mac Caption Size 12 pt Drawing Area Width x Height 19 79 x 27 15 cm Page Size A4 Reduction 100 Chem amp Bio Draw 12 0 181 User Guide 182 Preferences and Settings Appendix A Page Layout The presentation quality of your document is affected by how chemical structures and other objects are placed on the page Effective layout of a drawing includes proper alignment of chemical structures and other objects appro priate page size and page orientation The page layout tools include setup of the page and the use of the ruler tables layering aligning and distributing commands The Drawing Area The document window is not necessarily the same size as the drawing area of the page A document window in most cases actually cov ers only a portion of the drawing area The following options allow you to set the drawing area displayed on your screen Document Settings and Page Setup let you modify the page margins headers footers document type and size View menu options Actual Size Show Document Magnify and Reduce Magnification Controls enlarge and reduce Dragging to en
12. MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com With custom development CambridgeSoft works collaboratively with your team to create a system that meets your needs while executing our quality driven software development process We deliver what you need on time and within budget without surprises Product Development Development Consulting With custom development CambridgeSoft works collaboratively with your team to create a system that meets your needs while execut ing our quality driven software development process We meet your needs on time and within budget without surprises Systems Integration Process improvement often requires integrating systems designed for focused areas of work CambridgeSoft has integrated various E Notebook registration inventory and biological assay systems in a variety of settings Whether these are CambridgeSoft a third party product or an in house developed solution CambridgeSoft has the expertise to unite these systems in order to they improve business processes laboratory efficiency and decision making Application Configuration Your organization will see the benefit from implementing a CambridgeSoft application but would like to customize it for a unique environment Our professional services teams provi
13. Message Description The stereocenter has conflicting or ambiguous stereobonds specified Displayed for any stereo center tetrahedral atom asymmetric double bond etc where the absolute stere ochemistry cannot be deter mined from the structure as drawn For example this message would be shown for a carbon atom attached by bold bonds to four different ligands This message is displayed only when Show Stereochemistry is also turned on This label has an unrecognized isotopic mass Displayed for every label that has a numeric superscript immediately preceding an atomic symbol where the superscripted number does not correspond to a recog nized isotope For example 24CH3 Chem amp Bio Draw 12 0 User Guide 199 200 Chemical Interpretation Appendix C Property Calculations You can calculate predicted values of selected least squares analysis This method allows a physical and thermodynamic properties for calculation of logP with a standard devia structures of up to 100 atoms The following tion of 0 43 logP units and can handle mol topics describe how the values are determined ecules containing hydrogen oxygen nitrogen sulfur halogens and phosphorus atoms If this method is applied to mole NOTE The property calculations plug in is available for ChemBioDraw Ultra ChemDraw cules with internal hydrogen bonds the Ultra and ChemDraw Pro only standard deviation is 0 83 LogP
14. Setting Preferences Preferences affect how Chem amp Bio Draw 12 0 works regardless of the document with which you are working 1 To open the Preferences dialog box go to File gt Preferences 2 To restore the default settings click Use Defaults Default Document Location You can set the default file directory shown in the Open dialog box each time you want to open a file 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Directories tab 3 Click the Use Documents Location check box and type in or browse to the location to use Default Open File Format To set the default file format in the Open dia log box Chem amp Bio Draw 12 0 157 User Guide 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Open Save tab 3 Click Use Default File Format in the Opening Files section and choose the desired file format Setting the Default Tool You can choose which tool is selected when you open documents 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Open Save tab 3 Under Opening Files select a tool Autosave You can configure Chem amp Bio Draw 12 0 to periodically save an open documents at a spec ified time interval you set 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Open Save tab 3 Click the Autosave Every checkbox and enter the minutes to use The time star
15. When the alternative group definition is com plete the attachment point symbols appear in the parent compound EN Figure 10 15 R groups with multi attachment points By numbering your attachment points you have unambiguously specified that the methyl group must be adjacent to the amine group The conformations that are not of interest are excluded Attachment Rank Indicators You can hide the attachment rank indicators if required For example in publication quality drawings the numbering of attachment points is implicit and the numbered attachment rank indicators are superfluous NOTE Attachment rank indicators are avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To hide the attachment rank indicators and remove the numbers from the attachment points 1 Go to File gt Preferences 2 In the Preferences dialog box click Build ing Display 3 Deselect Show Attachment Rank Indicators This change affects all documents The figure below shows an alternative group definition and a parent structure with the attachment rank indicators hidden Figure 10 16 Hidden attachment indicators Attachment Point Numbering Numbered attachment points let you specify precisely how the structure fragments are con nected to your parent structure Chem amp Bio Draw 12 0 137 User Guide The numbering of the attachment points is related to the front to back order
16. 1 Select one or more labels in the sequence Hold down the Shift key to select more than one 2 Go to Structure gt Expand Label When you expand a label into its structure the label appears below the structure COLLAPSING LABELS To collapse the structure back to its label in the sequence 1 Double click the label to select the struc ture 2 Go to Structure Contract Label REMOVING RESIDUES When you remove a residue the adjacent labels close keeping the sequence intact 1 If the label is expanded collapse the struc ture back to its label 2 Using a sequence tool double click the label 3 Press DELETE on your keyboard REPLACING RESIDUES To replace a residue select the Marquee tool and hover your mouse over it Then type the new hotkey ADDING RESIDUES You can add one or more residues to an exist ing sequence To add a residue 1 Choose the appropriate sequencing tool 2 Select an existing label you want the new label to be adjacent to 3 Type the new label The new label is added to the right of the existing label NOTE To add a label so that it is the farthest left in the sequence select the amino group protein sequence or 3 group DNA RNA sequence CHANGING AMINO ACID TERMINI You can change the termini in the sequence or even hide them altogether To change the termini 1 Using a selection tool select the whole sequence 2 Go to Object gt Object Settings
17. 3 In the Object Settings dialog box select the Atom Labels tab 4 Under Amino acid Termini select either NH2 COOH or H OH 5 Click OK To hide or display the termini 1 Using a selection tool select the whole sequence 2 Go to Object gt Object Settings 3 In the Object Settings dialog box select the Atom Labels tab 4 Under Amino acid Termini select or dese lect Show Sequence Termini 5 Click OK Nonlinear sequences By default Chem amp Bio Draw builds a sequence from left to right across the page as you continue to enter residue codes However you can add a carriage return to a sequence so that it continues on the next line such as H Pro Cys Leu His Lys Cys OH To create a nonlinear sequence 1 Draw the sequence 2 Use the sequencing tool to select the resi due you want at the end of the first line such as His in the example above 3 Press ENTER on your keyboard Chem amp Bio Draw 12 0 4 User Guide Bonding from sequences 1 Draw a bond starting at the sequence label from which you want to create a branch The Modify Nickname dialog box appears displaying the sequence structure you selected 2 In the Modify Nickname dialog box dou ble click the atom in the structure on which you want to add the attachment point A new attachment point appears Gly COOH 3 Click OK Sequence labels typically have two attachment points However you can add attac
18. Finder List Error No database loaded in ChemFinder Load a database and perform your search Then return to Excel and redo the operation ChemFinder is running but no database is loaded Do the following 1 Click OK ChemFinder moves to the front 2 Open a database and perform a search 3 Return to Excel and go to ChemOffice12 gt Import Export gt Import Chem Finder List Error Form has no database or hit list has no records Load a database and perform your search Then return to Excel and redo the oper ation 1 Click OK ChemFinder moves to the front 2 Open a database and perform a search 3 Return to Excel and go to ChemOffice12 gt Import Export gt Import Chem Finder List Exporting Tables ChemDraw Excel lets you export tables to MDL SDFiles The first column of the area to export must have the word Structure in its top cell Structures outside the first column will be discarded To export data 1 Select the cells to export including the cell that contains the word Structure 2 Go to ChemOffice12 gt Import Export gt Export Table 3 Inthe Save Table To dialog box type the file name and click Save Adding Structures You can add chemical structures from any file format supported by Chem amp Bio Draw 12 0 to a spreadsheet The names of added structures are retained If the structure does not have a name Chem amp Bio Draw 12 0 assigns the name Structure lt n
19. Helix Proteins To create a helix protein 1 Select the Helix Protein tool 2 Drag in the document window or click to draw the default size When orienting the protein note that if the Fixed Angles option on the Object menu is selected you are constrained to 15 degree Chem amp Bio Draw 12 0 37 User Guide increments To override the constraint hold down the Alt or Option key as you drag The helix protein has four adjustment handles height width of the strands width of the cylin ders and spacing C B Figure 4 2 Adjustment handles on a helix protein A height adjustment B width of strands C width of cylinder D spacing between cylinders DNA Molecules To create a DNA molecule 1 Select the DNA tool 2 Drag in the work space or click to draw the default size When orienting the DNA note that if the Fixed Angles option on the Object menu is selected you are constrained to 15 degree increments You can override the default by holding down the Alt or Option key as you drag 38 BioDraw Chapter 4 DNA has four adjustment handles height width of the strands offset of the second strand and spacing A 29 Figure 4 3 DNA adjustment handles A height adjustment B spacing C width D offset Coloring Residues After you draw a protein or DNA strand you can color each residue using any of the color ing options Shading Fading or Filled 1 Using the Marquee or Lasso tool s
20. See the lower left corner of the Chem amp Bio Draw 12 0 window for useful information Learning Chem amp Bio Draw Perhaps the best way to learn Chem amp Bio Draw is to follow the tutorials found in this guide As you advance beyond the basics you will find many powerful features to be quite useful in drawing structures Just a few of the advanced features are described below Chemical structures in Excel Chem amp Bio Draw 12 0 Excel provides a unique plug in to help you manage chemical structures in Microsoft Excel for Windows Chem amp Bio Draw 12 0 Excel enables you to Add structures and data from Chem amp Bio Draw 12 0 or a ChemFinder database to an Excel spreadsheet Search using the same features in Chem Finder Perform calculations on chemical struc tures Converting Structures to Names One of the most significant and useful features in Chem amp Bio Draw is Struct Name Draw or open a chemically correct structure and Chem amp Bio Draw displays the IUPAC name See Chapter 7 Naming Structures for more information About ChemNMR Use this powerful feature to estimate proton and carbon 13 chemical shifts in molecules you draw See ChemNMR on page 203 Chem amp Bio Draw 12 0 5 User Guide 6 Introduction Chapter 1 Getting Started This section will help you install Chem amp Bio Draw 12 0 and become familiar with the user interface Installing Chem amp
21. To create a scrap or clipping file 1 Select an object in a document 2 Drag the selection out of the document win dow onto the desktop The file appears on the desktop To view the file contents double click its icon To use contents in a document drag the file into an open window of an application that supports drag and drop Transferring Objects In this section we explain how some features in Chem amp Bio Draw 12 0 behave when you transfer objects using the Clipboard or drag and drop from one document to another AUTOSCALING When you transfer objects the objects are scaled to match the document settings of the destination document BONDS When a structure is copied or moved to another document the structure adopts the new document s fixed length value However it retains its scaling factor For example assume the Fixed Length is set to 1 0 cm in a source document A benzene ring is resized to 200 The bond length is then 2 0 cm In the destination document the Fixed Length set to 1 7 cm When the benzene ring is pasted into the destination document the bonds are scaled by a factor of 2 to a final bond length of 3 4 cm ATOM LABELS Atom labels are scaled the same way as bonds For example in the source document the atom label font size is set to 16 points One or two atom labels in the source document are resized to 8 points a ratio of 8 16 or a scale factor of 0 5 The destination document has an a
22. 2 Select the appropriate option in the Edit menu ADDING A TEMPLATE To add a template click in an empty template pane and begin drawing the template in the document window Go to File gt Save DELETING A TEMPLATE 1 Select the template pane for the template to delete 2 In the document window select the entire drawing 3 Go to Edit gt Clear 4 Go to File gt Save Orienting Templates To make templates that you create simple to use orient the template structure so that you can modify the bonds you use most often Resizing Template Panes To resize the Template panes in the Template panel drag the lower right corner of the Tem plate panel If needed first click and drag the resize handle Defining Nicknames A nickname is an alphabetic abbreviation that represents part of a structure Nicknames are useful for drawing large structures or struc tures that repeatedly use similar features NOTE The Nicknames feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Chem amp Bio Draw 12 0 comes with a library of nicknames for various commonly used func tional groups and monomers For example if you typically draw protein structures you may consider using amino acid nicknames in your drawings rather than drawing each amino acid structure yourself Oz es Figure 6 21 Leucine as found in the Nicknames Library Attachment points A nickname can have
23. 89 Chemical Symbols 90 Chemical Properties 9 Viewing Chemical Properties 92 Stoichiometry Grid 92 IV ou 93 Ry Display 95 Resizing Spots 95 Custom 95 Chemn NMR eseeton 95 NMR 95 Assigning Structures to Spectra 96 Viewing Spectral Assignments 96 Removing Spectral Assignments 97 Custom Shift Correction Data 97 Chapter 9 ChemDraw Excel eee 103 Setting Up ChemDraw Excel 103 Importing 103 Converting Worksheets 104 Upgrading Workbooks sss 104 Importing Hit Lists 104 Error Messages 104 Exporting Tables et eres 104 Adding Structures ssss 105 Adding a Structure From a File 105 SMILES Strings esse 105 Adding Structures by Name 105 Saving Structures eere 106 Searching ETE 106 Opening a database 106 Normal Searches sss 106 Similarity Searches sess 106 R Group Analysis 107 Interpreting Analysis Results 107 Working with Structures 107 Naming Structures 107
24. Acid Halides Carboxylic Esters Salts Anhydrides Hydrazides Imides Amides Hydrazines Nitriles Amines and Imines S Se and Te Acids S Se and Te Esters S Se and Te Acid Halides S Se and Te Amides Sulfides and chalcogen analogs Sulfoxides and chalcogen analogs Heteroatomic acids P B As Heteroatomic esters Heteroatomic acid halides Aldehydes and chalcogen analogs Ketones and chalcogen analogs Alcohols and chalcogen analogs Hydroperoxides Peroxides Non ringed structures 80 Isolating and naming the functional groups Naming Structures Chapter 7 Identifying the base chain of the molecule Identifying and building substituents Nomenclature of groups cited only by pre fixes Heteroacyclic compounds Naming of substituent groups Locants Name generation alphabetization punctua tion etc Ringed structures Struct gt Name supports the these types of ringed structures Carbomonocyclic structures Heteromonocyclic structures Fused polycyclic structures e Fused polycyclic trivially named struc tures Ring fusions of multiple rings Ring fusions of two multiple ring systems Ring fusions of more than two ring sys tems Bridged monocyclic structures Spiro ring systems Some of these ring structures are defined below RING ASSEMBLIES A ring assembly consists of two or more cyclic systems that are directly joined to each other by single or double bonds All the cyclic sys tems
25. Appendix C ba diii AND zii NH2 H2 Figure C 8 The Racemic flag indicates a mixture of the exact stereoisomer as drawn and its enantiomer Polymer Representations Polymers are represented by brackets used to enclose repeated structures or structural frag ments Bracket properties specify the orienta tion and context of the repeating units An explanation of the bracket properties is given in Setting Bracket Properties on page 131 NOTE The polymer drawing feature is avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only References Graphic Representations Chemical Formu lae of Macromolecules Recommendations 1994 Pure Appl Chem 66 2469 2482 1994 Source Based Nomenclature for Copolymers Recommendations 1985 Pure Appl Chem 57 1427 1440 1985 Also available at http www iupac org publications books pbook Pur pleBook C7 pdf Basic Definitions of Terms Relating to Poly mers 1974 Pure Appl Chem 40 479 491 1974 Also available at http www iupac org reports 1996 68 12jenkins index html Also see the Guide for the authors of papers and reports in polymer science and technology from IUPAC Analysis Messages When a structure cannot be analyzed fully two general types of messages are displayed Status messages that report a problem that may not affect the final analysis Critical messages that may affect the fi
26. Go to File gt Preferences 2 Click the Warnings tab 3 Select the types of warnings and click OK Chem amp Bio Draw 12 0 33 User Guide 34 Basic Drawings Chapter 3 BioDraw Chem amp Bio Draw provides a variety of tools for you to create biology related drawings Before reading this section you should famil larize yourself with the general behavior of Chem amp Bio Draw 12 0 drawing tools See Basic Drawings on page 13 BioDraw Tools The BioDraw toolbar contains tools to draw metabolic pathways such as enzymes and receptors To display the BioDraw toolbars go to View gt Show BioDraw Toolbar Standard shapes such as circles ellipses and arrows can be added from the Drawing Ele ments tool palette or the Arrows tool palette You can also use the Curve tool to create cus tom shapes As with Chem amp Bio Draw 12 0 Drawing Ele ments you can change the color of an object with the Color menu and the line and fill prop erties with the Curves menu You can also rotate or change the size You create a BioDraw object by either clicking or dragging on the page where you want it to appear Clicking gives you the default size and shape dragging allows you to not only to enlarge the object but also to distort it by drag ging on the x and y axes Linear objects elon gate in the direction they are dragged The membrane and protein tools DNA and helix add more subunits as they are dragged and dis play
27. Inventory Enterprise has the capabili ty to import datafiles from other computer systems such as liquid dispensers handlers Microsoft Excel spreadsheets etc to accom modate automated updating of information in the Inventory database us 1 800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 Regulated Materials Management Request Dispense Reference Standard Materials from Central Group to Sites Certification Expiration Certificate of Analysis of Containers and Aliquots Create Manage Container History and Genealogy Searching Every field in a record is searchable The application includes a number of specially designed inventory search forms Search results are returned in list form and can be exported into a docu ment PDE HTML via the report engine Workflow Support Supported user transactions include the ability to request dispense modify duplicate dispose etc entities throughout the system These and other transactions are an integral part of Inventory workflows For example a user logs on finds the substance s theyd like to request and makes a request entry in the system the request is ful filled directly by changing the location the substance or by taking an aliquot and creating a new co
28. Newman projection 1 Point within the Selection Rectangle so the pointer changes to a hand 2 Drag the selection until the tertiary carbon is centered within the orbital as shown below NOTE If chemical warnings are turned on you will see a red warning box when you over lay the structure because the center atoms are on top of each other Chem amp Bio Draw 12 0 55 User Guide 3 Release the mouse button and click outside the Selection Rectangle to deselect the structure Figure 5 21 Completed Newman projection Save and close the document 1 Go to File gt Save 2 Go to File gt Close Tutorial 6 Stereochemistry This tutorial demonstrates using Stereochemis try markers and the flip command As you draw the structure below you may notice that some of the steps are similar to those needed earlier to draw isobutane Create a new document 1 Go to File gt New Document 2 Go to File gt Save as 3 Type tut7 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save First we draw the following structure O OH NH 2 amino 3 methylbutanoic acid 56 Tutorials Chapter 5 Drawing the structure To draw the structure 1 Click the Solid Bond tool 2 In the document window click and drag downward to create the first bond 3 Point at the lower atom and click to add a second bond 4 Continue pointing at the same atom and click again to
29. To expand a generic structure 1 Select one or more generic structures to expand NOTE For alternative group R tables both the alternative group label and the table must be selected If the label is selected but not the table the label will not be modified by the expansion and will appear as a label in all gen erated structures 2 Go to Structure Expand Generic Structure The structures are generated in a new docu ment R Logic Queries After you have your generic structure and a set of R groups you can use them to run queries against a structure database This 1s called an R Logic query When you run an R Logic query you search for structures that all have the generic structure and a combination of your R groups The com binations are based on a Boolean expression that you define To prepare an R Logic search go to Structure gt R Logic Query to open the R Logic Query dialog box To define a query select one or more R groups in your structure and how many times it must occur You can also indicate that if the first R group condition is met another R group must also be found before the structure is returned as Chem amp Bio Draw 12 0 139 User Guide a result For example consider the following structure This structure indicates that both sites must consist of either a fluorine or chlorine atom and that the site must be either a bromine or iodine atom Assume you want to find all
30. User Guide not the content for the toolbars the pop up text and the status bar text The toolbar XML files The Toolbars directory contains the subdirec tory where the toolbars xml files are stored The files are stored according to the skins in which they are used These are the files you will most commonly edit to customize the tool bars Editing the XML files Since the files are xml based you can edit them using any xml or text editor After you save them exit and restart Chem amp BioDraw Your changes will take effect CAUTION Create a backup of all XML files that you intend to edit Editing toolbar icons In addition to customizing the toolbars you can also replace the icons themselves For example you can replace the eraser icon with the word Erase NOTE All images files you use as icons must be in png format Document and Object Settings Document and object settings are user defin able settings that are applied to the current doc ument Settings include Drawing settings set drawing options such as the fixed length used to draw bonds 160 Preferences and Settings Appendix A Caption and label text settings set text options such as the font used for atom labels and captions Color settings set available colors for objects and the document background Print Page Setup set options such as the page size used and text displayed in footers You can apply document settin
31. abnormal valence 126 description 120 122 128 implicit hydrogens 123 in query structures 120 options 122 reaction changes 124 reaction stereo 125 resetting defaults 122 ring bond count 123 substituents 122 unsaturation 124 viewing 121 atom changing to a different 11 atom to add an 10 atoms moving 30 atom to atom mapping 140 attached data 153 attachment point defining 135 numbering 137 symbol 136 tool 91 135 attachment points 63 75 attachment order 75 numbering 137 attachment points multiple 136 220 Index attachment points viewing 64 attachment rank indicators showing 137 auto update 81 automatic alignment 165 drawing of structure 82 justification atom labels 165 autosave 158 autoscale template color 171 when transferring 149 B background and foreground 169 background color printing 171 Balaban index 115 baseline style captions 163 benzene ring changing orientation 22 drawing 22 BioDraw 9 drawing a helix protein 37 drawing a membrane arc 37 drawing a membrane line 37 drawing DNA 38 templates 73 BioDraw objects color 35 customizing 36 line and fill properties 35 BioDraw templates 1 35 bitmap fonts Macintosh 158 bitmap fonts using when available 158 bitmapped printing quality 161 boiling point 111 calculation 202 definition 91 bold width 162 bond crossings changing 16 white space 162 bond properties defining 127 query indicators 127 reaction center 129 removing 128 topol
32. estimate physical properties such as logP boiling point melting point and more Visualize Connolly surface areas and molecular volumes EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com SOFTWARE ChemFinder amp Chemlnfo Structure Searching and Scientific Databases ChemFinder Ultra is chemically intelligent database man agement and search system designed for chemical and biological data ChemFinder Ultra can be used with local MSDE or shared Oracle databases Either way the face of ChemFinder is the same friendly form oriented interface BioViz included in ChemFinder Ultra provides data visualization features to help the user understand relationships between biological data and chemical structures These features allow you to plot structural and biological data in a variety of styles perform statistical analy sis filter plots based on your criteria highlight intersecting sets on plots generate histograms of data distributions and more BioViz included in ChemFinder Ultra provides statistical analysis and visualization tools for structural and biological data BioViz transforms ChemFinder database information into easy to under stand graphics allowing users to discern structure activity rela tionships more easily With BioViz it is easy to retrieve a set of compounds using filters or searching capabilities and generate an interactive window showing a wide variety of useful graphical infor
33. http www CambridgeSoft com services Other resources are also available 1 Chem amp Bio Draw 12 0 Readme file This file includes known limitations or conflicts 2 Review System requirements See the beginning of this manual for minimum requirements for installing and running Chem amp Bio Draw 12 0 3 Ifyou still need assistance fill out a copy of the CS Software Problem Report Form at http www cambridgesoft com services mail When you fill out the form Try to reproduce the problem before con tacting us If you can reproduce the prob lem please record the exact steps that you took to do so Record the exact wording of error mes sages Record what you have tried to correct the problem You can deliver your form to Technical Sup port using either of Online www cambridgesoft com services mail E mail support cambridgesoft com Locating your serial number For Windows users the serial number is on the outside of the Chem amp Bio Draw 12 0 box For Macintosh users the serial number is on a card inside the box You can also find the serial number online or in the Chem amp Bio Draw menu ONLINE If you have downloaded Chem amp Bio Draw 12 0 you can find your serial number at the CambridgeSoft Web site 1 Go to www cambridgesoft com 2 Log into your CambridgeSoft account 3 Click My Downloads in the list of Services WINDOWS In Chem amp Bio Draw for Windows go to Help gt Abou
34. on page 29 Chemical Properties You can enter predicted values for the physical and thermodynamic properties of a chemical structure of up to 100 atoms NOTE Chemical properties are available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only The properties are calculated using the most reliable methods for the given structure Log P and CMR values based on literature values rather than a calculation are included in the report file The reported properties are Boiling Point Reported in Kelvin at 1 atm Melting Point Reported in Kelvin at 1 atm Critical Temperature The temperature above which the gas form of the structure cannot be liquefied no matter the applied pressure Reported in Kelvin Critical Pressure The minimum pressure that must be applied to liquefy the structure at the critical temperature P Reported in bars Critical Volume The volume occupied at the compound s critical temperature and pressure V Reported in cm3 mol Gibbs Energy The Gibbs free energy AG for the structure Reported in kJ mol at 1 atm and 298 15K Henry s Law The inverse of the logarithm of Henry s law constant log H no units Chem amp Bio Draw 12 0 91 User Guide Heat of Formation AH for the structure Reported in kJ mol at 1 atm and 298 15K tPSA Calculation of polar surface area based on fragment contributions CLogP CMR Use CLogP to calculate n octanol wat
35. quadruple bonds 14 queries multiple rings 134 query indicators editing 122 query properties 3D 142 exported 144 query structures 119 exporting 144 quick reference card description 5 QuickDraw print quality 160 quickdraw bitmapped image 161 R R groups 134 racemic flag drawing 142 radicals 193 drawing 90 specification 193 radius 116 reaction atom to atom mapping 140 reaction center 129 reaction changes 124 reaction intermediates 70 reaction interpreter 70 reaction mapping automatic 141 clearing 142 exporting 142 manual 141 overview 140 reaction stereo 125 reactions 67 red boxes on objects 33 reduce document window 183 object 186 page size 185 references 196 registration marks 184 registration online 215 relative flag drawing 142 relative stereochemistry 88 remove colors 170 removing atom properties 121 removing bond properties 128 removing colors 170 repeat command rotations 29 repeat pattern 133 repeating actions 9 repeating atom labels 17 replacing residues 41 repositioning stereochemistry indicators 87 reset defaults atom properties 122 bond properties 128 residues replacing 41 resizing arcs 26 template panes 74 resizing and rotating 25 resizing objects 29 resizing structures 108 resizing template panes 74 resonance delocalized rings drawing 22 resonance structures 22 46 Rest H 140 retrosynthesis tool 67 returning to the document window 78 reversing actions 9 Rfd
36. reaction center for the reactants and products When a reaction map is established you can point to an atom in one structure with the Reaction Atom Atom Map tool selected to highlight the mapped atom in the other struc ture Displaying and Printing To make the symbols always appear and print on the atoms when mapping reactions 1 Go to File gt Preferences 2 In the Preferences dialog box click the Building Display tab 3 Select Always Display and Print Reaction Mapping 4 Click OK Deselect Always Display and Print Atom Map ping to show the symbols only when you select the Reaction Atom Atom Map tool When this option is deselected atom mapping symbols do not print even though a reaction map has been created Automatic Mapping To create a reaction map 1 Draw the reaction you want to map and select the reaction TIP Double click the arrow with a selection tool to select the entire reaction 2 Go to Structure Map Reaction Atoms The symbol Rxn appears next to the bonds in the reactant and product that are perceived by the algorithm as being modified by the reac tion These symbols are bond properties that are applied For more information about the Reaction Center bond property see Bond Properties on page 127 OSMes Rxn Rxn p a xn gt Ph Figure 10 18 Automatic reaction mapping Manual Mapping In situations that require manual mapping of atoms you can use the Reaction Ato
37. view available appears With the preview window open you can change the structure s appearance several ways in either the document window the pre view window In the document window Even with the preview window open you can still change your drawing in the document win dow to look how you want You can alter the structure rotate it or add new structures The preview window updates to reflect the changes Chem amp Bio Draw 12 0 77 User Guide In Chem amp Bio 3D Preview The preview window offers several options to view structures Launch Chem 3D The structure will appear in Chem amp Bio 3D as a model that you can edit Display Mode Choose display options for the model wire frame stick ball amp stick cylindri cal bonds and space filling Select Select the structure or parts of it Translate Move the structure Rotate Rotate the structure in three dimen sions the image rotates only in the ChemBio3D Preview Zoom Enlarge or reduce the apparent size of the structure Spin rotate the structure horizontally in one direction Rock rotate the structure horizontally back and forth Returning to the document window To exit the Chem amp Bio 3D Preview close the preview window To edit the 3D structure 1 Double click the 3D structure Chem amp Bio 3D opens 78 Advanced Drawing Techniques Chapter 6 2 Edit the structure and close Chem amp Bio 3D The edited structure a
38. 142 atemplate 74 chemical names 79 frames 69 rows and columns 74 structures 105 structures by name 105 structures in ChemDraw Excel 105 adjustment handles 23 Adv Synth Catal 174 advanced drawing techniques 59 aligning objects align submenu 32 overview 32 rulers 187 with crosshair 188 aligning structures 70 108 aligning text 164 alignment automatic 165 alternative groups 134 attachment point numbering 137 attachment point symbol 136 attachment rank indicators 136 defining 135 description 134 multiple attachment points 136 analysis 133 information 85 messages 197 analysis and properties 163 analysis messages 197 analysis results interpreting 107 analysis window 85 anion drawing 90 anonymous alternative groups 138 apply settings command 161 applying object settings 161 arcs 26 drawing 26 resizing 26 arrows adjustment handles 23 autoscaling 150 changing direction 24 cursor types 23 hollow arrows 24 rotating 25 undo 24 assigning atom mapping 140 asymmetry see stereochemistry indicators 195 atom numbers 64 65 query properties 120 atom label text boxes closing 158 Chem amp Bio Draw 12 0 219 User Guide atom labels 164 191 automatic justification 165 justification 164 layering 167 margin width 167 multi attached 61 specification 191 text boxes creating new line 158 white space 167 atom labels adding 10 atom numbers editing 65 showing and hiding 64 atom properties
39. 202 Topological Polar Surface Area 202 Other Properties sss 202 Appendix E ChemNMRL eese eescit aechi eroe enecen 203 ChemNMR Limitations sss 203 NMR References 204 Appendix F Technical Support 205 Locating your serial number 205 Appendix G Shortcuts and Hotkeys 207 Ato KEYS CT 207 Bond Hotkeys 208 Function 208 SIDES RH 209 Fe eue ue te 209 Dog 209 jur MH 209 OD 209 iron 210 Chem amp Bio Draw 12 0 User Guide Drawing eese een 210 NICKNAMES cado edi tabo EUR 212 Appendix H The CambridgeSoft Web Site 215 Registering 1 215 User s Guide sss 215 Technical Support ssssss 215 vi Contents Suppliers on 216 ACX Structures and Numbers 216 Chem amp Bio 3D ActiveX Control 216 151 216 CambridgeSoft com sss 216 Using the ChemOffice SDK 217 Dill MED FM PIED ARM What s New Chem amp Bio Draw has long been the preferred tool for illustrating chem
40. 5 x gt 4 0 Save as ChemDraw 3 x chm lt 3 5 x Save as ChemDraw and add chm to the file name Chem amp Bio Draw 12 0 155 User Guide 156 Sharing Information Chapter 11 Preferences and Settings You can customize Chem amp Bio Draw 12 0 by configuring Preferences and Document Set tings for the way you work Preferences allow you to change the default behavior of certain options that apply to every open document Document Settings allow you to change the default behavior of options that will affect only the active document Theme Options The theme defines the appearance of the Chem amp Bio Draw GUI but does not affect any of the functions By default Chem amp Bio Draw 12 0 is installed with the version 12 0 theme How ever other themes such as Classic and I Draw are also available To change themes 1 Go to File gt Preferences and select the Gen eral tab 2 Select a theme in the Theme dropdown list Click OK Macintosh only Exit and relaunch Chem amp Bio Draw 12 0 A l Draw The I Draw theme changes the look of the Main and Ring toolbars However in addition to changing these toolbars you can select the I Draw mode to activate two other helpful fea tures Sprout rings as opposed to spiro rings The default style sheet is changed to I Draw Styles cds To activate the I Draw mode go to File gt Prefer ences and click l Draw
41. 87 see also indicators 195 showing 86 terms supported 86 stereochemistry tutorial 56 stoichiometry grid 92 editing with the context menu 93 setting the limiting compound 92 Struct Name 5 79 82 Struct Name structure types supported 83 structure checking 32 chemical warning 33 clean up structure command 62 converting to name 79 selecting 28 shortcut keys 210 show stereochemistry 86 structure perspective 65 structure perspective tool using with ob jects 25 structure based polymers 132 structures adding by name 105 displaying 108 style indicators 164 style sheet document settings 160 page setup settings 185 saving document settings 161 style sheets color palette 171 style caption 163 styles default 160 subscript command 163 substituents 122 sum of valence degrees 116 superscript command 163 supplier finding online 216 Chem amp Bio Draw 12 0 233 User Guide supported structures 79 83 suppress chemical warnings 33 45 SVG 1 syntax checking 32 Synthesis and retrosynthesis 67 Synthesis Synlett 180 Synthesis Synlett document 180 system requirements 7 T technical support 205 templates 73 BioDraw 1 35 coloring 171 creating 74 customizing 74 deleting 74 new drawings 73 orientating 74 overview 73 resizing panes 74 tutorial 57 templates and color 171 terminal carbon labels 162 text atom label format 164 atom labels automatic justification 165 formatting 163 shortcut keys 210 tex
42. Bio Draw Before installing Chem amp Bio Draw see the ReadMe html file and other ReadMe docu ments on the installation CD ROM System Requirements Requirements for installing Chem amp Bio Draw 12 0 on a Windows system Operating System Windows 2000 XP Pro 32 bit only Vista 32 bit only Browsers Microsoft Internet Explorer 7 x or 6 x Mozilla Firefox 1 5 and higher Netscape 7 x Mozilla 1 x Microsoft Office Microsoft Office 2000 Office XP Office 2003 Office 2007 Screen Resolution Chem amp Bio 3D supports a PC screen resolution of 800 x 600 or higher Requirements for install Chem amp Bio Draw 12 0 on a Macintosh system Operating System Mac OS X 10 4 PowerPC Mac OS X 10 4 Intel Mac OS X 10 5 Pow erPC Intel Browsers Safari 1 4 and higher Firefox 1 x Mozilla 1 7 5 and higher Netscape 7 0 x Screen Resolution Chem amp Bio 3D supports a screen resolution of 800 x 600 or higher Site License Networks If you have a site license see the network installation instructions at http www cambridgesoft com services Desk topSupport Documentation NetworkInstalls The Work Area The work area appears whenever you launch Chem amp Bio Draw 12 0 By default the work area displays commonly used toolbars the Chem amp Bio Draw 12 0 7 User Guide main menu and document status bar The work area appears below b EP b bo lc 2uvm title ba
43. BioViz offers automated statistical analysis curve fitting and customized structure activity reports including a user friendly interface for importing viewing validating and plotting chemical and biological data Handle reagent Inventory manages your reagent and biological tracking needs Using MSDE as the desktop database you organize store racking and search over your inventory Inventory integrates with the ChemACX database of available chemicals and ChemMSDX safety data providing chemical sourcing and purchasing Efficient notebook E Notebook is an efficient accurate way to write notebooks It stores Microsoft Office documents ChemDraw keeping structures and reaction drawings and related data in a notebook searchable by text or chemical structure Organize pages by project experiment or in your own style Use CombiChem Excel to build libraries Access info Databases include ChemINDEX including the NCI and AIDS databases The ChemACX database contains nearly 400 with ease catalogs from leading suppliers and ChemMSDX Database contains over 20 000 material safety data sheets for commonly used laboratory chemicals US 1 800 315 7300 INT L 1 617 588 9300 FAX 1617 588 9390 EMAIL infoGcambridgesoft com EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 44 1223 464900
44. CambridgeSoft extended its software to include enterprise wide solutions with ChemOffice Enterprise in 1998 E Notebook in 2000 and biology with BioAssay in 2001 Today CambridgeSoft products are used by hundreds of thousands of chemists biologists scientists and engineers who work in pharmaceutical biotechnology and chemical industries including government and academic research These systems work within your research discov ery development trials and manufacturing and information technology to help you capitalize on your organizations intellectual assets By turning information into explicit knowledge you accelerate innovation and drive organizations forward Created with Passion Chemists biologists scientists and engineers need timely convenient access to critical information whether structured or unrefined CambridgeSoft which began by helping scientists manage desktop chemical and biological information with Chem amp Bio Draw now addresses enterprise wide scientific information problems with Chem amp Bio Office Enterprise and Workgroup These solutions are flexible and powerful to deal with today s complex projects which span functional organizations and geographi cal boundaries Eliminating data barriers and bringing information to all in the form they need to interpret it aligns all of the mem bers of your teams focusing their collective knowledge and diverse skills toward the common goals of problem solvin
45. ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Link nodes must have exactly two connecting bonds The atom label must conform to the fol lowing conditions It must consist of a generic name or no more than a single element symbol The last part of the label in the form num ber hyphen number with the number and hyphen subscripted 134 Query Structures Chapter 10 Parentheses or braces may be used instead of brackets Brackets can be omitted if not needed for clarity for example with O1 3 To create a link node 1 Open an atom label text box 2 Type in the following format 2 7 Flip For ladder polymers those polymers with two connecting bonds on each side the connection order may be undefined You can assign the Flip Type property to define it This property is appropriate only for brackets with exactly two crossing bonds Because of its prevalence the No Flip type does not receive special annotation The figure below illustrates a flip type in ladder polymers amp H H Alternative Groups You can create a search query that contains variable functional groups or substructures Instead of submitting multiple queries on structures that share a common substructure you can submit a single query with the parent structure The parent structure can have attach ment points to a list of alternative groups that you can define NOTE The alte
46. ChemDraw Laser Prep The ChemDraw Laser Prep contains specific instructions that enable the printer to interpret the PostScript com mands contained in a Chem amp Bio Draw 12 0 document INCLUDE POSTSCRIPT To transfer Chem amp Bio Draw 12 0 pictures to another document that will be printed on a PostScript printer 1 Go to File gt Preferences 2 Click Include PostScript Chem amp Bio Draw 12 0 171 User Guide 3 Click OK When Include PostScript is deselected no PostScript commands are generated This usu ally results in lower quality printing particu larly of drawings cut and pasted into other applications However because the representa tion used for printing when Include PostScript is not selected is the same as that used for drawing to the screen better correspondence between the screen and printed output may be observed INCLUDE CHEMDRAW LASER PREP Selecting the include ChemDraw Laser Prep lets you print to a printer that cannot be initial ized using Chem amp Bio Draw 12 0 If you cre ate drawings with this option off they will not print on PostScript printers without the use of Chem amp Bio Draw 12 0 To include ChemDraw Laser Prep 1 Go to File gt Preferences 2 Click Include ChemDraw Laser Prep 3 Click OK When you select Include ChemDraw Laser Prep you should also select Include Post Script 172 Preferences and Settings Appendix A Document Settings Chem amp Bio Draw 12 0 i
47. Com puter Inc InChI is a trademark of the International Union of Pure and Applied Chemistry Jaguar is a trademark of Schr dinger LLC THE MERCK INDEX is a trademark of Merck amp Company Incorporated Whitehouse Station New Jersey USA and is registered in the United States Patent and Trademark Office Oracle is a registered trademark of Oracle Corporation and or its affiliates Other names may be trademarks of their respective owners All other trademarks are the property of their respective holders Any use of the marks in connection with the sale offering for sale distribution or advertising of any goods and services including any other Web site or in connection with labels signs prints packages wrappers receptacles or adver tisements used for the sale offering for sale distribution or advertising of any goods and services including any other Web site which is likely to cause confusion to cause mistake or to deceive is strictly prohibited Copyright Notice The materials contained in CambridgeSoft Database Products including but not limited to Che mACX ChemIndex and The Merck Index are protected by copyright laws and international copy right treaties as well as other intellectual property laws and treaties Copyright in the materials contained on the CD and internet subscription products including but not limited to the textual material chemical structures representations artwork photographs computer
48. Ctrl drag Text Copy a selected object Shift Ctrl drag constrained to X and Y Flush left Distort limit resize to X Shift drag with Y axis resize handle Center Shift Ctrl C Toggle the Lasso and the Ctrl Alt Tab Flush right Shift Ctrl R previous drawing tool Justified Shift Ctrl J 210 Shortcuts and Hotkeys Appendix G Change direction of a chain Ctrl Drag with alkane chain tool Change orientation of Shift Click double bonds with saturated double bondring tools Create resonance delocal Ctrl Click with ized ring ring tools except chairs Remove a curve segment Alt Shift Click with the pen tool Chem amp Bio Draw 12 0 211 User Guide Nicknames Ac Bz c C7H13 cyclopropyl DPIPS i C4H9 Ad BOM c C8H15 Cys DPTBS i C5HI11 Ala Bs c Hx Dan DTBMS i Pr Alloc Bt C10H20 DEAE DTBS Ile Allyl Btm C10H21 DEIPS Et Im Am Bu Cbz DMIPS Fmoc Leu Arg Bzh cHx DMPM Gln Lys Asn Bzl CoA DMPS Glu m C6H4 Asp BzOM Cy DMTr Gly m Phenylene Benzoyl c C3H5 cyclobutyl DNP His m Tolyl Benzyl c C4H7 cycloheptyl Dnp i Am MDIPS Bn c C5H9 cyclooctyl Dns i Bu MDPS Boc c C6H11 cyclopentyl DNS i C3H7 Me MEM n Pr Phenyl s Butyl TBDMS Thr Mes N3 Pht s C4H9 TBDPS TIPDS Met neo Am Piv s C5H11 TBMPS TIPS MMTr neo C5H11 PMB SEM TBS TMS MOM Np PMBM Ser TDS Tos
49. Group name Formula cannot be computed for queries Displayed for every label that contains a generic nickname an element list or an alterna tive group This is a status message only analysis continues as if the problem atic label were not selected Chem amp Bio Draw 12 0 197 User Guide Message Description Message Description Text not in Formula style won t be inter preted Displayed for the first caption that is not an atom label or Alternative Group name and which contains any text not in Formula Subscript or Super script style This is a status message only and appears only once regardless of how many captions are in the selection This isolated bond is probably not intended to have chemical significance Displayed for unlabeled single bonds unattached to other bonds All bonds are interpreted chemically usually as C gt H and may cause unexpected results 1f intended as a graphical line only This is a status message only This named alternative group contains no attachment point Displayed for any structure within an Alternative Group Box where the structure lacks an attachment point This is a status message only The atom is very close to another atom or bond Displayed for any atom that is nearly touching another atom or bond but not bound to it If a bond really was intended the analysis of the structure produces incorrect resul
50. If it is attached to a collection of atoms and bonds and a set of brackets it will be converted to two different Data SGroups To attach data to objects 1 Select an object 2 Go to Object gt Attach Data The Attach Data dialog box appears 3 Enter the field name and click OK NOTE Field names cannot be edited in Chem amp Bio Draw 12 0 after they are created While Chem amp Bio Draw 12 0 will allow any field name length MDL formats have restrictions that users should be aware of before creating names Likewise Chem amp Bio Draw 12 0 will allow data to be attached to any object When saving to MDL formats this data will be lost unless the object meets the rules noted above 4 Enter the data in the text box under the object Modifying Attached Data Chem amp Bio Draw 12 0 treats attached data as normal text for most purposes However two additional commands appear on the context menu when attached data is selected Select Linked Objects changes the selection to include all of the objects associated with the data Position opens up the same dialog that is used to position ObjectTags allowing you to position the data relative to the associ ated structure NOTE Positioning information is lost when saving to MDL formats Graphics export border preference You can specify the size of the border when exporting pictures This preference affects the output of all graphical formats including
51. Label Size 9 pt Caption Font Win Mac Caption Size 9 pt Drawing Area Width x Height 8 9 cm x 25 4 cm 1 column 19 cm x 27 7 cm Page Size US Letter Reduction 100 178 Preferences and Settings Appendix A Science of Synthesis Fixed Length 17 pt Bold Width 2 pt Line Width 0 8 pt Margin Width 2 25 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Atom Label Size 10 pt Caption Font Win Mac Caption Size 10 pt Drawing Area Width x Height 19 79 cm x 27 15 cm Page Size A4 Reduction 96 100 HO Chem amp Bio Draw 12 0 179 User Guide Synthesis Synlett HO Fixed Length 17 pt Bold Width 2 pt Line Width 0 8 pt Margin Width 1 3 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Atom Label Size 10 pt Caption Font Win Mac Caption Size 10 pt Drawing Area Width x Height 12 cm x 26 7 cm Page Size A4 Reduction 100 Verlag Helvetica Chimica Acta HO Fixed Length 17 pt Bold Width 2 9 pt Line Width 0 54 pt Margin Width 2 pt Hash Spacing 2 pt Chain Angle degrees 120 Bond Spacing of length 14 Atom Label Font Win Mac Atom Label Size 10 pt Caption Font Win Mac Caption Size 12 pt Drawing Area Width x Height 368 x 720 pts Page Size US Letter Reduction
52. Management Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK 44 1223 464900 FAX JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com MANAGEMENT General R amp D IP Protection and Regulatory Compliance General R amp D CambridgeSoft s E Notebook is a solution that enables pharmaceutical and biotechnology companies to improve the efficiency of the process from diseased target identification to prod uct launch Its core Oracle database manages the workflow to be compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and the FDAS 21 CFR Part 11 while the client interface is highly configurable and flexible Anywhere a shared drive is used E Notebook can offer a better solution Through the R amp D process using CambridgeSoft s E Notebook in each subsequent stage adds increasing scientific and economic value by providing workflow automation and knowledge sharing Research and Discovery E Notebook Enterprise is capable of providing knowledge manage ment chemical and biological focused solutions in virtually all areas of discovery Researchers can record and share their experi mental informati
53. OH m OH Figure 5 15 Adding the OH labels 3 Move the pointer to the other atoms as shown and triple click to repeat the atom label TIP If placing the labels is difficult because of the drawing size go to View gt Magnify Add the CH5OH label 1 Triple click the upper atom of C5 2 Press the Enter Windows or Return Mac intosh key to open the atom label text box Type CH2 before the OH H Figure 5 16 Adding the CH OH label NOTE When used with a bond tool active Enter Windows or Return Macintosh is a Hotkey that opens a text box for the last atom labeled Change the type of the front bonds 1 Click the Bold Bond tool 2 Point to the center of the bond shown below CH20OH 3 Click to change to the new bond type 4 The cursor changes to a bold arrow as you point at the bond 5 Click the Bold Wedge bond tool 6 Click each of the ring bonds adjacent to the bold bond For each bond point slightly off center in the direction that you want the wide end of the wedge to be oriented and click TIP If you move the pointer too far the high light box disappears If you find placing the pointer difficult go to View gt Magnify NOTE If the wedge is pointed in the wrong direction click the bond again to flip its orien tation The resulting structure is shown in below CH20H OH Save and close the document 1 Go to File gt Save 2 Go to File gt Close
54. R stereochemistry 1s preserved Save and close the document 1 Go to File gt Save 2 Go to File gt Close Tutorial 7 Templates Chem amp Bio Draw 12 0 comes with an exten sive template library of predrawn structures and images to help you work more quickly You can use a template to either start a new drawing or to modify one that already exists Chem amp Bio Draw 12 0 57 User Guide In this tutorial we use the phenanthrene tem plate to create peroxydibenzene The template and final drawing are shown below phenanthrene peroxydibenzene There are two simple steps to follow when using a template First add the template to your drawing second modify the template to look the way you want To add the template for phenanthrene 58 Tutorials Chapter 5 1 Go to File gt Open Style Sheets gt New Docu ment 2 In the Main toolbar select the template tool The list of template palettes appears 3 In the Aromatics palette select the phenan threne template it is in the fourth row third column 4 Click anywhere in the document window Phenanthrene appears Now that phenanthrene is in the document you will want to remove two bonds from the center ring and add two oxygen atoms To modify phenanthrene 1 In the Main toolbar select the Eraser tool 2 Click the bottom bond in the center ring 3 Click the double bond at the top of the ring It is now a single bond 4 In the Main too
55. Reduction 100 Chem amp Bio Draw 12 0 User Guide 173 Adv Synth Catal Fixed Length 17 pt Bold Width 2 pt Line Width 1 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Atom Label Size 10 pt Caption Font Win Mac Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 J Chin Chem Soc HO e Fixed Length 18 pt Bold Width 2 5 pt Line Width 1 pt Margin Width 2 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 20 Atom Label Font Win Mac Atom Label Size 12 pt Caption Font Win Mac Caption Size 12 pt Drawing Area Width x Height 693 pt x 918 pt Page Size US Letter Reduction 80 174 Preferences and Settings Appendix A J Mol Mod 1 column HO HO Fixed Length 14 4 pt Bold Width 2 pt Line Width 0 6 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Times New Roman Times Atom Label Size 10 pt Caption Font Win Mac Times New Roman Times Caption Size 10 pt Drawing Area Width x Height 8 5 cm x 25 4 cm 1 column 17 cm x 25 4 cm 2 column Page Size US Letter Reduction 96 100 Chem amp Bio Draw 12 0 175 User Guide New Document HO Fix
56. Solutions Narurwinenwhafitiche Unternehmenslsungen Solutions globales pour les sciences de la vie 2427 TVA X78 FX VU CAMBRIDGESOFT Vision Passion Research Discovery Development CambridgeSoft Software Solutions and Databases SOLUTIONS amp Innovation Trials and Manufacturing Motivated by Vision Innovation is an organizational must in pharmaceutical biotechnology and chemical industries Effective new ideas developed through collaboration and communication free from organizational boundaries will determine your long term success In today s connected world information flow within organization can be overwhelming Large amounts of data some structured and some unstructured can cloud an R amp D organization s ability to focus on what is important Since 1986 CambridgeSoft has been solving the problem of electronic storage and communication of chemical structures models and informa tion Starting with ChemDraw then broadening to ChemOffice in 1992 and BioOffice in 2004 CambridgeSoft extended its software to include enterprise wide solutions with ChemOffice Enterprise in 1998 E Notebook in 2000 and biology with BioAssay in 2001 Today CambridgeSoft products are used by hundreds of thousands of chemists biologists scientists and engineers who work in pharmaceutical biotechnology and chemical industries including government and academic research These systems work with
57. The arrow indi cates the bond connected to the attachment point of the nicknamed functional group 3 Go to Structure Define Nickname The number of connection points is shown by radicals in the formula 4 Type a short name for the nickname 5 Click OK If you use a nickname that is the same as an element name a message indicates that the ele ment is replaced with the nickname For exam ple using Ac for an acetyl group replaces the element Actinium The Check Structure com mand recognizes the label as an acetyl group rather than Actinium The Nicknames list provides the following default Nickname Element conflicts Symbol Nickname Element Ac Acetyl Actinium 76 Advanced Drawing Techniques Chapter 6 Symbol Nickname Element Am Amyl Americium Np para Nitrophenyl Neptunium Pr Propyl Praeseodymium To remove the overriding Nicknames go to File gt List Nicknames and delete the overriding nickname definition Deleting Nicknames You can also delete nicknames from the Nick names dialog box To delete a nickname 1 Go to File gt List Nicknames 2 Select the nickname and click Delete Troubleshooting Nicknames If the Define Nicknames command is disabled check for the following Aconnection point that is not present More than two connection points that are defined Aconnection point that is not a single bond In Figure a below the entire functional group was selected Becaus
58. a cross hair when you click You can drag to a different region to change the hue and saturation 3 Click in the Luminosity box to set the brightness of the color 4 If necessary change the hue saturation luminosity and RGB components by typing the values in the text boxes 5 Click Add to Custom Colors 6 Click OK Macintosh Color Settings To change the palette of colors used in the cur rent document 1 Go to File gt Document Settings The Docu ment Settings dialog box appears 2 Click the Colors tab 170 Preferences and Settings Appendix A 3 Click New Color Layout f Footer Y Drawing Captions Atom Labels Colors Background Color 1 4 New Color Foreground Color ae Other Colors Remove Color j Pa ae Set Background Color Color Picker Original GS CMYK a Crayon Cyan Gee 0 e Magenta e 50 HSV Yellow 100 Y Black TT 0 Figure A 3 The Macintosh Color Picker dialog box 4 Use one of the icons on the left to select a method of defining your color then select a color For more information about the Macintosh color options see your System documentation 5 Click OK The new color appears in the Colors tab in place of the original color and is added to the color menu To add a new color to the Color menu 1 Click New Co
59. amp Bio Draw 12 0 checks differences up to 15 atoms distant from the stereocenter Stereochemical Indicators After the ligands are ranked an indicator is assigned as shown in the following table Stereo Indicator center Double bond Z 1f the highest ranking ligand of each pair are on the same side of the bond otherwise E Tetrahedra When the lowest ranking atom ligand is located behind the central atom R when remaining 3 ligands are arranged clockwise in descending order S when remaining 3 ligands are arranged counterclock wise in descending order rors is used for pseudo asymmetric atoms Stereochemical Flags While the chirality of a specific stereocenter can be indicated with the appropriate wedged hashed or plain bond sometimes it is useful to indicate the relative stereochemistry of a mole cule as a whole considering the relationship between all stereo centers Stereochemical flags apply to the nearest structure if no struc ture is within the distance specified by the Chem amp Bio Draw 12 0 195 User Guide Fixed Length value the stereochemical flag is not assigned to any structure Abs COOH NH2 COOH NHz Figure C 6 The Absolute flag indicates the exact stereoisomer as drawn ill e COOH NH NH2 Z jine H2 Figure C 7 The Relative flag indicates the exact stereoisomer as drawn or its enantiomer 196 Chemical Interpretation
60. amp Finds compounds where the Change selected bonds are formed bro ken or undergo a change in bond order Not Center Finds compounds where the selected bonds are not part of the reaction center Not Modi Finds compounds where the fied selected bond s orders do not change but which may or may not be part of the reaction cen ter Unmapped Finds all compounds Element Lists By labeling an atom position with a list of ele ments you specify that one of these elements must match in the structure for which you are searching An example of an element list is S Se Te The elements in the list must be separated by commas A space after each comma and brack ets are optional NOTE An element list may contain only atomic symbols plus D deuterium and T tri tium To create an element list 130 Query Structures Chapter 10 1 Open an atom label text box 2 Type an open bracket followed by a list of elements separated by commas Br I followed by a close bracket 3 Close the text box Br 1 Figure 10 6 An element list as an atom label The figure below shows a query structure cre ated to find compounds matching the follow ing criteria B A 20 5 Se Te A indicates that the atom must match atom except hydrogen The indicator B near the bond indicates that the bond must be single or double S D
61. and BioViz All are integrated with Microsoft Office to speed Inventory amp E Notebook research tasks ChemBioFinder Gateway SCIENTIFIC DATABASES Good research depends on reference information starting with the structure searchable The Merck Index P 9 ChemACX Database of commercially available chemicals and Sigma Aldrich MSDS The Merck ChemACX Database Index and other scientific databases provide necessary background about chemicals their prop erties and reactions Development PROFESSIONAL SERVICES Training amp Support CambridgeSoft s scientific staff has the industry experience and the chemical and biological knowledge to maximize the effectiveness of your information systems ENTERPRISE amp Chem amp Bio Office Enterprise Integrated Research Discovery Development Desktop to Enterprise Since the company s founding CambridgeSoft s desktop soft ware starting with its industry leading Chem amp Bio Draw has been the cornerstone application for scientists who draw and annotate molecules reactions and pathways This suite of enter prise applications has developed and now provides solutions in all areas of discovery Research and Discovery Researchers record and share their experimental information using E Notebook while protecting intellectual prop erty with digital signatures and 21 CFR Part 11 compliance They can design both single experiments or design combinatorial libraries of compoun
62. and pharmaceutical laboratories and E Votebook for manufacturing compliance management Desktop Software includes Chem e Bio Office a powerful suite of software consisting of ChemBioDraw ChemBio3D ChemFinder and ChemACX for chemists BioDraw BioAssay and BioViz and for biologists and Inventory and E Notebook for all Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma Aldrich MSDS The Merck Index and other scientific databases provide information about chemicals their properties and reactions Professional Services include custom development system deployment educational training and technical support for pharmaceutical biotechnology and chemical customers including government and academia by experienced staff Web www cambridgesoft com Email info cambridgesoft com Ca m b ridge Soft America 1 800 315 7300 United Kingdom 44 1223 464900 Ti Science Enterprise Solutions Europe 00 800 875 20000 Germany 49 69 2222 2280 Naturwissenschafiliche Unternehmenslomungen Solutions globales pour les sciences de la vie Japan 0120146700 France 33 170 7198 80 Sess SR x b 94 Vig MAE 04980 0902 CambridgeSoft Solutions peaturtug x E Notebook DESKTOP SOFTWARE ENTERPRISE SOLUTIONS CHEMICAL amp BIOLOGICAL RESEARCH INFORMATICS LABORATORY DEVELOPMENT amp MANUFACTURING INFORMATICS KNOWLEDGE MANAGEMENT SCIENTIFIC DATABASES CambridgeSofr Life Science Enterprise
63. as you modify the structure To add analysis data to a caption 1 Right click the caption and select Analysis on the context menu 2 Choose the properties to add Rings You can draw aliphatic and aromatic rings of different sizes and types 1 In the Main toolbar select a ring tool 2 Click and drag in the document window to orient the ring If you click an atom or bond with a ring tool in an existing structure the ring is fused to it Spiro and sprout rings By default clicking an atom in a ring using a ring tool forms a spiro link Chem amp Bio Draw 12 0 21 User Guide You can change this behavior so that a sprout bond appears instead Go to File gt Preferences On the Building Display tab check the box next to Sprout Rings Instead of Spiro When Clicking N Aromatic Structures Delocalized rings You can draw a resonance delocalized ring using any ring tool except for the cyclohexane chairs 1 Click a ring tool 2 Press the Ctrl Windows or Command Macintosh key and drag or click in the document window Resonance structures You can draw cyclopentadiene or benzene in either of their two orientations 22 Basic Drawings Chapter 3 To draw click in the document window with either the cyclopentadiene or benzene drawing tool To draw a different orientation Shift click in the drawing window Acyclic Chains To draw long hydrocarbon chains 1 Select the Acyclic Chain
64. ately aligned centered amp c right amp r left default amp 1 Page Setup You can customize the size orientation and margins for the document page To setup the page go to File gt Page Setup Options for cus tomizing the page appear below Paper Choose the size of the paper on which you want to print the document and the printer tray where the paper is located Orientation Select either Portrait or Land scape Margins By default all margins are set to 0 5 inches Printer Click to select a printer and set prefer ences You can also choose the printer in the Print Options dialog box as described below Printing Chem amp Bio Draw 12 0 uses the standard sys tem commands to print documents The options that you have available to you depend on the printer that you are using See your printer s documentation for more information In general to print a document 1 Go to File gt Page Setup 2 Make all appropriate selections for the printer you are using and click OK 3 Go to File gt Print 4 Make your selections in the Print dialog box and click OK To print a document from Windows Explorer or from the Finder 1 Select the document you want to print 2 Go to File gt Print The Chem amp Bio Draw 12 0 application is opened and the Print dia log box appears 3 Make your selections in the Print dialog box and click OK Print Options Select Printer This window lists all printers co
65. basic computational tools such as 3D Molecular Overlay and Dihedral Driver and utilizes MOPAC Jaguar Gaussian GAMESS and extended Hiickel to com pute molecular properties ChemProp computes Connolly surface areas molecular volumes and properties including ClogP molar refractivity critical temperature and pressure ChemFinder is a chemically intelligent database manager and search engine ChemFinder provides support for a database searching compound profiling R Group Analysis subforms tight integration with ChemDraw Excel and Combichem Excel statistical analysis and visualization through BioViz all in a friendly form based environment ChemFinder Office searches documents spreadsheets and files for chemical structures and references ChemFinder Oracle provides enterprise solution integration BioOffice is the ultimate suite for management analysis and visualization of biological data using 2voDraw for drawing pathways and BioAssay BioFinderand BioVizfor data analysis Includes 58 230 Draw Excel CombiChem Excel Inventoryand E Notebook BioDraw provides support for biological pathway drawing and annotation A wide variety of customizable drawing tools are available including membranes DNA enzymes receptors tRNA ribosomes and a plasmid map tool BioAssay manages both high and low throughput biological screening data Designed for complex lead optimization experiments the software supports the quick set up of biological models
66. batch process records from the pilot plant studies using Jnventory E Notebook and Registration systems Good Laboratory and Manufacturing Processes GxP under The handling of materials including chain of custody require ments material documentation material workflow such as avail ability states and recertification dates are tracked and handled by the system These systems meet the requirements and provide the basis to manage materials and records during clinical trials Clinicians can design and record results from protocols and all of these web based software systems provide the access required by clinicians who are removed from the sponsoring company Chem amp Bio Office Enterprise Chem amp Bio Office Enterprise is a comprehensive knowledge management and informatics solution covering electronic note books biological screening and chemical registration over your intranet ChemBioOffice Enterprise Ultra includes E Notebook for record keeping BioAssay for low and high throughput screening with integrated plate inventory BioSAR for SAR reports Registration System Inventory for reagents and biologicals and ChemACX database of available chemicals Technologies include ChemDraw ActiveX and Oracle Cartridge Chem amp Bio Office Workgroup Chem amp Bio Office Workgroup Ultra is a comprehensive knowl edge management and informatics solution covering electronic notebooks biological screening and more over your
67. bound by the copyright laws just like everyone else Such conduct exposes the company and possibly the persons involved to liability for copyright infringement Consequently more and more corporations concerned about their liability have written policies against such softlifting Employees may face disciplinary action if they make extra copies of the company s software for use at home or on additional computers within the office A good rule to remember is that there must be one authorized copy of a software product for every computer upon which it is run 0 Can take a piece of software owned by my company and install it on my personal computer at home if instructed by my supervisor A A good rule of thumb to follow is one software package per computer unless the terms of the license agreement allow for multiple use of the program But some software publishers licenses allow for remote or home use of their software If you travel or telecommute you may be permitted to copy your software onto a second machine for use when you are not at your office computer Check the license care fully to see if you are allowed to do this 0 What should do if become aware of a company that is not compliant with the copyright law or its software licenses A Cases of retail corporate and Internet piracy or non compliance with software licenses can be reported on the Internet at http www siia net piracy report asp or by call
68. but not necessarily limited to WMF PICT EPS TIFF GIF BMP and PNG It applies to the clipboard and saved files The default value is 2 points 0 278 1n 0 071 cm File Formats Chem amp Bio Draw 12 0 supports importing and exporting the file formats listed below To export in one of these formats use the Save As option Not all formats are supported in all Chem amp Bio Draw 12 0 153 User Guide Chem amp Bio Draw 12 0 products Also see Importing on page 152 Format Import Export ChemDraw CD X YES YES ChemDraw XML CDXML YES YES ChemDraw 3 5 CHM YES YES ChemDraw 2 0 and YES NO ChemDraw 2 1 CHM ChemDraw Template CTP YES YES ChemDraw Template Style YES YES Sheet CTS ChemDraw Stationary Pads YES YES Style Sheets CDS Connection Table CT YES YES Chemical Markup Language YES YES CML a Bitmap BMP YES YES Encapsulated PostScript NO YES Macintosh PostScript EPS Windows Graphic Image Format GIF YES YES ISIS SKC TGF YES YES JCAMP JDX DX YES NO JPEG JPG JPEG YES NO MDL V3000 MolFile MOL yES YES 154 Sharing Information Chapter 11 Format Import Export MDL MolFile MOL YES YES MDL RGFile RGF 8 YES YES Macintosh Accelrys YES YES MolFile MSM PICT Macintosh YES YES Portable Network Graphics YES YES PNG Standard Molecular Data YES YES SMD Struct
69. button over the Chemical Symbols tool and drag to select the charge symbol from the palette 2 Click and drag the atom to which you want the charge to correspond The number of hydrogen atoms increases or decreases as appropriate for the addition of the charge Attachment Points The ability to indicate an attachment point is useful in polymer bound combinatorial synthe sis protein chemistry and other situations The Chemical Symbols toolbar includes four stan dard attachment point drawing tools that allow you to indicate a point of attachment while maintaining chemical meaning p 7 i ia o Figure 8 4 Attachment point symbols The bead tool are specifically intended to indi cate attachment to a resin Any of these tools may be used for variable attachments in que ries see Attachment Points on page 63 but only the diamond tool shows rank numbers This means that as you add diamond symbols to a structure the points will have sequential numbers Rotating a Symbol You can rotate the radical anion cation and lone pair symbols around the same end from which they were originally drawn For exam ple the radical cation symbol is rotated and resized from the charge The Info window shows the angle that one of the ends of a sym bol makes with the X axis as you rotate To rotate a chemical symbol 1 Select the chemical symbol 2 Drag the rotation handle on the chemical symbol See Rotating Objects
70. check mark appears next to the Fixed Lengths command 2 Using the Solid Bond tool begin drawing a structure The bonds in the new structure appear at default lengths Drawing fixed angle bonds When you fix bond angles all bond that you draw are constrained to angles that are multi ples of 15 relative to the X axis Chem amp Bio Draw 12 0 13 User Guide 1 Go to Object gt Fixed Angles and ensure that a check mark appears next to the Fixed Angles command 2 Select a bond tool 3 Begin drawing a structure The bonds in the new structure appear at stan dard 120 angles relative to the X axis Changing fixed values By default bond lengths are drawn at 4167 in and bond angles in a chain are shown at 120 by default To change the default fixed values 1 Go to File gt Document Settings and click the Drawing tab 2 Enter a value in the Fixed Length text box Use in cm pt or iu for units default is 4167 in 3 Enter a value in the Chain Angle text box 4 Click OK NOTE To suppress fixed lengths and fixed angles press the ALT Windows or Option Macintosh key as you drag the bond Bond Types Double Bonds There are four ways to draw a double bond Draw a bond using the Double bond tool Draw a single bond over an existing single bond Using any bond or selection tool point to an existing bond and type 2 Right click any bond and select Dou ble gt Plain in the co
71. com pounds where distant polar interaction is present Chem amp Bio Draw 12 0 201 User Guide Molar Refractivity Molar refractivity T wo fragmentation methods are used to estimate the molar refrac tivity value Method one includes 93 atomic contribu tions evaluated from 504 molecules by using a constrained least squares technique This method works with a standard devia tion 1 27 cm3 mol and can handle mole cules containing hydrogen oxygen nitrogen sulfur and halogens The second method is an extension of method one that includes 120 atomic contri butions evaluated from 538 molecules by using a constrained least squares analysis technique In addition to the atoms intro duced for method one this method can han dle molecules with phosphorus and selenium atoms This method works with a standard deviation of 0 77 cm mol CLogP and CMR Specific algorithms for calculating LogP and molar refractivity from fragment based meth ods developed by the Medicinal Chemistry Project and BioByte NOTE CLog P and CMR are available in ChemBioDraw Ultra and ChemDraw Ultra only 202 Property Calculations Appendix D Topological Polar Surface Area The polar surface area of a molecule mea sured in square angstroms can be used to pre dict of pharmaceutical transport properties in the body Historically this property has been calculated using time consuming 3D tech niques However but a recent paper has
72. cre ate high quality chemical drawings The ChemDraw series includes ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 ChemDraw Pro 12 0 and ChemDraw Standard 12 0 ChemDraw Standard 12 0 is designed for users who only need a fundamental method for drawing structures However if you need a more powerful application one that is designed for creating advanced chemical struc tures and analysis you may consider ChemDraw Pro 12 0 or ChemDraw Ultra 12 0 If you need an advanced drawing application that also includes the ability to draw biological structures and pathways you will want to refer to ChemBioDraw Ultra 12 0 ChemBioDraw Ultra 12 0 includes all features that are avail able in the Chem amp Bio Draw 12 0 Series and BioDraw Series For more information on Chem amp Bio Draw 12 0 see www cambridgesoft com The BioDraw Series Designed to complement the Chem amp Bio Draw 12 0 Series the BioDraw series of appli cations has been developed specifically for the biology and biochemistry communities of users The BioDraw series includes BioDraw Pro 12 0 BioDraw Ultra 12 0 ChemBioDraw Ultra 12 0 also part of the Chem amp Bio Draw 12 0 series In addition to all the standard chemical draw ing tools the BioDraw series also includes tools specifically designed to illustrate biologi cal pathway and biochemical structure For example use the BioDraw tools to describe binding sites for enzyme inhibitors illustra
73. crossed all fragments on each side of the line are considered together If the only bond crossed is a ring bond a single formula mass pair is displayed You can reposition the formula and mass dis plays they are text objects or delete them altogether Synthesis and Retrosynthesis Chem amp Bio Draw 12 0 includes two tools to help you draw synthesis reactions The Synthe sis tool draws synthesis reaction based on a product structure that you specify Alterna tively the Retrosynthesis tool draws the reac tion with the product on the left and a broad arrow pointing to the reactants These tools are in the fragmentation tools palette of the main tools palette To demonstrate these features we use the Beyer Method for quinolines starting with the structure below You can create either type of reaction using the appropriate tool and dragging through bonds indicated by the dotted line For example if you use the retrosynthesis tool you will create the reaction N R NH R Uu gt t 22 Figure 6 8 Reaction created with the Retrosynthesis tool NH UR SS o O S AN Figure 6 9 Reaction created with the Synthesis tool By dragging through the bonds in the structure below as indicated by the dashed lines we can create either of two reactions depending on the tool that is used Drawing Reactions To demonstrate how to draw reactions we will use this example e OH Ma p 2 propanone 4
74. draw a bond to a multi center attachment point 1 Click the Bond tool Chem amp Bio Draw 12 0 63 User Guide 2 Point to the asterisk and either click or drag to create a bond TIP Go to Object gt Fixed Lengths to either dis able or toggle Fixed Lengths to draw the bond so that it extends from the ring Variable Attachment Points To create a variable attachment point 1 Draw the structural fragment to which to assign a variable attachment node 2 Select the fragment 3 Go to Structure gt Add Variable Attachment 4 Point to the asterisk in the structure and drag to draw a bond NOTE Either disable or toggle Fixed Lengths to draw the bond so that it extends from the ring Br Br Br Figure 6 6 Using a variable attachment point Viewing Attachment Points After you draw a bond from a variable or multi center attachment point the asterisk dis appears To view an attachment point position the cursor over the attachment point with either 64 Advanced Drawing Techniques Chapter 6 a bond tool or a selection tool The attachment point is highlighted Atom Numbering You can add sequential numbering indicators to atoms The types of indicators are Numbers 1 2 3 and so on Text ending with a number atom1 Greek letters in the Symbol font Letters a b c and so on The default indicator is numbers TIP To use text instead of numbers number an atom then edit the n
75. draw a new arrow starting at the midpoint of an existing arrow 1 Select from the Arrows palette an arrow type for the new arrow 2 Place your cursor over the midpoint of the existing arrow and hold down the Shift key 3 With the shift key held down draw the new arrow starting from the existing arrow s midpoint You can also drag existing arrows and connect them Here are a few examples A R Finally arrows can be rotated with the Struc ture Perspective tool as well as the Lasso or Marquee Combining these methods lets you draw an unlimited number of arrows that are otherwise difficult to create EQUILIBRIUM ARROWS For equilibrium arrows changing the length changes both arrows proportionately changing the shape of the arrowhead changes both arrowheads identically To change the length of only one arrow hold down the Alt or Option key Two new adjustment handles appear When you have created a unbalanced equilib rium arrow only the shorter side can be adjusted further A NONE ud y gt Drawing Elements Drawing elements are simple shapes such as circles and rectangles that you can add to your drawing Drawing elements cannot belong to a structure Therefore if you double click on a bond atom or atom label with a drawing tool they are not selected To group drawing ele ments with a structure go to Object gt Group See Grouping Objects on page 31 The Info window indicates the
76. gt where n is a number unique to the worksheet The simplest way to insert a new structure in a cell is by using Chem amp Bio Draw 12 0 1 Double click in a cell The ChemDraw for Excel dialog box appears 2 Click Yes Chem amp Bio Draw 12 0 opens Draw the structure 4 n Chem amp Bio Draw 12 0 go to File gt Exit and Return to New Molecule The new struc ture appears in the cell Adding a Structure From a File 1 In Excel select the cell into which you want to add the structure 2 Go to ChemOffice12 gt Molecule gt Load The Choose Molecule To Load dialog box appears 3 Type or select the file name of the structure to add and click Open SMILES Strings You can insert SMILES strings into cells and convert them to structures NOTE This feature is available in ChemBio Draw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only 1 Type or paste the SMILES strings into one or more cells 2 Select the cells to convert NOTE Optional To keep the original text copy and paste it elsewhere 3 Go to ChemOffice12 gt Convert gt SMILES to Molecule The cell will display a text string starting with Structure followed by a number 4 To display the structure click the Show Pictures icon If the cell did not contain a valid SMILES string the string remains Adding Structures by Name You can type or paste the names of chemicals into cells and convert them into str
77. guides together show the height and width of the selected object The Crosshair Use the crosshair to align objects relative to each other and to space objects an equidistant apart The axes of the crosshair can be moved within a document window Displaying the Crosshair To toggle the Crosshair on and off go to View gt Show Crosshair To assist you in aligning objects the Crosshair includes grid lines that extend from the major division marks on each axis You can also show the rulers while the crosshairs are displayed so that you can see the unit measurement associated with each divi sion on the crosshair axes Chem amp Bio Draw 12 0 187 User Guide Moving the Crosshair 1 Position the pointer where the Crosshair axes intersect The pointer changes to an arrow when it is near the center of the crosshair 2 Click and drag the crosshair To constrain crosshair to move in the X or Y direction shift drag the crosshair Positioning Objects To align two or more objects do anyone of the following Move the Crosshair axes and align it with the object Select an object and drag it until it is aligned with either axis of the Crosshair or a grid line 188 Page Layout Appendix B In either case if a bond or side of the object is parallel to one of the axis it disappears when it is exactly positioned over a Crosshair axis 3 Select a second object 4 Drag the second object to the crosshair axis o
78. in the folder C Documents and Settings All Users Application Data CambridgeSoftNChemOffice2010 ChemDrawNChemDraw Items The Hotkeys in the file are organized by object type Atom Hotkeys used to modify atoms Bond Hotkeys used to modify bonds Generic Hotkeys used to select tools and open dialog boxes Each Hotkey is encoded in this format lt Hotkey key key command command value value description description gt key Key 1s the keyboard key that invokes the com mand You can assign a particular key to dif ferent functions as long as the functions are defined in different object types For example b changes an atom to Boron in the Atom object type a bond to bold in the Bond object type and could be assigned to the Benzene tool in the Generic object type You can use any key except the hard coded keys function keys Enter Space Backspace and arrow keys When you edit the xml file remember that 1f you create capital and lowercase Hotkeys for the same object type the Hotkey will be case sensitive If a key appears more than once in the file for the same object type the one closest to the end of the file takes precedence command Command is any one of the predefined com mand names All available commands are described in the hotkeys xml file NOTE You cannot add to the command list value This is the parameter value associated with the command For e
79. in the periodic table and click the atom in the document you want to change TO EDIT A LABEL To modify the atom label double click the atom in the document window NOTE Some element names conflict with Chem amp Bio Draw 12 0 Hotkeys and may not be interpreted correctly Character Map Use the character map to add ASCII and other symbols to your document in various font styles To show or hide the map go to View gt Show Character Map Window The character map is active only when a text box is open for editing With a text box open mouse over the character map to view a larger version of the characters in the top right corner of the window Click any character in the table to enter it in the text box The selected font shown in the character map window is applied to that character only It does not change the active font in the text box NOTE To cancel a selection drag it to another character before releasing The eight most recently used characters appear at the top of the window These characters retain their font and are not affected by changes to the window A character may appear more than once in this section if the versions use different fonts Click the back but ton to toggle among all the displayed charac ters Chem amp Bio Draw 12 0 11 User Guide 12 Getting Started Chapter 2 Basic Drawings Chem amp Bio Draw 12 0 provides a variety of tools for drawing everything from simple che
80. is an important com ponent of today s research institutions A key document that aids in the management of EH amp S tasks is the Material Safety Data Sheet also commonly referred to as MSDS In every organization there are several groups of personnel who require access to MSDSs Everyone who comes into contact with chemicals needs Scientific Databases REFERENCE DATA The Merck Index 11 000 monographs R amp D Insight Chemists 20 000 substances ChemlNDEX Database 75 000 substonces NCI AIDS amp Cancer 270 000 substances Troditional Chinese Medicines 10 000 substances Drugs Synonyms amp Properties 8 000 drugs Nanogen Index 1 000 pesticides Medicinal Chemistry 540 000 substances ChemACX Database 480 catalogs ChemMSDX Database 23 000 MSDSs Sigma Aldrich MSDS 130 000 MSDSs REACTION amp SYNTHESIS DATA ChemReact500 450 000 reactions ChemReacl 8 68 000 reaclions ChemSynth 178 000 reactions US 1800315 7300 INT L 1 617 588 9300 FAX 1617 588 9390 EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com ChemACX is fully structure searchable with more than 1 million products from nearly 500 catalogs ChemACX and the Sigma Aldrich MSDS are updated semi annually to meet the needs of scientis
81. length and angle relative to the X axis while you use any of the drawing element types 1 Select a rectangle tool from the Drawing Elements toolbar 2 Click and drag the box to the size you want Circles and Ovals To draw a circle or oval 1 Select one of the circle or oval tools 2 Point to where you want the center of the circle 3 Drag outward from the center RESIZING AND ROTATING You can modify rectangles circles and ovals the way you modify arrows 1 Point to a shape with its drawing tool or a selection tool to display adjustment han dles 2 Click and drag to modify the shape Circles have only a radius adjustment but you can resize and reshape ovals and rectangles for both length and width Rectangles also have corner handles that adjust length and width proportionately Lines Lines drawn with the line tool differ in two sig nificant ways from bonds drawn with the bond tools Chem amp Bio Draw 12 0 25 User Guide Lines are not included in chemical interpre tation of the drawing Lines that cross appear solid bonds do not To draw a line 1 In the Drawing Elements toolbar select a line tool 2 Click and drag in the drawing window where you want the line Arcs Use the Arc tools to draw solid or dashed arcs of different angles 90 120 180 and 270 To draw an arc 1 Do one of the following In ChemDraw Standard point to an Arc tool and drag in the palette to s
82. molecules with little thought for the world of formulations and mixtures CambridgeSoft has developed a system specifically designed for this registration need called Formulations amp Mixtures ChemFinder Enterprise ChemFinder Enterprise is a multiple user system designed for sites with comprehensive chemical and biological data needs ChemFinder Enterprise contains its own engine for working with local and shared databases and it is also delivered with the CambridgeSoft Oracle Cartridge the powerful Oracle hosted structure engine based on ChemFinder search technology The face of ChemFinder Enterprise is the same friendly form oriented inter face as the desktop version but underneath is a fast direct connec tion to Oracle and the robust scalable Oracle Cartridge running on the server Substance Barcode Expires On Ordered On PPSORUORICAC Ouen Aurotenzene sura 22592 TERAMEIMILAPMENUMH 2 Gene snap isai s Gap anspoo 7601 552 ES sr wr gelcs pemtaerythel Tevanwiate Sr saga es 1942455 l rn snap nre Suse Supp Quante Conners EH Cit You are logzedinas Troma PiniLabel 41 kh tast modifed at 11 5 2003 30300 PM shown below ofthe document changes necessary before submission v Index Documents esr kd sio Cortaner Sc S d Comarer Type
83. nicknames together an atom label with a bond attached GIyAlaOH Stringing nicknames together without bonds HGIyAIaOH Disulfide Bridges Creating a disulfide bridge between cysteine residues is as simple as drawing a bond Bridges between chains To draw a disulfide bridge between two chains 1 Draw two chains each containing cysteine 2 Draw the bond between the cysteine resi dues H Asn Pro Cys OH H lle Leu Cys OH Figure 4 4 Before drawing the disulfide bridge H Asn Pro Cys OH H lle Leu Cys OH Figure 4 5 After drawing the disulfide bridge Bridges within a chain To draw a disulfide bridge within a chain Chem amp Bio Draw 12 0 43 User Guide 1 Draw a chain that includes two cysteine res The bonded residues appear below idues such as the one below H Pro Cys Leu His Lys Cys OH peo PIOS MPH EMPSHEBEOH Eyes wen 2 Using the single bond tool draw a bond from one cysteine residue to the other 44 BioDraw Chapter 4 Tutorials Overview The tutorials illustrate fundamental drawing techniques Each tutorial introduces new tech niques or variations of techniques learned in previous tutorials We therefore suggest that you follow the tutorials in order Before you begin review Conventions for this guide on page 4 to familiarize yourself with the terminology You may also want to use your quick reference card while
84. of the double bracket tools 3 To draw the brackets click and drag across the structure you want to enclose This method will give a default value for com ponent order multiple group repeat count or SRU label Setting Bracket Properties You can change the properties of brackets by the context menus or Bracket Properties dialog box To use the Bracket Properties dialog box 1 Select a bracket using a selection tool 2 Go to Structure Bracket Properties The Bracket Properties dialog box appears The Flip Type option appears only for ladder polymers See Flip Type on page 134 You can customize the text that appears to the bottom right of the bracket for the following bracket types Component c the component order must be a non negative integer and is dis played as the letter followed by an inte ger or alone if an order of zero is specified Multiple Group the repeat count must be a positive integer SRU n the SRU label can be any text You can also edit the text for these bracket usage types directly in the document using the Text tool You cannot edit the text displayed for other bracket usage types Chem amp Bio Draw 12 0 131 User Guide Bracket Usage Representations of polymers are either struc ture based or source based The type of bracket you use depends on which type of rep resentation you need Structure based Polymers Structure based rep
85. or side ticks Change the order of lanes Right click or Control click in the plate and select the appropriate action Use the Transparent option to overlay the TLC plate on a scanned plate Drag the origin tick to the new location Display or set the Re for a spot add a custom spot Right click or Control click on a spot 2 Point to TLC Spots and take the appropri ate action To display R for all spots right click or Control click in the plate and select Show Rf from the TLC Spots submenu Add delete or duplicate a lane Position the cursor on the lane you want to delete or duplicate or between lanes to add 2 Right click or Control click in the plate 3 Select the appropriate action You can also delete lanes with the Eraser tool Change the style or color of a spot Right click or Control click in a spot 2 Choose the style or color To change the style for all spots Right click or Control click in the plate and choose the style from the TLC Spots submenu Move a spot Drag the spot The Rr displays as you drag Duplicate a spot Ctrl drag or Option drag the spot 94 Chemistry Features Chapter 8 If you want to then Enlarge or smear Shift drag the spot When a spot you position the cursor on a spot and press Shift the cursor assumes one of three shapes depending on how it is positioned
86. or the magnifica tion controls Magnification Magnifying your drawings changes how large or small it appears without changing its actual dimensions You can either select a value in the magnification dropdown list or enter your own value between 1 and 999 Magnify 1 Select an object you want to keep in view as you magnify the drawing NOTE If you do not select an object the last object drawn is the center point of the magnifi cation 186 Page Layout Appendix B 2 Go to View gt Magnify or press F7 The magnification occurs around the center of the selected object The magnification percent age appears in the Magnification control on the General toolbar Actual Size To return to the actual size from any other magnification go to View gt Actual Size Reduce To reduce the magnification 1 Select an object around which you want to reduce the magnification NOTE If you do not select an object the last object drawn is the center point of the magnifi cation 2 Go to View gt Reduce The reduction in magnification appears in the Magnification drop down list You can reduce the magnification until the entire page fits on the screen In the reduced view you can continue to use all of the draw ing tools In particular you can use a selection tool to rearrange the drawing to take better advantage of the space available Show Document Show Document reduces the magnification until the enti
87. organizations Oracle Cartridge manages chemical structures and reactions in a common data repository layered with detailed security and is 21CFR Part 11 Compliant audit trails digital signatures The enterprise edition works with procurement databases and services including ChemACX database and Inventory management systems to save time locating chemicals and entering structures Flexible and Configurable Architecture The E Notebook architecture is designed to provide organizations with an unparalleled level of flexibility A powerful configuration layer is provided to make it possible to modify substantially the look and feel of the application in order to meet very diverse work flows Detailed workflow support in the same application is pro vided for researchers in early stage discovery through early clinical development even though the requirements for these groups are totallydifferent Beyond configuration a rich API is provided for custom development and system integration E Notebook is also in production with integrated inventory sys tems including CambridgeSoft s Inventory manager as well as in house systems analytical data capturing systems and com pound registration systems E Notebook supports limiting access to certain information at the project or group level if desired as secu rity is granular Information can be shared or secured as desired throughout the framework RESEARCH amp CHEMISTRY A
88. powerful data catalog technique with knowledge gained through years of working closely with scientist users The result is a SAR application that is as intuitive as it is powerful Security within BioSAR Enterprise is highly granular different roles exist for administrators publishers and browsers Administrators may add assays to the data catalog engine publish ers may create reports and publish them and browsers may use data query and analysis Most data mining tools provide a mech anism to store queries but the interface for creating queries is too complex With BioSAR each set of assays is a complete report with a query form a view form and a table view combining the convenience of a ChemFinder or ISIS application with the power and flexibility of a data catalog driven mining program Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 BioSAR is a catalog driven mining and structure activity analysis program BioSAR provides both form and table views within a simple and powerful web interface BioViz provides one step in depth analysis of several variables BioSAR is a catalog driven data mining and structure activity analysis program BioSAR provides both form and table views within a simple and powerful web int
89. pro vided a remarkably accurate way of predicting it very rapidly Chem amp Bio Draw 12 0 imple ments a more innovative algorithm Other Properties Normal Boiling Point and Melting Point Esti mated in K using two methods Joback s fragmentation method The Joback method as modified by Stein All boiling points are estimated for a pres sure of 1 atm Miscellaneous properties Heat of Formation Gibbs Free Energy Ideal Gas Thermal Capac ity Freezing Point Critical Temperature Criti cal Pressure and Critical Volume are estimated using Joback s fragmentation method The algorithm is based on Ertl P Rohde B and Selzer P 2000 Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment Based Contribu tions and Its Application to the Prediction of Drug Transport Properties J Med Chem 43 3714 3717 ChemNMR NOTE The ChemNMR Feature is available in ChemBioDraw Ultra and ChemDraw Ultra only ChemNMR estimates chemical shifts for all hydrogen or carbon atoms for which additivity rules are available Following a hierarchical list it first identifies key substructures ofa molecule A substructure provides the base value for the estimated shift For example ben zene would be identified as the key substruc ture of trinitrotoluene When a substructure is a ring system not avail able in the data ChemNMR approximates its base shift using embedded rings and if neces sary i
90. returns all molecules in the query database that include a template structure that you provide For example assume you want to find all molecules in the database that include toluene in its structure such as p cresol or o xylene assuming your database includes these molecules Simply draw toluene as your template and the analysis will return all molecules that contain at least one toluene structure Interpreting Analysis Results To illustrate we will assume that you have a small database that consists of four molecules o m and p cresol and bromobenzene Fur ther assume you want to run an R group analy sis on this database to find all the molecules that contain toluene in its structure You will find that the results include three main parts The list of molecules that contain the tolu ene template In this example the results include o m and p cresol Bromobenzene is not included because it does not contain the template The toluene template with all variations of R group attachments that were found in the database In this example the attachments are represented by functional groups These are the locations of the R groups found in the analysis results the hydroxyl groups for o m and p cresol The functional group found at each R posi tion for each search result For a given returned molecule view across its row to view the functional group at each R group position In this
91. ring 4 Click to fuse another ring 6 The create the double bond in the second ring hover the mouse over the bond and type 2 or simply click it gt Figure 5 4 Fusing rings 5 In the final structure there is supposed to be only one double bond in the second ring To correct the current structure hover the mouse over one of the double bonds in the second ring and type 1 Do the same for 7 Using the bond tool click the carbon atoms circled in the figure below Three new bonds will appear the other double bond 8 Hover your mouse over one of the bond Figure 5 5 To change the bond order type I shown below and type 2 Do the same for the other bond N Chem amp Bio Draw 12 0 47 User Guide 9 Hover the mouse over the right most termi Tutorial 3 Fischer Projections nal carbon and type the letter o to create the ketone functional group This tutorial demonstrates creating a Fischer projection of glucose shown below CHO H OH HO H H OH H OH 10 To connect the left terminal carbons select the solid bond tool and click drag a bond CH OH from one carbon to the other The structure is complete Chemical Formula C Hi2O Exact Mass 180 06 Molecular Weight 180 16 m z 180 06 100 0 181 07 6 9 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 53 29 Figure 5 6 Fischer projections 1 Go to File gt Open Style Sheets and choose ACS Document
92. sepa rate the items in the anonymous alternative group A space after each comma and the brackets are optional Examples of anonymous alternative groups are shown below OME OPh B C OCH OH X S SE Figure 10 17 Anonymous alternative groups To create anonymous alternative groups 1 Open an atom label text box 2 an open bracket followed by a list of elements fragments nicknames or generic nicknames separated by commas followed by a close bracket Expand Generic Structures You can generate multiple structures from an abbreviated combinatorial structure with the Expand Labels tool The tool is designed for small expansions and is limited to a maxi mum of 500 generated structures For large combinatorial expansions use CambridgeSoft s CombiChem for Excel NOTE This feature is available in ChemBio Draw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Four kinds of abbreviated combinatorial defi nitions may be used definition example Alternative Groups and R4 R tables Anonymous OMe OH Alternative dii EU Groups Element LKR 1 Br CI Variable CH Attachment 3 BEES Definitions are expanded into multiple com plete molecules If more than one site is present in the selection the expansion will include all permutations of substitutions Expansions are generated in a new document
93. several posters to help emphasize the message that unauthorized copying of software is illegal To order any of these materials please send your request to SHA Anti Piracy Materials Software amp Information Industry Association 1090 Vermont Ave Sixth Floor Washington D C 20005 202 289 7442 We urge you to make as many copies as you would like in order to help us spread the word that unauthorized copying of software is illegal Workgroup Solutions Desktop Applications Software Databases A Guide to CambridgeSoft Manuals Manuals Chem amp Bio Draw Chem amp Bio Office Chem amp Bio Office Chem amp Bio Desktop Software Workgroup Solutions Drawing Standard ChemBio 3D and Databases Includes Finder amp BioViz Including E Notebook Chem amp Bio 3D BioAssay Desktop Inventory Desktop ChemDraw Excel ChemNMR ChemFinder Office CS Gaussian Jaguar Interface BioAssay Workgroup Inventory Workgroup Compliant SDMS R amp D Insight Chemists Traditional Chinese Medicines Nanogens Index Medicinal Chemistry Sigma Aldrich MSDS Contents What s New e 1 Chapter 1 Introduction eser arent ako rti 3 The ChemDraw 3 The BioDraw Series 3 About This 4 Conventions for this guide 4 Additional Information s 4 L
94. shall CS be liable for any indirect special or consequential damages such as but not limited to loss of anticipated profits or other economic loss in connection with or arising out of the use of the software by you or the services provided for in this agreement even if CS has been advised of the possibility of such damages CS s entire liability and your exclusive remedy shall be at CS s discretion either A return of any license fee or B correction or replacement of software that does not meet the terms of this limited warranty and that is returned to CS with a copy of your purchase receipt Database Representations and Limited Warranty The User shall indemnify defend and hold CS Merck and or other Supplier harmless from any damages expenses and costs including reasonable attorneys fees arising out of any breach or alleged breach of these Terms and Conditions represen tations and or warranties herein by the User or any third party to whom User shares her his password or otherwise makes available this Subscription Service The User shall cooperate in the defense of any claim brought against CambridgeSoft Merck and or other Database Suppliers In no event shall CS Merck and or other Supplier be liable for any indirect special or consequential damages such as but not limited to loss of anticipated profits or other economic loss in connection with or arising out of the use of the software by you or the services provided for in
95. software audio and visual elements is owned or controlled separately by CS CS is a distributor and not a publisher of information supplied by third parties Accordingly CS has no editorial control over such information Database Suppliers Supplier individually own all right title and interest including copyright in their database and retain all such rights in providing information to Customers The materials contained in The Merck Index are protected by copyright laws and international copy right treaties as well as other intellectual property laws and treaties Copyright in the materials con tained on the CD and internet subscription products including but not limited to the textual material chemical structures representations artwork photographs computer software audio and visual elements is owned or controlled separately by Merck amp Co Inc Merck and CambridgeSoft Corporation CS The ChemReact68 ChemSynth ChemReact500 and ChemSelect Reaction Database is copyrighted O by InfoChem GmbH 1997 AspTear is copyrighted O by Softwing InChI is a trademark of the International Union of Pure and Applied Chemistry InChITM Material in ChemDraw is O IUPAC 2005 schr dinger Jaguar GAMESS is copyrighted O by Ames Laboratory Copyright O 1986 2009 CambridgeSoft Corporation Cambridge Scientific Computing Inc Al Rights Reserved Printed in the United States of America All other trademarks
96. specifies whether selected atoms can have a valence other than normal Normal valences for each element are defined in the Isotopes Table file in the Chem amp Bio Draw 12 0 Items folder NOTE The Abnormal Valence atom property does not provide a visual indicator Option Search Result Notallowed Default Finds compounds where the selected atoms only have valences that are normal for that element If necessary hydrogen atoms are added to or removed from the atom before transferring it to the chemical database If the Check Structure When Copying to Clipboard or Exporting preference is turned on an error message warns of abnormal valences Allowed Finds compounds with the specific valence drawn NOTE If Abnormal Valence is Allowed any Invalid Valence messages for those atoms are ignored by the Check Structure command Bond Properties Assigning query properties to bonds is similar to assigning query properties to atoms Bond query indicators that appear next to a bond show the properties that have been assigned to it NOTE The bond property feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Assigning Bond Properties To define bond properties 1 Select one or more bonds in a structure 2 Doone of the following Right click point to Bond on the context menu point to the property you want and choose the desired options Go to Str
97. structures in your database that have either a F or Cl atom at both locations and either Br or I at 1 Go to Structure gt R Logic Query 2 In the R Group dropdown list select Ry 3 For Occurrence range select 2 This indi cates that two instances of an R group must Occur in a structure for it to be returned as a result 4 For If R 1 select R2 This indicates that the R2 location must consist of either Br or I 5 Click Add 6 Click OK Rest H Select Rest H in the R Logic Query dialog box to indicate that if you have two possible R group locations and only one is filled the 140 Query Structures Chapter 10 other must be a hydrogen to return a positive result Atom to Atom Mapping You can create correspondences between atoms in different structures for use in creating queries for searching a reaction database The reactions mapped can be single or multi step You can assign atom to atom mapping for cre ating records for a reaction database and for creating queries for searching a reaction data base NOTE Atom to atom mapping is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only You can assign atom mapping in two ways Automatic mapping go to Structure Map Reaction Atoms Manual mapping using the Reaction Atom Atom Map tool on the main tools palette During either type of mapping process the mapping algorithm perceives and assigns a
98. subunit Membrane size of subunit ellipse Micelle size of subunit Plasmid map Add adjust markers and regions Ribosomes resize color tRNA resize color These tools cannot be customized G protein alpha subunit 2 Substrate Enzyme Ion channel G protein beta subunit Immunoglobulin Golgi body Endoplasmic Mitochondrion reticulum Cloud resize color Membrane Line 1 Select the membrane line tool 2 Click and drag to draw a membrane line of the size you want or just click for the default size When orienting the membrane note that if Fixed Angles is selected you are constrained to 15 degree increments To override the con straint hold down the Alt or Option key as you drag The membrane line has one adjustment handle at its center that you can drag to change the size of the membrane subunits PPP POR OOOOQUOOO Figure 4 1 Drag the cursor to change the size of the membrane subunits TIP To change the length of the membrane select it and drag the left or right handle of the selection box You may then deselect it and readjust the subunit size Membrane Arc To create a membrane arc click and drag in a curve using the Membrane Arc tool The membrane arc tool has three adjustment handles the handle at the starting point controls the length the center handle controls the subunit size the handle at the leading edge controls the arc
99. supplied with copy protection Do not duplicate any of the copyrighted materials except for your personal backups without written permission from CS To do so would be in violation of federal and international law and may result in criminal as well as civil penalties You may use ChemBioOf fice ChemOffice BioOffice ChemBioDraw ChemDraw BioDraw ChemBio3D Chem3D CS MOPAC ChemFinder BioViz Inventory E Notebook and BioAssay ChemOffice ChemDraw Chem3D CS MOPAC ChemFinder Inventory E Notebook BioAssay and ChemInfo on any com puter owned by you however extra copies may not be made for that purpose Consult the CS License Agreement for Software and Database Products for further details Trademark Notices ChemBioOffice ChemOffice BioOffice ChemBioDraw ChemDraw BioDraw ChemBio3D Chem3D ChemINDEX ChemFinder ChemInfo and ChemACX are registered trademarks of CambridgeSoft Corporation Cambridge Scientific Computing Inc The Merck Index is a registered trademark of Merck amp Co Inc 2006 All rights reserved MOPAC 2002 is a trademark of Fujitsu Limited Microsoft Windows Windows 2000 Windows XP and Microsoft Word Microsoft Excel Microsoft PowerPoint Microsoft Access and SQL Server 2005 are registered trademarks of Microsoft Corpo ration Apple Events Macintosh Laserwriter Imagewriter QuickDraw and AppleScript are registered trademarks of Apple Computer Inc Geneva Monaco and TrueType are trademarks of Apple
100. that require unambiguous structures Chemically significant text must be entirely in formula or for isotopes and charges super script style Chem amp Bio Draw 12 0 does not recognize a chemical formula embedded within a larger block of text If you draw a bond add an NH atom label and then delete the bond you have a chemically meaningful text block whose font size and style match other atom labels If you create a caption with the H30 text tool and set it to Formula style you have a chemically meaningful text block whose font size and style match other captions Charges Charges may be created as part of a textual atom label or with the appropriate symbol from the Chemical Symbols palette Charges are always assigned to a specific element in the atom label whose acceptable valences become those of the similar isoelectronic neutral ele ment NH3 n N H3 NH N H3 CO CO O NH Fet Fe Fe NH N H3 A charge following an element is assigned to that element A charge that does not follow an element is assigned to the next element Charges that follow a monova lent element with a repeat count are assigned to the element before that element Charges that follow other repeating units are distributed among those units Charges may be superscripted Multiple charges are recog nized appropriately Ch
101. the Rectangle shadowed tool 3 Point to the upper left corner of the reaction scheme Click and drag diagonally down ward to the right to draw the box Grouping Objects Some objects such as arrows are not associ ated with each other automatically You can manually group the objects together using the Group command You can then manipulate or move them as a single object To group objects 1 Click the Marquee tool 2 Doone of the following Draw a box around the arrow caption and symbol to select them Click the arrow then hold the shift key down while you click the OH caption and the charge symbol The Shift key lets you add objects to a selec tion without deselecting other objects NOTE If you click a selected object while holding Shift that object is deselected Chem amp Bio Draw 12 0 69 User Guide 3 Go to Object Group NOTE You can select individual objects within a group by clicking them Aligning the structures To align the structures 1 Select both structures with the Lasso or Marquee 2 Go to Object gt Align gt T B centers The Reaction Interpreter The reaction interpreter identifies the reactants products catalysts and annotations in a reac tion The interpreter color codes each part to help you identify them NOTE The Reaction Interpreter is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To use the reactio
102. the penalties for copyright infringement A The Copyright Act allows a copyright owner to recover monetary damages measured either by 1 its actual damages plus any additional profits of the infringer attributable to the infringement or 2 statutory damages of up to 150 000 for each copy righted work infringed The copyright owner also has the right to permanently enjoin an infringer from engaging in further infringing activities and may be awarded costs and attorneys fees The law also permits destruction or other reasonable disposition of all infringing copies and devices by which infringing copies have been made or used in violation of the copyright owner s exclusive rights In cases of willful infringement criminal penalties may also be assessed against the infringer SIIA also offers a number of other materials designed to help you comply with the Federal Copyright Law These materials include It s Just Not Worth the Risk video This 12 minute video available 10 has helped over 20 000 organizations dramatize to their employees the implications and consequences of software piracy Don t Copy that Floppy video This 9 minute rap video available for 10 is designed to educate students on the ethical use of software Other education materials including Software Use and the Law a brochure detailing the copyright law and how software should be used by educational institutions corporations and individuals and
103. the scientist s E Notebook which appear in the person s E Notebook inbox and are then accepted into the experi ment if desired To establish chain of custody each step of sam ple ownership is tracked recorded and made compliant with FDA s 21 CFR Part 11 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com Workflow LIMS Automation CambridgeSoft s Workflow LIMS is a scientific data and workflow management tool for lab automation and zz se experimentation Workflow LIMS eliminates the need for custom programming by providing a visual experiment design and work flow layout with built in laboratory automation and analytics By using Workflow LIMS researchers can connect their laboratory processes instruments and decision points in a conceptual manner that directly couples to instrumentation for both automation and data gathering and provide real time results The Workflew LIMS solution enables a scientific team to design procedures execute those procedures capture the results and integrate lab equipment to automate part or all of the process Procedures typically revolve around lab activ ities but may also draw in decision support tools on a scientist s desktop and queries updates to databases Interactivity and Integrity 1 The modeling environment Workshop Configur
104. the structure with the Marquee or Lasso Tool 2 Go to Object gt Flatten All z coordinate information is removed from the structure Mass Fragmentation The Mass Fragmentation mimics the molecular fragmentation in a mass spectrometer but does not have any predictive qualities so you must specify what bonds are to be broken NOTE The Mass Fragmentation command is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To fragment a structure use the Mass Frag mentation Tool to drag the cursor across one or 66 Advanced Drawing Techniques Chapter 6 more bonds When you release the mouse but ton bonds that you cross are broken Te Chemical Formula Exact Mass 42 05 Chemical Formula C3H Exact Mass 42 05 Figure 6 7 Using the mass fragmentation tool By default the line you draw disappears when you release the mouse button NOTE To draw a curved line or to keep the line visible hold down the Alt windows or Option Macintosh key while drawing To keep the line visible release the mouse button first To draw a curved line release the Alt or Option key first When the line crosses a bond the formula and exact mass for the fragments on either side of the bond are displayed as if the bond were homolytically broken That is a single bond turns into a monoradical on each fragment a double bonds turns into a pair of diradicals If multiple bonds are
105. the subunit count NOTE BioDraw tools are available in Chem BioDraw Ultra 12 0 BioDraw Ultra 12 0 and BioDraw Pro 12 0 only BioDraw Templates BioDraw and ChemBioDraw Ultra include a variety of templates that are useful for illustrat ing biological systems in full color for publica tion To view the templates go to File gt Open Templates and select the template toolbar you want A few of the available templates are shown below Anatomy templates Chem amp Bio Draw 12 0 User Guide 35 Animals MES Xa Bio Instruments Microorganisms For more information on using templates see Templates on page 73 Customizable Objects The table below describes which BioDraw objects you can customize When customizing 36 BioDraw Chapter 4 a BioDraw object you must use a selection tool or the same tool used to create it Tool Customization Options 1 Substrate Enzyme size of the enzyme mouth Receptor width G protein shape subunit Helix Protein height width of the strands width of the cylin ders spacing DNA height width of the strands offset of the second strand spacing size of subunit The overall length remains constant and the number of subunits changes in inverse propor tion to the size Membrane line Membrane arc length arc size of
106. to pilot an application before a major commitment to an enterprise wide implementation is made CambridgeSoft will work closely with you to plan the evaluation deploy the application and gather feedback regarding systems design APT s and technology specifications Training Effective user administrator and help desk training is often an afterthought in many systems deployments However the produc tivity returns generated by an investment in systems training can be dramatic CambridgeSoft offers a complete array of powerful user focused training services PLANNING Strategic Op Planning Requirements Analysis DEVELOPMENT Data Integration Application Development DEPLOYMENT MANAGEMENT Systems Optimization Systems Integration Product Tailoring Software Evaluations Training Services 1 617 588 9300 FAX Project Readiness 21CFRTI Compliance Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Managed Informatics allows your organization to focus on science while CambridgeSoft plans implements and manages your technology environment Systems Management Managed Informatics Informatics outsourcing provides the people processes and tech nology to develop a unique level of service for your organization For a mont
107. units Henry s Law LogP Two methods are used to predict Henry s Law constant Three fragmentation methods are used to pre dict the logP values The first is an approach based on the bond Method one is based on 94 atomic contribu tions evaluated from 830 molecules by least squares analysis This method works with a standard deviation of 0 47 logP units and can handle molecules containing hydrogen oxygen nitrogen sulfur and halogens Method two is an extension of method one but is based on 120 atomic contributions evaluated from 893 molecules by least squares analysis In addition to the atoms introduced for method one it can handle molecules that contain phosphorus and selenium atoms This method works with a standard deviation of 0 50 logP units Method three is based on 222 atomic contri butions calculated from 1868 molecules by contribution method This method uses 59 bond contribution values and 15 correction factors The contributions were calculated by least squares analysis using a data set of 345 chemicals This method estimates with a mean error of 0 30 units and a standard deviation of 0 45 units and can handle mol ecules containing carbon hydrogen oxy gen nitrogen sulfur phosphorus and halogens In the second method Henry s Law con stant 1s estimated from an equation found using linear regression Multifunctional compounds were omitted from this study This method should not be used for
108. will update when you modify the structure To toggle the auto update feature right click the caption and select Auto update A check mark appears next to the command when it 1s selected Successive clicks toggle the command on and off Chem amp Bio Draw 12 0 81 User Guide When auto update is on default the label updates each time you modify the structure NOTE For large complex structures it may take the new label a few seconds to appear on the screen depending on the speed of your pro cessor You do not have to wait for the new label to appear before continuing to modify your structure Name Struct Name Struct creates structures from chemical names you provide NOTE Name Struct is available only in ChemBioDraw Ultra and ChemDraw Ultra Name Struct recognizes most organic nomen clature It also recognized inorganic chemistry especially when the rules closely match those for organic chemistry However there area few types that are not supported Coordination complexes Polyboranes Polymers Some highly bridged ring systems includ ing fullerenes and porphyrins porphines Some stereochemistry designators D L DL endo exo syn anti r t c Although some trade names are supported Name Struct is not intended to interpret trade or common names A chemical database such as ChemBioFinder com is more appropriate 82 Naming Structures Chapter 7 for obtaining struct
109. workflow enforcement that monitors data entry and ensures that the forms are complet ed in sequence for proper method execution For example rules can be configured such that the Day 3 form of a multi day process will not accept any entries unless all required fields on the Day 2 form are first completed The forms can contain automatic calculations to compute totals averages differences and much more E Norebook can further streamline the procedure by allowing for electronic management of solutions equipment and other resources that are needed for experiments Drug Metabolism E Notebook supports the DMPK laboratories in testing the metab olism and longevity of compounds in various zz vitro and in vivo models DMPK data capture needs can vary significantly and the flexibility of the E Notebook solution addresses this For example an in vivo enzyme induction test may create relatively small amounts of data for which scientists utilize E Notebook integra tion with Microsoft Excel Conversely large quantities of data such as those generated by zz vitro enzyme inhibition studies are often collected and analyzed by applications such as BioAssay Therefore integration with BioAssay and Excel are fundamental to DMPK E Notebook usage us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02
110. workgroups to large enterprises collaborate and share information more effectively Knowledge Management with Notebook including Reaction Explorer CombiChem E Signatures for intellectual property protection and 27 CFR11 Compliance streamlines daily record keeping with rigorous security and efficient archiving Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant SDMS for storage of your data Biological Informatics scientists use BioDraw BioAssay BioSAR and BioViz to set up biological models and visualize information generate spreadsheets correlating structure and activity search by structure and draw and annotate pathways Chemical Informatics including Registration organizes new compound information Inventory provides complete management of chemical and biological inventories including GxP Validation DocManager indexes chemical structures in documents Manufacturing Informatics include Inventory to meet the chemical reagent sample and compound tracking needs of large multi site chemical and pharmaceutical laboratories and E Votebook for manufacturing compliance management Desktop Software includes Chem e Bio Office a powerful suite of software consisting of ChemBioDraw ChemBio3D ChemFinder and ChemACX for chemists BioDraw BioAssay and BioViz and for biologists and Inventory and E Notebook for all Scientific Databases include the ChemACX Database of commercially available chemi
111. you follow the tutorials Chem amp Bio Draw 12 0 checks for correct chemical syntax as you draw If there is an error a red box is displayed around the errone ous object the red box appears on screen only and does not print To disable the automatic warning on a specific object right click the object and deselect Display Warnings on the context menu Tutorial 1 Drawing a Structure In this tutorial we explain how to draw the structure below 2 To create the bonds 1 Go to Object gt Fixed Lengths and Fixed Angles NOTE Fixed lengths and fixed angles lets you create structures with consistent bond lengths and angles The fixed length dimension is set in the Drawing tab of the Document Settings dia log box The fixed angle dimension increments angles by 15 degrees 2 Go to View gt Show Main Toolbar 3 On the main toolbar select the Solid Bond tool 4 Position the cursor anywhere in the doc ument window and click A bond appears 5 To add a second bond click the right end of the bond you just created A B ae 3 du Figure 5 1 Attaching a bond to an existing bond The two bonds form a 120 degree angle NOTE The angle used when clicking to add bonds is controlled by the Chain Angle setting in the Drawing tab of the Document Settings Chem amp Bio Draw 12 0 45 User Guide dialog box If this bond angle cannot be estab lished the next sm
112. 00 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Register and Track Chemicals amp Biologicals throughout the enterprise Freezer Rack Plate Handling Targeting Workflow and HTS Support Supports Barcoding Report Generation amp Audit Trails Registration Enterprise Registration Enterprise is built around robust data model for pure compounds batches salt management automatic duplicate checking and unique ID assignments Built on the Oracle Cartridge it handles stereochemistry including advances in rela tive stereochemistry tautomerization and structure normaliza tion for duplicate checking Using ChemScript it also can enforce drawing business rules such as orientation around a scaffold and functional group normalization Compounds may be entered individually through a user friendly web form through the use of a batch loader from Inventory or directly from E Notebook As compounds are registered regardless of whether through the web user interface E Notebook or from a batch file they are com pared for uniqueness via a configurable stereoselective duplicate check and assigned a registry number All information about the compound including its test data and other syntheses is tracked by the registry number and this is used to lin
113. 00 0 5 00000000 0 0 8 2927 0 0000 0 00000 0000000000 0 3 7950 1 2962 0 0000C 3 7950 0 0000 0 0000C 0000000000 0 2 2489 2 1708 0 0000C 000000000 0 0 1 1401 1 5149 0 0000 Cc 000000000 0 0 0 0000 2 1552 0 00000 0 0 00 00 0 0 0 0 0 1 1401 0 2186 0 00000 0 0 00 00 0 0 0 0 0 1 2 wd 595 00 0 13 2000 0 17 10000 2 4 2 0 0 0 0 3 5 1 0 0 0 0 4 61 0 5 6 2 0 510 1 0 7 8 1 0 0 7 9 2 0 0 0 0 1011 1 0 0 0 0 I0 12 X 0 0 lt 0 0 1213 1 0 0 0 0 1314 2 0 0 0 0 1315 1 0 0 0 0 M ZZC 15 M ZZC 26 M ZZC 34 M ZZC 41 M ZZC 5 3 M ZZC 62 M CHG 2 7 1 8 1 M ZZC 79 M ZZC 8 14 M ZZC 9 10 M ZZC 10 7 M ZZC 11 8 ZZC 12 11 M ZZC 13 12 M ZZC 14 13 END gt AIDS 2 100 Chemistry Features Chapter 8 Chem amp Bio Draw 12 0 101 User Guide 102 Chemistry Features Chapter 8 ChemDraw Excel ChemDraw Excel is an add in for Microsoft Excel for Windows ChemDraw Excel enables you to Add chemical structures and other data from Chem amp Bio Draw 12 0 or a Chem Finder database to an Excel spreadsheet Search using the same search features as ChemFinder Perform calculations on chemical struc tures When you install the add in a ChemOffice menu is added to the Excel menu and a toolbar appears Setting Up ChemDraw Excel When you install ChemDraw or Chem amp Bio Draw ChemDraw Excel is also installed To open a ChemOffice w
114. 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 WWW www cambridgesoft com CambridgeSoft MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 www cam b ridgesoft com SOFTWARE Chem amp Bio Office Software Standard for Scientists The ultimate sofiware suite for scientists The standard achieves the ultimate Computational chemistry made easy Desktop to enterprise searching Ultimate suite for biologists Draw pathways Screening data Visualize data Chem amp Bio Office isa powerful suite of software consisting of ChemDraw Chem3D ChemFinder and ChemACX for chemists BioDraw BioAssay and BioViz for biologists and Inventory and E Notebook for all types of scientists Chem amp Bio Office is available for Microsoft Windows Chem amp Bio Draw includes Struct Name ChemDraw Excel and ChemNMR BioDraw a biological sequence tool hotlinks to 3D structures Stoichiometry grid live linked chemical property calculations a TLC plate tool and more The ChemDraw ActiveX Plugin adds chemical intelligence to your browser for querying databases and displaying information ChemBio3D provides state of the art visualization and display of protein structures molecular surfaces molecular orbitals electrostatic potentials charge densities and spin densities Chem3D provides
115. 02140 USA e ChemDraw s improved Struct Name feature produces names for more types of compounds Live ChemDraw window embedded in Chem3D application allows simultaneous 2D and 3D editing Chem3D brings workstation quality molecular graphics and rigorous computational methods to your desktop ChemNMR be used to accurately estimate 13C and 1H chemical shifts The structure and the spectrum appear with the chemical shifts displayed on the molecule and the spectrum is linked to the structure so that clicking on a peak in the spectrum highlights the corresponding fragment on the molecule ChemBio3D Ultra includes visualization and molecular mod eling capabilities for both small molecules and protein structures designed for the bench chemist Small molecule computational methods include Molecular Overlay and Dihedral Driver It also includes interfaces to the MOPAC Jaguar Gaussian and GAMESS semi empirical and ab initio computational packages High quality Chem3D graphics can be viewed on the web using the Chem3D Activex Chem3D Pro brings workstation quality molecular visualiza tion and display to your desktop Convert ChemDraw and ISIS Draw sketches into 3D models View molecular surfaces orbitals electrostatic potentials charge densities and spin densi ties Use built in extended Hiickel to compute partial atomic charges Use MM2 to perform rapid energy minimization and molecular dynamics simulations Chem3D can also be used to
116. 140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com Service Request Workflow Sample Management Method Execution Framework Pharmacokinetics DMPK There is a holistic approach to Drug Metabolism and Pharmacokinetics No single study describes the behavior of a compound it is the combination of data from disparate experi ments that represents the pharmacological profile for a com pound It is here where E Notebook reveals one of its most signifi cant capabilities the reporting feature E Notebook reports are flexible any field e g compound ID study type etc can be used to query the system and any field e g conclusion dose etc or field aggregate e g average radioactivity can be displayed in the report Reports are dynamic and navigable results are displayed with links that provide quick access to experiments Reports are viewed directly in the E Notebook interface but they can also be exported to Microsoft Word or PDF to share with those who do not have E Notebook access v Inventory Enterprise TT i As EMAIL info cambridgesoft com CambridgeSoft www cambridgesoft com MANAGEMENT Sample Management Compliance Execution and Sample Tracking Drug Safety Toxicology Paper notebooks have traditionally been considered to be the record source for the entirety of an experiment but they o
117. 15 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP MAIL CambridgeSoft Corporation 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Chemical Synthesis Scale up and Analytical DMPK Screening Biology Genetics and Microscopy LIMS Method Execution 21 CFR Part 11 and GxP Assay amp Screening Biology One of E Notebook 5 strengths is its ability to integrate with exist ing electronic methods of data capture including using it with CambridgeSoft s BioAssay module to provide full screening exper imental support In addition to this Microsoft Word and Excel are also embedded directly in E Notebook as is image and movie capture Scientists benefit from the functionality of these tools implanted in a rich searchable environment Biological experi ments can be managed and organized in a way that is not possi ble with a traditional file system In vivo Experiments Animal Management In vivo experiments are important aspects of target discovery and validation and are critical paths to determine the efficacy of selective therapeutic candidates CambridgeSoft s E Notebook becomes the centralized location to collect store and interpret im vivo experiment results Again when used with BioAssay the full end to end experimental workflow is supported from creation to data analysis and quality control to summary and reporting
118. 1996 Special Documents are stylesheets or station ary pads They allow you to have pre config ured settings for different tasks NOTE In this tutorial the ACS template pro vides the required settings for structures to be published in all ACS journals One column lay out Page Setting Bonds with a Fixed length of 0 2 inches Drawing Setting Atom Labels in 10 point Arial or Helvetica font Text Setting 2 Go to File gt Save As 3 Type tut3 cdx in the appropriate text box 4 Select a folder in which to save the file 48 Tutorials Chapter 5 5 Click Save To draw the first bond 1 Click the Solid Bond tool 2 Point in the document window Drag down ward vertically to draw the first bond 3 Point to the lower atom and drag down ward again to draw the second bond The red wavy box appears because Show Chemical Warnings is selected We will keep it selected for now 4 Repeat step 3 three more times to draw a total of five bonds Figure 5 7 Drawing the backbone NOTE When you drag the pointer along the length of the bonds the pointer alternates between an arrow and a cross The arrow indi cates you are pointing over the center of a bond and the cross indicates you are pointing to an atom Add horizontal bonds to the second atom in the string of bonds you created 1 To add a perpendicular bond point to the uppermost Chemical Warning box and click it Note that the red wavy box disa
119. 2 3 5 zh A o 3 Macworld rem V y eroe n nn aum umi BA ox The RTK RAS pathway is one of the main signal transduction pathways Extracellular f Mit Ves mua wes Co Omer We CambridgeSoft Life Science Enterprise Solutions Naturwissenschafiliche Unternehmenslisungen Solutions globales pour les sciences de la vie 2794I7A I754 724X VY a vay noe ma 222 Ne oU 9 2 cC cu F Register your CambridgeSoft Product Please complete the registration card at right Registering your prod uct makes you eligible to receive update and upgrade information technical support and a free subscription to ChemBioNews Com a publication for Scientists with Computers www cambridgesoft com Visit our homepage for more information about CS products and services Technical Support Warranty technical support available For details please see www cambridgesoft com services contact CS Product Registration Name For faster response and accuracy use the Web www cambridgesoft com register USER INFORMATION Register today and Title receive free Firm Street Warranty technical support City State Zip ChemBioNews Com Country publication for Scien
120. 3 setting preferences 20 157 setting the baseline style 163 setting up ChemDraw Excel 103 settings document 160 settings for new text 166 settings from other documents 161 shape attribute 116 shape coefficient 116 sharing information 147 shortcut keys 4 structure 210 text 210 shortcuts 207 209 show atom numbering 64 show crosshair 187 show document 183 186 show rulers command 187 show stereochemistry 86 showing atom numbers 64 showing palettes 8 Sigma orbitals drawing 89 similarity searches in ChemDraw Excel 106 single bonds drawing 13 single brackets 26 single lobe orbitals drawing 89 site license 7 SLN strings 148 copy as 147 SMILES strings 105 copy as 147 creating 147 viewing clipboard 148 SMILES string 111 SMIRKS overview 147 S orbitals drawing 89 source based polymers 132 specifying line spacing 164 specifying the margin width 167 spectra removing assignments 97 spectrum structure assignments removing 97 viewing 96 spiro and sprout rings 21 squiggly bond tool see tools wavy bond 13 starting ChemDraw Excel 103 stationery pad default 170 document settings 170 page setup settings 185 saving document settings 158 Status 5 status bar 5 8 160 status messages 197 stereochemical flags 195 stereochemical indicators 195 stereochemical symbols drawing 142 stereochemistry drawing mirror images 59 flags 195 indicators 86 195 indicators repositioning 87 relative 88 removing markers
121. 4900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemFinder offers improved searching and hit list management along with new property generation ChemFinder is tightly integrated with CambridgeSoft s Oracle Cartridge Search ChemACX and other CambridgeSoft ChemACX Database includes over 1 million chemical products available for purchase from 472 supplier catalogs search able with a single query by structure substructure name syonym partial name and other text and numeric criteria ChemMSDX Database provides material safety datasheets and is integrated into ChemACX and contains over 23 000 Material Safety Data Sheets MSDS in PDF format ChemINDEX Database includes 100 000 chemicals public NCI compounds AIDS data and more NCI Database contains over 200 000 compounds with anti cancer drug dose response data AIDS Database is an NCI compiled database for AIDS anti viral compounds ChemRXN Database is a collection of 30 000 fully atom mapped reactions selected and refined from chemical literature It also includes reactions from InfoChem s ChemSelect database and 151 ChemPrep database ChemBioFinder Com is the award winning web site with and WWW links for 100 000 chemicals Users can search by name o
122. 5 0 0000C 0 0000000000 0 4 6062 3 9825 0 0000N 0 0 0 3 4547 1 9992 0 0000C 0 0000000000 0 3 4547 3 3267 0 0000C 0 0000000000 0 6 9094 1 3275 0 0000 N 0 0 8 0609 1 9992 0 00000 0 5 0 0 0 6 9094 0 0000 0 00000 0 0000000000 0 2 3031 1 3275 0 0000C 0 0000000000 0 2 3031 0 0000 0 0000C 0 0 0 1 1516 1 9992 0 0000C 0 0 0 1 1516 3 3267 0 00000 0 0 0 0 0000 1 3275 0 00000 0 0 0 12 10000 i 3 2 9 20 90 17 10000 2 4 2 000 0 3 5 i O 202 0 0 4 6 1 0 0 0 0 5 6 2 0 0 0 0 510 1 0 0 0 0 7 8 1000 0 7 9 2 0 1011 1 0 0 0 O0 2 d 0 0 0 0 1213 2 0 0 0 0 1214 1 0 0 0 0 ZZC 15 ZZC 26 ZZC 34 M ZZC 41 M ZZC 5 3 M ZZC 62 M CHG 2 7 1 8 1 M ZZzC 79 M ZZC 8 13 M ZZC 9 10 ZZC 10 7 ZZC 118 M ZZC 12 11 M ZZC 13 12 M END gt ID 1 98 Chemistry Features Chapter 8 Chem amp Bio Draw 12 0 99 User Guide ACD Labs07190711112D 1515 0 0 0 00 16 V2000 7 1683 1 9521 0 0000 7 1683 3 2484 0 0000C 0000000000 0 6 0438 1 2962 0 0000C 0 0000000000 0 6 0438 3 8887 0 0000N 0 4 9194 1 9521 0 0000C 0000000000 0 4 9194 3 2484 0 0000C 0 0000000000 0 8 2927 1 2962 0 0000 N 0 9 4171 1 9521 0 000
123. ACX Numbers from Structure The ACX number appears in the Find ACX Numbers from Structure dialog box Chem amp Bio 3D ActiveX Control http www cambridgesoft com services Desk topSupport Documentation Chem3DControl SciStore com SciStore offers life science desktop software enterprise solutions chemical databases and consulting services to biotechnology pharma ceutical and chemical industries Visit SciS tore at www scistore com CambridgeSoft com To open the CambridgeSoft Home Page go to Online gt Browse CambridgeSoft com Check the CambridgeSoft Web site for new product information You can also get to Chem News Com and other pages through CambridgeSoft Com Using the ChemOffice SDK The ChemOffice Software Developer s Kit SDK lets to customize your applications To browse the ChemOffice SDK go to Online gt Browse ChemOffice SDK The ChemOffice SDK page contains docu mentation sample code and other resources for the Application Programming Interfaces APIs Chem amp Bio Draw 12 0 User Guide 217 218 The CambridgeSoft Web Site Appendix H Index Numerics UD lH shifts estimating 95 35 mm slide boundary lines 185 3D model 77 3D query properties 142 3D viewing 77 A abnormal valence 126 absolute flag drawing 142 accessing documents 159 ACS Document 1996 173 ACX information finding 216 acyclic chains changing direction 22 drawing 23 adding 3D query property
124. CCW for counterclockwise rotation 3 Optional To rotate the atom label text select Rotate Atom Labels 4 Click Rotate Objects are rotated around the center of the selection rectangle Chem amp Bio Draw 12 0 29 User Guide To repeat the same rotation on any object in the document window 1 Immediately after rotating an object select the other objects to rotate 2 Go to Edit gt Repeat Rotate Moving the center of rotation By default an object turns around its center when you rotate it However you can move the center of rotation so that the object rotates around an atom or some other location on the page To move the center of rotation 1 Select the object A center of rotation indi cator appears in the center of the object 2 While pressing the ALT key click and drag the indicator to another location 3 To rotate the object click and drag the rota tion handle To reset the center of rotation to its default position deselect the object Moving Objects 1 Select an object to move using a selection tool 2 Click and drag the object to a new location To constrain the movement to the horizontal or vertical direction Shift drag the selected objects Small incremental movements are often useful for aligning objects To move an object a incre mentally 1 Select the object 30 Basic Drawings Chapter 3 2 Press an arrow key The selected object moves 1 point in the direction o
125. Chem amp Bio Draw 12 0 53 User Guide Tutorial 5 Newman Projections This tutorial demonstrates how to draw a New man projection of ethane Create a new document 1 Go to File gt New Document 2 Go to File gt Save As 3 Type tut6 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Draw ethane 1 Click the Solid Bond tool 2 In the document window click and drag downward to create the first bond 3 Point at the lower atom and click to add a second bond 4 Continue pointing at the same atom and click again to add a third bond Figure 5 17 Creating the initial structure Duplicate the structure 1 Click a selection tool The last structure you drew is selected 54 Tutorials Chapter 5 2 Create a duplicate by holding down the Ctrl Windows or Option Macintosh key while dragging the selection rectangle upward to the right of the original The selection box disappears while you are dragging Figure 5 18 Creating a duplicate structure Add a bond between the duplicated structures 1 Click the Solid Bond tool 2 Click and drag from the tertiary carbon atom of the lower fragment to the tertiary carbon of the upper fragment NOTE When connecting existing atoms the Fixed Length and Fixed Angles commands are ignored When you release the mouse button the ethane structure is complete Now create its Newman projection Drawing the Newman P
126. ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 Regulated Materials Management Request Dispense Reference Standard Materials from Central Group to Sites Certification Expiration Certificate of Analysis of Containers and Aliquots Create Manage Container History and Genealogy Searching Every field in a record is searchable The application includes a number of specially designed inventory search forms Search results are returned in list form and can be exported into a docu ment PDE HTML via the report engine Workflow Support Supported user transactions include the ability to request dispense modify duplicate dispose etc entities throughout the system These and other transactions are an integral part of Inventory workflows For example a user logs on finds the substance s theyd like to request and makes a request entry in the system the request is ful filled directly by changing the location the substance or by taking an aliquot and creating a new container of the substance The new substance container is also tracked in the system and inherits all of the critical properties of its parent container If a quality con trol test is run on the parent then the results are viewable in the daughter s properties The multi select capability allows the user to select several con tainers and perform a transaction on all of the selected containers simultaneo
127. Click the Lasso or Marquee tool 2 Select the objects from which to remove the assignment 3 Go to Structure gt Clear Spectrum Structure Custom Shift Correction Data You can add your own shift correction data for proton prediction to supplement the existing data that the ChemNMR algorithm uses You provide your data in an SDF file and then use the file to update the Chem amp Bio Draw Chem NMR database Using a third party tool such as ACD Labs software or MestreNova you may be able to create your SDF file with the supplementary data already included Consult your applica tion s user manual for instructions Alterna tively you can use ChemBioFinder to add your data to an SDF file NMR DATA FORMAT The correction data that you add to your SDF file must be in this format gt lt SHIFT gt lt atom_id gt lt shift_value gt lt ignored gt For example gt SHIFT1 27 92 615050 gt lt SHIFT2 gt 378 927030 The correction data for each molecule must appear after the molecule s structural data For example if your SDF file includes benzene the NMR data must immediately follow the benzene structural data Updating the ChemNMR database Once you have an SDF file that contains the supplementary follow these steps to update the ChemNMR database 1 Exit Chem amp Bio Draw 2 Locate the Chem amp Bio Draw ChemNMR directory By default the directory is at C Documents and Settings All Use
128. Ctrl v Select all Ctrl a Undo Ctrl z Redo Shift Ctrl z Repeat last Ctrl y command Clear Delete View Actual size F5 Magnify F7 Reduce F8 Fit to window F6 Toggle ruler Toggle crosshair Ctrl h Object Toggle fixed length Ctrl L Toggle fixed angles Ctrl E Select multiple objects Shift Click with Lasso Marquee or Structure Perspec tive tools Group selected objects Ctrl g Ungroup objects Shift Ctrl g Chem amp Bio Draw 12 0 209 User Guide Join selected objects Ctrl J Automatic justifica Shift Ctrl M tion Bring to front F2 Plain Ctrl Send to back F3 Bold Ctrl B Flip horizontal Shift Ctrl H Italic Ctrl I Flip vertical Shift Ctrl V Underline Ctrl U Rotate 180 horizontal Alt Shift Ctrl H Formula Ctrl F Rotate 180 vertical Alt Shift Ctrl V Subscript selected F9 in a label Rotate opens Rotate Ctrl R character or next Objects dialog box character typed Scale opens Scale Ctrl K Superscript selected F10 in a label Objects dialog box character or next character typed Structure Adds a degree sign Alt 248 in a label BE Drawing Clean up structure Shift Ctrl K Convert name to structure Shift Ctrl N Convert structure to name Alt Ctrl N Copy a selected object
129. DS Database is an NCI compiled database for AIDS anti viral compounds ChemRXN Database is a collection of 30 000 fully atom mapped reactions selected and refined from chemical literature It also includes reactions from InfoChem s ChemSelect database and 151 ChemPrep database ChemBioFinder Com is the award winning web site with and WWW links for 100 000 chemicals Users can search by name or partial name view struc ture drawings or use the ChemDraw ActiveX Plugin for structure and substructure searches in formation over 1 617 588 9390 EMAIL info cambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP BioAssay BioViz BioDraw Biological Assay Visualization and Pathways BioAssay Ultra BioAssay Ultra the cornerstone of BioOffice provides flexible storge retrieval and analysis of biological data BioAssay easily manages both high and low throughput biological screening data Designed for complex lead optimization experiments the soft ware supports quick set up of biological protocols automated calculations and curve fitting and the creation of customized structure activity reports BioAssay brings all of this functionality to your desktop BioAssay Ultra compatible with the MSDE database offers a user friendly interface for importing viewing validating and plotting your biological assay data BioViz Combining biological data with chemical structures is of the utmost importance
130. Figure 10 1 Two example structure queries A The results will include any connected atom at the loca tion specified by R B The results will include either a single or double bond at the location speci fied by S D To perform a query you first draw the query structure in Chem amp Bio Draw You then enter the structure in a database application such as ChemBioFinder 12 0 The application then searches one or more databases that you spec ify and returns the query results Search limitations Several factors determine the search results that are returned To get the results you expect you must first ensure that the structure you draw accurately represents the query you want to perform For example if your query struc ture requires that no carbon atoms in an aro matic structure can be part of any ring you are likely to return no results or an error depend ing on the query system used Your search application you use can also affect your query If the application does not accu rately interpret your query structure or the structures in the database you may receive inaccurate results Generic Nicknames A generic nickname represents a nonspecific attachment It can be either an unspecified atom functional group or structural feature When you perform a query the query will look for structures based on the type of generic nickname you use and where it is located in the Chem amp Bio Draw 12 0 119 User Guid
131. For simple structures typing the atomic sym bol in a text box is easy However for compli cated structures using Hotkeys and Nicknames is easier Using Hotkeys Using Hotkeys you can add functional groups to your structures with one keystroke For example to add tert butyl to the end of a hydrocarbon chain 1 Draw the chain 2 Hover the cursor where you want the func tional group 3 Press 3 the hotkey for tert butyl on the keyboard t Bu is added to the structure 4 Select t Bu in the structure and go to Structure gt Expand Label Using the Hotkeys n nitrogen O oxygen and I iodine you can turn ethylbenzene into pyridin 2 yl hypoiodite 18 Basic Drawings Chapter 3 You can also label several atoms at a time For example you can change neopentane figure A below into methanetetraamine figure B A B qw To change neopentane into methanetetraamine 1 Create the neopentane structure 2 Use Shift click to select all the terminal car bon atoms and press n on the keyboard For a complete list of Hotkeys see Shortcuts and Hotkeys in the online Help NOTE The Automatically Rectify Hydrogens in Atom Labels feature see Setting Preferences on page 20 does not affect Hotkeys To add a substructure press a hotkey To change how many hydrogens are added to the substructure select the hotkey again Using Nicknames Using Nicknames you can add short names for functio
132. Hotkey entry using the appropriate format and values or edit an existing hotkey in the list 5 Save the hotkeys xml file 6 Close and reopen Chem amp Bio Draw 12 0 Working with Color You can create full color presentations of your chemical drawings to appear on your monitor print on a color printer or create 35mm slides using a film printer Most computers can display any of 16 million colors but the number of colors that can appear at any one time may be limited by your monitor and display card What you can color In Chem amp Bio Draw 12 0 you can change the color of the background foreground or indi vidual objects Background Color The color of the document window By default the background color is white Foreground Color The color of object you draw By default the foreground color is black Individual objects You can assign colors to objects to help then stand out against other parts of your drawing Changing colors You can change the color of the background foreground groups or objects to emphasize parts of your drawing Background and foreground The background and foreground define the col ors used in your drawing To change the col ors 1 Go to File gt Document Settings and select the Colors tab 2 Select the Background and Foreground col ors 3 Click OK NOTE Changing the foreground color does not affect objects you have colored The Color palette Use the
133. Hs A series of any combi CH COOC OPh nation of the above Chem amp Bio Draw 12 0 analyzes atom labels from left to right applying standard valence rules to determine which atoms are bonded together The exception is with an atom label in Automatic alignment on the left side of a compound This type of atom label is displayed in reverse H4CO instead OCH3 and is parsed from right to left Standard valences for each atom are defined in the Isotopes Table By definition a simple atom label has all bonds attached to the first or last character A multi attached atom label has bonds connected to more than one character or has all of its bonds attached to a character in the middle of the atom label Multi attached atom labels are always parsed from beginning to end but the beginning might be on the right if the atom label was in Automatic style and on the left side of the original structure A multi attached label that is parsed from left CH CCH to right A multi attached label that is parsed from right to left H34CCH C CH OH A bond attached to the open parenthesis of a repeating group is treated as if bonded to the first of those CHACH sOH groups Chem amp Bio Draw 12 0 191 User Guide bond attached to the close parenthesis or repeat count of a repeating group is CH5 CH5 CH treated as if bonded to the last of those groups Multiple fragm
134. In conjunction with zz vivo experiments animal housing and breeding can also be tracked Traditionally the work flow consists of paper based record keeping across the animal facility lab bench and researchers desktop With E Notebook paper tracking and recording is eliminated Instead form tools can be designed to Track animal status Track animal pedigree Record Genotype Create mating records Create litter records 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com KNOWLEDGE Analytical Services amp Electronic Journal and Record Keeping Formulation and Validation E Notebook s formulation module is designed to support the dual workflows and regulatory compliance needs of formulation engi neers The flexibility allows any number of formulations to be created and security allows only designated administrators to create a new formulation Analytical amp Quality Control Analytical and Quality Control Laboratories must execute defined procedures to test material that may be administered during pre clinical and clinical trials This work must also be compliant with both GxP and 21 CFR Part 11 Templates for standard analytical tests are provided and analytical procedures are implemented as E Notebook forms which are easily designed and controlled Equally important Votebook provides
135. Isis a x Xx ox X Mol Rxn Exported Query Properties Double Bold Aromatic Tautomeric Triple Quadruple X Any X S D D A S A X Topology x Unspecified d Ring X Chain e Reaction Center X Unspecified X Center Make Break f Change X Make amp Change X Not Center Isis P KR x X ox Mol h h X X 1 i X X 1 1 X X X X X X X X X X X X X X X X X X X X Chem amp Bio Draw 12 0 User Guide Rxn 145 Exported Query ISIS Mol Rxn Properties Other Query Attributes Generic Nick Xj Xj Xj names Element Lists Xko Xko Element Not Xk Xk Xk Lists Alternative X Xm Groups Anonymous Alternative Groups Link Nodes e Bracket proper X X ties Atom Atom X X mapping Variable Attachment Positions 3D query properties a Converted to the appropriate number of exact substituents 146 Query Structures Chapter 10 b Free Sites counts of zero translated to Substitution as drawn all other Free Sites values written as substitution counts equal to the total current valence plus the free sites value c Substituent counts of greater than 5 are translated to 6 or more d Converted to Wedged Hashed e Converted to Wedged f Converted to a Single with a positive charge applied to that atom at the base of the dative bond and a negative charge applied to the atom at the poin
136. JP 0120 146 700 WWW www cambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP ChemDraw Chem3D Structure Drawing and Molecular Modeling ChemBioDraw Ultra adds BioDraw ChemFinder BioViz and E Notebook to ChemDraw Ultra Easily draw and annotate publication quality biological pathway illustrations with the BioDraw tools The combination of the BioDraw tools with ChemDraw and E Notebook creates an excellent environment for smooth communication between Chemists and Biologists ChemDraw Ultra adds Struct Name ChemDraw Excel ChemNMR Stoichiometry Grid CLogP tPSA as well as the added capabilities of Chem3D Pro and ChemFinder Std to the ChemDraw Pro application With rich polymer notation gener ic structure expansion fragmentation tools and a modern user interface ChemDraw is more powerful than ever before Create tables of structures identify and label stereochemistry estimate NMR spectra from ChemDraw structures obtain structures from chemical names assign names from structures and create multi page documents and posters ChemDraw Pro will boost your productivity more than ever Draw quality publications with structures reactions chemical queries polymers relative stereochemistry generic structures TLC plate depictions and a biological sequence tool Publish on the web using the ChemDraw Plug in Create precise database queries by specifying atom and bond properties and stereochem istry Display spect
137. MPM o C6H4 PNB SES Tf trans Cinnamyl 212 Shortcuts and Hotkeys Appendix G Ms o Phenylene Poc t Am Tfa Troc MTM o Tolyl PPi t BOC TFA Trp n Am p C6H4 Pr t Boc Thexyl Trt n Bu p Phenylene Pro t Bu THF Ts n C3H7 p Tolyl Pv t Butyl Thf Tyr n C4H9 Ph s Am t C4H9 THP Val n C5H11 Phe s Bu t C5H11 Thp Xyl Chem amp Bio Draw 12 0 213 User Guide 214 Shortcuts and Hotkeys Appendix G The CambridgeSoft Web Site The CambridgeSoft Web site is a valuable source of helpful information There you can Register your software Search for chemical information by name or ACX number or insert a structure into a worksheet Get technical support documentation soft ware downloads and more You can navigate to the site directly from Chem amp Bio Draw by selecting the appropriate option in the Online menu Registering Online To activate any Chem amp Bio Office 2009 application register with the CambridgeSoft Web site to receive a registration code Upon filling out a registration form you will receive the registration code by e mail this registra tion scheme does not apply to site licenses If your serial number is invalid or you do not have an internet connection contact CambridgeSoft Support to receive a registra tion code You may use your Chem amp Bio Office 12 0 application a limited number of times while waiting for the registration process to fin
138. MS solution enables a scientific team to design procedures execute those procedures capture the results and integrate lab equipment to automate part or all of the process Procedures typically revolve around lab activ ities but may also draw in decision support tools on a scientist s desktop and queries updates to databases Interactivity and Integrity 1 The modeling environment Workshop Configuration Editor in which the scientific team models the capabilities of the lab for example the kind of basic processes which are available in the lab and their inputs and outputs 2 The design environment Workbench in which researchers create workflows from these basic processes 3 The runtime Operations Manager which manages the assign ment of tasks to agents tracks the progress of tasks and workflows and manages the storage of captured data 4 The agent tier made up of a number of applications that han dle specific types of task either manually through a user inter face or automatically by driving equipment through a control interface or performing automated data processing 5 The monitoring tier consists of a reporting tool that provides historical utilization information and a live activity viewer that allows scientists to drill into individual workflows and samples 1 617 588 9390 0120 146 700 us 1 800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP MAIL CambridgeSoft Corporati
139. PPLIED ANALYTICAL SAMPLE DEVELOPMENT RESEARCH BIOLOGY SERVICES MANAGEMENT E Notebook Drug Safety amp Configured to Comprehensive Toxicology Individual Function Integrated Corporate Workflow Knowledge Development Ed Compliance Requirements Management amp Testing Execution for Development for Research amp _ Trials amp Discovery Trials amp KAFARA Lifecycle Manufacturing 228 Ese Management Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK 44 1223 464900 FAX JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com MANAGEMENT General R amp D IP Protection and Regulatory Compliance General R amp D CambridgeSoft s E Notebook is a solution that enables pharmaceutical and biotechnology companies to improve the efficiency of the process from diseased target identification to prod uct launch Its core Oracle database manages the workflow to be compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and the FDAS 21 CFR Part 11 while the client interface is highly configurable and flexible Anywhere a shared drive is used E Notebook can offer a better solution Through the R amp D
140. Right click the formula and select Expand Label or go to Structure Expand Label Ph CH CHIIH CH Ph CH CH CHCH Figure 6 3 Adding bonds to a label After the label expands it behaves the same way as any other part of the structure Clean Up Structure You may find it difficult to draw atoms in the sterically correct position Use the Clean Up Structure command to redraw the structure so that bond lengths are fixed and atoms are in the correct location Clean Up Structure does not position molecules relative to other objects So some overlap may occur For some compounds the Clean Up Structure command produces a structure that extends beyond the bounds of the page To view the entire structure scale the structure or increase the size of the printed page See Scaling 62 Advanced Drawing Techniques Chapter 6 Objects on page 32 and Page Setup on page 184 NOTE The Clean up Structure command is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only The Clean Up Structure feature follows these rules The Fixed Length setting on the Drawing tab of the Document Settings dialog box determines optimum bond lengths A ring is redrawn only if all of its bonds are selected Multi attached atom labels variable attach ment points and multi center bonds cannot be cleaned Structures are rotated so that as many bonds as possible are d
141. TICAL PRESSURE cell ref Examples In cell CHEMPROP CRITICAL PRESSURE A2 Result 49 8035 In cell CHEMPROPPRO CRITICAL PRESSURE A2 Result 49 804 Critical temperature The temperature above which the gas form of the structure cannot be liquefied no matter the applied pressure Units Kelvin 112 ChemDraw Excel Chapter 9 Functions CHEMPROP CRITICAL TEMP cellref CHEMPROPPRO CRITICAL TEMPERATURE C ell ref Examples In cell CRITICAL TEMP 2 Result 615 351 In cell CHEMPROPPRO CRITICAL TEMPERATURE A2 i i Result 615 351 Critical volume The volume occupied at the compound s criti cal temperature and pressure Units cm3 mole Functions CHEMPROP CRITICAL VOLUME cell ref CHEMPROPPRO CRITICAL VOLUME cell ref Examples In cell CHEMPROP CRITICAL VOLUME A2 Result 562 5 In cell CHEMPROPPRO CRITICAL VOLUME A2 Result 562 5 Gibbs Free Energy The Gibbs free energy for the structure at 298 15 K and 1 atm Units kJ mole Functions CHEMPROP GIBBS cell ref CHEMPROPPRO GIBBS FREE ENERGY cell ref Examples In cell GIBBS 2 Result 84 77 In cell CHEMPROPPRO GIBBS FREE ENERGY A2 Result 84 77 Henry s Law Constant The inverse of the logarith
142. TRUCTURE cell ref Example In cell ISSTRUCTURE A2 Result False Does cell have reaction drawing Returns TRUE if the cell has a ChemOffice Excel structure drawing of a reaction drawings returns FALSE otherwise Function ISREACTION cell ref Example In cell ISREACTION 2 Result True Boiling point The boiling point for the molecule at one atm Units Kelvin Functions CHEMPROP BOILING cell ref CHEMPROPPRO BOILING POINT cell ref Examples In cell CHEMPROP BOILING A2 Result 540 059 In cell LING POINT A2 Result 540 059 Melting freezing point The melting freezing point for the structure at 1 atm Units Kelvin Functions CHEMPROP FREEZING cell ref CHEMPROPPRO MELTING POINT cell ref Examples In cell CHEMPROP FREEZING 2 Result 331 31 In cell CHEMPROPPRO MELTING POINT A2 Result 331 31 Chem amp Bio Draw 12 0 111 User Guide Vapor pressure The vapor pressure for the structure at 25 C Units P a Function CHEMPROPPRO VAPOR PRESSURE cell ref Example In cell CHEMPROPPRO VAPOR PRESSURE 2 Result 0 Critical pressure The minimum pressure that must be applied to liquefy the structure at the critical temperature Units bar Functions CHEMPROP CRITICAL PRESSURE cell ref CHEMPROPPRO CRI
143. The element list C specifies that one of these elements must match in the target structures Element Not Lists The element not list specifies that the elements in the list match must not match in the struc ture for which you are searching Commas must separate the elements in the element not list A space after each comma and brackets are optional The word NOT must be in all caps and must be followed by a space Alternatively the word NOT may be replaced with a minus sign For example NOTIF Br NOT F Br Figure 10 7 Element NOT lists F Br NOTE An element not list may contain only atomic elements plus D deuterium and T tri tium To create an element not list 1 Open an atom label text box 2 Type an open bracket the word NOT and a space followed by a list of ele ments separated by commas Br 1 followed by a close bracket J Polymers Polymers are indicated by brackets parenthe ses and braces that enclose repeating struc tures or structural fragments The bracket properties lets you specify the context and ori entation of the repeating units NOTE The polymer feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only For example NH To enclose structures with brackets 1 To display to Bracket toolbar go to View Other Toolbars gt Bracket 2 On the Bracket toolbar select one
144. UPAC codes sss 42 Peptides ei FREE RON 43 Disulfide Bridges 43 Chapter 5 liri 45 OVERVIEW I 45 Tutorial 1 Drawing a Structure 45 Tutorial 2 Using Rings 46 Tutorial 3 Fischer Projections 48 Tutorial 4 Perspective Drawings 21 Tutorial 5 Newman Projections 54 Tutorial 6 Stereochemistry 56 Tutorial 7 Templates 57 Chapter 6 Advanced Drawing Techniques 59 Mirror Imag68u de cotton tod tor ore 59 ii Contents Coloring DBPECES sicisesensasssesessassadsendinarans 59 Coloring groups esee 60 HT 60 Expanding Labels sss 60 Contracting Labels sss 61 Multiple atoms sse 61 Clean Up Structure 62 Attachment Points 63 Multi Center Bonds ses 63 Variable Attachment Points 64 Viewing Attachment 64 Atom Numbering 64 Showing Atom 64 Hiding atom numbers 64 Editing Atom Numbers sss 65 Positioning Atom Numbers 65 Structure Perspective 65 Flatten Command sss 66 Mass 66 Synthesis and Retro
145. Use Defaults The bond properties are removed and the indi cators do not appear To remove specific bond properties 1 Select the bond 2 Doone of the following Right click point to the appropriate prop erty and click the property to remove Go to Structure gt Bond Properties and click the bond property to remove Bond Property Options The properties you can assign to bonds are described below Bond Types This property specifies the bond type of the selected bonds The default bond type corre sponds to the current type of the bond single double etc as drawn Option Search Result Single all Finds compounds with the and Dative bond type you select for the selected bonds Double or Finds compounds whose Double Bold selected bonds are double Double Finds compounds whose Either selected bonds are double bonds and have either cis trans stereochemical configu ration Aromatic Finds compounds whose selected bonds are aromatic Tautomeric Finds compounds whose selected bonds are tautomeric Triple Finds compounds whose selected bonds are triple Quadruple Finds compounds whose selected bonds are quadruple Any Finds compounds regardless of the bond type of the selected bonds S D Finds compounds whose selected bonds are single or double D A Finds compounds whose selected bonds are double or aromatic S A Finds compounds whose selected bo
146. Using the Clipboard 108 Displaying Structures sss 108 ChemDraw Excel Functions 108 Chapter 10 Query Structures 119 Search limitations sss 119 Generic Nicknames 119 Generic Nickname Hotkeys 120 Defining Generic Nicknames 120 Atom 2 120 Assigning atom properties 121 Query Indicators sss 121 Removing Atom Properties 122 Atom Property Options sss 122 Bond Properties 127 Chem amp Bio Draw 12 0 iii User Guide Assigning Bond Properties 127 Viewing Bond Properties 128 Removing Bond Properties 128 Bond Property 128 El ment Lists 130 Element Not Lists o 130 POL VIPIGES 131 Setting Bracket Properties 131 Bracket Usage sse 132 Repeat Pattern esse 133 Link NOUS oi eo er interit 134 Flip TVpQ aceti eter ot tees 134 Alternative GITOUpS sescenti 134 Multiple Attachment Points 136 Attachment Rank Indicators 137 Attachment Point Numbering 137 Anonymous Alternative Group
147. WLEDGE Chemistry amp Electronic Journal and Record Keeping Chemistry Under the R amp D value chain chemistry can be further divided into three separate stages synthetic chemistry research discovery analytical chemistry pre clinical and process chemistry development The flexibility and configura bility of E Notebook enables a successful data repository analysis sharing reporting and searching efficiently and paper free Synthetic Chemistry Synthetic Chemists take advantage of many features tied into a smooth interface within CambridgeSoft s Enterprise E Notebook Reactions are drawn with in place editing stoichiometry grid dynamically fills with the formulas molecular weights and chem ical names Reagents can also be imported from other systems such as available chemicals from the ChemACX database or Registration system CombiChem is one important aspect of library generation for Synthetic Chemists For some E Notebook serves as the complete CombiChem solution taking advantage of features such as the enumeration of products from a virtual library on a flexible plate layout a multiple reaction site checker and multiple step parallel synthesis Others simply import a list of compounds from an external source or SDFile so that they can record and calculate data on a library wide stoichiometric table Analytical Chemistry E Notebook serves as a repository for analytical data and it also acts as a commun
148. Y SOLVENT EXCLU DED VOLUME cell ref Example In cell CHEMPROPSTD CONNOLLY SOLVENT EXCL UDED VOLUME A2 Result 170 277 Ovality The ratio of the molecular surface area to the minimum surface area The minimum surface area is the surface area of a sphere having a value equal to the solvent excluded volume of the molecule Computed from the Connolly Molecular Surface Area and Solvent Excluded Volume properties Function CHEMPROPSTD OVALITY cell ref Example In cell CHEMPROPSTD_OVALITY A2 Result 1 428947 Principal Moments of Inertia X Y Z The moments of inertia when the Cartesian coordinate axes are the principal axes of the molecule Units grams mole Angstroms Function CHEMPROPSTD PRINCIPAL MOMENT cell ref Example In cell CHEMPROPSTD PRINCIPAL MOMENT A2 Result 249 546 1409 279 1658 824 Balaban index Function MOLECULAR TOPOLOGY BALABAN INDEX ell ref Example In cell MOLECULAR TOPOLOGY BALABAN INDEX A2 Result 29909 Cluster count Function MOLECULAR TOPOLOGY CLUSTER COUNT C ell ref Example In cell MOLECULAR TOPOLOGY CLUSTER COUNT 2 Result 13 Topological index Function MOLECULAR TOPOLOGY MOLECULAR TOPOL OGICAL INDEX cell ref Example In cell MOLECULAR TOPOLOGY MOLECULAR TOPO LOGICAL INDEX 2 Result 1998 Chem a
149. a sss 159 The toolbar XML files sss 160 Editing the XML files sss 160 Editing toolbar icons sss 160 Document and Object Settings 160 Default Styles sss 160 Saving Customized Styles 161 Settings From Other Documents 161 Drawing Settings sess 161 Analysis and Properties 163 Formatting Captions 163 Setting Font parameters suus 163 Setting the Baseline Style 163 Style Indicators sss 164 Specifying Line 5 164 Aligning Text sse 164 Changing the Default Format 165 Customizing Hotkeys 167 Working with Color 168 What you can color esses 169 Changing colors sss 169 The Color palette esses 169 Removing Colors sess 170 Templates and 171 Saving Color palette Settings 171 Printing Background Color 171 Document 172 Publishing Documents sss 173 Appendix B Page po Ida pedit 183 The Drawing 183 Setting up erinnern 183 Page
150. a chemical compound mixture sample etc Inventory Enterprise manages an unlimited number of diverse locations containers and substances Containers are created to represent the actual storage vessels used by the organization Each container is assigned a unique barcode identifier which can be printed using customizable report tem plates from the Inventory interface Updating the inventory becomes as easy as scanning barcodes into the system and adjust ing parameters for one or multiple containers Users are able to order check in out move split and merge containers at will Typicalcontainers include ttles vials tubes cylinders boxes racks multi well plates etc Multi well Plates Inventory Enterprise manages multi well plate information In addition to creating storing moving and deleting plates the application allows users to create daughter plates reformat plates and utilize plate maps Inventory also supports user interfaces or machine interfaces for these operations including reading files from liquid handler robots Inventory Enterprise has the capabili ty to import datafiles from other computer systems such as liquid dispensers handlers Microsoft Excel spreadsheets etc to accom modate automated updating of information in the Inventory database us 1 800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice
151. a from your desktop BioAssay effectively manages data from complex biological assays involved with lead optimization BioViz integrates with BioSAR for one step in depth data analysis from a BioSAR report Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK 44 1223 464900 FAX JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 BIOLOGICAL BioAssay BioViz Assay Screening and Visualization Effectively manage data from complex biological assays involved with lead optimization Scalable HTS amp HTTS Use BioDraw to document cellular pathways BioDraw Diagramming and presenting cellular pathways is made easier and more effective with BioDraw Formerly called Pathworks BioDraw does for biologists what ChemDraw has done for chemists saving time and producing a more professional representation of the science BioDraw makes drawing and annotating biological pathways quick and easy adding a level of uniformity and detail which is unmatched Common pathway elements such as membranes enzymes receptors DNA and reaction arrows are built into the BioDraw toolbar BioDraw also allows the import of images in PNG or JPEG formats BioDraw offers many ways to share your drawings and accompanying data Users can export data to Microsoft Office applications for inclusion in presentations and grant proposals
152. abeled Switching to another structure resets the counter 3 To edit the atom number style select the atom number indicator with the Text tool and use the Text menu or Text formatting toolbar Positioning Atom Numbers Atom number indicators are positioned auto matically and move appropriately when you modify a structure You can reposition them by dragging them to the desired position or use the Position Indicators dialog box To reposition an indicator 1 Right click the indicator to move and click the Position command on the context menu The Position Indicators dialog box appears from the atom or bond by offset hori center to bottom left of zontal and vertical indicator baseline at specified coordinates absolute horizon tal and vertical Structure Perspective You can tilt molecules or portions of mole cules through three dimensions with the Struc ture Perspective tool To tilt a structure 1 Select the structure by dragging over it with the Structure Perspective tool 2 Place the cursor inside the marked rectangle and drag in any direction 3 Use Shift drag to limit the rotation to the X or Y axes only Chem amp Bio Draw 12 0 65 User Guide You can also select part of a complex molecule and rotate it around a particular bond NOTE Structure Perspective cannot be applied to orbitals Flatten Command To remove the Structure Perspective Tool effect 1 Select
153. action by weight of the given element in the structure Functions CHEM COMPOSITION cell ref CHEM COMPOSITION cell ref atomic sym bol Examples In cell CHEM COMPOSITION 2 Result C 82 72 H 8 10 0 9 18 In cell CHEM COMPOSITION A2 C Result 0 827188133 Chemical formula Displays the chemical formula for the struc ture s in the cell Functions CHEM FORMULA cell ref CHEMPROPSTD MOL FORMULA cell ref Examples In cell FORMULA A2 Result C12H14O In cell CHEMPROPSTD MOL FORMULA A2 Chem amp Bio Draw 12 0 109 User Guide Result CI2H14O Molecular weight Displays the average molecular mass of the structure where atomic masses are based on the weighted average of all isotope masses for the element Units atomic mass units Functions CHEM MOLWEIGHT cell ref CHEMPROPSTD MOL WEIGHT cell ref CHEMPROPSTD MASS cell ref Examples In cell MOLWEIGHT A2 Result 174 23896 In cell CCHEMPROPSTD MOL WEIGHT A2 Result 174 238960 In cell CHEMPROPSTD MASS 2 Result 174 238960 Exact mass Displays the exact molecular mass of the mole cule where atomic masses of each atom are based on the most common isotope for the ele ment Units g mole Function CHEMPROPSTD EXACT MASS cell ref Example In cell CCHEMPROPSTD EXACT MASS 2 Result 174 104465 110 ChemDraw Excel Chapter 9 Numbe
154. add a third bond ILA Figure 5 22 Creating the initial structure 5 Point to the bond shown in the figure below and type 9 the Hotkey to sprout two bonds Figure 5 23 Repeating the bond sprouting Now turn the single bond at the upper right into a double bond using any of the methods described in the earlier tutorials Adding Atom Labels 1 Double click the alpha carbon atom and type NH2 in the text box that appears Press the Esc key when finished 2 Add the and OH with the text box or the HotKey o OH lt Adding Stereochemical properties We now add stereochemical properties to the structure First we change the carbon nitrogen bond to a solid wedge bond tutorial 5 intro duced the wedge bond tool however you can also use a HotKey Afterward we display the stereochemical markers R and S for the two isomers To add the solid wedge point to the carbon nitrogen bond and do one of the following Select the Wedge Bond tool and click the bond Point to the bond and type the letter w OH To add the markers 1 Select the entire structure with the Lasso or Marquee tool 2 Go to Object gt Show Stereochemistry The S marker appears NH 3 Select the structure and go to Object gt Flip Horizontal The R marker appears NH2 4 With the structure selected go to Object gt Rotate 180 Vertical Hz H The Wedged bond becomes hashed and the
155. added to your spreadsheet NOTE You can import a table only into a new ChemOffice worksheet Converting Worksheets You can convert a normal Excel worksheet into a ChemDraw Excel worksheet Go to ChemOffice12 gt Convert Worksheet ChemDraw for Excel appears in the Excel title bar Upgrading Workbooks Older ChemDraw Excel workbooks may be incompatible with the latest add in Therefore you may need to upgrade them To upgrade go to ChemOffice12 gt Upgrade Workbook Importing Hit Lists You can search records in ChemFinder and import the hit list structures with data into Excel using the Import ChemFinder List com mand ChemFinder must be open with a hit list present To import a hit list 1 Go to ChemOffice12 gt Import Export gt Import ChemFinder List 2 In the message box click Yes to import the hit list The records are imported into Excel Error Messages If all conditions required to use the Import ChemFinder List command are not met one of the following error messages may appear 104 ChemDraw Excel Chapter 9 Error ChemFinder is not running would you like to start it up Do the following 1 Click Yes The message After loading your desired database and performing your search return to Excel and redo the opera tion appears 2 Click OK ChemFinder opens 3 Open a database and perform a search 4 Return to Excel and go to ChemOffice12 gt Import Export gt Import Chem
156. advantage of the wide variety of the publishing capabilities avail able in ChemDraw such as the ability to import and export images in GIE PNG or JPEG formats In addition the integration of ChemDraw BioDraw Chem Bio Draw application pro vides a great communication mechanism between chemists and biologists v Notebook Pages a Data Visualization EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com SOFTWARE Inventory amp E Notebook Materials Management and Electronic Journal Inventory Ultra Inventory Ultra allows users to manage the tracking needs of chemical and non chemical inventory data for laboratories and research centers The system manages data associated with both commercially procured and internally produced chemical sub stances from their procurement or initial production through their depletion and disposal Inventory Ultra is an MSDE based product and includes the CZez4CX database with over 450 cat alogs of chemical reagents The three primary entities in an Inventory system are locations containers and substances Users or administrators con figure a network of locations which represent locations within an organization Containers are created to represent actual containers in your facility Each container is assigned a unique barcode whic
157. alette 2 Click an atom in the drawing where the orbital will be centered Single Lobe Orbitals To draw a single lobe orbital 1 Hold down the mouse button over the Orbital tool and drag to select the single lobe orbital tool from the palette 2 Click an atom where the narrow end of the orbital is to be attached p orbitals To draw a p orbital 1 Hold down the mouse button over the Orbital tool and drag to select the p orbital tool from the palette 2 Click an atom where the node of the orbital is to be attached Hybrid Orbitals To draw a hybrid orbital sp3 Chem amp Bio Draw 12 0 89 User Guide 1 Hold down the mouse button over the Orbital tool and drag to select the hybrid orbital tool from the palette 2 click an atom where the node of the orbital is to be attached d orbitals To draw a d orbital dxy 1 Hold down the mouse button over the Orbital tool and drag to select the d orbital tool from the palette 2 Click an atom where the node of the orbital is to be attached d orbitals To draw a d orbital 1 Hold down the mouse button over the Orbital tool and drag to select the d 2 orbital tool from the palette 2 Click an atom where the node of the orbital will be attached Chemical Symbols When you attach a symbol other than H dot or H dash to an atom it remains at a fixed dis tance from the central character of the atom label even when you move the symbol Ho
158. aller and logical bond angle is used 6 To create a tertiary carbon click in the same place as you did in step 5 Figure 5 2 Adding a third bond CHANGING BOND ORDER To create the double bond either click and drag over the vertical bond you drew in step 6 or simply double click it P RENE Figure 5 3 Adding a double bond ADDING ATOM LABELS 1 Using the Text tool click the end of the double bond shown below A text box appears at the end of the bond g B ol 2 Type an uppercase in the text box 3 Close the text box by either pressing the Esc key or choosing another tool 46 Tutorials Chapter 5 ADDING A CAPTION We also want to name the molecule 1 Using the Text tool click below and to the left of the structure A text box appears 2 In the text box type 2 propanone 3 Press Esc or choose another tool Tutorial 2 Using Rings In this tutorial you use rings to create the struc ture below Create a new document 1 Go to File gt New Document 2 Go to File gt Save As 3 Type tut2 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Create the ring system 1 Click the Benzene tool 2 Shift click in an empty area of the docu ment NOTE Hold down the shift key to change resonance structures when using the cyclopentadiene or benzene tools 3 Point to the center of the lower right bond in the benzene
159. also required that such processes be compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and the FDA s 21 CFR Part 11 regulation E Notebook s process chemistry modules are designed to support these dual workflow and regulatory compliance needs of process chemists v Reaction Properties Fig 4A Medula 7 4a Gcr E Wi vum a PowerPoint Integration EMAIL info cambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com MANAGEMENT Biology DMPK Screening Biology Microscopy Discovery Biology These scientists are involved at the very start of the drug discovery process as genomics and genetics are essential disciplines used when identifying a disease target This work is methodical but unscripted and so requires an electronic note book pallet that is as free form as its paper predecessor This is where the benefit of E Notebook s flexibility is unmistakable While the system can be set up with rigid form based data entry appropriate for later stage research and development discovery biology configurations are typically open and boundless Genomic map and DNA RNA and protein sequence files can be dragged and dropped into E Notebook sequenc
160. and experiments linking such data directly to the sample ID and it acts as a communication portal with which scientists and analysts communicate with each other during the service request lifecycle Scientists create and send service requests directly to an analyst with the click of a button Paper is eliminated when results are obtained the analyst can send the images and chromatograms directly back to the scientist s E Notebook which appear in the person s E Notebook inbox and are then accepted into the experi ment if desired To establish chain of custody each step of sam ple ownership is tracked recorded and made compliant with FDA s 21 CFR Part 11 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com Workflow LIMS Automation CambridgeSoft s Workflow LIMS is a scientific data and workflow management tool for lab automation and zz se experimentation Workflow LIMS eliminates the need for custom programming by providing a visual experiment design and work flow layout with built in laboratory automation and analytics By using Workflow LIMS researchers can connect their laboratory processes instruments and decision points in a conceptual manner that directly couples to instrumentation for both automation and data gathering and provide real time results The Workflew LI
161. and Microsoft Word or Excel documents CombiChem Excel CambridgeSoft provides you with the tools to effectively plan combinatorial chemistry experiments in Excel The CombiChem Excel add in introduces additional functionality for handling combinatorial chemistry Users can generate products from a reaction and lists of reagents you can view all the products arising from a given reagent or all the reagents of a given product and you can lay out reagent and reaction plates info cambridgesoft com CambridgeSoft www cambridgesoft com SCIENTIFIC The Merck Index NCI AIDS Scientific Reference Chemical Reactions and Patents ChemBioFinder Gateway ChemBioFinder Gateway allows searching of the complete CambridgeSoft reference collection of databases with a single query Search such databases as The Merck Index R amp D Insight for Chemists and Traditional Chinese Medicines with only one click of a search button All results federate back to the spe cific databases for complete information The Merck Index Known for its integrity detail and longevity The Merck Index contains over 10 000 monographs on drugs chemicals and other biologically active molecules Each monograph contains informa tion on the compound and its derivatives common trade and systematic names trademarks and associated companies CAS Registry Numbers physical and toxicity data therapeutic and commercial uses literature citations as well as che
162. ant to dis play or hide structures 2 Select ChemOffice12 gt Picture gt Show or Hide Aligning Structures A structure may be too big for its cell or be improperly positioned To correct the problem select the Align All Pictures command To align structures go to ChemOffice12 gt Pic ture gt Align Pictures The cells adjust to display their entire contents 108 ChemDraw Excel Chapter 9 Resizing Structures 1 Select the cells whose pictures you want to resize 2 Select Resize Picture on the ChemOffice menu Resize handles appear on the selected structures 3 Click drag the resize handles to resize a picture Any changes you make to a picture is proportionately reflected in the other pic tures 4 To end resizing click a cell and the pictures are deselected NOTE When pictures are resized larger than their cells use Align Pictures to enlarge the cells Align Pictures does not make cells smaller ChemDraw Excel Functions ChemDraw Excel supplies a variety of func tions that return information about chemistry objects in a specified cell NOTE Functions that report chemical proper ties are available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only NOTE The surface area and volume calcula tions are performed with Michael Connolly s program for computing molecular surface areas and volume M L Connolly The Molecu lar Surface Package J Mol Graphics 1993 11
163. are the property of their respective holders CambridgeSoft End User License Agreement for Software Products Important This CambridgeSoft Software License Agreement Agreement is a legal agreement between you the end user either an individual or an entity and CambridgeSoft Corporation CS regarding the use of CS Software and Database Products which may include computer software the associated media any printed materials and any online or electronic documentation By installing copying or otherwise using any CS Software Product you signify that you have read the CS End User License Agreement and agree to be bound by its terms If you do not agree to the Agreement s terms promptly return the package within 30 days of purchase and all its contents to the place of pur chase for a full refund CambridgeSoft Software and Database License 1 Grant of License CambridgeSoft CS Software Products are licensed not sold CS grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product Soft ware in accordance with the terms of this Agreement This licensed copy of the Software may only be used on a single computer except as provided below You may physically transfer the Software from one computer to another for your own use provided the Software is in use or installed on only one computer at a time If the Software is permanently installed on your computer other than a network ser
164. are the same and are either a single ring fused system alicyclic von Baeyer system spiro system phane system or fullerene Also the number of ring junctions is the number of cyclic systems minus 1 Figure 7 23 An example of a ring assembly struc ture 1 1 2 1 terphenyl FUSED RING SYSTEMS Struct Name supports fused ring systems of two or more rings such as the structure below Figure 7 24 cyclopenta ij pentaleno 2 1 6 cde azulene is a fused ring system BRIDGED FUSED RING SYSTEMS Chem amp Bio Draw 12 0 supports bipodal both bivalent and polyvalent simple acyclic chained homogeneous atoms of only one element independent bridged fused ring sys tems An example appears below Figure 7 25 The bridged fused ring system 9 10 epidioxyanthracene Other compounds Phosphorous and Arsenic compounds Si Ge Sn and Pb compounds Boron compounds Organometallic compounds Stru1 1 2 1 terphenylct Name generates names with proper CIP stereochemistry descriptors It has no theoretical limits to the size of the structures that can be named Using Struct Name To insert the name of a structure into your drawing 1 Select the drawing for which you want to insert a name 2 Go to Structure gt Convert Structure to Name The name of the structure appears as a cap tion under your drawing Auto Update Chemical properties including the chemical name and analysis can be included in a cap tion and
165. arges may have repeat counts as long as both the charge and the repeat count are superscripted A floating charge placed with the Chemical Symbols Tool is assigned to the nearest atom If no atom is within the distance set as the Fixed Length the charge is ignored and not assigned to any atom A floating charge placed within a delocalized system is recognized by the Analyze Structure function but is discarded when saved to formats that require all charges to be associated with specific atoms Isotopes and Elements By default all isotopes are recognized in the full Table of the Elements This data is pro vided by CRC Press Inc Isotopes are defined in the Isotopes Table file You can edit this file in any text editor to add new isotopes 350 o 1 CD OD Radicals A superscripted number before the element symbol indi cates isotope numbers Isotopes can be included anywhere that regular elements can Deuterium and Tritium can be indicated by their one letter symbols Radicals are indicated with the appropriate symbol from the Chemical Symbols palette As with charges they are assigned to the nearest atom Radicals always occupy one free Chem amp Bio Draw 12 0 193 User Guide valence in addition to any charge effects Two examples are Ph Ph Sc i Ph ut H Dot H Dash H Dot and H Dash symbols from the Chemical Symbols palette indic
166. ariety of file formats and can open documents created in other appli cations To export a file Chem amp Bio Draw 12 0 151 User Guide 1 Go to File gt Save As 2 In the Save As dialog box do the follow ing a Type a name for the file and choose a location in which to save it Use Go To ChemDraw Items to quickly locate the ChemDraw Items folder b Select a file format c Click OK or Save Some file formats do not support atom labels that contain nicknames or structural fragments When you save in these formats Chem amp Bio Draw 12 0 expands all atom labels and saves the file using the expanded form The following formats do not support nick names or structural fragments Connection Table MSI MolFile SMD NOTE Some versions of Chem amp Bio Draw 12 0 do not support all the formats listed Some formats can be saved with different options If a format has no save options Options is grayed out The following text based formats can use the Text Options ChemDraw XML CML Connection Table ISIS TGF ISIS Reactions MDL MolFile Accelrys MolFile SMD 152 Sharing Information Chapter 11 Other format options are noted in format descriptions Importing You can import graphics or documents from other applications into Chem amp Bio Draw 12 0 Objects Inserted objects are OLE files and can be resized and rotated but cannot be flipped Since an object is embedded
167. as 149 include ChemDraw LaserPrep 151 indicators atom numbering 64 query editing 122 query positioning 122 stereochemistry 86 195 stereochemistry positioning 87 Info window 10 displaying fixed angles 13 insert name as structure 82 inserting name as structure 82 integral groups creating 31 intermediates 70 internet CambridgeSoft web site 216 ISIS V3000 support 153 isotopes specifications 193 isotopes and elements 193 isotopes table file 126 isotopes text file 126 isotopic abundance 126 J J Mol Mod 175 J Mol Mod 1 column 175 J Chin Chem Soc 174 Joback s Fragmentation method 202 joining objects 31 joining structures 31 justification atom labels 164 captions 164 Kekule structures 22 L lab supplies purchasing online 216 label to edita 11 labels 10 60 automatic terminal carbons 162 auto update 81 contracting 61 expanding 60 Lasso tool selecting objects 28 launch Chem amp Bio 3D 78 layering atom labels 167 Lewis dot symbol see lone pair symbol 90 ligand defined 195 limitations name to structure 82 line width 162 lines drawing 25 link nodes 134 LogP 201 lone pair symbol 90 Chem amp Bio Draw 12 0 227 User Guide m z displaying 85 magnification control 183 186 187 magnifying with magnification control 187 with View menu 186 Main toolbar 8 13 21 MakeChemNMRUserDB exe 97 manual mapping 141 clearing 142 overview 141 mapping atom 140 automatic 141 clearing 142 e
168. as an optional add on fea ture Using ChemNMR you can estimate and display proton and Carbon 13 chemical shifts for a selected molecule NMR Shifts To view or NMR information 1 Select a structure 2 Go to Structure gt Predict 1H NMR Shifts or Predict 13C NMR Shifts ChemNMR redraws the molecule with the esti mated shifts and displays the information and Chem amp Bio Draw 12 0 95 User Guide line spectrum in a new window as shown below Chee NMR H Estimaton Assigning Structures to Spectra ChemBioDraw Ultra lets you assign structures to spectra You can then display the structure associated with a specific peak by placing the pointer on that peak 1 Open a spectral file 2 Draw the structure or structures to assign to the spectrum 3 Select specific atoms and bonds in the structure 4 Shift click the peak or peaks to which you want the structure assigned 96 Chemistry Features Chapter 8 The selection rectangle surrounds the selected objects 5 Go to Structure gt Make Spectrum Structure Assignment The selected atoms and bonds in the structure are associated with the selected spectral peaks Viewing Spectral Assignments 1 Click the Lasso or Marquee tool 2 Place the pointer over a peak The assigned atoms or bonds are highlighted Figure 8 7 Viewing spectrum structure assignments Removing Spectral Assignments To remove spectrum to structure assignments 1
169. at the indi cators are converted into corresponding Data SGroups Whenever you open SKC or TGF files containing such Data SGroups they are converted into true Enhanced Stereochemistry values Chemical Annotations Chem amp Bio Draw 12 0 provides the following tools and tool palettes that enable you to add chemical annotations to your documents Orbital tools palette Draw orbitals Chemical Symbol Tools palette Draw charges radicals and other symbols Orbitals You draw orbitals so that the node appears first Then you can change the background color shading and solid color using the Color menu Display the Info window to view the orbital s length and angle relative to the X axis while you draw it To constrain the length and angle of an orbital go to Object gt Fixed Lengths or Fixed Angles NOTE Orbitals are not normally part of the structure they are drawn near and are not selected when you double click a bond atom or atom label with a selection tool To group the orbitals with the structure go to Object Group See Grouping Objects on page 31 S orbitals To draw an s orbital 1 Hold down the mouse button over the Orbital tool and drag to select the S orbital tool from the palette 2 Click an atom in the drawing where the orbital will be centered Sigma Orbitals To draw a c orbital 1 Hold down the mouse button over the Orbital tool and drag to select the c orbital tool from the p
170. ate the stereochemistry of a single hydrogen atom These symbols are most commonly used in fused systems such as below 20 90 Complexes Compounds with electron pairs can act as Lewis bases bonding with Lewis acids that are electron deficient Similar behavior can be seen between lone pairs and metals The best representation of these types of inter action is with a dative bond from the electron pair donor to the acceptor With a plain bond instead of the dative bond a valence error would be reported The dative bond more accu rately represents the electron donation Complexes may also be represented with explicit lone pairs and without any bonds If you use a simple bond to indicate a complex you may want to set Abnormal Valence to Allowed in the Atom Properties dialog Multi center Attachments Multi center attachments are meaningful only when created using Structure gt Add Multi Center Attachment This command creates a pseudo 194 Chemical Interpretation Appendix C atom that is disregarded during chemical cal culations but still lets you create diagrams that look meaningful to an experienced chemist A few examples are shown below 1P or z Allyl complex Ferrocene a n Aryl complex c Cp5TiCL another id complex CI 2 P n C5H5Mn CO Lo ON fe CO ey Cahn Ingold Prelog Absolute stereochemistry is calculated for tet rahedral atoms and double bonds according to the Cahn Ingold Prelog CIP p
171. ation Editor in which the scientific team models the capabilities of the lab for example the kind of basic processes which are available in the lab and their inputs and outputs 2 The design environment Workbench in which researchers create workflows from these basic processes 3 The runtime Operations Manager which manages the assign ment of tasks to agents tracks the progress of tasks and workflows and manages the storage of captured data 4 The agent tier made up of a number of applications that han dle specific types of task either manually through a user inter face or automatically by driving equipment through a control interface or performing automated data processing 5 The monitoring tier consists of a reporting tool that provides historical utilization information and a live activity viewer that allows scientists to drill into individual workflows and samples 1 617 588 9390 0120 146 700 us 1 800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com LABORATORY Workflow LIMS Visual LIMS Lab Automation Service Request Workflow allows scientists to communicate as they work Direct Communication from F Nofebook to create tasks and send r
172. ation flexible enough to model any assay regardless of complexity through an easy to use interface for importing storing and analyzing the data The software supports the quick set up of biological models auto mated calculations and curve fitting data validation and the cre ation of customized structure activity reports BioAssay Extends E Notebook BioAssay Enterprise is a scalable flexible biological screening solu tion utilizing Oracle s role based security and the Oracle Cartridge When used as part of ChemOffice Enterprise BioAssay is integrat ed with E Notebook for experimental data Inventory Enterprise for plate tracking and management Registration Enterprise for the reg istration of new compounds and BioSAR Enterprise for customized reporting BioAssay Ultra is designed to deliver much of the functionality of our enterprise level applications without a widespread roll out BioAssay Ultra coupled with BioViz offers a user friendly inter face for importing viewing validating and plotting your biolog ical assay data from your desktop BioAssay effectively manages data from complex biological assays involved with lead optimization BioViz integrates with BioSAR for one step in depth data analysis from a BioSAR report Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK 44 1223 464900 FAX JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are tra
173. ations 196 polymers 131 flip type 134 repeat pattern 133 source based 132 structure based 132 p orbitals drawing 89 positioning crosshair 187 objects 30 query indicators 122 rulers 187 stereochemistry indicators 87 positioning atom numbers 65 positioning query indicators 122 posters setup 184 PostScript commands 151 printing 161 preferences drawing see Drawing settings 161 include ChemDraw LaserPrep 151 include PostScript 151 initialize PostScript printer 151 overview 157 print 171 require CTRL ENTER 158 require Option Return 158 text see text settings 161 use bitmap fonts when available 158 preferences and settings 157 principal moments of inertia X Y Z 115 printing background color 171 ChemDraw laser prep 171 drawing elements fill 25 effect of PostScript commands 151 high resolution non PostScript 161 overview 184 PostScript atom labels 171 230 Index preferences 171 printing background color 171 properties atom in searching 120 atom abnormal valence 126 atom description 120 122 128 atom implicit hydrogens 123 atom query 120 atom reaction changes 124 atom reaction stereo 125 atom resetting defaults 122 atom ring bond count 123 atom substituents 122 atom unsaturation 124 bond 127 bond query indicators 127 bond types 128 bond reaction center 129 bond removing 128 bond topology 129 proton shifts see 13C 1H shifts estimating 95 publishing documents 173 Q
174. atom labels go to File gt Document Settings and click the Atom Labels tab You can modify the font style baseline style and whether terminal car bons and implied hydrogens appear CH C HC P C A a b c Figure 3 3 Isobutane with a terminal carbon labels and implicit hydrogens shown b implicit hydrogens hidden and c terminal carbons and implicit hydro gens hidden To set the default for a document 1 Go to File gt Documents and Settings 2 On the Atoms Labels tab check the Show Labels on Terminal Carbons checkbox 3 Click OK To set the default for one or more structures 1 Select and right click the structure s 2 Click Object Settings in the context menu The Object Settings dialog box appears 3 On the atom Labels tab check the box next to Show Labels on Terminal Carbons To add or remove a terminal carbon label right click the atom and select or deselect Show Terminal Carbon Labels Chemical Significance Whenever possible labels are recognized as chemically significant by default For example if you add a label such as CH4OH to your structure you can attach bonds to it and the label appears in the properties of the molecule To activate chemical significance right click the label and select Interpret Chemically Analysis Data You can add properties from the Analysis Window to a caption and if Auto update is on Go to File gt Document Setting gt Auto update tab the values will update
175. cals and Sigma Aldrich MSDS The Merck Index and other scientific databases provide information about chemicals their properties and reactions Professional Services include custom development system deployment educational training and technical support for pharmaceutical biotechnology and chemical customers including government and academia by experienced staff Web www cambridgesoft com Email info cambridgesoft com Ca m b ridge Soft America 1 800 315 7300 United Kingdom 44 1223 464900 Ti Science Enterprise Solutions Europe 00 800 875 20000 Germany 49 69 2222 2280 Naturwissenschafiliche Unternehmenslomungen Solutions globales pour les sciences de la vie Japan 0120146700 France 33 170 7198 80 Sess SR x b 94 Vig MAE 04980 0902
176. can interact with chemical structure data directly in the database The CambridgeSoft Oracle Cartridge supports CDX CDXML MolFile MolFile v 3000 RXN and SMILES formats making it flexible enough to be included with both new and legacy data applications without the need for file conversion Chemical infor mation can originate from either ChemDraw or ISIS Draw E Notebook Inventory or Registration Oracle Cartridge has extensive support for stereochemistry relative stereochemistry tautomers and structure normalization There is also a built in structure enu merator for nonspecific structures basic property predictors nomenclature algorithms names struct and dynamic utilities for molecular file format conversions 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com BioAssay For complicated supporting an ultra HTS platform BioAssay has become the lead ing choice for managing biological experimental data It is the only application of its kind to provide a best of breed solution for both ultra high volume laboratories and lower throughput set tings BioAssay includes support for laboratory automation calcu lation and statistics and also complicated low and medium throughput assays such as animal models and in vivo experiments modeling in vivo experiments BioAssay is designed to tackle the needs of high and low through put screening biologists alike by providing an applic
177. chiometry grid live linked chemical property calculations a TLC plate tool and more The ChemDraw ActiveX Plugin adds chemical intelligence to your browser for querying databases and displaying information ChemBio3D provides state of the art visualization and display of protein structures molecular surfaces molecular orbitals electrostatic potentials charge densities and spin densities Chem3D provides basic computational tools such as 3D Molecular Overlay and Dihedral Driver and utilizes MOPAC Jaguar Gaussian GAMESS and extended Hiickel to com pute molecular properties ChemProp computes Connolly surface areas molecular volumes and properties including ClogP molar refractivity critical temperature and pressure ChemFinder is a chemically intelligent database manager and search engine ChemFinder provides support for a database searching compound profiling R Group Analysis subforms tight integration with ChemDraw Excel and Combichem Excel statistical analysis and visualization through BioViz all in a friendly form based environment ChemFinder Office searches documents spreadsheets and files for chemical structures and references ChemFinder Oracle provides enterprise solution integration BioOffice is the ultimate suite for management analysis and visualization of biological data using 2voDraw for drawing pathways and BioAssay BioFinderand BioVizfor data analysis Includes 58 230 Draw Excel CombiChem Excel Inventoryand E Notebook
178. chment points An attach ment point symbol has been applied to the nitrogen atom When you create a parent compound that con tains an alternative group you defined an attachment point symbol appears next to the label The attachment point number matches that found in the definition OH o F Figure 10 13 Structure with R group table The number displayed in the attachment point symbol is the attachment rank order See the example in Multiple Attachment Points 136 Query Structures Chapter 10 Multiple Attachment Points You can also use R groups that contain more than one attachment point such as the one below Ry For this type of R group you will need to indi cate in your table the attachment point order If you have well defined multiple attachment points on your structure fragments you can search for specific materials This type of search is especially useful for searching for conformationally similar structures For example assume you want to find the two compounds in figure below but not the two compounds in figure Figure 10 14 Multiple attachment points By specifying the attachment point order you can exclude the unwanted compounds To specify the attachment points order 1 Draw the parent structure shown below Ry 2 Create an alternative group box labeled ee 3 Draw the structure fragments and label them with attachment points
179. color palette to specify the color of objects and text in the document in the active window A palette is stored in every document and style sheet called a stationery pad for Macintosh users You can use style sheets or stationary pads to create a series of documents with the same color scheme Customizing Colors Changes you make to the color palette affect the current document only You can save up to 20 colors For more information see Saving Customized Styles on page 161 NOTE If you select an object or group that contains multiple colors a check mark appears next to each of the colors in the Color menu The check mark alerts you that a change would affect more than one color To change the color palette in the current docu ment 1 Go to File gt Document Settings The Docu ment Settings dialog box appears 2 Click the Colors tab 3 Click the color to change either Back ground or Foreground and select Other The Color dialog box opens 4 Click the new color in the Basic Colors or the Custom Colors section 5 Click OK The color is changed to the new color and added to the Color menu To add a customized color Chem amp Bio Draw 12 0 169 User Guide 1 In the Color dialog box click Define Cus tom Colors Figure A 2 Setting custom colors A Color refiner box B Luminosity box 2 Clicka color in the Color Refiner box to set the hue and saturation The pointer turns into
180. com uiui ln aaa i ra mem eee ee Please remove this portion before mailing SALVLS GALINA JHL NI Q3TI VW dl AXVSS3O3N 1071504 ON VSN 2086 07 120 VW eBpuquin ogeBpuquo 001 33SS33QQV Ad Glvd 38 TIIM JDVLSOd VW 3oGllgWvO 4905 ON LIW33d SSVIO LS3IJ 1IVW Ald33 SSANISNG License Information All resources and application files in ChemBioOffice ChemOffice BioOffice ChemBioDraw ChemDraw BioDraw ChemBio3D Chem3D ChemFinder BioViz Inventory E Notebook BioAs say ChemINDEX ChemFinder and ChemInfo programs all resources in the ChemOffice ChemDraw Chem3D ChemFinder and ChemInfo application files and this manual are Copyright O 1986 2009 by CambridgeSoft Corporation CS with all rights reserved worldwide MOPAC 2002 is Copyright O 1993 2006 by Fujitsu Limited with all rights reserved Information in this document is subject to change without notice and does not represent a commit ment on the part of CS Both these materials and the right to use them are owned exclusively by CS Use of these materials is licensed by CS under the terms of a software license agreement they may be used only as provided for in said agreement ChemBioOffice ChemOffice BioOffice ChemBioDraw ChemDraw BioDraw ChemBio3D Chem3D CS MOPAC ChemFinder BioViz Inventory E Notebook and BioAssay and ChemInfo are not
181. compound information Inventory provides complete management of chemical and biological inventories including GxP Validation DocManager indexes chemical structures in documents Manufacturing Informatics include zzz z to meet the chemical reagent sample and compound tracking needs of large multi site chemical and pharmaceutical laboratories and E Notebook for manufacturing compliance management Desktop Software includes Chem amp Bio Office a powerful suite of software consisting of ChemBioDraw ChemBio3D ChemFinder ChemACX for chemists BioDraw BioAssay and BioViz and for biologists and Inventory and E Notebook for all Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma Aldrich MSDS The Merck Index and other scientific databases provide information about chemicals their properties and reactions Professional Services include custom development system deployment educational training and technical support for pharmaceutical biotechnology and chemical customers including government and academia by experienced staff Web www cambridgesoft com Email info cambridgesoft com Cambridagesoft America 1 800 315 7300 United Kingdom 44 1223 464900 Life Science Prey ihr se Solutions ne Unternehmensisungen Europe 00 800 875 20000 Germany 49 69 2222 2280 sions globales pour Japan 0120146700 France 33170719880 947M1vA XV8 79X Vx vay Chem amp Bio Office Deskto
182. construed according to the laws of the Commonwealth of Massachusetts United States of America SOFTWARE NO its not okay to copy your colleague s software Software is protected by federal copyright law which says that you can t make such additional copies without the permission of the copyright holder By protecting the investment of computer software companies in software development the copyright law serves the cause of promoting broad public availability of new creative and innovative products These companies devote large portions of their earnings to the creation of new software products and they deserve a fair return on their investment The creative teams who develop the software programmers writers graphic artists and 0 IS IT OK TO COPY MY COLLEAGUE S others also deserve fair compensation for their efforts Without the protection given by our copyright laws they would be unable to produce the valuable programs that have become so important to our daily lives educational software that teaches us much needed skills business software that allows us to save time effort and money and entertainment and personal productivity software that enhances leisure time Q That makes sense but what do get out of purchasing my own software A When you purchase authorized copies of software programs you receive user guides and tutorials quick reference cards the opportunity to purchase upgrades and technical support from t
183. crossed no go Chem amp Bio Draw 12 0 23 User Guide arrows equilibrium arrows of unequal lengths and elliptical arcs ARROW HEADS There are three arrow head shapes available solid hollow and angled To change the shape right click an existing arrow and choose the new shape from the context menu ARC ARROWS You can create an arc arrow one of two ways Click and drag the arc adjustment handle of a straight arrow Select an arc arrow from the Arrows pal ette You can customize arc arrows as easily as straight arrows Here are a few examples Click a modified arrow with the same arrow tool to undo all changes to the shape but not length of the arrow NOTE Click an unmodified arrow or one that has had only its length changed to reverse its direction 24 Basic Drawings Chapter 3 HOLLOW ARROWS You can rotate hollow arrows as well as change their length and width Changing the arrowhead width also changes the width of the line segment You can modify arrows with a context menu Some of the context menu commands are also available on the Curves menu Use the Context menu to create arrows for which there are no tools such as bold dashed or dipole CONNECTING ARROWS You can connect a new arrow to an existing arrow at either end or at the midpoint NOTE The terms left and right in the context menu are relative and refer to the direction the arrowhead is pointing For example to
184. cture gt Clear Reaction Map Exporting Reaction Mapping Reaction mapping and reaction center percep tion information are stored in the native file format cdx You can open the file in Chem amp Bio Draw 12 0 for transfer to other applica tions that read atom mapping such as Chem Finder You can also copy mapped reactions to these same applications using the Clipboard 142 Query Structures Chapter 10 Stereochemical Symbols There are three types of flags that indicate ste reochemistry Racemic A racemic mixture Absolute A pure enantiomer of known config uration Relative A pure enantiomer of unknown con figuration See Relative Stereochemistry on page 88 for changes in Chem amp Bio Draw 12 0 The default atom label size for the document determines font and size for stereochemical flags NOTE The stereochemical symbols feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To draw a stereochemical flag 1 To display the Query tools go to View gt Other Toolbars gt Query Tools or click the Query Tools icon on the Main Tool pal ette 2 Onthe Query tools palette click the tool for the flag you want to use 3 Click next to the structure to which you want to assign the flag 3D Properties 3D queries are particularly useful in pharma cophore searching where the user is looking for a 3D relationship among atoms and bonds for example in a serie
185. cument It shows the current values as you draw The Decimals setting applies to Exact Mass Molecular Weight and nvz only Formula The molecular formula showing the exact number of atoms of each element in the molecule and charges radicals and isotopes Exact Mass The exact molecular mass of the structure where atomic masses of each atom are based on the most common isotope for the element Molecular Weight The average molecular mass of the structure where atomic masses are based on the natural abundance of all isotopes of the element m z Mass charge where charge 1 The weights of the most common isotopes and a graphical representation of the isotopic abun dance is shown The molecular weight shown takes the isotopes for each atom and their natural abundance into account Where there 1s more than one abun dant isotope this feature computes multiple molecular weights Low abundance combina tions whether because the isotope is in low abundance or because it includes many moder ate abundance contributions are not taken into account Elemental Analysis The percent by weight of each element in the structure To paste information about a structure as a caption 1 Click the check boxes for the information that you want 2 Click Paste Chem amp Bio Draw 12 0 85 User Guide The information appears as a multiline caption below the structure You can edit this informa tion with the text tool OH OH
186. current document To apply object settings 1 Select the object 2 Go to Object gt Apply Object Settings from and choose the document from which to apply the settings A dialog box appears 3 Do one of the following To selected object only click No To selected an object and any new objects you draw click Yes Drawing Settings Drawing settings affect how bonds and other objects are drawn You can configure the drawing settings for an entire document or for a particular object as follows Chem amp Bio Draw 12 0 161 User Guide For the entire document go to File gt Docu ment Settings and select the Drawing tab Foranobject use the Object Settings dialog box Changes made to the drawing settings affect the active document window only Drawing settings can be saved in style sheets or station ary pads To apply settings from other documents to your document go to File gt Apply Document Settings Chain Angle Set the angle from 1 to 179 degrees between bonds created by the Acyclic chain tool or modified by the Clean Up Struc ture command See Acyclic Chains on page 22 and Clean Up Structure on page 62 Bond Spacing Set the distance between the lines in double or triple bonds The distance is set either as The percent of the length of the bond between 1 and 100 This allows for pro portional spacing if different bond lengths are used 1095 1496 1895 w An absol
187. d Document 183 Poster Documents 184 Headers and Footers sss 164 Page Setup 164 PEWYCIDES 184 Print Options 185 SCalihg un 185 Saving Page Setup Settings 185 35mm Slide Boundary Guides 185 Viewing Drawings 186 Magnification oaeee 186 The Magnification Control 187 IO 187 The Crosshair esses 187 Appendix C Chemical Interpretation 189 Chemical Intelligence 189 Database Conventions 189 Bond Conventions sss 190 Atom Labels see 191 Chemically Significant Text 192 Charges 192 Isotopes and 193 Radicals endete 193 H Dot H Dash esee 194 Complexes esses 194 Multi center Attachments 194 Cahn Ingold Prelog 194 Stereochemical Flags 195 Polymer Representations 196 Analysis Messages sese 197 Appendix D Property Calculations 201 LUBP uid easy 201 Henry s Law 201 Molar Refractivity sss 202 CLogP and CMR sse
188. d Wedged Bonds Dative bonds and wedged bonds are drawn with a fixed orientation in a document window To draw a dative bond 1 Select the Dative Bond tool 2 Drag from the positive to the negative end arrow head of the dative bond To draw a wedged bond 1 Click one of the wedged bond tools 2 Drag from the narrow end of the wedged bond to the wide end of the wedged bond 3 BOND ORIENTATION To change the orientation of the wedged bond click the center of the bond using the wedged bond tool To change the orientation of a dative bond click the center using the dative bond tool COOH COOH Or di HO CH3 HO CH3 NOTE Chem amp Bio Draw 12 0 treats hashed wedged bonds with the narrow end in the plane of the screen and the wide end behind the plane Editing Bonds You can modify the appearance of chemical bonds by Changing bond types Changing bond alignment and orientation Moving Atoms Layering bonds Changing Bond Types Change a single bond from one type to another by doing either of the following Select a bond tool and click the center of an existing bond Right click and select the new type from the context menu e Ctrl click the bond Changing Double Bonds To change one type of double bond to another 1 Select the Bold Dashed or Solid Bond tool 2 Click a double bond The double bond changes to the new bond type One of the bonds in the double bond i
189. d by CS 5 Limitations on Use a Desktop versions of E Notebook Inventory and BioAssay are licensed for use with SQL Server Express and are not licensed for use with SQL Server Licenses for use with SQL Server are available separately b Workgroup versions of E Notebook Inventory and BioAs say are licensed for use with SQL Server and SQL Server Express c Except as expressly provided by copyright law copying redistribution or publication whether for commercial or non commercial purposes must be with the express permission of CS Merck or other CS partner In any copying redistribution or publication of copyrighted material any changes to or deletion of author attribution or copyright notice or any other proprietary notice of CS Merck or other Database producer are prohibited 6 Separation of Components The Software is licensed as a single product Its component parts may not be separated for use on more than one computer except in the case of ChemBioOffice Enterprise ChemBioOffice Enterprise includes licenses for ChemBioDraw ActiveX and licenses for ChemBio3D ActiveX The ActiveX software products may be installed on computers other than that one on which ChemBioOffice Enterprise is installed However each copy of the ActiveX is individ ually subject to the provisions of Paragraphs 1 through 4 of this Agreement 7 Educational Use Only of Student Licenses If you are a student enrolled at an educational institu tion
190. d perhaps an infinite num ber of substituents Generic nicknames have meaning only in the context of the search sys tem you are using The generic nicknames recognized as chemi cally meaningful are listed in the Generic Nicknames file in the ChemDraw Items folder To edit the generic nickname files open the Generic Nicknames file in a text editor and make your changes Follow examples in the file for the correct format NOTE If you check a structure that has a generic nickname a message is displayed because the structure contains variable substit uents If you ignore this message the generic nicknames are ignored and the chemical for mula mass etc are reported as if the atom label containing the generic nickname were not selected Atom Properties Atom properties determine what structural fea tures are allowed at the site of an atom For example you can specify that a carbon atom must be part of a ring have at least two attach ments have no attachments or perhaps be a specific isotope You can specify a wide vari ety of properties for any atoms in your query structure NOTE The atom properties feature is avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Assigning atom properties To assign properties to selected atoms in a structure 1 Select one or more atoms 2 To open the Atom Properties dialog box do one of the following Right click select At
191. d under this license provided you transfer this Agreement and all copies of the Software including prior versions and all accompany ing materials The recipient must agree to the terms of this Agreement in full and register this transfer in writing with CS 4 Use of Included Data All title and copyrights in and to the Software product including but not limited to any images photographs animations video audio music text applets Java applets and data files and databases the Included Data are owned by CS or its suppliers You may not copy distribute or otherwise make the Included Data publicly available Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plug in software products may access search and view the Included Data and may transmit the results of any search of the Included Data to other users of the licensed ChemOffice Enterprise and Workgroup software products within your organization only provided that such transmission is via an internal corporate or university network and is not accessible by the public You may not install the Included Data on non licensed computers nor distribute or otherwise make the Included Data publicly available Youmay use the Software to organize personal data and you may transmit such personal data over the Internet provided that the transmission does not contain any Included Data All rights not specifically granted under this Agreement are reserve
192. d when you modify your drawing 7 Click OK Formatting Captions Text settings affect how captions and atom labels for the current document are drawn and formatted Formatting options include font font type size font size style font and baseline style line spacing alignment Setting Font parameters Changing text formats in the Document Set tings dialog box affects the current document only You can also change settings for individ ual objects by using the Object Settings dialog box the Text menu or the Style toolbar To edit the document text settings for captions and atom labels 1 Click File gt Document Settings 2 In the Document Settings dialog box click Captions or Atom Labels 3 Change the settings as desired The options are described in the following sections 4 Chck OK 5 The formatting is applied to the current document Setting the Baseline Style You can specify the following baseline styles Normal Use this for standard text Superscript Reduces the text size by about 25 percent and raises its baseline Subscript Reduces the text by about 25 percent and lowers the baseline Chem amp Bio Draw 12 0 163 User Guide Formula Formats in a way that is appropriate for most chemical formulas that is numbers are subscripted You must however capitalize manually You can apply several styles to the same selected caption You can also apply multiple styles to
193. data from disparate experi ments that represents the pharmacological profile for a com pound It is here where E Notebook reveals one of its most signifi cant capabilities the reporting feature E Notebook reports are flexible any field e g compound ID study type etc can be used to query the system and any field e g conclusion dose etc or field aggregate e g average radioactivity can be displayed in the report Reports are dynamic and navigable results are displayed with links that provide quick access to experiments Reports are viewed directly in the E Notebook interface but they can also be exported to Microsoft Word or PDF to share with those who do not have E Notebook access v Inventory Enterprise TT i As EMAIL info cambridgesoft com CambridgeSoft www cambridgesoft com MANAGEMENT Sample Management Compliance Execution and Sample Tracking Drug Safety Toxicology Paper notebooks have traditionally been considered to be the record source for the entirety of an experiment but they often miss non experimental information generated shortly after con ception For example toxicology studies are often initiated not by the scientist who ultimately runs the experiment but instead by a manager or coordinator who assigns the study to the scien tist Important material related to this first step in the process such as ideas emails and other communications are often left out of traditiona
194. date information of high quality ChemACX allows you to purchase chemicals fast efficiently and without worry or cumbersome paper catalogs The database can be accessed from both desktop and enterprise environments and boasts nearly 500 catalogs from major suppliers from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds in between Sigma Aldrich MSDS Environmental Heath and Safety EH amp S is an important com ponent of today s research institutions A key document that aids in the management of EH amp S tasks is the Material Safety Data Sheet also commonly referred to as MSDS In every organization there are several groups of personnel who require access to MSDSs Everyone who comes into contact with chemicals needs Scientific Databases REFERENCE DATA The Merck Index 11 000 monographs R amp D Insight Chemists 20 000 substances ChemlNDEX Database 75 000 substonces NCI AIDS amp Cancer 270 000 substances Troditional Chinese Medicines 10 000 substances Drugs Synonyms amp Properties 8 000 drugs Nanogen Index 1 000 pesticides Medicinal Chemistry 540 000 substances ChemACX Database 480 catalogs ChemMSDX Database 23 000 MSDSs Sigma Aldrich MSDS 130 000 MSDSs REACTION amp SYNTHESIS DATA ChemReact500 450 000 reactions ChemReacl 8 68 000 reaclions ChemSynth 178 000 reactions US 1800315 7300 INT L 1 617 588 9300 FAX 1617 588 9390 EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 MAIL CambridgeSof
195. de those specific features by developing market add ins or other modifications that are supported in the future Systems Deployment Installation and Configuration CambridgeSoft has a tested methodology for system deployment that consists of an IT architectural review a business workflow and process review as relates to specific scientific areas a process integration review and maintenance guidelines By care fully following this proven methodology CambridgeSoft installs and configures systems that are easy to maintain and have the flex ibility to accommodate variations in the science or business work flow that come from extensive experience in these areas EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com SERVICES Training amp Support Educational Training and Technical Support Systems Optimization CambridgeSoft s systems deployment team will work with you to make sure that your computing environment has been optimized for high performance Your systems networks applications and databases are assessed and designed to deliver maximum achieve ment Beta and Pre Release Programs Committed to maximizing your productivity through the use of our products as well as exposing you to the newest technologies our beta and pre release programs provide you with first hand product knowledge and allows CambridgeSoft to improve appli cations with your feedback Pilot Software Evaluations It makes sense
196. defined stereochemistry by duplicating and rotating it To create a mirror image 1 Draw a structure with defined stereochem istry for example wedged bonds 2 Select the structure and make a copy using Ctrl Drag or option drag 3 With the copy still selected go to Object gt Flip Horizontal or Flip Vertical To preserve the absolute stereochemistry while flipping go to Object gt Rotate 180 Coloring objects You can select and color objects specific bonds part or all of a chemical structure boxes curves arrows orbitals and reaction mechanism symbols The border of objects that are shaded or filled such as white filled s orbitals in the Orbitals palette are the same color as the shading or fill The border of objects that are hollow such as circles and hollow boxes in the Drawing Elements palette can be colored but the inside of the object cannot Chem amp Bio Draw 12 0 59 User Guide To color an object 1 Select the object 2 Doone of the following Click the Color button on the Style tool bar and select the color from the menu that appears e Choose color from the Color menu Go to Object gt Object Settings and select the color in the Drawing tab Click OK when finished Coloring groups Chem amp Bio Draw colors groups differently from integral groups When you color an inte gral group its objects acquire the new color but retain the original shading When you color anormal g
197. demarks of CambridgeSoft Corporation 2009 BIOLOGICAL BioAssay BioViz Assay Screening and Visualization Effectively manage data from complex biological assays involved with lead optimization Scalable HTS amp HTTS Use BioDraw to document cellular pathways BioDraw Diagramming and presenting cellular pathways is made easier and more effective with BioDraw Formerly called Pathworks BioDraw does for biologists what ChemDraw has done for chemists saving time and producing a more professional representation of the science BioDraw makes drawing and annotating biological pathways quick and easy adding a level of uniformity and detail which is unmatched Common pathway elements such as membranes enzymes receptors DNA and reaction arrows are built into the BioDraw toolbar BioDraw also allows the import of images in PNG or JPEG formats BioDraw offers many ways to share your drawings and accompanying data Users can export data to Microsoft Office applications for inclusion in presentations and grant proposals or save data as an image file for use in journal article submission Draw Biological Pathways EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com INFORMATICS BIoSAR amp BioDraw Data Mining and Pathway Drawing BioSAR BioSAR Enterprise a strate
198. des fully integrated Knowledge Management and Enterprise Informatics applications integrated with compliant storage Compliant DB makes this possible v Workbench Sample Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 0080087520000 UK 44 1223 464900 JP 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com Develop Centralized Validated Storage and GxP Compliant Storage Store Documents Machine Files amp Chemical Objects Oracle Cartridge is compatible with Linux Solaris AIX and Windows and includes structure searching property predictions and nomenclature Oracle Cartridge The CambridgeSoft Oracle Cartridge is used by all ChemOffice Enterprise applications for storing searching and analyzing chem ical data It can also be used in the development of your custom Oracle applications Chemical structure and reaction data is diffi cult to manipulate without utilizing special software and Oracle data cartridges define new recognized data types CambridgeSoft s Oracle Cartridge utilizes this technology making it possible to manipulate chemical structure and reaction data from within Oracle improving portability and consistency in applications Since the Oracle Cartridge is accessed through native Oracle SQL programmers
199. different portions of a single caption Style Indicators Select any text in the document window and go to Text gt Style to view the styles that have been applied to it A check indicates the style applies to all the selected text A hyphen indi cates the style applies to only some of the selected text Specifying Line Spacing You can specify the three types of line spacing Automatic Consistently spaced lines of text based on the height of the tallest character in the entire caption This is the default line spac ing Variable Lines of text with different spacing based on the tallest character and the lowest descender in each line Fixed Consistently spaced lines using a spac ing that you specify Aligning Text You can set the alignment of captions and atom labels to justify text to suit your needs The options available depend on whether you are aligning captions or atom labels Apply set tings in the Object Settings dialog box 164 Preferences and Settings Appendix A To open the object settings dialog box do the following 1 Select a caption or atom label 2 Go to Object gt Object Settings The Object Settings dialog box appears Captions You specify the caption justification and line spacing on the Captions tab of the Object Set tings dialog box All text in a single caption must have the same justification and line Spac ing There are four available justifications Flush Left creates left justi
200. document Chem amp Bio Draw 12 0 creates a QuickDraw representation and a PostScript representation of the docu ment contents If you are transferring information to another application from which you print Chem amp Bio Draw 12 0 pictures you include PostScript commands and the ChemDraw LaserPrep File with the pictures The Macintosh High Resolution Clipboard supports high resolution printers Most appli cations support the High Resolution Clipboard Because this was not always the case in the past this preference continues to be available for users to turn off if an application being used does not support the High Resolution Clipboard If you are unsure if the application uses a High Resolution Clipboard try transferring pictures with this check box selected and deselected and see which picture prints with higher qual ity If you are printing to a non PostScript printer deselect Include ChemDraw LaserPrep and Include PostScript to reduce the size of each picture Do not deselect this option if the docu ment will ever be printed to a PostScript printer Printers that use the PostScript page definition language use the PostScript representation The PostScript representation describes objects by using mathematical shapes that can be pre cisely imaged at whatever resolution is used by your printer The PostScript representation cre ated by Chem amp Bio Draw 12 0 is composed of two parts the PostScript commands and the
201. ds They can find and purchase reagents in ChemACX database store and use them from Inventory record newly made compounds within a proprietary Registration system record the results in BioAssay analyze the results with BioViz and generate reports linking activity and structure with BioSAR can Virtually every aspect of discovery from synthesis planning library enumeration reagent selection primary and secondary screening 77 vivo testing through to analysis of results and report ing is covered by this integrated application suite Development and Testing Building on productivity software CambridgeSoft created enter prise applications to meet the needs of an everexpanding research and development community that relies on data sharing across sci entific disciplines research campuses and even oceans as global ization has increased demands Since the software takes advantage of the latest web based technologies it is deployed readily throughout a research and development organization Using the integrated suite scientific teams are well armed to solve the daily challenges of development These teams include scientists who scale up and design manufacturing procedures toxicologists who determine the metabolic fate of drugcandidates formulation sci entists who determine drugdosing and delivery systems as well as many others Trials A suitable drug candidate is one that has the desired activity to provide disease therapy w
202. e query structure Records that match the query structure are returned in the search results NOTE The nicknames feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only For example the query structure below uses the letter to indicate that a nonhydrogen noncarbon atom must appear at the specified location Other generic nicknames may be used to indi cate other types of query criteria The generic nicknames that Chem amp Bio Office 12 0 sup ports is listed below all are recognized as chemically significant A represents one atom only M represents metal Q represents an atom that is neither hydro gen nor carbon X represents any halide R unrestricted represents zero or more connected atoms of any kind To label an atomic position with a generic nickname do one of the following Double click the atom to open a text box and type in the nickname 120 Query Structures Chapter 10 Right click the atom point to Insert Generic Label on the context menu and click the label you wish to insert on the sub menu Generic Nickname Hotkeys You can assign hotKeys to generic nicknames just like other nicknames For information on assigning a Hotkey to a nickname see Cus tomizing Hotkeys on page 167 Defining Generic Nicknames You cannot define the meaning of a generic nickname because generic nicknames can rep resent multiple an
203. e LI GAMESS We LI Gaussan Infertacc We a E Jaguor Interface We a a Interface We Ei s a 8 1 Win Mac m E ChemINDEX Ultra We a a E Chesf XN NCI amp AIDS We a 4xadcble Sepcrately zpacihicatare subject to change without notice US 1 800 315 7300 INT L 1617 588 9300 FAX 1617 588 9390 EMAIL info cambridgesoft com EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 WWW www cambridgesoft com CambridgeSoft MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 www cam b ridgesoft com SOFTWARE Chem amp Bio Office Software Standard for Scientists The ultimate sofiware suite for scientists The standard achieves the ultimate Computational chemistry made easy Desktop to enterprise searching Ultimate suite for biologists Draw pathways Screening data Visualize data Chem amp Bio Office isa powerful suite of software consisting of ChemDraw Chem3D ChemFinder and ChemACX for chemists BioDraw BioAssay and BioViz for biologists and Inventory and E Notebook for all types of scientists Chem amp Bio Office is available for Microsoft Windows Chem amp Bio Draw includes Struct Name ChemDraw Excel and ChemNMR BioDraw a biological sequence tool hotlinks to 3D structures Stoi
204. e All To stop checking for errors click Stop Checking copied structures To analyze a structure on the Clipboard 1 Go to File gt Preferences 2 On the General tab click the Check Struc ture When Copying to Clipboard or Exporting check box This change affects all documents Chemical Warnings Chem amp Bio Draw 12 0 checks for correct chemical syntax as you draw If it finds an error in your structure such as improper valences a wavy red box appears around the questionable object The box is displayed on screen only and does not print Disabling chemical warnings Warnings are displayed by default however you can turn them off To disable the automatic display of chemical warnings go to View gt Show Chemical Warnings To disable the automatic error checking on a specific object right click the object and dese lect Display Warnings on the context menu When Display Warnings is deselected for an object Red boxes are not displayed for question able objects Problems are reported by the Check Struc ture command Go to Structure Check Structure To view a description of the problem do one of the following Pointat the warning with the mouse to dis play a tool tip that describes the error Right click the warning and choose Explain This Warning Select the structure and go to Structure Check Structure Warning Preferences To select which types of chemical warnings to display 1
205. e Group to indicate that the enclosed items are repeated a specific known number of times Multiple group brackets may enclose entire structures or may enclose a portion of the structures only You can edit the numeric repeat count with the text tool Examples are shown in below OH O Figure 10 9 Brackets indicate multiple groups ANALYSIS Because multiple group brackets represent a specific repeat count unlike the unknown repeat count of the other bracket types it is possible to calculate accurate molecular weights and related data for such structures That data 1s displayed in the Analysis window as with any other structure Repeat Pattern For simple linear polymers the repeating units may connect head to tail or head to head or their repeat pattern might be a mixture or unknown You can also assign this property to brackets Because of its prevalence the head to tail type is assumed to be the default Repeat Pattern Chem amp Bio Draw 12 0 133 User Guide and does not receive any special annotation on the brackets as shown below A 477 of B C T Figure 10 10 Head to tail repeat pattern A and B represent the polymers shown C represents a mixture of A and B Link Nodes You can specify a variable length chain or ring by indicating that one of the atoms can be repeated some number of times using link nodes NOTE The link nodes feature is available in
206. e cyclohexane to tetrahydropyran 1 Click outside the structure to deselect it 2 Point to the atom indicated in the figure below and type the letter o ete Figure 5 14 Adding an atom label with a HotKey Resize horizontally 1 Go to Edit gt Select All or type Ctrl A 2 Using a selection tool click drag the right side handle to resize the ring horizontally Release the mouse button when the ring is is stretched about 200 201 05 Resize the ring Chem amp Bio Draw 12 0 User Guide 51 1 Go to Edit gt Select All or type Ctrl A 2 Click Drag the ring a corner adjustment handle increase the size of the ring to 150 A dialog box appears asking you whether you want to scale the drawing and text settings 3 In the dialog box click No Add vertical bonds 1 Click the Solid Bond tool 2 Pointto the atom shown in the figure below and drag upward to create a bond N Q 3 Point to the same atom and drag downward to create another bond 4 Repeat this procedure four more times add ing the pairs of vertical bonds shown below Create OH labels You can use the repeating bond label technique in Tutorial 4 or use Hotkeys For the HotKey method just point and type o The Text tool 52 Tutorials Chapter 5 method is repeated here with a slight varia tion 1 Select the Solid Bond tool point to the atom shown in the figure below and double click to open a text box Type
207. e the Paid Subscription Service materials to abide by all of the terms and conditions of this Agreement In all other cases only the Subscriber is permitted to access the Paid Subscription Service materials Should CambridgeSoft become aware of any use that might cause revocation of the license they shall notify the Subscriber The Subscriber shall have 90 days from date of notice to correct such violation before any action will be taken 6 Trademark Notice THE MERCK INDEX is a trademark of Merck amp Company Incorporated Whitehouse Station New Jersey USA and is registered in the United States Patent and Trademark Office CambridgeSoft and ChemACX are trademarks of CambridgeSoft Corporation Cambridge Massachusetts USA and are registered in the United States Patent and Trademark Office the Euro pean Union CTM Japan and other markets Any use of the marks in connection with the sale offering for sale distribution or advertising of any goods and services including any other Web site or in connection with labels signs prints pack ages wrappers receptacles or advertisements used for the sale offering for sale distribution or advertising of any goods and services including any other Web site which is likely to cause confu sion to cause mistake or to deceive is strictly prohibited 7 Modification of Databases Web sites or Subscription Services CS reserves the right to change modify suspend or discontinue any or all
208. e there is no atom that indicates a connection point you cannot define a nickname When a sulfonamide group is attached to an unselected bond you can define a nickname In Figure b there is more than one attachment point on a single atom in a nickname Incorrect Correct a b 3D Viewing As you create your drawing you may be curi ous to see it in three dimensions There are two features in Chem amp Bio Draw that let you do just that NOTE Chem amp Bio 3D must be installed on your computer to preview structures in three dimensions Chem amp Bio 3D Preview is avail able only in ChemBioDraw Ultra and Chem amp Bio Draw 12 0 Ultra 3D Model Use a 3D model to paste a 3D version of the structure into your drawing 1 Select the structure 2 Go to Edit gt Get 3D Model The 3D structure appears in the document window To view the model in Chem 3D double click it NOTE 3D Objects inserted in this way cannot be transferred between platforms For more information see File Formats on page 153 Chem amp Bio 3D Preview options The preview window displays structures in 3D that you have selected all structures if none are selected Chem amp Bio 3D Preview works only for chemical structures not biological structures To view go to View gt Show Chem3D Preview Window NOTE For molecules that cannot be viewed in the Chem amp Bio 3D Preview window No pre
209. e they are near Note that the red valence error warning disappears when you add the minus charge CURVED ARROWS For some reactions you may not want to be limited to drawing simple straight arrows In fact you may need a variety of curved or col ored arrows to enhance your drawings You can curve most arrows found on the Arrows toolbar After you paste an arrow in your draw ing click and drag the selection point in the middle of the arrow As you drag the selection point the size of the arc appears measured in degrees COLORED ARROWS To color an arrow 1 In the drawing window select the arrow to color 2 Selecta color from the Color menu COLORING BLOCK ARROWS For block arrows those that aren t made of just simple lines you can create various col 68 Advanced Drawing Techniques Chapter 6 ored effects using the filled faded and shaded options To use these effects 1 Select a block arrow from the Arrows pal ette and right click it 2 Select a color from the Color menu 3 On the context menu choose either Filled Faded or Shaded Drawing the product We now create 4 hydroxy 4 methyl 2 pen tanone using a copy of the 2 propanone struc ture You can also create the product from scratch but you may find copying another structure more convenient Copy the structure 1 Select the 2 propanone structure and its caption 2 Press and hold the Ctrl windows or Option Macintosh key The hand poin
210. ear with the chemical shifts displayed on the molecule and the spectrum is linked to the structure so that clicking on a peak in the spectrum highlights the corresponding fragment on the molecule ChemBio3D Ultra includes visualization and molecular mod eling capabilities for both small molecules and protein structures designed for the bench chemist Small molecule computational methods include Molecular Overlay and Dihedral Driver It also includes interfaces to the MOPAC Jaguar Gaussian and GAMESS semi empirical and ab initio computational packages High quality Chem3D graphics can be viewed on the web using the Chem3D Activex Chem3D Pro brings workstation quality molecular visualiza tion and display to your desktop Convert ChemDraw and ISIS Draw sketches into 3D models View molecular surfaces orbitals electrostatic potentials charge densities and spin densi ties Use built in extended Hiickel to compute partial atomic charges Use MM2 to perform rapid energy minimization and molecular dynamics simulations Chem3D can also be used to estimate physical properties such as logP boiling point melting point and more Visualize Connolly surface areas and molecular volumes EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com SOFTWARE ChemFinder amp Chemlnfo Structure Searching and Scientific Databases ChemFinder Ultra is chemically intelligent database man agement and search system designed for chem
211. earch discovery development trials and manufacturing organization is able to respond swiftly and effectively to opportunities and market changes promote innovation and accelerate product delivery you are working smarter to outpace your competitors As the speed of busi ness continues to accelerate leading organizations constantly seek faster and better informed decision making as well as new business efficiencies For the individual chemist biologist scientist and engi neer who needs to capture organize and communicate chemical and biological data through the complex and widespread workgroup and enterprise scientific information systems needs CambridgeSoft Solutions can help CAMBRIDGESOFT Chem amp Bio Office Desktop KNOWLEDGE MANAGEMENT CHEMICAL BIOLOGICAL Desktop Chemistry Biology BioAssay amp E Notebook E Notebook ChemBioViz Process Workflow BioSAR E Notebook LIMS Enterprise Enterprise Chem amp Bio Office Enterprise E Notebook Enterprise Chemistry amp Biology Analytical Services Sample Management Workflow LIMS Compliant DB Oracle Cartridge BioAssay Enterprise BioDraw BioSAR amp BioViz Registration Enterprise ChemBioFinder Enterprise Compliance E Notebook DocManager Enterprise Enterprise KNOWLEDGE MANAGEMENT Research organizations thrive when information is easily captured well organized and readily avail able Nofebook E
212. earning Chem amp Bio Draw 5 Chemical structures in Excel 5 Converting Structures to Names 3 About ChemNMR sss 2 Chapter 2 Getting Started seessooesssesssesssesssoosssossss 7 Installing Chem amp Bio Draw 7 System Requirements eese 7 Site License 7 The Work NIE 7 8 The Main Toolbar sss Tearing Off Toolbars sss 8 Docking and Floating sss 9 BioDraw Toolbar sss 9 soi troi tecto n daa oen 9 Creating Documents esee 9 Opening Documents eee 9 Discarding Changes sss 9 Undo Redo and Repeat 9 Saving Documents esee 10 Selecting an open document 10 WAIDGOWS M 10 The Info Window sss 10 Periodic Table sss 10 Character 11 Chapter 3 Basic Drawings ence ecce ecoes cc eaa caosa ecu 13 TONGS RT n 13 Fixed Bonds sse 13 Bond Types 14 Editing Bonds sss 15 Captions and Atom labels 16 Formatting captions and labels 17 Hotkeys and Nicknames 18 Expanding 19 Annotations
213. ears as a caption below the structure CHO H OH HO H H OH H OH HOH Chemical Formula CsH1206 Exact Mass 180 06 Molecular Weight 180 16 m z 180 06 100 0 181 07 6 9 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 53 29 Figure 5 12 Fischer projection with analysis Save and close the document 1 Go to File gt Save 2 Go to File gt Close Tutorial 4 Perspective Drawings In this tutorial we explain how to create a per spective drawing by creating a model of a D glucose as a Haworth projection CH20H OH Figure 5 13 Perspective drawings Create a new document using the default style 1 Go to File gt Open Style Sheets gt New Docu ment NOTE If you are following the tutorials in order Chem amp Bio Draw 12 0 will remember your last drawing used the ACS style sheet and open it as the default Step 1 resets the default to New Document 2 Go to File gt Save As 3 Type tut4 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Draw a ring 1 Click the Cyclohexane Ring tool 2 Click in an empty area of a document win dow A cyclohexane ring appears Rotate the ring 1 Go to Edit gt Select All or type Ctrl A 2 Go to Object Rotate or type Ctrl R 3 In the Rotate Objects dialog box enter 30 degrees for an angle and click Rotate The cyclohexane ring is rotated i peee H H I Chang
214. eb based user interfaces to speed use but substan tial gains come in the automated reporting and alerting Examples include notifying all users of samples derived from a single stan dard of some change in status such as different analytical results or failure to recertify v Inventory Enterprise al iej x Google CambridgeSoft Inventory Enterprise Disce l Location iin gui ViewSimpleRackL ayau Pharmacy MyRack esaa 2 sae E Expiration Date 08 21 2008 owner Status Available Container Links Parent Container Fami 6295 teh 1 Amount on Hand Current User la sila T T fbi 5 amp 5 S3 5e OS wm a seran o 1B 3e a 0e mal Ye 5 0e WH e Mu ewe Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP MAIL CambridgeSoft Corporation 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Validated for GxP Environments with Audit Trails Container History Store Datafiles with Samples such as Batch and Certificates of Analysis Allows for Flexible Reporting Electronic Data Files In addition to storing moving and disposing containers the a
215. ecting Objects Use the Lasso or the Marquee tool to select any object You use the Lasso for freehand selec tion and the Marquee to select rectangular regions To set one selection tool to behave like the other click the Lasso or Marquee tool while holding the Alt or Option key down To toggle a selection tool and the last drawing tool used press Ctrl Alt Tab or Com mand Optionttab If you haven t used either selection tool it defaults to the Lasso tool When you select a structure or object the selection is displayed with a light blue frame Chem amp Bio Draw 12 0 27 User Guide around it with three types of selection handles with a resize handle on each side and corner Figure 3 7 A Drag this handle to rotate the object B Drag any corner to resize C Drag any side handle to distort The Lasso Tool Use the Lasso tool to make freehand selection of irregular areas To select objects using the Lasso tool 1 Select the Lasso tool 2 Press the mouse button while the pointer is not over any object 3 Drag around part of a structure or other object As you drag a line appears that defines the selection area Bonds structures or other objects are selected only if they are entirely within this area The end points of the Lasso are connected when you release the mouse but ton The Marquee Tool Use the Marquee tool to select objects and structures within a rectangular area 1 Select the Marquee too
216. ed Length 30 pt Bold Width 2 pt Line Width 1 pt Margin Width 2 pt Hash Spacing 2 7 pt Chain Angle degrees 120 Bond Spacing of length 12 Atom Label Font Win Mac Atom Label Size 10 pt NS Caption Font Win Mac BO Caption Size 12 pt Drawing Area Width x Height 7 5 in x 10 in Page Size US Letter or A4 as selected Reduction 96 100 New Slide Fixed Length 30 pt Bold Width 4 pt Line Width 1 6 pt Margin Width 2 pt Hash Spacing 2 7 pt Chain Angle degrees 120 Bond Spacing of length 15 Atom Label Font Win Mac Atom Label Size 12 pt Caption Font Win Mac Caption Size 16 pt Drawing Area Width x Height 7 5 in x 10 in Page Size US Letter Reduction 100 176 Preferences and Settings Appendix A Phytomedicine HO HO Fixed Length 20 pt Bold Width 1 33 pt Line Width 1pt Margin Width 1 25 pt Hash Spacing 3 pt Chain Angle degrees 120 Bond Spacing of length 8 Atom Label Font Win Mac Atom Label Size 12 pt Caption Font Win Mac Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 Chem amp Bio Draw 12 0 User Guide 177 RSC Fixed Length 0 43 cm Bold Width 0 056 cm Line Width 0 016 cm Margin Width 0 044 cm Hash Spacing 0 062 cm Chain Angle degrees 120 Bond Spacing of length 20 Atom Label Font Win Mac Atom
217. ed in parentheses The default is to dis play parentheses Removing Indicators To remove an indicator click it using the Eraser tool Positioning Indicators Stereochemistry indicators are positioned auto matically and move appropriately if a structure 1s modified However you can move them either by dragging them or by indicating an exact location To indicate an exact location 1 Select the indicator to move 2 Right click and choose Position The Posi tion Indicator dialog box appears 3 Click the appropriate option and type a value described below To Position Type a value for the position by from the atom or bond angle in degrees center to indicator Or center clock in clock time from the atom or bond offset horizontal center to bottom left of and vertical indicator baseline at specified coordinates absolute horizontal and vertical Chem amp Bio Draw 12 0 87 User Guide Relative Stereochemistry You can specify relationships between groups of stereocenters within a molecule NOTE ChemBioDraw Ultra Chem amp Bio Draw 12 0 Ultra and Chem amp Bio Draw 12 0 Pro support ISIS compatible stereochemistry This notation enables you to describe stere ochemical properties and individual stereo centers rather than the entire molecule As a result you can illustrate properties of several enantiomers using only a few or even just one structure The notati
218. ed the award winning ChemFinder Com database since 1995 Now the data on ChemFinder Com is integrated into ChemOffice as ChemINDEX ChemINDEX contains data from over 75 000 compounds including structures names and synonyms physical properties and Internet links Additionally three informative databases have been integrated into one power ful application with the NCI and AIDS database a collection of over 200 000 molecules studied by the National Cancer Institute ChemReact and ChemSynth These reaction database collections from InfoChem GmbH com prising essential information on chemical reactions published in the literature between 1974 and 2001 The largest is ChemReact500 with almost 500 000 reactions selected with an eye toward synthetic utility ChemSynth is a subset of the reac tions found in ChemReact500 chosen because they have greater than 50 yield and have been sited in leading journals more than once ChemReact68 has 68 000 reactions that have greater than 50 yield and have appeared in more than five example reactions EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com DATABASES ChemACX amp Sigma Aldrich MSDS Available Chemicals and Material Safety Data Sheets ChemACX Database Sifting through chemical catalogs is a poor use of time for any researcher ChemACX database solves this problem by offering a complete tool for research chemical sourcing and purchasing With an emphasis on up to
219. elect Regions in the context menu 2 In the Regions dialog box enter in the Start and End text boxes the base pair numbers for a fragment For example if a fragment includes all base pairs from 1 to 1000 type 1 and 1000 in the text boxes 3 If you want the Start and End base pair numbers for the fragment to appear in the drawing select Add Markers At Region Ends 4 Chck Add 5 To add more regions repeat steps 2 4 6 Click OK ADDING MARKERS Markers let you annotate base pairs in the plas mid map For example to label a specific base pair or fragment you add a marker to it To add a marker 1 Right click the plasmid map and select Markers in the context menu 2 In the Markers dialog box enter in the Posi tion text box the number for the base pair to which you want to add a marker 3 In the Label text box enter the text to iden tify the marker 4 click Add 5 Click OK MOVING MARKERS To move a marker label click and drag the label Chem amp Bio Draw 12 0 39 User Guide RESIZING REGIONS you can resize region arrows to indicate differ ent base pairs or extend them outward to emphasize them 1 Hover over the end of the region s arrow using a selection tool The arrow s resize handles appear and the cursor changes to a double arrow Ry 2 Click and drag a resize handle to adjust the size of the arrow You can extend a region s arrow outward as shown below 5000 To exte
220. elect a residue to color 2 Select the desired color from the Color menu 3 On the Curves menu select either Filled Shaded or Faded tRNA To create a tRNA molecule 1 Select the tRNA tool 2 Click and drag in the workspace until the tRNA object is the desired size Having drawn the tRNA molecule you can modify it as desired Ribosomes A and B These are two separate tools available on the BioDraw toolbar To draw either Ribosome A or Ribosome B 1 On the BioDraw toolbar select a Ribosome tool 2 Click and drag in the workspace until the Ribosome object is the desired size Having drawn the object you can modify its appearance Plasmid Maps To draw a plasmid map you first enter the number of base pairs you want your map to represent and then add markers A simple plas mid map of an infectious R factor is shown below NOTE The tRNA and Plasmid Map tools require ChemBioDraw Ultra or BioDraw Ultra CREATING A PLASMID MAP 1 Onthe BioDraw Toolbar select the Plasmid Map tool 2 Click in the drawing window where you want to draw the plasmid map The Insert Plasmid Map dialog box opens 3 In the dialog box enter the number of base pairs you want in the map and click OK The plasmid map is drawn ADDING REGIONS Regions represent the fragments in the plas mid You can add as many regions to you map as you want or have none at all To add regions 1 Right click the plasmid map and s
221. elect the angle n other Chem amp Bio Draw 12 0 applica tions point to the Drawing Elements tool and drag in the tool palette to select the angle 2 Drag from left to right for a convex arc or from right to left for a concave arc EDITING ARCS To resize or rotate an arc 1 Position the Arc tool over the arc Drag points appear on the ends and in the middle 2 Drag either end of the arc to change its length 3 Drag the center point to change the curva ture 4 Usea selection tool to change its size or ori entation The Info window indicates the distance between the ends of the arc and the angle the clockwise end makes with the X axis 26 Basic Drawings Chapter 3 When you drag the resize handle the Info win dow indicates the percentage enlarged or reduced When you drag the Rotation handle the Info window indicates the degree rotated The Bracket Tools palette Brackets includes braces brackets and parentheses Single Brackets You can draw a single bracket in any orienta tion Select a single bracket tool from the Drawing Elements palette 1 Point where you want the bracket to start 2 Drag from one end of the bracket to the other end Paired Brackets Paired brackets can only be placed in a vertical orientation A rectangle or box defines their position To draw a paired brackets 1 Select a paired bracket tool from the Draw ing Elements palette 2 Point where you
222. ents within a single label can be specified in the following ways COO Na Implicitly using standard valence rules COO Na Explicitly using a space period unsuperscripted or COO Na unsubscripted bullet or COO Na combination COO Na CHOO 3Na An unsuperscripted unsub scripted integer at the start of a fragment is recognized as a stoichiometric multiplier and Is treated as if the appropriate number of fragments were drawn explicitly CHOO eNa Na Na Chemically Significant Text Often it is simpler to write a chemical formula like MeOH or H50 than it is to draw out an entire atoms and bonds structure Chem amp Bio Draw 12 0 correctly interprets any unambigu ous structural formula For example CH3COCH CH is recognized as methyl ethyl ketone and MeOH is recognized as methanol On the other hand CgH might mean benzene or it might mean one of over 200 other iso mers C6H6 is not recognized by Chem amp Bio 192 Chemical Interpretation Appendix C Draw 12 0 and generates an error message if you try to analyze it Generally empirical for mulas and H5SO are not recognized but structural formulas and HOSO OH are Molecular weight and elemental analyses of empirical structures is possible but the Expand Label command does not work with them Empirical structures are discarded when they are transferred to other applications
223. er 20 000 material safety data sheets for commonly used laboratory chemicals US 1 800 315 7300 INT L 1 617 588 9300 FAX 1617 588 9390 EMAIL infoGcambridgesoft com EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 44 1223 464900 JP 0120 146 700 WWW www cambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP ChemDraw Chem3D Structure Drawing and Molecular Modeling ChemBioDraw Ultra adds BioDraw ChemFinder BioViz and E Notebook to ChemDraw Ultra Easily draw and annotate publication quality biological pathway illustrations with the BioDraw tools The combination of the BioDraw tools with ChemDraw and E Notebook creates an excellent environment for smooth communication between Chemists and Biologists ChemDraw Ultra adds Struct Name ChemDraw Excel ChemNMR Stoichiometry Grid CLogP tPSA as well as the added capabilities of Chem3D Pro and ChemFinder Std to the ChemDraw Pro application With rich polymer notation gener ic structure expansion fragmentation tools and a modern user interface ChemDraw is more powerful than ever before Create tables of structures identify and label stereochemistry estimate NMR spectra from ChemDraw structures obtain structures from chemical names assign names from structures and create multi page document
224. er partition coefficient log Pow LogP values based on literature rather than cal culations are included in the report file Use CMR to calculated Molar Refractivity MR values based on literature rather than cal culations are included in the report file NOTE CLogP and CMR values appear only in ChemBioDraw Ultra and ChemDraw Ultra Viewing Chemical Properties 1 Select the structure whose properties you want to view 2 Go to View gt Show Chemical Properties Win dow The Chemical Properties window appears 3 To paste the basic properties into your doc ument click Paste 4 To create a report and view results for other fragmentation methods click Report The report is produces as a text file Stoichiometry Grid Use the Stoichiometry Grid to calculate sto ichiometric data for a reaction The grid is filled in as you modify a reaction drawing NOTE The stoichiometry grid is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only 92 Chemistry Features Chapter 8 To create a stoichiometry grid 1 Draw a reaction or open a file containing a reaction and select the entire reaction 2 Go to Structure gt Analyze Stoichiometry The grid appears under the reaction NOTE If a catalyst or condition label is dis played above the reaction arrow right click the label and deselect Interpret Chemically in the context menu before creating the grid To enter data in
225. erface e BioDraw makes it easy to and biological pathways including common elements such as mem draw annotate branes enzymes receptors and DNA BioViz BioViz with ChemFinder transforms the numbers in your database into graphics on your screen Retrieve or search for a set of com pounds choose the data you want to see whether it is biological test results in Oracle tables physical property values calculated automatically or prices in a catalog and BioViz will generate an interactive window showing a scatterplot histogram or other useful data graphic The Plot Window the key to data visualization in BioViz is able to show two variables plotted against each other in a scatterplot with each point representing a structure from the current hit list If you for example modify the list by performing a search the plot updates to show the new set of points You can drag a rectan gle around a set of points to select them or zoom in to see them more closely 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com CHEMICAL Inventory Registration Chemical and Biological Inventory Freezer Management Chemicals and Biologicals Inventory is an application designed to manage the chemical and biological reagent tracking needs of laboratories and research cen ters in multiple contexts lab reagents freezer
226. es of acids Alcohols and chalcogen Anhydrides analogs Nitriles Ringed structures Aldehydes and chalcogen analogs Carbonic acids Bridged monocyclic struc tures Heteromonocy clic structures Amides Imides Carbomonocyclic structures Ring fusions of only two rings Amines and Imines Nitric acids Fused polycyclic trivially named structures Ring fusions of two multiple ring systems Other compo unds Carboxylic Acids Peroxy acids Carboxylic Esters Salts Heteroatomic acid halides Sulfides and chal cogen analogs Boron compounds Si Ge Sn and Pb compounds Heteroatomic acids P B As Sulfoxides and chalcogen analogs Organometallic compounds Phosphorous and Arsenic compounds Heteroatomic esters Peroxides Hydrazides S Se and Te Amides Chem amp Bio Draw 12 0 83 User Guide 84 Naming Structures Chapter 7 Chemistry Features Chemical Analysis The Analysis window displays the chemical formula exact mass molecular weight m z and elemental analysis for the entire document a structure part of a structure or a caption in Formula style To view analysis information go to View gt Show Analysis Window Values for selected objects in the document window are shown If no structure is selected in your document values for the entire docu ment are shown You can have this window open as you draw in the do
227. esoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA The Merck Index offers encyclopedic reference for over 10 000 chemicals drugs and biological agents R amp D Insight for Chemists has information on more than 20 000 drug products in various stages of development world wide from over 1 700 sources All databases are updated contain information unavailable in print and are searchable by structure as well as text and numeric range by structure as well as text and numeric range Traditional Chinese Medicines Access to this wealth of knowledge is now available with the Traditional Chinese Medicines database The database consists of monographs for 10 458 chemicals isolated from 4 625 natural sources used in traditional Chinese remedies The monographs feature bio activity data for many of the compounds effects and indications of the medicines English Latin and Chinese names for the natural sources and over 2 000 references ChemINDEX NCI AIDS amp Cancer Scientists have used the award winning ChemFinder Com database since 1995 Now the data on ChemFinder Com is integrated into ChemOffice as ChemINDEX ChemINDEX contains data from over 75 000 compounds including structures names and synonyms physical properties and Internet links Additionally three informative databases have been integrated into one power ful application with the NCI and AIDS database a collection of
228. esults Method Execution Framework to enable standard operation procedures and compliance Applied Technologies and Benefits Workflow management enables discovery teams to rapidly trial new procedures capture best practices and scale successful designs from a manual prototype right up to a fully automated high throughput lab But discovery and research by its very nature demands that processes be flexible and that workflow execution rapidly adapt to new techniques and equipment Conventional laboratory information workflow applications can not meet this requirement because of their heavyweight configu ration needs their lack of adaptability and the cost and complex ity of integrating them with rapidly changing lab technology Workflow LIMS addresses these problems by providing a visual easy to use environment for describing processes and building workflows out of those processes enabling scientists to rapidly trial new procedures and by offering a rapid development tool kit for equipment integration which supports gradual automation to minimize up front costs and ongoing risk CambridgeSoft s Workflow LIMS simplifies even manual lab pro cedures by managing the breakdown of a procedure into tasks and by automating the majority of data capture and transfer tasks but by capturing process as well as data Pathways reduces the costs and risks of implementing discovery techniques and enables companies to accelerate the entire disc
229. et tings 3 Click OK TERMINAL CARBON LABELS By default Chem amp Bio Draw 12 0 does not display terminal carbons To display them 1 Go to File gt Document Settings 2 Select the Atom Labels tab 3 Check the box next to Show Labels On Ter minal Carbons Configuring Objects To configure the drawing settings for a selected object 1 Select the object 2 Go to Object gt Object Settings 3 Configure the settings and click OK The settings you chose are applied only to the selected object Analysis and Properties You can paste fundamental structure properties directly into your drawing There may be a time where you may decide to change the names of these properties For instance you may consider using MW rather than Molecular Weight to save room on the page How these properties are named and updated is controlled by the document settings The changes you make apply only to the prop erties you paste in your drawing The names in the Analysis and Chemical Properties dialog boxes remain unaffected To change the names of the properties 1 Go to File gt Document Settings 2 Select the Auto update tab 3 In the Analysis window select the property whose name you want to change 4 In the Label text box type the new name 5 Repeat steps 3 4 as desired for the Chemi cal Properties window 6 Select Automatically update upon chemistry changes if you want the property values to be update
230. example the search results consist of a hydrogen and hydroxyl group for Ry and R3 Working with Structures ChemDraw Excel lets you rename structures and use the clipboard to cut copy and paste structures Naming Structures Excel recognizes certain characters as formu las To prevent the system from interpreting a chemical structure name as an Excel formula you can rename a structure To name a structure 1 Select the structure 2 Go to ChemOffice12 gt Molecule gt Name All Selected The Name Molecule dialog box appears 3 Type the name and click OK Chem amp Bio Draw 12 0 107 User Guide Using the Clipboard You can cut copy and paste structures using the clipboard To cut a structure from a cell 1 Select the structure 2 Go to ChemOffice12 gt Molecule gt Cut The structure is removed from the cell and is placed on the clipboard To copy a structure from a cell 1 Select the structure 2 Go to ChemOffice12 gt Molecule gt Copy The structure remains in the cell and a copy is placed on the clipboard To paste a structure 1 Select the area where you want to paste the structure 2 Go to ChemOffice12 gt Molecule gt Paste The structure is pasted from the clipboard Displaying Structures ChemDraw Excel lets you select whether to display structures You can also adjust the size of cells to display their entire contents To show structures 1 Select the cells in which you w
231. f the arrow NOTE To move in a larger increment hold down the Alt or Option key while dragging the object The selected objects move 10 points in the direction of the arrow Moving Atoms You can move an atom in a chemical structure click and drag it using a selection tool The bonds connected to the atom stretch To move multiple atoms select only the bonds that have atoms on both ends that you want to move The unselected bonds attached to the selected atoms are stretched NOTE You can also move atoms using the bond tool used to draw the atom See Moving Atoms on page 16 Copying Objects 1 Select one or more objects 2 Ctrl drag or Option drag the object s to create a copy and position it To constrain the copy to move only vertically or horizontally while positioning it hold down the Shift Ctrl or Shift Option keys Deleting Objects To delete selected objects do one of the fol lowing Press the Delete key Go to Edit gt Clear Joining Objects To join two structures so that they share a bond 1 Select a bond in the first structure 2 Shift click to select the bond in the second structure 3 Go to Object Join To join two structures so that they share an atom 1 Position the two chemical structures so that the atoms you wish to fuse are oriented near each other 2 Select the two atoms to be joined 3 Go to Object gt Join NOTE Attempts to fuse atoms that are
232. fied caption text Centered creates centered caption text Flush Right creates right justified caption text Justified creates right left justified caption text Atom Labels Use the Centered Flush Left Flush Right Stacked Above or Automatic justifications to create labels that identify atoms and functional groups in your chemical structure without obscuring bonds or other atom labels NOTE When using Stacked Above justifica tion enter the tokens from top to bottom using Alt Enteror Option Return to go to a new line If you change the justification after the label is entered it will in most cases generate a warn ing Examples of the atom label justifications are shown below OMe CH O 2 cH OMe OMe Figure A 1 Atom label justification A stacked above B centered C flush left D flush right Automatic Alignment When you justify atom labels automatically Chem amp Bio Draw 12 0 breaks the label into tokens A token consists of an uppercase letter followed by any numbers or lowercase letters The first token is attached to the atom and the rest of the label appears without obscuring other parts of the chemical structure For example to create N methylpiperidine label an atom in cyclohexane with the atom label NCH3 which contains the three tokens N C and H3 If you label C3 the tokens are placed from left to right because there are bonds to the left of the atom If you
233. ften miss non experimental information generated shortly after con ception For example toxicology studies are often initiated not by the scientist who ultimately runs the experiment but instead by a manager or coordinator who assigns the study to the scien tist Important material related to this first step in the process such as ideas emails and other communications are often left out of traditional paper notebooks The E Notebook toxicology work flow addresses this concern studies are first created by a manager and subsequently assigned to the scientist for execution Compliance Execution E Notebook is also useful for capturing the Standard Operating Procedure SOP corresponding to the experiment These docu ments are often stored separately from the actual data leading to error and confusion thus causing risk to the validity of the data Storing and displaying procedures and other related documents in concert with the data eliminates this risk and helps build perspec tive on the study Sample Lifecycle Management E Notebook can manage the entire sample lifecycle through tight integration with nventory Sample lifecycle management is essen tial for the registration testing evaluation and reporting in vari ous analytical and manufacturing stages Manual tracking of sam ples and test results is labor intensive and time consuming and compliance with GxP guidelines requires expensive manual audits The controlled flex
234. g If the Clipboard contains structures and you are pasting into another Chem amp Bio Draw 12 0 document the pasted information is scaled to the settings in the current document For more information see Autoscaling on page 149 If you are pasting the Chem amp Bio Draw 12 0 drawing into a document from which you are planning to print to a PostScript printer see Transferring PostScript Macintosh on page 151 Text Line Notation Use text line notation to expand a line of text into the structure that it represents A SMILES string is a line of text that represents the struc ture of a molecule Several software packages use SMILES strings to enter and store chemi cal structure information NOTE Text line notation is available in Chem BioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only A SMIRKS string describes chemical reactions in text If you select a reaction and use the Copy As SMILES command a SMIRKS string is copied to the clipboard If you use the Paste Special SMILES command when a SMIRKS string is on the clipboard a reaction 1s pasted into your document Creating SMILES Strings To create the SMILES string for a structure 1 Select the structure Chem amp Bio Draw 12 0 147 User Guide 2 Go to Edit gt Copy As gt SMILES The SMILES string is transferred to the Clip board NH rH O C H 1CCCC C H 1N Figure 11 1 Using SMILES strings To display the SMILES
235. g box appears 3 Type the number of atoms in the chain 4 Click Add To add another chain of the same length any where in a document window Alt click Win dows or Option click Macintosh where you want the chain to begin Arrows and Shapes Use the tools and tool palettes on the main toolbar to add shapes to your documents A tool palette is indicated on the main toolbar by an arrow You can tear off the palettes and place them where you want Objects except for daggers and some symbols can be rotated and scaled Arrows You can customize arrows not only for length and angle but for arrowhead width and shape You can also drag an arrow from its middle to create an arc of any length When you mouse over an arrow with the Lasso Marquee or an Arrow tool selected the application switches to edit mode and adjust ment handles appear on the arrow length adjustment arrowhead shape arc adjustment arrowhead length and width Figure 3 5 Arrow adjustment handles Drag the adjustment handles to change the arrow length angle or shape When changing the angle of an arrow you are restricted to multiples of 15 if the Fixed Angles is selected Hold down the Alt or Option key to drag to any angle Arrow Types There are many arrows types available letting you add a wide variety of reactions and annota tions to your drawings Chem amp Bio Draw 12 0 offers a variety of arc types and arrow types such as
236. g and innovation The results can be dramatic Information transparency and group collaboration improve productivity and reduce costs Faster and smarter research decisions cut time to market and increase productive efforts Empowered employees contribute increased value to the research discovery development trials and manufacturing organization Advanced through Innovation When your research discovery development trials and manufacturing organization is able to respond swiftly and effectively to opportunities and market changes promote innovation and accelerate product delivery you are working smarter to outpace your competitors As the speed of busi ness continues to accelerate leading organizations constantly seek faster and better informed decision making as well as new business efficiencies For the individual chemist biologist scientist and engi neer who needs to capture organize and communicate chemical and biological data through the complex and widespread workgroup and enterprise scientific information systems needs CambridgeSoft Solutions can help CAMBRIDGESOFT Chem amp Bio Office Desktop KNOWLEDGE MANAGEMENT CHEMICAL BIOLOGICAL Desktop Chemistry Biology BioAssay amp E Notebook E Notebook ChemBioViz Process Workflow BioSAR E Notebook LIMS Enterprise Enterprise Chem amp Bio Office Enterprise E Notebook Enterprise Chemistry amp Biology Anal
237. geSoft and Reel Two will give users access to all the chemical compounds named in a patent and enable them to search by structure keyword or chemical name us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA The Merck Index offers encyclopedic reference for over 10 000 chemicals drugs and biological agents R amp D Insight for Chemists has information on more than 20 000 drug products in various stages of development world wide from over 1 700 sources All databases are updated contain information unavailable in print and are searchable by structure as well as text and numeric range by structure as well as text and numeric range Traditional Chinese Medicines Access to this wealth of knowledge is now available with the Traditional Chinese Medicines database The database consists of monographs for 10 458 chemicals isolated from 4 625 natural sources used in traditional Chinese remedies The monographs feature bio activity data for many of the compounds effects and indications of the medicines English Latin and Chinese names for the natural sources and over 2 000 references ChemINDEX NCI AIDS amp Cancer Scientists have us
238. ged fused ring systems than was possi ble with earlier versions of Chem amp Bio Draw Struct Name supports ring assemblies that consist of two or more rings or ring sys tems Struct gt Name in earlier versions of the Chem amp Bio Draw supported fused ring systems that consisted of only 2 3 rings In Chem amp Bio Draw 12 0 Struct gt Name has been enhanced to recognize much more complex systems Struct Name supports bridged fused ring systems in Chem amp Bio Draw 12 0 For information on Struct gt Name see Struct Name on page 79 Name gt Struct Improvements Name gt Struct in Chem amp Bio Draw 12 0 reports whether a chemical name is ambiguous For example if you enter dichloronaphthalene Chem amp Bio Draw 12 0 displays an isomer of the structure but also report that the name is ambiguous This new feature is quite useful in an auto mated environment such as with ChemScript where many names are converted at the same time Enhanced Color Palette Chem amp Bio Draw 12 0 supports 16 million colors Advanced BioDraw Templates BioDraw and ChemBioDraw Ultra include a set of high color templates for creating publication quality illustrations of biological systems To open the Advanced BioDraw and other templates go to Chem amp Bio Draw 12 0 1 User Guide File gt Open Templates gt Advanced BioDraw or go to View gt Templates Just a few of the BioDraw templates that are new in Chem am
239. gic must for any discovery organization interested in serious data mining is a data dictionary driven structure activity analysis program Users may choose among assays registered in the dictionary or search for assays of interest The power of BioSAR lies in the researcher s freedom from dependence on IT support for dynamically working with all avail able scientific data For example once an assay is registered into the data dictionary it is automatically included in the powerful analysis framework By reducing the time between question and answer BioSAR gives researchers the ability to explore new ideas and avoids this issue by placing SAR report creation in the researcher s control BioSAR Enterprise allows the researcher to create custom reports and views of their data You decide what is displayed and BioSAR takes care of the rest While most SAR tools provide only a table based interface BioSAR provides both a form view and table view and connects to BioViz for high dimensional analysis BioSAR merges the sophisti cation of a powerful data catalog technique with knowledge gained through years of working closely with scientist users The result is a SAR application that is as intuitive as it is powerful Security within BioSAR Enterprise is highly granular different roles exist for administrators publishers and browsers Administrators may add assays to the data catalog engine publish ers may create reports and publish the
240. gs in the fol lowing ways Customize settings for the entire document using the Document Settings dialog box Apply settings to the entire current docu ment from an existing document re Apply settings to selected objects in the current document from an existing docu ment Default Styles Chem amp Bio Draw 12 0 saves default styles as either a style sheet Windows or stationary pad Macintosh When you launch Chem amp Bio Draw 12 0 the last style sheet or stationery pad used opens as the default If you choose different one that file becomes the default You can set a default that is not changed 1 Go to File gt Preferences Macintosh ChemDraw 2 On the Open Save tab browse to the default style sheet stationery pad 3 Deselect Opening Any Style Sheet Statio nery Pad Changes Default 4 Click OK To view the default style click the File menu The New menu item displays the name of the Style Sheet or Stationery Pad Saving Customized Styles Every new document created with Chem amp Bio Draw 12 0 uses a style sheet or stationary pad file to obtain its document settings These files can also contain predefined objects When you create a new document you actually create an untitled copy of the style sheet or stationary pad Any changes you make to the copy do not affect the file itself You can create a style sheet or stationary pad with your own customized setting by saving it as a CDS file If yo
241. h can be printed using a customized template from the Inventory interface Each container stores a substance Additional text fields are avail able to track other chemical contents such as the solvent Custom fields may also be defined To keep track of substances the system maintains its own internal chemical structure database containing unique substances that can be associated with inventory contain ers Advanced duplicate checking is incorporated in the system Every field in a record including the chemical structure molecu lar formula and molecular weight are searchable The application includes a number of specially designed invento ry search forms Search results are returned in list form and can be exported into a document PDF HTML using the report engine The nventory interface allows for printing labels as well as generating reports Inventory uses a report application that incor porates wizards that allow for the quick creation of simple reports and label templates that can be shared across an organization Inventory Pro Inventory Pro contains the same features as CambridgeSoft s Inventory Ultra application except without CambridgeSoft s ChemACX database Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 1617 588 9390 EMAIL 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporatio
242. h more E Norebook can further streamline the procedure by allowing for electronic management of solutions equipment and other resources that are needed for experiments Drug Metabolism E Notebook supports the DMPK laboratories in testing the metab olism and longevity of compounds in various zz vitro and in vivo models DMPK data capture needs can vary significantly and the flexibility of the E Notebook solution addresses this For example an in vivo enzyme induction test may create relatively small amounts of data for which scientists utilize E Notebook integra tion with Microsoft Excel Conversely large quantities of data such as those generated by zz vitro enzyme inhibition studies are often collected and analyzed by applications such as BioAssay Therefore integration with BioAssay and Excel are fundamental to DMPK E Notebook usage us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com Service Request Workflow Sample Management Method Execution Framework Pharmacokinetics DMPK There is a holistic approach to Drug Metabolism and Pharmacokinetics No single study describes the behavior of a compound it is the combination of
243. hat is designed for multiple users with diverse container types racks and multi well plate formats Entities in the nventory system include locations containers and substances A location is defined as any physical location where a container plate or another location can be stored An inventory container represents a container capable of storing chemical sub stances An inventory substance represents a chemical compound mixture sample etc Inventory Enterprise manages an unlimited number of diverse locations containers and substances Containers are created to represent the actual storage vessels used by the organization Each container is assigned a unique barcode identifier which can be printed using customizable report tem plates from the Inventory interface Updating the inventory becomes as easy as scanning barcodes into the system and adjust ing parameters for one or multiple containers Users are able to order check in out move split and merge containers at will Typicalcontainers include ttles vials tubes cylinders boxes racks multi well plates etc Multi well Plates Inventory Enterprise manages multi well plate information In addition to creating storing moving and deleting plates the application allows users to create daughter plates reformat plates and utilize plate maps Inventory also supports user interfaces or machine interfaces for these operations including reading files from liquid handler robots
244. he software publishers For most software programs you can read about user benefits in the registration brochure or upgrade flyer in the product box 0 What exactly does the law say about copying software A The law says that anyone who purchases a copy of software has the right to load that copy onto a single computer and to make another copy for archival purposes only or in limited circumstances for purposes only of maintenance or repair It is illegal to use that software on more than one computer or to make or distribute copies of that software for any other purpose unless specific permission has been obtained from the copyright owner If you pirate software you may face not only a civil suit for damages and other relief but criminal liability as well including fines and jail terms of up to one year Q So I m never allowed to copy software for any other reason A That s correct Other than copying the software you purchase onto a single computer and making another copy for archival purposes only or purposes only of maintenance or repair the copyright law prohibits you from making additional copies of the software for any other reason unless you obtain the permission of the software company Q At my company we pass disks around all the time We all assume that this must be okay since it was the company that purchased the software in the first place A Many employees dont realize that corporations are
245. hile meeting drug safety requirements can be manufactured in a cost effective and reproducible fashion under 21 CFR Part 11 and Good Manufacturing Processes GMP guidelines and is stable under normal formulation and storage conditions With a drug candidate in hand the final chal lenge is to determine safety and efficacy in a patient population 7 Avy ato en e 5 e en a AN K ory hem i ley e Pry I LS Includes tit o o ae E Notebook Enterprise or Workgroup a BioAssay Enterprise or Workgroup L BioSAR Enterprise BioViz Desktop Registration Enterprise Li Inventory Enterprise or Workgroup a n ChemACX Database ChemlNDEX Database Oracle Cartridge SQL Server Compatible ChemFinder Ultra E All specifications subject to change without notice 1 617 588 9390 EMAIL 0120 146 700 Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 info cambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com WORKGROUP and Workgroup Solutions Trials and Manufacturing Workflow Manvfacturing Manufacturing requires the transfer of data and
246. hly fee CambridgeSoft will deliver the informatics applications and the technology staff required to maximize pro ductivity This service allows your organization to focus on sci ence while CambridgeSoft plans implements and manages your technology environment Systems Hosting A hosting service that allows customers to use our state of the art enterprise applications over the extranet from any location 24 hours a day seven days a week is available With this hosting serv ice our customers can shift the responsibilities of application devel opment and IT infrastructure management to CambridgeSoft allowing more time to focus on core science research discovery and development functions Ultra Services The Ultra Services program is CambridgeSoft s personalized pre mium service for supporting our customers Organizations can take advantage of both telephone and electronic access to CambridgeSoft s support scientists who can address Usage and installation questions Product compatibility and interoperability questions Diagnostic review to help isolate the cause of a problem Configuration assistance Planning information for software updates and upgrades Assistance with problem resolution Technical Support amp Remote DBA Services Technical Support and Remote DBA Services for Oracle and SQL Server are also available 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Dr
247. hment points so that the sequence branches For exam ple Ala Leu Although you modify the sequence in the R4 Modify Nickname dialog box the structure for the label in the nickname library does not When you add an attachment point you spec change ify the atom in the expanded label to which the bond will attach IUPAC codes To bond from a sequence Use these codes to enter nucleotides and amino acids in your sequence A Adenine A Ala Alanine C Cytosine Cys Cysteine G Guanine D Asp Aspartic Acid T or U Thymine or E Glu Glutamic Acid Uracil R A orG F Phe Phenylalanine Y CorT G Gly Glycine S GorC H His Histidine W AorT I Ile Isoleucine K GorT K Lys Lysine M AorC L Leu Leucine B CorGorT M Met Methionine D AorGorT N Asn Asparagine H AorCorT P Pro Proline 42 BioDraw Chapter 4 V or C or G Q Gln Glutamine N any base R Arg Arginine Or gap S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan Y Tyr Tyrosine Peptides The definition in the figure below was used for the amino acid alanine The unselected bond at each end of the structure indicates the connec tion points nitrogen on the left and carbon on the right o Hf You can draw a peptide chain by either Stringing nicknames together Gly OH H Stringing
248. ht Measured Mass Molarity Purity Density 807 50g4 788 00gA Product Mass Volume 00 00mi Product Moles Reactant Moles 760 76mmol 760 76mmol Y ield Reactant Mass 80 75 33 51g Figure 8 6 Calculated stoichiometric values You can edit the grid for presentation with the context menu showing or hiding either rows or columns You can also change the color of the text TLC The TLC Tool lets you depict thin layer chro matography plates The tool creates a rectangu lar plate with an origin line solvent front and one or more lanes The lanes can be populated with spots of different size shape or color NOTE The TLC tool available in ChemBio Draw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To create a TLC plate 1 Select the TLC tool from the Main toolbar 2 Drag in any direction from the point of ori gin The number of lanes is a function of the width of the plate you create Chem amp Bio Draw 12 0 93 User Guide You can modify the plate as follows If you want to then Change the height or width of the plate Drag a border or corner Move the origin or solvent front Click and drag the origin or solvent front line If you want to then Delete a spot Click the spot with the Eraser tool If you erase all spots in a lane the lane will be deleted Show or hide the origin solvent front borders
249. hydroxy 4 methylpentan 2 one Drawing an arrow Starting with 2 propanone draw the reaction arrow 1 On the Main Tool toolbar click the Arrow tool to display the Arrow toolbar 2 While holding the mouse button down move the mouse to the palette title bar then release the button The palette becomes a floating toolbar 3 Click the third arrow from the left in the top TOW 4 In the document window click and drag the mouse horizontally to the right of the 2 pro panone structure The arrow appears 5 Select the Text tool 6 Click above the arrow A text box appears 7 Type OH and press Esc Realign the text box as necessary using a selection tool NOTE If Show Chemical Warnings is turned on the default a red box will appear around the OH label when change tools or open another text box indicating an error Ignore this for now Add a charge symbol using the specialized symbols available in the Chemical Symbols tool palette Chem amp Bio Draw 12 0 67 User Guide 1 In the Main Tool toolbar click the Chemi cal Symbol tool 2 Holding the mouse button down select the circled Circle Minus symbol 3 Point to the center of the OH label Move the cursor slightly right or left to select the O 4 With the oxygen atom selected drag the charge symbol around the atom to the desired position bu 5 Objects added from the Chemical Symbols palette are associated chemically with the structur
250. i pur pose and enterprise scalable it provides a solution to a large set of requirements across R amp D and manufacturing E Notebook s foun dation layer of features includes support for 21 CFR Part 11 37 CFR and GxP compliance on top of which a widely configurable design interface provides support for specific scientific and regula tory workflows Because this diverse portfolio of requirements is met in a single applicationplatform E Notebook both lowers the total investment required to meet these needs and provides a sub stantial increase in productivity due to a far more integratedenvi ronment for scientists and technical staff E Notebook Architecture CambridgeSoft s E Notebook provides a comprehensive easy to use interface designed to replace paper laboratorynotebooks in a variety of settings Underneath is a fullyconfigurable secure sys tem for organizing the flow ofinformation generated by your organization Scientists can enter chemical reactions Microsoft documents Word Excel PowerPoint spectra biological data and images and other types of information and documents It also allows you to search by text chemical substructure metadata tags organizational hierarchy or other keys KNOWLEDGE Overview amp E Notebook s Flexible Architecture E Notebook Architecture E Notebook Enterprise edition is a globally deployable Oracle based application designed for everyone from small research groups to global
251. ibility of CambridgeSoft s E Notebook is well suited for these detail and compliance oriented environments E Notebooks Sample Lifecycle Management module is compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and 21 CFR Part 11 Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Track amp Barcode Samples Create Any Report from Database Full Audit Trail Sample Login E Notebook is able to easily configure sample logins registration of sample assignment of barcode label and initiation of sample tracking by incorporating CambridgeSoft s Inventory application Through E Notebook forms can be created to keep track of newly synthesized or acquired compounds tracking their physical prop erties and tests and assigning unique identifiers New compounds are entered directly via the E Notebook form and chemical along with non chemical data is kept alongside the sample When a proprietary compound is registered if desired it is compared for uniqueness via a configurable stereoselective duplicate check and assigned a registry number Sample Tracking Iracking samples requesting analysis and establishing chain of custody can all be simply managed within the E Notebook inter face E Notebook serves as a repository for analytical data
252. ical and biological data ChemFinder Ultra can be used with local MSDE or shared Oracle databases Either way the face of ChemFinder is the same friendly form oriented interface BioViz included in ChemFinder Ultra provides data visualization features to help the user understand relationships between biological data and chemical structures These features allow you to plot structural and biological data in a variety of styles perform statistical analy sis filter plots based on your criteria highlight intersecting sets on plots generate histograms of data distributions and more BioViz included in ChemFinder Ultra provides statistical analysis and visualization tools for structural and biological data BioViz transforms ChemFinder database information into easy to under stand graphics allowing users to discern structure activity rela tionships more easily With BioViz it is easy to retrieve a set of compounds using filters or searching capabilities and generate an interactive window showing a wide variety of useful graphical information ChemFinder Pro is a fast chemically intelligent relational database search engine for the Desktop The integration with Microsoft Excel and Word adds chemical searching and database capability to spreadsheets and documents Compatibility with MDL ISIS databases is provided by SDfile and RDfile import export Us 1800 315 7300 INT L 1 617 588 9300 EU 0080087520000 UK FAX 44 1223 46
253. ical concepts Chem amp Bio Draw 12 0 introduces a variety of improvements and new features not found in earlier versions The new features in this latest version of Chem amp Bio Draw are briefly described below You can find more informa tion on these and other features throughout the manual and online Help Disulfide Bridges When you create a disul fide bond between cysteine residues Chem amp Bio Draw 12 0 will create the disulfide bridge for you For information see Disulfide Bridges on page 43 Bonding from Sequence Atoms In Chem amp Bio Draw 12 0 you can create bonds from spe cific atoms in DNA RNA and protein sequences The bonds are retained even if you expand or collapse the sequence labels See Bonding from sequences on page 42 Rotation Centers Using Chem amp Bio Draw 12 0 you can rotate your drawing around an atom an arbitrary center or any other location on screen See Rotating Objects on page 29 Export to SVG In Chem amp Bio Draw 12 0 you can export your drawings in the Scalable Vector Graphics SVG format SVG is an XML based format often used to describe two dimensional vector graphics To save a draw ing as an SVG file go to File gt Save As Struct gt Name Improvements Ring structure recognition has been greatly improved in the Struct Name feature for Chem amp Bio 12 0 You can now apply Struct Name to more complex ring assemblies fused ring systems and brid
254. ication portal with which scientists and analysts communicate with each other Scientists can create and send service requests directly to an analyst with the click of a button Paper is eliminated when results are obtained the analyst can send the images and chromatograms directly back to the scientist s E Notebook Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Chemical Synthesis Scale up and Analytical 37 CFR Electronic Signatures Service Requests and Discovery Workflow Process Chemistry The objective of process research is to identify efficient processes for the synthesis of active pharmaceutical agents at the scale required for clinical trials and commercial use It is necessary to provide precise descriptions of these processes so that they can be executed by different groups in different locations It is also required that such processes be compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and the FDA s 21 CFR Part 11 regulation E Notebook s process chemistry modules are designed to support these dual workflow and regulatory compliance needs of process chemists v Reaction Properties Fig 4A Medula
255. ickname THP is defined the label appears as See Aligning Text on page 164 Expanding Nicknames A nickname is a type of label Therefore you expand and contract nicknames the same way When you expand a nickname into its struc ture the nickname itself disappears unless the nickname represents an amino acid or nucleic acid Trifluoroacetone is shown here F TFA F F ri You can use nicknames to select and help you modify the functional groups they represent For example assume you have a chain of three amino acids glycine isoleucine and leucine HN Leu le3 Gly COOH jn After you expand the nicknames you can select any of the amino acids by double click ing its nickname as shown HaN Leu NH Gly COOH Chem amp Bio Draw 12 0 19 User Guide To contract nickname go to Structure gt Con tract Label Annotations Annotations are useful for adding text informa tion that helps to identify your drawing in a database search Annotations are categorized using keywords There are several default key words Name Description Type and Other Info You can also add your own keywords NOTE Annotations are available in ChemBio Draw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To annotate an object 1 Select the object 2 Go to Object gt Annotate The Annotate dia log box opens 3 In the Keyword list do one of
256. idual components are known not to repeat them selves or they alternate with the other compo nents For example und mer co Copolymers represent substances with more than one repeating unit In general you can use bracket type Component co You can also use Copolymer alternating alt Copoly mer random ran and Copolymer block blk to represent different specific types of copolymers in a source based representation The bracket type Mixture unordered mix may be used to represent a collection of sub stances that may all be present but not neces sarily in known amounts Bracket type Component c indicates individual mixture elements as shown below COOH coo c1 c2 COOH coo c3 c Figure 10 8 Brackets used to indicate mixtures Bracket type Mixture ordered f is prima rily used to describe manufacturing processes where the ordering of components is a critical part of the process and where a different ordering might produce a different final prod uct As with unordered mixtures individual elements of an ordered mixture should be sur rounded by brackets with a bracket usage of Component c Unlike with unordered mix tures however components of ordered mix tures must represent their ordering You can do this by editing the c label with the text tool to include a number 1 c2 and so on You use the bracket type Multipl
257. iew of strategic goals and the barriers to achievement The delivery of a phased technology transition plan Requirements Analysis amp Proof of Concept With years of experience meeting the needs of the scientific com munity CambridgeSoft understands the user The prototyping process allows definition and testing of the functional and techni cal feasibility of potential technology solutions The process pro vides a baseline for the future development and deployment of a tailored solution Users gain valuable first hand knowledge in experiencing how the system can help achieve individual and workgroup goals Legacy System Migration Legacy systems with private data structures and architecture can be barriers for migrating systems to new technologies Our con sultants have significant experience with these systems and can successfully migrate chemical and biologial data business work flow and other aspects of legacy informatics technologies 21 CFR Part 11 Compliance and GxP Validation As an integral part in creating 21 CFR Part 11 and GxP validated applications CambridgeSoft offers services to Audit the software and process Create conforming systems design specifications Create IQ OQ PQ documentation Generate test plans and validation matrices Insure systems compliance with functional guidelines Us 1800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700
258. ilure to perform any such term or condition by the other party Governing Law This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts Export You agree that the Software will not be shipped transferred or exported into any country or used in any manner prohibited by the United States Export Administration Act or any other export laws restrictions or regulations End User License Agreement for CambridgeSoft Database Products Important This CambridgeSoft End User License Agreement is a legal agreement between you either an individual or a single entity and CambridgeSoft Corporation for the CambridgeSoft sup plied database product s and may include associated media printed materials and online or elec tronic documentation By using the database product s you agree that you have read understood and will be bound by this license agreement Database Product License 1 Copyright Notice The materials contained in CambridgeSoft Database Products including but not limited to ChemACX ChemIndex and The Merck Index are protected by copyright laws and international copyright treaties as well as other intellectual property laws and treaties Copyright in the materials contained on the CD and internet subscription products including but not limited to the textual material chemical structures representations artwork photographs computer software audio and visual elements is owned or contr
259. imary and secondary screening 77 vivo testing through to analysis of results and report ing is covered by this integrated application suite Development and Testing Building on productivity software CambridgeSoft created enter prise applications to meet the needs of an everexpanding research and development community that relies on data sharing across sci entific disciplines research campuses and even oceans as global ization has increased demands Since the software takes advantage of the latest web based technologies it is deployed readily throughout a research and development organization Using the integrated suite scientific teams are well armed to solve the daily challenges of development These teams include scientists who scale up and design manufacturing procedures toxicologists who determine the metabolic fate of drugcandidates formulation sci entists who determine drugdosing and delivery systems as well as many others Trials A suitable drug candidate is one that has the desired activity to provide disease therapy while meeting drug safety requirements can be manufactured in a cost effective and reproducible fashion under 21 CFR Part 11 and Good Manufacturing Processes GMP guidelines and is stable under normal formulation and storage conditions With a drug candidate in hand the final chal lenge is to determine safety and efficacy in a patient population 7 Avy ato en e 5 e en a AN K ory he
260. in any drug discovery environment BioViz allows you to visually analyze and perform statistical analysis on structure related data combined with biological data in ChemFinder Users can search over structural and biological data and construct various plots such as scatterplots or histograms The plots are interactive allowing you to select subsets of your data perform statistical analysis filter plots based on your criteria highlight lists and intersecting sets on plots generate histograms of data distributions and more BioDraw Reporting on and presenting findings is a task familiar to every biologist Making this process easier and more effective benefits everyone involved BioDraw is doing for biologists what ChemDraw has done for chemists for years saving time and resulting in a more professional representation of the science BioDraw makes drawing and annotating biological pathways quick and easy adding a level of uniformity and detail which is unmatched Typical drawings of biological pathways include us 1 800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 BioAssay offers flexible storage retrieval and analysis of biological data BioViz provides statistical analysis and graphical representations of the data loaded into a ChemFinder for
261. in your research discov ery development trials and manufacturing and information technology to help you capitalize on your organizations intellectual assets By turning information into explicit knowledge you accelerate innovation and drive organizations forward Created with Passion Chemists biologists scientists and engineers need timely convenient access to critical information whether structured or unrefined CambridgeSoft which began by helping scientists manage desktop chemical and biological information with Chem amp Bio Draw now addresses enterprise wide scientific information problems with Chem amp Bio Office Enterprise and Workgroup These solutions are flexible and powerful to deal with today s complex projects which span functional organizations and geographi cal boundaries Eliminating data barriers and bringing information to all in the form they need to interpret it aligns all of the mem bers of your teams focusing their collective knowledge and diverse skills toward the common goals of problem solving and innovation The results can be dramatic Information transparency and group collaboration improve productivity and reduce costs Faster and smarter research decisions cut time to market and increase productive efforts Empowered employees contribute increased value to the research discovery development trials and manufacturing organization Advanced through Innovation When your res
262. includes an extensive library of templates to help you quickly create your own structures and reactions You can use a template either as a starting point for a new drawing or to fuse structural features to an existing drawing NOTE Templates are available in ChemBio Draw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only The templates you define are not limited to atoms and bonds Templates can contain any features such as captions colors boxes arcs orbitals arrows reaction mechanism symbols and curves You can also paste pictures from other applications into a template pane Selecting a template Chem amp Bio Draw 12 0 provides several ways for you to select a template 1 Go to File gt Open Templates 2 Select a template toolbar from the Main toolbar 3 Go to View gt Templates gt and select a tem plate toolbar from the list New Drawings 1 Select the template to use 2 In the document window click and drag the mouse until the template is oriented the way you want or simply click in the window TIP To modify template size while drawing it hold down the ALT key Chem amp Bio Draw 12 0 73 User Guide Fusing a Template In addition to starting new drawings you can use templates to add structural features to existing drawings To fuse a template to a drawing first select the template you want using the template tool Then click a bond in the existing drawing to add the tem
263. index of the document and extracts chemical informa tion into a chemically aware substructure searchable database Chemical information can originate from either ChemDraw or ISIS Draw DocManager Enterprise includes a batch loading utility for admin istration level users to load multiple documents at one time The system can be configured to submit a batch of documents as one event or as a reoccurring submission to be executed daily The administrator specifies a time for the submission to take place and the location of the files DocManager Enterprise utilizes the search ing intelligence of the ChemOffice Enterprise suite 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com MANUFACTURING Reference Standards Inventory Enterprise CambridgeSoft s Inventory Enterprise application is designed to manage the chemical reagent sample and compound tracking needs of large multi site chemical and pharmaceutical laboratories Inventory Enterprise is Oracle based ChemOffice Enterprise product that is designed for multiple users with diverse container types racks and multi well plate formats Entities in the nventory system include locations containers and substances A location is defined as any physical location where a container plate or another location can be stored An inventory container represents a container capable of storing chemical sub stances An inventory substance represents
264. ing online 215 troubleshooting nicknames 76 Tutorial 1 Drawing a Structure 45 Tutorial 2 Using Rings 46 Tutorial 3 Fischer projections 48 Tutorial 4 Perspective Drawings 51 Tutorial 5 Newman Projections 54 Tutorial 6 Stereochemistry 56 Tutorial 7 Templates 57 tutorials 45 types of bonds 190 U undo redo and repeat 9 ungroup command 31 ungrouping objects 31 unsaturation 124 unspecified atom properties in queries 123 unsupported structures 79 up to in queries 123 upgrading workbooks 104 use defaults atom properties 122 bond properties 128 bracket properties 131 user guide online 215 using nicknames 18 V V3000 support for 153 vapor pressure 112 variable attachment points 64 Verlag Helvetica Chimica Acta 180 view shortcut keys 209 viewing 92 analysis information 85 spectrum structure assignments 96 viewing drawings 186 W warning preferences 33 warnings chemical 33 water solubility 114 Web site CambridgeSoft accessing 216 wedged bonds drawing 15 what you can color 169 What s New 1 white space adjusting in atom labels 167 Wiener index 117 Wiley document 181 Window menu 10 Windows to Macintosh 155 work area 7 working with color 168 Chem amp Bio Draw 12 0 235 User Guide working with structures 107 ideal gas thermal capacity 113 X LogP 113 melting freezing point 111 molecular weight 110 Z number of atoms 110 sum of degrees 116 topological diameter 117 xml fi
265. ing Biology One of E Notebook 5 strengths is its ability to integrate with exist ing electronic methods of data capture including using it with CambridgeSoft s BioAssay module to provide full screening exper imental support In addition to this Microsoft Word and Excel are also embedded directly in E Notebook as is image and movie capture Scientists benefit from the functionality of these tools implanted in a rich searchable environment Biological experi ments can be managed and organized in a way that is not possi ble with a traditional file system In vivo Experiments Animal Management In vivo experiments are important aspects of target discovery and validation and are critical paths to determine the efficacy of selective therapeutic candidates CambridgeSoft s E Notebook becomes the centralized location to collect store and interpret im vivo experiment results Again when used with BioAssay the full end to end experimental workflow is supported from creation to data analysis and quality control to summary and reporting In conjunction with zz vivo experiments animal housing and breeding can also be tracked Traditionally the work flow consists of paper based record keeping across the animal facility lab bench and researchers desktop With E Notebook paper tracking and recording is eliminated Instead form tools can be designed to Track animal status Track animal pedigree Record Genotype Create mating
266. ing Biology Genetics and Microscopy LIMS Method Execution 21 CFR Part 11 GxP Development and Testing CambridgeSoft s Enterprise E Notebook meets the needs of ever expanding research and development communities that rely on data sharing across scientific disciplines and campuses as globaliza tion has increased demands E Notebook allows custom integration of a large array of modules in house applications lab instruments and back end data storage to provide a true end to end solution for development and testing Designing workflows and calculations is much faster and requires far less programming using the E Notebook than existing lab infor mation systems End users include scientists and process chemists who scale up and design manufacturing procedures toxicologists who determine the metabolic fate of drug candidates formulation scientists who determine drug dosing and delivery systems as well as many others Trials and Manvfacturing A suitable drug candidate has the desired activity to provide dis ease therapy while still meeting safety requirements can be man ufactured in a cost effective fashion under 21 CFR Part 11 and GMP and is stable formulation conditions The handling of guidelines under normal and storage materials including chain of custody requirements material documentation material workflow such as availability states and recertification dates are tracked and handled by the E Notebook applica
267. ing results can be sent directly from instruments to electronic experiments and protocols and data can be managed with familiar tools such as Microsoft Word and Excel The beauty of capturing data in E Votebook is that information can be compiled and viewed in a meaningful way For example the creation of a new biological strain entails many steps potentially involving nonconsecutive workdays of various individ uals E Notebook can generate customized reports that meaning fully summarize the process in real time These reports are navigable clicking on each step will bring you to the corresponding experiment v Database Structure d 4134 001 Specia E ler BUTOH CAREDNTLL FRDLINE Compou Solvent Temper Time Yield Remarks ih AnPreps A134001 MS Esca Spreadsheet E Yeldirtemaion Ey sospes nd ature Hr 20 scars PEL Bo DMsoF 5 4 D Sarele Shes au J Bo n B eu ena lue Comm 5 cs tomo Boe piso 236 70 2 equis TMG Ens las D DMSO 25 18 89 2 equiv TMG Gama laf 5 4 62 CHA st eD DMSO 40 40 78 CHA sat ear DMSO 50 48 62 2eqdv TMG DOHA sak continuous estrscton with Boe 25 25 80 Regu TMG as Boe l DMSO 40 72 n Bo 25 TB Calo as henihydrate tez Fes Mansa Us 1800 3
268. ing the Anti Piracy Hotline 800 388 7478 Q Do the same rules apply to bulletin boards and user groups always thought that the reason they got together was to share software A Yes Bulletin boards and user groups are bound by the copyright law just as individuals and corporations However to the extent they offer shareware or public domain software this is a perfectly acceptable practice Similarly some software companies offer bulletin boards and user groups special demonstration versions of their products which in some instances may be copied In any event it is the responsibility of the bulletin board operator or user group to respect copyright law and to ensure that it is not used as a vehicle for unauthorized copying or distribution 0 I ll bet most of the people who copy software don t even know that they re breaking the law A Because the software industry is relatively new and because copying software is so easy many people are either unaware of the laws governing software use or choose to ignore them It is the responsibility of each and every software user to understand and adhere to copyright law Ignorance of the law is no excuse If you are part of an organization see what you an do to initiate a policy statement that everyone respects Also suggest that your management consider conducting a software audit Finally as an individual help spread the word that users should be software legal 0 What are
269. inged structures 80 normal searches 106 number of hydrogen bond acceptors 110 number of hydrogen bond donors 110 number of rotatable bonds 116 numbering atoms 64 O objects 3D rotation 25 aligning 188 copying 30 deleting 30 distributing 32 framing 27 grouping 31 joining 31 moving 30 selecting 27 ungrouping 31 using crosshair with 187 using rulers with 187 objects ungrouping 31 OLE 150 Online menu browse SciStore com 216 CambridgeSoft home page 216 ChemBioOffice SDK 217 CS Chem3D technical support 215 lookup suppliers on SciStore com 216 register online 215 217 open documents 10 open templates 10 opening ChemDraw Excel 103 opening a database 106 or labels formatting 166 orientation benzene ring tool 22 cyclopentadiene ring tool 22 double bonds 16 orienting templates 74 ovality 115 overlap multipaged documents 184 oxidation state changing 10 P page border 183 overlap 184 page definition language quickdraw 161 page setup saving settings 185 paged documents 183 paired brackets 26 palette arcs 26 brackets 26 color 169 showing 8 single bonds 13 tearing off 8 palettes creating 74 parentheses 26 pen tools 27 peptides defining with nicknames 43 periodic table 10 perspective drawings tutorial 51 phytomedicine 177 picture layers atom labels 167 plasmid map 39 adding markers to 39 resizing regions 40 Chem amp Bio Draw 12 0 229 User Guide polar surface area 116 polymer represent
270. integrity detail and longevity The Merck Index contains over 10 000 monographs on drugs chemicals and other biologically active molecules Each monograph contains informa tion on the compound and its derivatives common trade and systematic names trademarks and associated companies CAS Registry Numbers physical and toxicity data therapeutic and commercial uses literature citations as well as chemical strucures formulas andmolecular weights The electronic versions include archived monographs from previous editions and is updated twice a year R amp D Insight Chemists Information on current drug products under development is essential for those working in research and development licensing and marketing at pharmaceutical and healthcare institutions R amp D Insight for Chemists a collaborative product from Wolters Kluwer Health and CambridgeSoft combines the power of chem ical structure searching with a wealth of drug development data to give subscribers a competitive edge when making decisions rele vant to the direction of their research Updated weekly users can search the collection of over 20 000 compounds by structure substructure names partial names and synonyms Patent Database Researchers chemists and patent analysts are now able to easily search full text patents for chemical structures using CambridgeSoft s powerful search and analysis tools The new CambridgeSoft Patent Database portal co developed by Cambrid
271. intranet Chem amp Bio Office Workgroup Ultra includes E Notebook for record keeping BioAssay for low and high throughput screen ing BioViz for visualization nventory for reagents and ChemACX database of available chemicals Technologies also include SQL Server for affordability and ease of administration Research Discovery Development Trials amp Manufacturing Workflow E Notebook Experiment ChemACX Reagent Procurement ow LIMS Laboratory Analytical Registration Batch Tracking BioAssay amp BioSAR Toxicity Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK FAX 44 1223 464900 JP MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com BioAssay Biologicol Activity BioViz amp BioSAR Structure Activity E Notebook Manufacture Clinical Trials DrugDeg Degradation BioAssay amp DrugDeg Metabolism 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com E Notebook Used for collaboration and knowledge sharing regulatory compli ance intellectual property protection LIMS document manage ment project management and workflow support E Notebook is the leader in a new class ofapplications Configurable mult
272. ion 24 hours a day seven days a week is available With this hosting serv ice our customers can shift the responsibilities of application devel opment and IT infrastructure management to CambridgeSoft allowing more time to focus on core science research discovery and development functions Ultra Services The Ultra Services program is CambridgeSoft s personalized pre mium service for supporting our customers Organizations can take advantage of both telephone and electronic access to CambridgeSoft s support scientists who can address Usage and installation questions Product compatibility and interoperability questions Diagnostic review to help isolate the cause of a problem Configuration assistance Planning information for software updates and upgrades Assistance with problem resolution Technical Support amp Remote DBA Services Technical Support and Remote DBA Services for Oracle and SQL Server are also available 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com Chem amp Bio Office Desktop Software to Enterprise Solutions KNOWLEDGE CHEMICAL LABORATORY amp SCIENTIFIC MANAGEMENT BIOLOGICAL MANUFACTURING DATABASES Dui mE CombiChem kflew BioAssay Registration Inventory E grins Merck ons em i amp BioViz Enterprise Enterprise ioSAR f
273. ion Definition Equal Default Matches specific to specific or generic to generic terms Broad Translates specific query atoms to corresponding superatoms in the database Narrow Translates query superatoms to corresponding specific atoms or groups in the database Any Translates generic or specific terms to any term For more information see the Markush DARC User Manual Isotopic Abundance The Isotopic Abundance property lets you dis tinguish between different isotopic com pounds for example between mono and 126 Query Structures Chapter 10 hexa deuterobenzene by specifying a nuclide at any location NOTE The isotopic abundance property is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Option Search results Unspeci fied Default Any For ChemFinder the same as default Included for compati bility with other systems where the default may be different Natural Indicates an isotopically unmodified nuclide Enriched Indicates a mixture of isotopi cally substituted and isotopi cally unmodified nuclides Deficient Indicates a depleted label that is the nuclide is present in less than the natural ratio Nonnatural Indicates an isotopically substituted nuclide that is essentially all the molecules of the compound have only the indicated nuclide Abnormal Valence The Abnormal Valence property
274. irected at a multiple of 15 degrees Clean Up Structure preserves stereochemi cal meaning rather than the precise identity of wedged or hashed bonds as shown below san Before HO After Figure 6 4 Preservation of stereochemical meaning Using Clean Up Structure 1 Select the structure or part of the structure to clean up 2 Go to Structure gt Clean Up Structure or type Shift Ctrl K NOTE The Clean Up Structure command redraws your structure in iterations Therefore you may need to select the command more than once Attachment Points You can draw polyhapto structures such as fer rocene or an abbreviated notation for different positional isomers of a compound using attachment centers The procedure is similar and in both cases the structure retains chemical significance rd cy Figure 6 5 Drawing a polyhapto structure Isomers of dibromobenzene can be represented as Br Br Abbreviated notation for Br Br Br A Br Br Multi Center Bonds To create a multi center attachment point 1 Select the structure whose center you want defined as a multi center attachment point 2 Go to Structure gt Add Multi Center Attach ment An asterisk indicates a multi center node The asterisk is not visible once a bond is drawn to it However you can view the attachment point using a bond or selection tool See Viewing Attachment Points on page 64 To
275. ish After you reach the limit you must register the software In addition to registering your software you can request literature or register for limited free access to ChemBioFinder com Che mACX com ChemClub com and the e mail edition of ChemNews To register online go to Online gt Register Online The CambridgeSoft Professional Services page opens in your browser User s Guide The Online menu also provides a way for you to easily find current and previous versions of all CambridgeSoft documentation To access the CambridgeSoft Manuals page go to Online gt Browse CambridgeSoft Documentation The Desktop Manuals Web page appears You can select PDF versions of the CambridgeSoft manuals from the dropdown list NOTE If you do not have a CambridgeSoft User account you will be directed to a sign up page first Technical Support The online menu link Browse CambridgeSoft Technical Support also opens the CambridgeSoft Professional Services page Here you can find a variety of Desktop Support resources including the CambridgeSoft Knowledge Base product Downloads Q amp A FAQ Documentation and so on Chem amp Bio Draw 12 0 215 User Guide 1 Go to Online gt Browse CambridgeSoft Tech nical Support The Professional Services Web page opens 2 Click Desktop Support Suppliers on ACX com ChemACX Available Chemicals Exchange is a Webserver application that accesses a data base of commercially avai
276. isplay 94 95 R group analysis 107 ribosome 38 39 ribosomes A and B 38 ring assemblies 80 ring bond count 123 ringed structures 80 83 rings drawing with fixed length 21 rings tutorial 46 R logic queries 139 rotate chemical symbols 91 command 29 dialog box 29 objects 29 rotating objects 29 RS see stereochemistry indicators 195 Chem amp Bio Draw 12 0 231 User Guide RSC 178 RSC document 178 ruler guides 187 rulers showing 187 running scripts 78 S sample code SDK web site 217 save command default file format 158 saving defaults 161 structures in ChemDraw Excel 106 saving changes automatically 158 saving color palette settings 171 saving customized settings 161 saving customized styles 161 saving documents 10 saving page setup settings 185 saving structures 106 scaling fixed length 32 objects 32 when transferring information 149 scaling objects 32 Science of Synthesis 179 SciStore com 216 scrap files 149 scripts 78 SDK Online accessing 217 searching 106 ChemDraw Excel 106 export compatibility 144 selecting bonds 28 entire structure 28 with lasso 28 with marquee 28 selecting an open document 10 232 Index selecting multiple objects 28 selecting objects 27 by clicking 28 selection tool deleting 30 deselecting objects 28 29 highlight box 28 joining 31 sequences drawing 40 nonlinear 41 setting preferences 157 setting bracket properties 131 setting font parameters 16
277. ive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com Chem amp Bio Office Desktop Software to Enterprise Solutions KNOWLEDGE CHEMICAL LABORATORY amp SCIENTIFIC MANAGEMENT BIOLOGICAL MANUFACTURING DATABASES Dui mE CombiChem kflew BioAssay Registration Inventory E grins Merck ons em i amp BioViz Enterprise Enterprise ioSAR frm Signatures mem 1 Compliant p Bc Em IP Protection Compliance zum p Bc I Enterprise E73 Research Discovery Development Trials Manufacturing Enterprise Solutions include Chem amp Bio Office with Oracle Cartridge and Chem amp Bio Office Workgroup based on SQL Server to help organizations from small workgroups to large enterprises collaborate and share information more effectively Knowledge Management with E Norebook including Reaction Explorer CombiChem E Signatures for intellectual property protection and 27 CFR11 Compliance streamlines daily record keeping with rigorous security and efficient archiving Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant DB for storage of your data Biological Informatics scientists use BioDraw BioAssay BioSAR and BioViz to set up biological models and visualize information generate spreadsheets correlating structure and activity search by structure and draw and annotate pathways Chemical Informatics including Registration organizes new
278. ivity returns generated by an investment in systems training can be dramatic CambridgeSoft offers a complete array of powerful user focused training services PLANNING Strategic Op Planning Requirements Analysis DEVELOPMENT Data Integration Application Development DEPLOYMENT MANAGEMENT Systems Optimization Systems Integration Product Tailoring Software Evaluations Training Services 1 617 588 9300 FAX Project Readiness 21CFRTI Compliance Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Managed Informatics allows your organization to focus on science while CambridgeSoft plans implements and manages your technology environment Systems Management Managed Informatics Informatics outsourcing provides the people processes and tech nology to develop a unique level of service for your organization For a monthly fee CambridgeSoft will deliver the informatics applications and the technology staff required to maximize pro ductivity This service allows your organization to focus on sci ence while CambridgeSoft plans implements and manages your technology environment Systems Hosting A hosting service that allows customers to use our state of the art enterprise applications over the extranet from any locat
279. k Experiment ChemACX Reagent Procurement ow LIMS Laboratory Analytical Registration Batch Tracking BioAssay amp BioSAR Toxicity Us EU 1800 315 7300 INT L 1 617 588 9300 00 800 875 20000 UK FAX 44 1223 464900 JP MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com BioAssay Biologicol Activity BioViz amp BioSAR Structure Activity E Notebook Manufacture Clinical Trials DrugDeg Degradation BioAssay amp DrugDeg Metabolism 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com E Notebook Used for collaboration and knowledge sharing regulatory compli ance intellectual property protection LIMS document manage ment project management and workflow support E Notebook is the leader in a new class ofapplications Configurable multi pur pose and enterprise scalable it provides a solution to a large set of requirements across R amp D and manufacturing E Notebook s foun dation layer of features includes support for 21 CFR Part 11 37 CFR and GxP compliance on top of which a widely configurable design interface provides support for specific scientific and regula tory workflows Because this diverse portfolio of requirements is me
280. k data throughout ChemOffice Enterprise Registration Enterprise is the only true n tiered application of its kind that is designed around thin clients and thin servers with interfaces directly to Inventory batch file registration and E Notebook Oracle is supported on a variety of platforms and operating systems Using Oracle secures your pro prietary data through the use of Oracle s role based security and allows all chemical and non chemical data to be stored directly in the Oracle tables EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com INFORMATICS DocManager amp ChemFinder GxP Registration and Enterprise Infrastructure Formulations amp Mixtures Formulation scientists face different challenges from those work ing with individual molecules yet many of the tools they are forced to use emerge from the drug discovery world where single molecule research is the norm Take an essential task such as com pound registration and you will find that most systems are designed for registration of single molecules with little thought for the world of formulations and mixtures CambridgeSoft has developed a system specifically designed for this registration need called Formulations amp Mixtures ChemFinder Enterprise ChemFinder Enterprise is a multiple user system designed for sites with comprehensive chemical and biological data needs ChemFinder Enterprise contains its own engine for working with
281. ktop Software includes Chem amp Bio Office a powerful suite of software consisting of ChemBioDraw ChemBio3D ChemFinder ChemACX for chemists BioDraw BioAssay and BioViz and for biologists and Inventory and E Notebook for all Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma Aldrich MSDS The Merck Index and other scientific databases provide information about chemicals their properties and reactions Professional Services include custom development system deployment educational training and technical support for pharmaceutical biotechnology and chemical customers including government and academia by experienced staff Web www cambridgesoft com Email info cambridgesoft com Cambridagesoft America 1 800 315 7300 United Kingdom 44 1223 464900 Life Science Prey ihr se Solutions ne Unternehmensisungen Europe 00 800 875 20000 Germany 49 69 2222 2280 sions globales pour Japan 0120146700 France 33170719880 947M1vA XV8 79X Vx vay Chem amp Bio Office Desktop Software to Enterprise Solutions KNOWLEDGE CHEMICAL LABORATORY amp SCIENTIFIC MANAGEMENT BIOLOGICAL MANUFACTURING DATABASES BioAssay amp BioViz Enterprise Research Discovery Development Trials amp Manufacturing Enterprise Solutions include Chem amp Bio Office with Oracle Cartridge and Chem amp Bio Office Workgroup based on SQL Server to help organizations from small
282. l compounds For example if you re investigat ing organic acids a compound with the struc tural formula CH3COO would probably represent acetic acid Present the same formula in a paper on transition metal chemistry and you might be describing a novel methylated cobalt oxide If you had asked Chem amp Bio Draw 12 0 to interpret it beforehand you would have received a message reporting a valence error and you might have been prompted either to add a negative charge or to change the capitalization Chem amp Bio Draw 12 0 can offer only sugges tions If you and your audience understand what you are trying to depict then you can ignore these suggestions In many cases you can teach Chem amp Bio Draw 12 0 to under stand the notation you re using For more information see Applying Nicknames on page 19 Database Conventions Most databases require not only that you draw a structure in a way that makes sense but that you draw it in the way that the database expects it Consider ferrocene which is repre Chem amp Bio Draw 12 0 189 User Guide sented in at least four different ways in major databases Or gg 0 other isomers Merck Index Beilstein g Y Figure C 5 Representations of ferrocene HC I H H A successful search in one database might not produce any results in another When in doubt consult the documentation for the conventions y
283. l 2 Click and drag diagonally over the struc tures or other object As you drag a rectangle appears that defines the selection area Bonds and other objects are 28 Basic Drawings Chapter 3 selected only if they are entirely within the rectangle Selecting entire structures To select an entire chemical structure dou ble click a bond or atom in the structure using a selection tool If the chemical structure or other object is part of a group the group is selected Selecting objects by clicking 1 Select the Lasso or the Marquee tool 2 Point to an object in a document window A highlight box appears over the selected object If you point at a bond the highlight box appears over the length of the bond 3 Click the object The selected objects appear within the Selec tion Rectangle and the cursor changes to a hand NOTE If the bond or other object is part of a group you can select it as an individual object See Grouping Objects on page 31 Selecting multiple objects When you select multiple objects each object displays a selection box so that you can see exactly what is chosen To add more objects to the selection press Shift and select the other objects To select all objects go to Edit gt Select All Deselecting all objects To deselect all objects do one of the follow ing Click an empty area outside the selection rectangle Press Esc Select a different tool Select a
284. l paper notebooks The E Notebook toxicology work flow addresses this concern studies are first created by a manager and subsequently assigned to the scientist for execution Compliance Execution E Notebook is also useful for capturing the Standard Operating Procedure SOP corresponding to the experiment These docu ments are often stored separately from the actual data leading to error and confusion thus causing risk to the validity of the data Storing and displaying procedures and other related documents in concert with the data eliminates this risk and helps build perspec tive on the study Sample Lifecycle Management E Notebook can manage the entire sample lifecycle through tight integration with nventory Sample lifecycle management is essen tial for the registration testing evaluation and reporting in vari ous analytical and manufacturing stages Manual tracking of sam ples and test results is labor intensive and time consuming and compliance with GxP guidelines requires expensive manual audits The controlled flexibility of CambridgeSoft s E Notebook is well suited for these detail and compliance oriented environments E Notebooks Sample Lifecycle Management module is compliant with Good Laboratory Practices GLP Good Manufacturing Processes GMP and 21 CFR Part 11 Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw am
285. label C5 the tokens are placed from right to left because there are bonds to the right of the atom NCH HCN You can force an entire multi atom label to be a token by defining it as a nickname This pre vents the label from flipping when applied to the left side of a structure For example if you define the Nickname CH3 and label C5 with the combined label and nick name NCH the final orientation is CH3N instead of H4CN In this case the Nickname CH3 is a token If you label C1 the second and third tokens are placed above the first token since there are bonds below the atom If you label C4 the second and third tokens are placed below the first token CH3 N N CH Changing the Default Format Each new caption or atom label uses default document settings for the font size and style of captions and atom labels You can change the format by Changing the document settings for subse quent drawings in the current document Chem amp Bio Draw 12 0 165 User Guide Choosing a new format for an individual caption or label from the Text menu or tool bar before you type Selecting text and applying a new format to an individual label after you type Settings for New Text To specify the text settings for new captions and atom labels in the current document 1 Go to File gt Document Settings 2 Click Captions or Atom Labels in the Docu ment Settings dialog box 3 Select the appropriate option
286. lable chemicals The database contains catalogs from research and industrial chemical vendors You can use Chem amp Bio Draw 12 0 to link to the chemacx com database record of suppliers for compounds that you draw 1 In Chem amp Bio Draw 12 0 select a struc ture you have drawn that you want to look up 2 Go to Online gt Find Suppliers on Che mACX com The ChemACX Com page opens in your browser with information on the selected struc ture For more information on using the ChemACX Web site see the ChemOffice Enterprise Workgroup amp Databases Manual ACX Structures and Numbers Chem amp Bio Draw 12 0 searches ACX and returns information about related structures and numbers You can place the returned infor mation in your document ACX Structures There are two ways to find ACX structures by ACX number or by name To find a structure by ACX number 1 Go to Online gt Find Structure from ACX Num ber 216 The CambridgeSoft Web Site Appendix H The Find Structure from ACX number dialog box appears 2 Type the ACX registry number 3 Click OK The structure appears in your document To find a structure by name 1 Go to Online gt Find Structure from Name at ChemACX com 2 In the dialog box type either a chemical name or trade name 3 Click OK The structure appears in your document ACX Numbers 1 To Find an ACX number for a structure 1 Select the structure 2 Go to Online gt Find
287. large the drawing area Windows Point to a border or corner of a document window and drag to resize Macintosh Drag the Size box in the lower right corner of the document window The size of drawing area displayed depends on the size and resolution of your monitor In some cases you can see the entire document If you magnify a document the drawing area size and drawing objects become bigger If you increase the magnification so that the page size becomes bigger than the screen scroll bars become available Setting up Pages You can create two types of documents Pages A single document containing one or more sheets each of which is printed on a sin gle piece of paper Posters A single large document composed of as many pieces of paper as necessary Paged Document Setup To create a document with one or more pages 1 Go to File gt Document Settings The Docu ment Settings dialog box appears 2 On the Layout tab check that Pages is selected 3 Specify the number of pages in the Docu ment Size section The size of the pages is determined by the Page Setup settings For more information see Page Setup on page 184 4 Type the Margin settings The units of the margins are set in the Preferences dialog Chem amp Bio Draw 12 0 183 User Guide box The paper size minus the margins determines the drawing area 5 Create Headers and Footers as described in Headers and Footers 6 Click OK A new d
288. lbar select the Text tool 5 Select one of the carbon atoms in the hydro carbon chain what was the middle ring 6 Type O to change it to an oxygen atom 7 Select the other carbon atom and change it to an oxygen Peroxydibenzene is now shown Advanced Drawing Techniques The advanced features in Chem amp Bio Draw are designed to either help you save time or to perform functions that simply can t be accom plished using the basic tools For example you can see your drawing as 3D models or create stereoisomers at the click of your mouse With the Chem amp Bio Draw 12 0 advanced drawing features you can Create mirror images Clean up structures Add bonds to characters in atom labels Create bonds whose attachment is not explicitly defined Add atom numbers Contract and expand sections of structures View structure perspective Create mass fragmentation retrosynthesis and synthesis drawings Draw with templates Create and edit templates Label functional groups with nicknames NOTE The Clean Up Structure and template features are available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Mirror Images You can reflect structures through planes per pendicular to the X axis or Y axis By copying a structure you can create its mirror image to represent racemic mixtures and other stereoi somers You can also create a mirror image of a structure that has
289. lectronic data files Not only can machine readable instrument data files be stored but also images multimedia files presentations human readable word processing and Adobe PDF documents spreadsheets and hundreds of other formats This data can serve as source data instrument data to BioAssay and also repository Although Compliant DB can operate as a stand alone application only CambridgeSoft provides fully integrated Knowledge Management and Enterprise Informatics applications integrated with compliant storage Compliant DB makes this possible v Workbench Sample Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 0080087520000 UK 44 1223 464900 JP 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com Develop Centralized Validated Storage and GxP Compliant Storage Store Documents Machine Files amp Chemical Objects Oracle Cartridge is compatible with Linux Solaris AIX and Windows and includes structure searching property predictions and nomenclature Oracle Cartridge The CambridgeSoft Oracle Cartridge is used by all ChemOffice Enterprise applications for storing searching and analyzing chem ical data It can also be used in the development of your custom Oracle applications Chemical structure and reaction data i
290. les editing 160 zooming see changing perspectives 186 exact mass 110 heat of formation 113 236 Index CambridgeSoft Solutions peaturtug x E Notebook DESKTOP SOFTWARE ENTERPRISE SOLUTIONS CHEMICAL amp BIOLOGICAL RESEARCH INFORMATICS LABORATORY DEVELOPMENT amp MANUFACTURING INFORMATICS KNOWLEDGE MANAGEMENT SCIENTIFIC DATABASES CambridgeSofr Life Science Enterprise Solutions Narurwinenwhafitiche Unternehmenslsungen Solutions globales pour les sciences de la vie 2427 TVA X78 FX VU CAMBRIDGESOFT Vision Passion Research Discovery Development CambridgeSoft Software Solutions and Databases SOLUTIONS amp Innovation Trials and Manufacturing Motivated by Vision Innovation is an organizational must in pharmaceutical biotechnology and chemical industries Effective new ideas developed through collaboration and communication free from organizational boundaries will determine your long term success In today s connected world information flow within organization can be overwhelming Large amounts of data some structured and some unstructured can cloud an R amp D organization s ability to focus on what is important Since 1986 CambridgeSoft has been solving the problem of electronic storage and communication of chemical structures models and informa tion Starting with ChemDraw then broadening to ChemOffice in 1992 and BioOffice in 2004
291. ll ref Example In cell MOLECULAR TOPOLOGY TOPOLOGICAL DI AMETER A2 Result 7 Total connectivity Function MOLECULAR TOPOLOGY TOTAL CONNECTIV ITY cell ref Example In cell MOLECULAR TOPOLOGY TOTAL CONNECTI VITY A2 Result 0 009821 Total valence Function connectivity CE C MOLECULAR TOPOLOGY TOTAL VALEN ONNECTIVITY cell ref Example In cell MOLECULAR TOPOLOGY TOTAL VAL ENCE CONNECTIVITY A2 Result 0 001157 Wiener index Function MOLECULAR TOPOLOGY WIENER INDE l ref Example In cell MOLECULAR TOPOLOGY WIENER INDE 2 Result 249 X cel Chem amp Bio Draw 12 0 User Guide 117 118 ChemDraw Excel Chapter 9 Query Structures A query is simply a search for information that is stored in a database If you have ever searched the Internet using a Web browser then you have performed a simple query The query parameter is the alphanumeric text you enter in the search engine text field and the list of Web sites that are returned is the query result A query structure is a parameter you use to search chemical databases the database must include structures for the query to be useful The query structure can include bond and atom properties that you specify to narrow or broaden the list of search results Here are two query structure examples K B
292. lled on a server With a concurrent license the software can be installed on any number of computers at the organization but the number of computers using the software at any one time cannot exceed the number of concurrent licenses purchased For example a 10 user concurrent license can be installed on 20 computers but no more than 10 users can be using it at any one time If the number of users of the software could potentially exceed the number of licensed copies then Licensee must have a rea sonable mechanism or process in place to assure that the number of persons using the software does not exceed the number of copies CambridgeSoft reserves the right to conduct periodic audits no more than once per year to review the implementation of this agreement at the Licensee s site At CambridgeSoft s request Licensee will provide a knowledgeable employee to assist in said audit 2 Ownership The Software 1s and at all times shall remain the sole property of CS This ownership is protected by the copyright laws of the United States and by international treaty provisions Upon expiration or termination of this agreement you shall promptly return all copies of the Software and accompanying written materials to CS You may not modify decompile reverse engineer or disas semble the Software 3 Assignment Restrictions You may not rent lease or otherwise sublet the Software or any part thereof You may transfer on a permanent basis the rights grante
293. local and shared databases and it is also delivered with the CambridgeSoft Oracle Cartridge the powerful Oracle hosted structure engine based on ChemFinder search technology The face of ChemFinder Enterprise is the same friendly form oriented inter face as the desktop version but underneath is a fast direct connec tion to Oracle and the robust scalable Oracle Cartridge running on the server Substance Barcode Expires On Ordered On PPSORUORICAC Ouen Aurotenzene sura 22592 TERAMEIMILAPMENUMH 2 Gene snap isai s Gap anspoo 7601 552 ES sr wr gelcs pemtaerythel Tevanwiate Sr saga es 1942455 l rn snap nre Suse Supp Quante Conners EH Cit You are logzedinas Troma PiniLabel 41 kh tast modifed at 11 5 2003 30300 PM shown below ofthe document changes necessary before submission v Index Documents esr kd sio Cortaner Sc S d Comarer Type ES ss pos LN oo Caner a E f che PATI Assay Procedure o atest S i SETET Coney Sie 4 Manage your Inventory Properties Rhombohedeal platelets from 95 alchol mp 220 224 some decompa when heated evac capillary gs 209 c 1 2 in 98 alcoho af 0 125 in benzene f 2488 c 0 1
294. lor or Set Other Color on the Color tab The Color Picker dialog box appears 2 Click a color in the Color Wheel 3 If necessary adjust the hue saturation brightness and RGB components by typing in the values 4 Click OK The new color is added to the list of Other Colors Removing Colors To remove a color from the Color menu 1 Click the color A highlight box appears around the color 2 Click Remove Color Objects that were drawn in the removed color are changed to the foreground color Templates and Color The background and foreground colors used in a template from the template pop up palette are not used when the template is drawn in a docu ment window However any other colors used in the template are added to the color palette of the current document if they are not already present This is part of the autoscale feature For more information see Autoscaling on page 149 Saving Color palette Settings You can save the Color palette in a style sheet or stationery pad The Color palette is saved in addition to other document settings such as page setup settings text settings and drawing settings Printing Background Color Print Background Color controls whether the background color contained in your document is printed To change whether the background color is printed 1 Go to File gt Preferences 2 Click Print Background Color 3 Click OK Macintosh Print Preferences When you print a
295. lots based on your criteria highlight lists and intersecting sets on plots generate histograms of data distributions and more BioDraw Reporting on and presenting findings is a task familiar to every biologist Making this process easier and more effective benefits everyone involved BioDraw is doing for biologists what ChemDraw has done for chemists for years saving time and resulting in a more professional representation of the science BioDraw makes drawing and annotating biological pathways quick and easy adding a level of uniformity and detail which is unmatched Typical drawings of biological pathways include us 1 800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 BioAssay offers flexible storage retrieval and analysis of biological data BioViz provides statistical analysis and graphical representations of the data loaded into a ChemFinder form BioDraw allows for quick and easy drawing and annotation of biological pathway depictions many elements that are difficult to draw with the standard presen tation and word processing software Common pathway elements such as membranes enzymes receptors DNA tRNA and plas mid maps are built into the BioDraw toolbar BioDraw is built into the same backbone as ChemDraw allowing users to take
296. m BioDraw allows for quick and easy drawing and annotation of biological pathway depictions many elements that are difficult to draw with the standard presen tation and word processing software Common pathway elements such as membranes enzymes receptors DNA tRNA and plas mid maps are built into the BioDraw toolbar BioDraw is built into the same backbone as ChemDraw allowing users to take advantage of the wide variety of the publishing capabilities avail able in ChemDraw such as the ability to import and export images in GIE PNG or JPEG formats In addition the integration of ChemDraw BioDraw Chem Bio Draw application pro vides a great communication mechanism between chemists and biologists v Notebook Pages a Data Visualization EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com SOFTWARE Inventory amp E Notebook Materials Management and Electronic Journal Inventory Ultra Inventory Ultra allows users to manage the tracking needs of chemical and non chemical inventory data for laboratories and research centers The system manages data associated with both commercially procured and internally produced chemical sub stances from their procurement or initial production through their depletion and disposal Inventory Ultra is an MSDE based prod
297. m and browsers may use data query and analysis Most data mining tools provide a mech anism to store queries but the interface for creating queries is too complex With BioSAR each set of assays is a complete report with a query form a view form and a table view combining the convenience of a ChemFinder or ISIS application with the power and flexibility of a data catalog driven mining program Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 BioSAR is a catalog driven mining and structure activity analysis program BioSAR provides both form and table views within a simple and powerful web interface BioViz provides one step in depth analysis of several variables BioSAR is a catalog driven data mining and structure activity analysis program BioSAR provides both form and table views within a simple and powerful web interface e BioDraw makes it easy to and biological pathways including common elements such as mem draw annotate branes enzymes receptors and DNA BioViz BioViz with ChemFinder transforms the numbers in your database into graphics on your screen Retrieve or search for a set of com pounds choose the data you want to see whether it is biological test results in Oracle tables physical property
298. m i ley e Pry I LS Includes tit o o ae E Notebook Enterprise or Workgroup a BioAssay Enterprise or Workgroup L BioSAR Enterprise BioViz Desktop Registration Enterprise Li Inventory Enterprise or Workgroup a n ChemACX Database ChemlNDEX Database Oracle Cartridge SQL Server Compatible ChemFinder Ultra E All specifications subject to change without notice 1 617 588 9390 EMAIL 0120 146 700 Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 info cambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com WORKGROUP and Workgroup Solutions Trials and Manufacturing Workflow Manvfacturing Manufacturing requires the transfer of data and batch process records from the pilot plant studies using Jnventory E Notebook and Registration systems Good Laboratory and Manufacturing Processes GxP under The handling of materials including chain of custody require ments material documentation material workflow such as avail ability states and recertification dates are tracked and handled by the system These systems meet the require
299. m Atom Map tool This might be necessary when the automatic mapping is applied to complicated reactions and gives incorrect results In these cases you can manually readjust the reaction mapping The figure below shows the initial mapping being amended by using the Reaction Atom Atom Map tool Rxn Rxn Figure 10 19 Automatic mapping to be amended When you manual map reactions with the Reaction Atom Atom Map tool you can sup press automatic re mapping of atoms other than your target atom To suppress automatic re mapping 1 Go to File gt Preferences 2 On the General tab select Automatic Reac tion Mapping 3 Click OK To use the Reaction Atom Atom Map tool to supplement the automatic mapping 1 Click the Reaction Atom Atom Map tool on the Query toolbar 2 Point to the atom in the reactant whose mapping you want to establish For exam ple in the following drawing you would point to the acyclic carbon adjacent to the ether oxygen Chem amp Bio Draw 12 0 141 User Guide 3 Drag from the reactant atom to the corre sponding product atom The remaining atoms are mapped based on the manual mapping Figure 10 20 Finalized mapping You can continue to set or change the mapping for other atoms in the reaction if necessary until you get exactly the mapping you want Clearing Reaction Mapping To clear all reaction mapping 1 Select the structures whose mapping you want to remove 2 Go to Stru
300. m of Henry s Law constant Functions CHEMPROP HENRY LAW CONSTANT cell ref Example In cell CHEMPROP HENRY LAW CONSTANT A2 Result 4 78182 Heat of Formation The heat of formation for the structure at 298 15 K and 1 atm Units kcals mole Functions CHEMPROP HOF cell ref CHEMPROPPRO HEAT OF FORMATION cell ref Examples In cell CHEMPROP A2 Result 105 73 In cell CHEMPROPPRO HEAT OF FORMATION A2 Result 105 73 Ideal Gas Thermal Capacity The constant pressure 1 atm molar heat capacity at 298 15 K for an ideal gas com pound Units J mole K Functions CHEMPROP IDEAL GAS cell ref CHEMPROPPRO IDEAL GAS THERMAL CAPA CITY cell ref Examples In cell IDEAL GAS 2 Result 201 036 In cell CHEMPROPPRO IDEAL GAS THERMAL CAP ACITY A2 Result 201 036 LogP The logarithm of the partition coefficient for n octanol water Functions CHEMPROPPRO LOGP cell ref CLOGP DRIVER PARTITION COEFFICIENT cell ref Examples In cell CHEMPROPPRO LOGP A2 Result 2 233 In cell CLOGP DRIVER PARTITION COEFFICIEN T A2 5 E Result 2 243 Molar refractivity The molar refraction index Chem amp Bio Draw 12 0 113 User Guide Units cm mole Functions CHEMPROPPRO MOL REFRACTIVITY cell ref CLOGP DRIVER MOL REFRACTIVITY cell ref
301. mNMR directory 97 ChemNMR about 5 ChemOffice SDK accessing 217 ChemProp critical pressure 202 ChemScript 78 chirality see stereochemistry flags 195 clean up structure 62 clearing mapping 142 spectrum structure assignments 97 stereochemical markers 86 clearing reaction mapping 142 Clipboard 33 82 108 127 142 147 148 149 clipboard 82 107 147 clipping files 149 CLogP 92 202 closing text boxes 158 cluster count 115 CMR 92 color autoscaling 150 changing 169 menu 169 overview 168 saving settings 171 color palette 169 colored arrows 68 coloring block arrows 68 colors customizing 169 colors maximum number of 150 168 169 commands new 9 open 9 save 10 complexes 194 configuring documents 162 configuring objects 163 Connolly molecular surface area 114 Connolly solvent accessible surface area 114 Connolly solvent excluded volume 114 contracting labels 61 conventions text 4 convert name to structure limitations 82 convert structure to name automatic cap tions 79 converting name to structure 82 converting names to structures 82 converting worksheets 104 copy as SLN command 148 with clipboard 147 copying objects 30 creating Hotkeys 167 SLN strings 148 critical pressure calculation 202 critical pressure definition 91 critical pressure 112 critical temperature calculation 202 critical temperature definition 91 critical temperature 112 critical volume calculation 202 critical volume defini
302. mation ChemFinder Pro is a fast chemically intelligent relational database search engine for the Desktop The integration with Microsoft Excel and Word adds chemical searching and database capability to spreadsheets and documents Compatibility with MDL ISIS databases is provided by SDfile and RDfile import export Us 1800 315 7300 INT L 1 617 588 9300 EU 0080087520000 UK FAX 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemFinder offers improved searching and hit list management along with new property generation ChemFinder is tightly integrated with CambridgeSoft s Oracle Cartridge Search ChemACX and other CambridgeSoft ChemACX Database includes over 1 million chemical products available for purchase from 472 supplier catalogs search able with a single query by structure substructure name syonym partial name and other text and numeric criteria ChemMSDX Database provides material safety datasheets and is integrated into ChemACX and contains over 23 000 Material Safety Data Sheets MSDS in PDF format ChemINDEX Database includes 100 000 chemicals public NCI compounds AIDS data and more NCI Database contains over 200 000 compounds with anti cancer drug dose response data AI
303. mbridgeSoft grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product Software in accordance with the terms of this Agreement This licensed copy of the Software may only be used on a single computer except as provided below You may physi cally transfer the Software from one computer to another for your own use provided the Software is in use or installed on only one computer at a time If the Software is permanently installed on your computer other than a network server you may also use the Software on a portable or home com puter provided that you use the software on only one computer at a time You may not a electroni cally transfer the Software from one computer to another b distribute copies of the Software to others or c modify or translate the Software without the prior written consent of CambridgeSoft d place the software on a server so that it 1s accessible via a public network such as the Internet e sublicense rent lease or lend any portion of the Software or Documentation or f modify or adapt the Software or merge it into another program The Software may be placed on a file or disk server connected to a network provided that a license has been purchased for every computer with access to that server You may make only those copies of the Software which are necessary to install and use it as permitted by this agreement or are for purposes of backup and archival record
304. ments and provide the basis to manage materials and records during clinical trials Clinicians can design and record results from protocols and all of these web based software systems provide the access required by clinicians who are removed from the sponsoring company Chem amp Bio Office Enterprise Chem amp Bio Office Enterprise is a comprehensive knowledge management and informatics solution covering electronic note books biological screening and chemical registration over your intranet ChemBioOffice Enterprise Ultra includes E Notebook for record keeping BioAssay for low and high throughput screening with integrated plate inventory BioSAR for SAR reports Registration System Inventory for reagents and biologicals and ChemACX database of available chemicals Technologies include ChemDraw ActiveX and Oracle Cartridge Chem amp Bio Office Workgroup Chem amp Bio Office Workgroup Ultra is a comprehensive knowl edge management and informatics solution covering electronic notebooks biological screening and more over your intranet Chem amp Bio Office Workgroup Ultra includes E Notebook for record keeping BioAssay for low and high throughput screen ing BioViz for visualization nventory for reagents and ChemACX database of available chemicals Technologies also include SQL Server for affordability and ease of administration Research Discovery Development Trials amp Manufacturing Workflow E Noteboo
305. meration of products from a virtual library on a flexible plate layout a multiple reaction site checker and multiple step parallel synthesis Others simply import a list of compounds from an external source or SDFile so that they can record and calculate data on a library wide stoichiometric table Analytical Chemistry E Notebook serves as a repository for analytical data and it also acts as a communication portal with which scientists and analysts communicate with each other Scientists can create and send service requests directly to an analyst with the click of a button Paper is eliminated when results are obtained the analyst can send the images and chromatograms directly back to the scientist s E Notebook Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Chemical Synthesis Scale up and Analytical 37 CFR Electronic Signatures Service Requests and Discovery Workflow Process Chemistry The objective of process research is to identify efficient processes for the synthesis of active pharmaceutical agents at the scale required for clinical trials and commercial use It is necessary to provide precise descriptions of these processes so that they can be executed by different groups in different locations It is
306. mical structures to complex reactions In this section we introduce basic drawing tech niques to help you create your first structures We also explain how to add features such as arrows and shapes to enhance structures and reactions For more drawing features see BioDraw on page 35 and Advanced Draw ing Techniques on page 59 Bonds The Main toolbar and Multiple Bonds toolbar offer numerous options for drawing bonds Some of the tools are for drawing specific types of bonds while others represent nonspe cific bonds for drawing structures for database queries Drawing bonds To draw the first bond of your structure select the solid bond tool in the Main toolbar and click in the document window To draw another bond click either end of the first bond Figure 3 1 Adding a bond to an atom You can draw a bond in any direction Using a bond tool click and drag from an existing atom or an empty area in the document window The bond is drawn in the direction you drag the cursor Figure 3 2 Adding a bond by dragging Fixed Bonds The Info window displays the bond length and angle as you drag the bond You can draw any bond length or create any angle relative to the X axis However it is generally more useful to draw bonds that are constrained to a fixed length and a fixed angle Drawing fixed length bond To draw bonds constrained to a fixed length 1 Go to Object gt Fixed Lengths and ensure that a
307. mical strucures formulas andmolecular weights The electronic versions include archived monographs from previous editions and is updated twice a year R amp D Insight Chemists Information on current drug products under development is essential for those working in research and development licensing and marketing at pharmaceutical and healthcare institutions R amp D Insight for Chemists a collaborative product from Wolters Kluwer Health and CambridgeSoft combines the power of chem ical structure searching with a wealth of drug development data to give subscribers a competitive edge when making decisions rele vant to the direction of their research Updated weekly users can search the collection of over 20 000 compounds by structure substructure names partial names and synonyms Patent Database Researchers chemists and patent analysts are now able to easily search full text patents for chemical structures using CambridgeSoft s powerful search and analysis tools The new CambridgeSoft Patent Database portal co developed by CambridgeSoft and Reel Two will give users access to all the chemical compounds named in a patent and enable them to search by structure keyword or chemical name us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridg
308. mp Bio Draw 12 0 115 User Guide Number of rotatable bonds Function MOLECULAR TOPOLOGY NUM ROTATABLE B ONDS cell ref Example In cell MOLECULAR TOPOLOGY NUM ROTATABLE BONDS A2 Result 2 Polar surface area Function MOLECULAR TOPOLOGY POLAR SURFACE A REA cell ref Example In cell MOLECULAR TOPOLOGY POLAR SURFACE AREA A2 Result 17 07 Radius Function MOLECULAR TOPOLOGY RADIUS cell ref Example In cell MOLECULAR TOPOLOGY RADIUS A2 Result 4 Shape attribute Function EE MOLECULAR TOPOLOGY SHAPE ATTRIBUTI cell ref 116 ChemDraw Excel Chapter 9 Example In cell MOLECULAR TOPOLOGY SHAPE ATTRIBUT E A2 Result 11 076923 Shape coefficient Function MOLECULAR TOPOLOGY SHAPE COEFFICIE NT cell ref Example In cell MOLECULAR TOPOLOGY SHAPE COEFFICI ENT A2 Result 0 Sum of degrees Function MOLECULAR TOPOLOGY SUM OF DEGREES cell ref Example In cell MOLECULAR TOPOLOGY SUM OF DEGREES A2 Result 28 Sum of valence degrees Function MOLECULAR TOPOLOGY SUM OF VALENCE DEGREES cell ref Example In cell MOLECULAR TOPOLOGY SUM OF VALENCE _ DEGREES A2 Result 40 Topological diameter Function MOLECULAR TOPOLOGY TOPOLOGICAL DIA METER ce
309. mp Bio Draw 12 0 121 User Guide Go to Structure gt Properties and view the settings on the Atom Properties tab Showing indicators for a structure To display query indicators for a structure 1 Select the structure 2 Right click and go to Atom or Bond gt Show Query Indicator on the context menu To display query indicators for an atom or bond 1 Right click the atom or bond 2 Choose Show Query Indicator on the context menu Positioning Query Indicators Query indicators are positioned automatically and move appropriately if a structure is modi fied You can reposition them by dragging them to the desired position or with the Indica tor Position dialog box To reposition an indicator numerically 1 With a selection tool click the indicator to move 2 Right click and choose Position The Posi tion Indicator dialog box appears 3 Click the appropriate Position option and type a value To Position Type a value for from the atom or bond angle degrees center to indicator cen clock o clock ter from the atom or bond offset horizontal and center to bottom left of vertical indicator baseline at specified coordi absolute horizontal nates and vertical 122 Query Structures Chapter 10 Hiding a query indicators To hide an indicator 1 Right click the indicator 2 Choose Hide Indicator on the context menu Removing Atom Properties To remove all prope
310. n 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Inventory manages the chemical and reagent tracking needs of laboratories and research centers Inventory maintains its own internal chemical structure database with advanced duplicate checking E Notebook stores Microsoft Office documents ChemDraw structures reaction drawings and related data in a convenient searchable format E Notebook Ultra E Notebook Ultra is an efficient accurate way to store lab note book information It stores Microsoft Office documents ChemDraw structures reaction drawings and related data in an electronic notebook that is searchable by text or chemical struc ture You can organize pages by project experiment or in your own style with the MSDE database CombiChem Excel builds combinatorial libraries E Notebook is configured exactly like a chemist would like his or her own notebook to be Reactions can be easily drawn into the reaction template by either selecting from the generous list of preloaded reagents or by entering or drawing one s own chemicals Commonly used reagents can be stored in a separate folder for easy access Another fantastic feature is the pro cedural section This section contains pre written procedural sen tences with the ability to easily drop in the specific names of reagent chemicals present in the reaction One can also easily add other data to the notebook page such as spectra
311. n interpreter 1 Go to View gt Show Reaction Interpretation 2 Hover your cursor over the reaction arrow The various parts of a reaction are color coded as follows Red reactants Magenta products Cyan Anything above the reaction arrow Blue Anything below the reaction arrow 70 Advanced Drawing Techniques Chapter 6 Guidelines For a reaction to be interpreted Each reactant and product must contain at least one atom Each reactant and product must be described using a single label Multiple reactants and products must be linked by a sign Reaction conditions must reside completely within the left and right boundaries of the reaction arrow The reaction cannot include a curved arrow Drawing an Intermediate In this tutorial you draw the intermediate structure shown below starting from a ring and add arrows with the arrow and Draw Curve tools CoH D Create a new document Go to the File gt New Document Go to File gt Save As command Type tut2 cdx in the appropriate text box Select a folder in which to save the file Click Save M dm Draw a ring 1 Select the Cyclohexane Ring tool 2 Click in the document window to add a ring Delete an atom and its bonds from the ring 1 Click the Eraser tool 2 Click any atom as shown in Figure 6 13 A A B Figure 6 13 Erasing an atom NOTE Click the center of a bond to delete it or drag the era
312. nal analysis Message Description An atom in this label has an invalid valence Displayed in cases where a place cannot be found to place a bond or a bond cannot be found to place an atom Valid valences for each element are listed in the Isotopes Table file ChemDraw can t interpret this label Displayed when text is found that cannot be identified as an element nickname generic nickname or alternative group name Message Description There are too many bonds to this unlabeled Carbon Displayed for every unlabeled atom with more than four filled valences Filled valences include sum of bond orders charge radicals and free sites Aromatic bonds count 1 5 each rounded down unless it is the only bond to the atom Charge is signed and includes charge implied by dative bonds The Substit uents query property treats free sites up to and exactly the same way an atom with two explicit bonds and Substituents Up To 3 or Substituents Exactly 3 or Substituents Free Sites 1 has three filled valences Parentheses don t match This label has conflicting or unassignable charges Displayed when parentheses cannot be matched into nested open close pairs Displayed when a plus and minus charge have been assigned to the same element charges have been assigned in more than one way or a charge has been assigned to a nickname generic nickname or Alternative
313. nal groups to use as an atom label or part of a label When you label an atom with a nickname the expanded structure retains its chemical significance Commonly used nicknames such as Me Et and Ph are stored in your ChemDraw Items folder You can edit this list within the GUI however you should not attempt to edit this file directly NOTE Nicknames may be edited in ChemDraw Pro ChemDraw Ultra or Chem BioDraw Ultra 12 0 only See Generic Nick names on page 119 You can assign Hotkeys to Nicknames For example in the Nicknames and Hotkeys pro vided the Hotkey 4 labels an atom with Ph which represents a phenyl group Applying Nicknames You may select a nickname from the Nick names list or type it in manually To select from the list 1 Point to an atom 2 Press the Hotkey equal sign The Nickname list appears 3 Select a nickname from the list TIP You can jump to the approximately cor rect place in the Nickname list by typing the first letter of the Nickname 4 Click OK To type the nickname 1 Double click an atom with a bond tool or click an atom with the Text tool 2 Type the nickname in the text box NOTE Nicknames are tokens and do not flip orientation when applied to the left side of a structure when using Automatic Justification For example in the absence of a defined Nick name the label OTHP appears as However since the N
314. name OH To expand atom labels 1 Select a selection tool 2 Select the label to expand or double click the structure to expand all possible labels 3 Go to Structure Expand Label Your struc ture 1s redrawn in its expanded form Contracting Labels You can compress an area of a structure and replace it with a text label Contracted labels are similar to nicknames but they are for one time use only in the current document To create a contracted label 1 Select the area of the structure to contract Figure 6 1 Selecting a structure to contract 2 Go to Structure gt Contract Label The Con tract Label dialog box appears 3 Type a label for the contracted structure and click OK The label replaces the selected portion of the structure Hexylbenzene Figure 6 2 Contracted label NOTE If the area of the structure you contract contains errors an error dialog box appears Click Ignore to view other errors Click Ignore All to ignore all errors or Stop to end the con tract process Multiple atoms Labels can comprise a group of atoms When you expand the label it expands to create the structure Expanded H Y Contracted CH5CH NHCCH Chem amp Bio Draw 12 0 61 User Guide Adding a Label of multiple atoms 1 Using the text tool click an atom in the structure where to place the label 2 Type the formula such as CHoNHC3 3 Using a selection tool select the formula 4
315. ncludes a library of document settings based on those found in many well known scientific publications For example some journals may require submitted articles be formatted with specific margins fonts page size etc If you plan to submit your document to a specific journal open in Chem amp Bio Draw 12 0 the style sheet for that jour nal If you want you can also create style sheets of your own NOTE Style sheets are called stationary pads in the Macintosh operating system To create your own style sheet 1 Create a new document 2 Enter the settings in the Page Setup Draw ing Text Settings and Color palette dialog boxes 3 Go to File gt Save As 4 In the Save As dialog box a Select the Chem amp Bio Draw 12 0 style sheets or stationary pads file format b Type a name for the document c Select the ChemDraw Items folder as the location for saving the template 5 Click OK or Save Publishing Documents This following table contains a sample struc ture for each of the style sheets used in many popular publications ACS Document 1996 e e e Fixed Length 14 4 pt Bold Width 2 pt Line Width 0 6 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Atom Label Size 10 pt Caption Font Win Mac Caption Size 10 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter
316. nd position of text drawn using Bitmap fonts change somewhat when printed For accurate correspondence between what you see on the screen and what is printed dese lect Use Bitmap Fonts When Available This change affects all documents Highlight Box Tolerance You determine the size of the highlight box and how close you must get to activate an object by setting the Tolerance The default setting for the Tolerance is 5 pixels At this set ting the highlight box appears on bonds if the pointer is located 5 pixels or less from any point on the bond To set the Tolerance 1 Go to File gt Preferences 2 On the General tab select or type the toler ance This change affects all documents The ChemDraw Items Folder The location of the ChemDraw Items folder is based on your operating system If you are using ChemOffice 2009 the folder is at Windows XP C Documents and Settings All Users ApplicationData CambridgeSoft ChemOffice2009 ChemDraw Windows Vista C Program Data CambridgeSoft ChemOffice2009 Chem Draw Macintosh By default the ChemDraw Items Folder is in the same folder as your Chem amp Bio Draw 12 0 application The folder contains the preferences Hotkeys nicknames and isotopes files scripts and the generic nicknames file It also contains tem plate documents and template Stationery Pads You can have multiple ChemDraw Items fold ers This is useful in corporate installations for maintaining pe
317. nd an arrow click and drag its center handle as indicated by the cursor f in the figure above ENHANCING THE DRAWING A plasmid map is like any other drawing You can add color and shading to it changing line widths or modifying its text You can modify all or part of it Drawing sequences You can draw protein and RNA sequences using labels assigned to nucleic and amino 40 BioDraw Chapter 4 acids Then you can expand contract or remove labels to complete the drawing To draw a sequence 1 On the Main Toolbar click the Sequence icon and choose one of the following sequence tools Single letter amino acid tool Create a protein chain using a one letter label to represent each amino acid Three letter amino acid tool Create a protein chain using three letter amino acid labels DNA tool Create a DNA chain using labels that represent each of the nucleic acids RNA tool Create an RNA chain using nucleic acid labels 2 Click in the drawing window where you want to start the sequence A text box appears 3 In the text box enter the single or three letter label for the residue NOTE For a list of all residue labels see IUPAC codes on page 42 4 Repeat step 3 for each residue 5 When your chain is complete click any where in the drawing window or choose a different tool EXPANDING SEQUENCES After creating a sequence you can expand the whole sequence or just specific labels
318. ndow Right click the toolbar and select Float Tool bar BioDraw Toolbar The BioDraw toolbar contains drawing tools for adding biological and biochemical ele ments to your drawings BioDraw is available in ChemDraw ActiveX Pro ChemBioDraw Ultra and BioDraw Pro and Ultra versions See Chapter 4 BioDraw for more informa tion Documents A document is a workspace where you create and edit structures Creating Documents You can create a new document using the default settings or use a Style Sheet or Statio nery Pad with customized settings To create a document go to File gt New Document Using Styles To create a new document using a different style sheet or stationery pad 1 Go to File gt Open Style Sheets 2 Choose a Style Sheet or Stationery Pad from the list Chem amp Bio Draw 12 0 provides pre defined style sheets or stationary pads in the ChemDraw Items folder For example the ACS Document 1996 is configured to create documents that are set with the bond lengths bond width spacing and fonts used in the 2 column format of all ACS journals For a list of the settings stored in these docu ments see Appendix A Preferences and Set tings NOTE Predefined style sheets or stationary pads may restrict your options in unexpected ways For example not all Save As format options are available For general use keep the default settings Opening Documents To open a document do o
319. nds are single or aromatic NOTE Not all bond types are supported in all file formats When an unsupported bond type is saved to a given file format it is converted to the closest equivalent that is supported Topology The Topology property specifies the ring envi ronment of the selected bonds Option Search Result Unspecified Default Finds compounds regardless of environment Ring Finds compounds where the selected bonds are part of a ring Chain Finds compounds where the selected bonds are part of a chain and are specifically not part of a ring Ring or Chain Finds compounds where the selected bonds are part of either a ring or a chain Reaction Center The Reaction Center property specifies how the selected bonds are affected in a reaction This property is only meaningful when search ing a database containing chemical reactions Option Search Result Unspecified Default Finds compounds regardless of whether the selected bonds are affected by the reaction Center Finds compounds where the selected bonds are affected by a reaction but the type of change is unspecified Chem amp Bio Draw 12 0 129 User Guide Option Search Result Make Break Finds compounds where the selected bonds are either bro ken or created in a reaction Change Finds compounds where the bond order of the selected bonds changes in a reaction Make
320. ne of the following Goto File gt Open In the Open dialog box select the name and location of the file and click Open Inthe File menu choose the document from the list at the bottom Discarding Changes To retrieve the last saved version of a file go to File gt Revert Undo Redo and Repeat Chem amp Bio Draw 12 0 tracks your actions To undo redo or repeat your last action select the Chem amp Bio Draw 12 0 9 User Guide appropriate option in the Edit menu The num ber of actions that can be tracked is limited only by the amount of memory RAM and vir tual memory available NOTE Chem amp Bio Draw 12 0 tracks only those actions you have performed since you last saved the document Saving Documents Go to File gt Save Choose a folder in which to store the file Type a file name in the Save As text box Select a file format Click Save gt UNG CAUTION Chem amp Bio Draw 12 0 uses the CDX file for mat by default Other formats store a picture of your drawing but may not retain relevant infor mation For example the EPS format does not store the chemical significance of the connec tions between atoms and bonds Selecting an open document The Window menu lists all open documents and templates The document you choose from the list becomes the active window Windows Windows are useful for viewing information about your drawing and even adding informa
321. nerate elaborate reports Inventory Desktop and Workgroup use a report engine that incorporates wizards that allow for the quick creation of simple report label templates that can be shared across an organization A user has the ability to design a label based on tem plates for a number of commercially available label sheets e g Avery Dennison The Inventory manager makes extensive use of barcodes and web based user interfaces to speed use but substan tial gains come in the automated reporting and alerting Examples include notifying all users of samples derived from a single stan dard of some change in status such as different analytical results or failure to recertify v Inventory Enterprise al iej x Google CambridgeSoft Inventory Enterprise Disce l Location iin gui ViewSimpleRackL ayau Pharmacy MyRack esaa 2 sae E Expiration Date 08 21 2008 owner Status Available Container Links Parent Container Fami 6295 teh 1 Amount on Hand Current User la sila T T fbi 5 amp 5 S3 5e OS wm a seran o 1B 3e a 0e mal Ye 5 0e WH e Mu ewe Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP MAIL CambridgeSoft Corporation 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are t
322. nglish chemical names into chem ical structure diagrams It is designed to inter pret chemical names as they are actually used by chemists In other words it recognizes the shorthand and slang of everyday usage in addition to recognizing most of the official IUPAC IUBMB and CAS rules and recom mendations In addition it has an extensive algorithm for identifying common typing errors to help accurately generate structures NOTE Struct gt Name and Name gt Struct are available only in ChemBioDraw Ultra and ChemDraw Ultra Struct Name Struct Name is designed to interpret a wide variety of chemical structures This means that you can draw a structure in the document win dow and using the Convert Structure to Name command Struct Name will provide its name It also updates the name whenever you modify the structure NOTE Struct Name is available only in ChemBioDraw Ultra and ChemDraw Ultra Unsupported structures Although quite useful this feature has a few limitations for interpreting some structures such as Sulfones and chalcogen analogs Polymers Isotopically modified compounds Radicals ions and radical ions Supported Structures However the nomenclature types Struct Name will interpret include Stereochemistry Principal group in rings and chains Carboxylic Acids Chem amp Bio Draw 12 0 79 User Guide Peroxy acids Amide derivatives of acids Carbonic acids Nitric acids
323. nnected to your computer You can either use the default printer or select another printer Print to File The document is saved as a prn file that also includes your printer preferences The document can then be sent later to a printer Find Printer Click to map to a printer that is not currently listed in the Select Printer win dow Page Range Select the pages you want to print If you wan to print only specific parts of your document select the parts using the selec tion tool and then choose Selection in the Print Options dialog box to print Number of copies By default only one copy is printed Scaling Some printers include an option to reduce or enlarge your drawings by a variable percentage 25 400 This option scales all objects and text in the document window by the percentage specified This is not a change in magnifica tion The size of objects is changed relative to the paper size margins and orientation you have specified The enlarge or reduce option is useful for changing the size of the available drawing area while keeping the images on the screen at the normal size when you are drawing If your document is set so that the drawing fills the page on one printer and you use another printer that requires larger margins the drawing my disappear off the edge of the document win dow You can reduce the size of the drawing with the reduce option so that it fits in the doc ument window Saving Page Set
324. not approximately lined up will lead to incorrect results NOTE When you join two differently colored bonds or atom labels the color of the front object becomes the color of the resulting joined object When you join two atoms that are labeled the front atom label becomes the atom label of the resulting atom For more informa tion about front to back ordering of objects see Chapter Page Layout Grouping Objects A group is a collection of objects that act as a single object You can select all grouped objects by double clicking with a selection tool Objects within a group can be selected individually and manipulated while still remaining part of the group To group objects so that the individual objects in the group cannot be selected you create an integral group When you select any object in an integral group the entire group is selected Grouping does not lock the position or orienta tion of objects Grouped objects maintain their relative positions when they are centered on the page aligned or distributed Atoms and bonds making up a single chemical structure are always grouped If you group part of a structure with other objects the resulting group contains the entire structure If you add atoms or bonds to a grouped structure the new atoms and bonds are part of the group To group several objects 1 Select the objects to group using a selection tool 2 Go to Object gt Group To select an indi
325. nother object without holding down Shift Deselecting one object To deselect only one of several selected objects hold down the Shift key and click the object with a selection tool NOTE As shown in the figure below objects may appear within the borders of the selection rectangle but not be selected s 4 Figure 3 8 Removing selected objects Blue dots on the surrounding rings indicate these rings have been selected The center ring has not been selected Resizing Objects To resize a selected object click and drag a handle resize proportionately by dragging any cor ner resize with either X axis or Y axis distor tion by dragging any side resize freely X and Y axis distortion by holding the Shift key down while dragging Rotating Objects 1 Select an object to rotate The Rotation han dle is at the top of the selection rectangle 2 Drag the Rotation handle clockwise or counterclockwise To rotate an atom label with a structure press the Ctrl or Command key while dragging the structure yo pe 4 Se NOTE If an atom is unselected when a struc ture is rotated the structure rotates around the unselected atom To rotate a selected object by a specified angle 1 Doone of the following Go to Object Rotate Double click the rotation handle The Rotate Objects dialog box appears 2 Enter a number and click either degrees CW for a clockwise rotation or degrees
326. ntainer of the substance The new substance container is also tracked in the system and inherits all of the critical properties of its parent container If a quality con trol test is run on the parent then the results are viewable in the daughter s properties The multi select capability allows the user to select several con tainers and perform a transaction on all of the selected containers simultaneously including check in out move retire delete and update For instance if a request is made of the system that is fulfilled by another user such as dispensing the requester can automatically receive e mail notification of the progress Likewise users can be alerted to pending requests in the system EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com INFORMATICS Inventory amp GxP Document Storage Batch Records Conflict Resolution The Conflict Resolution processes and duplicates in the system automatically You may also search for duplicates at any time If a conflict is found the screen identifies the conflicting field s by highlighting it in red The user has the option to select the existing substance and edit the con flicting substance or create a duplicate substance and resolve the conflict later flags corrects Printed Reports amp Labels The Jnventory interface allows for printing labels and can ge
327. nterprise GxP Validation MANUFACTURING INFORMATICS CambridgeSoft s chemical chemical and pharmaceutical laboratories Inventory Enterprise is an Oracle based ChemOffice Enterprise product that container types racks and multi well plate formats Inventory Enterprise Materials Management Compliance Management ChemDraw amp Chem3D Compliant SDMS Gateway Inventory Enterprise reagent sample and designed needs of application is compound tracking to manage the large multi site is designed for multiple users with diverse DESKTOP SOFTWARE ChemFinder amp Chemlnfo Success begins at the desktop where scientists use ChemOffice ChemDraw BioOffice and BioDraw to pursue ideas and communicate with the natural language of chemical structures BioDraw BioAssay amp biological pathways and models Scientists organize information and manage data with BioViz 5 Notebook and nvenfory ChemBio3D provides modeling ChemBioFinder aids searching while BioOffice adds BioDraw BioAssay and BioViz All are integrated with Microsoft Office to speed Inventory amp E Notebook research tasks ChemBioFinder Gateway SCIENTIFIC DATABASES Good research depends on reference information starting with the structure searchable The Merck Index P 9 ChemACX Database of commercially available chemicals and Sigma Aldrich MSDS The Merck ChemACX Database Index and other scientific databases pro
328. nterprise streamlines record keeping with rigorous security and efficient archiv ing and facilitates text and structure searching Nofebook provides organizations with a powerful mechanism to transfer mission criticalwork product from shared drives to a well organized compli ant and searchable Oracle application MS Office chemical structures and workflow support modules are provided for the full range of research and development activities LABORATORY INFORMATICS Laboratory Informatics includes Workflow LIMS for instrumentation automation Compliant DB for stor age of your data and the Oracle Cartridge which is the industry s only enterprise content manage ment system developed by a large pharmaceutical company BIOLOGICAL INFORMATICS Finding structural determinants of biological activity requires processing masses of biological assay data Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models and visualize information The BioViz application allows you to create graphical representations of data CHEMICAL INFORMATICS Managing huge data streams is a key challenge Registration Enterprise organizes information about new compounds according to an organization s business rules SOLUTIONS to Enterprise Solutions LABORATORY amp MANUFACTURING A 2 Inventory Enterprise ChemACX Database SCIENTIFIC DATABASES moe The Merck Index Registration E
329. ntext menu 14 Basic Drawings Chapter 3 Double Either Bonds To draw a double either bond use the double either bond tool from the Multiple Bonds tool bar or 1 Draw a bond using the Wavy Bond tool 2 Click the center of the bond to create a dou ble bond 3 Click again to create a double either bond Triple Bonds There are three ways to draw a triple bond Draw a bond using the Triple bond tool Using the Solid Dashed or Bold bond tool drag from one end of an existing double bond to the other end Using any bond or selection tool point to an existing bond and type 3 Quadruple Bonds There are four ways to draw a quadruple bond Draw a bond using the quadruple bond tool Using the Solid Dashed or Bold bond tool drag from one end of an existing triple bond to the other end Using any bond or selection tool point to an existing bond and type 4 To change a quadruple bond into a single bond 1 Select any bond tool 2 Drag from one end of an existing quadruple bond to the other The quadruple bond changes into a single bond corresponding to the tool used to draw over the bond You can also draw multiple bonds by right clicking a bond and selecting the bond type from the shortcut menu using the bond properties dialog box or using Hotkeys See Bond Properties on page 127 NOTE To reduce the bond order select the Eraser tool and click the bond Dative an
330. o At Rn Fr Ra Ac Th Pa U Nep Pu Am Cm Bk Cf Es Fm Md No Lr Functional groups are expanded automatically In the case of H NMR it estimates shifts of about 90 of all CH groups with a standard deviation of 0 2 0 3 ppm The use of polar sol vents may strongly increase these deviations It does not estimate shifts of hydrogen atoms bonded to heteroatoms because they are signif icantly affected by solvents concentration impurities and steric effects Chem amp Bio Draw 12 0 203 User Guide In case of 5C NMR it estimates over 95 of the shifts with a mean deviation of 0 29 ppm and standard deviation of 2 8 ppm NMR References Sources for Chem amp Bio Draw 12 0 NMR data include the following publications F rst A Pretsch E Anal Chim Acta 1990 229 17 204 ChemNMR Appendix E Pretsch E F rst A Badertscher M B rgin R Munk M E J Chem Inf Comp Sci 1992 32 291 295 B rgin Schaller R Pretsch E Anal Chim Acta 1994 290 295 B rgin Schaller R Arnold C Pretsch E Anal Chim Acta 1995 312 95 105 B rgin Schaller R Munk M E Pretsch E J Chem Inf Comput Sci 1996 36 239 243 Technical Support Telephone and Internet technical support is available to registered users Be sure to provide your serial number Technical Support on the internet includes answers to frequently asked questions FAQs and general information You can find it at
331. ochemistry Show Stereochemistry calculates the absolute stereochemistry according to the Cahn Ingold Prelog CIP priority rules For more informa tion about CIP rules see Cahn Ingold Prelog on page 194 Only tetrahedral and double bond stereochem Istry are supported and only non racemic ste reochemistry is interpreted Stereochemical indicators for aromatic bonds are not dis played The stereochemistry feature calculates and dis plays the following R S Standard tetrahedral stereochemistry r s Tetrahedral stereochemistry deter mined by other stereochemical centers For example cis decalin and myo inositol E Z Standard double bond stereochemis try Displaying Stereochemistry Indicators 1 Select the entire structure 2 Right click and click Object Settings 3 In the Drawing tab under Atom Indicators and Bond Indicators select Show Stere ochemistry The stereo centers are marked as shown in the following example cholesterol Figure 8 2 Stereochemistry indicators If you make changes to the drawing that affect the stereochemistry the stereochemistry is recalculated Hiding Indicators 1 Select the indicator to hide 2 Right click and choose Hide Indicator Formatting Indicators The atom label settings determine the font style and size of the terms A setting on the Building Display tab of the Preferences dialog box determines whether or not the term will be display
332. ocument opens using your settings Poster Documents Setup You can create a poster by creating a single large drawing area which will be printed on as many separate pages as necessary When you set the document size and how much each page overlaps Chem amp Bio Draw 12 0 calculates the number of pages needed and the margin sizes You can set registration marks which mark the overlap setting on each page to use as a guide when assembling the poster from the separate pages To create a poster document 1 Go to File gt Document Settings 2 On the Layout tab click Poster 3 Type the Height Width and Page Overlap The number of pages and the margin dimensions are calculated 4 Select whether to Print Registration Marks 5 Create Headers and Footers 6 Click OK Headers and Footers In poster documents only one header and footer appear for the entire document To create headers and footers 1 Go to File gt Document Settings 2 Click the Hdr Ftr tab 3 Enter the position from the edge of the page that you want the header or footer to appear 4 Type the text to appear in the header or footer 184 Page Layout Appendix B 5 Type additional information in the Text box from the following file name amp f page number amp p date printed amp d time printed amp t 6 Position the text horizontally by typing the appropriate characters listed below Any text following these characters is appropri
333. of the attach ment points To set the order of the attachment points click the ends of the bonds in the order you want to number them using the Attachment Point tool The last point clicked has the highest number To change the ordering of the attachment points do one of the following Click the attachment points with the Attachment Point tool With a selection tool select the bond to which the attachment point is connected and go to Object gt Bring to Front or Send To Back The attachment point numbers are highest in the front Anonymous Alternative Groups NOTE Anonymous alternative groups are available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Anonymous alternative group are a cross between an element list and an alternative group Element lists are restricted to single ele ments but anonymous alternative groups can contain any structure that can be represented by text Nicknames and generic nicknames are allowed in anonymous alternative groups Anonymous alternative groups are shortcut notation for regular alternative groups elimi nating the need to specify a name such as RI 138 Query Structures Chapter 10 You can define your search query more con cisely with the anonymous alternative group By labeling an atom position as a list of sub structures you specify that one of these sub structures must match in the structure for which you are searching Commas must
334. ogy 129 types 128 viewing 128 bond spacing description 162 bond types in queries 128 bonding from sequences 42 bonds adding to an atom label 62 autoscaling 149 changing type 15 double either 129 drawing 13 editing 15 fixed angle 13 layering 16 margin width 162 multi center attachment 63 orientation for dative or wedged bonds 15 quadruple 14 selecting 28 types 190 border of page 183 braces 26 brackets drawing 26 paired 26 single 26 tool 26 usage 132 C Cahn Ingold Prelog 194 calculating chemical properties 91 elemental analysis 85 exact mass 85 formula 85 molecular weight 85 CambridgeSoft Web site accessing 216 CambridgeSoft com 216 caption text boxes closing 158 creating new line 158 captions 164 analysis information 85 autoscaling 150 formatting 163 166 formula 163 inserting from structure 79 justification 164 setting font size and styles 166 subscript 163 superscript 163 carbon 13 shifts see C shifts esti mating 95 cation drawing 90 CDX see file formats 10 chain angle description 162 chain length 23 specifying 23 changing default settings 161 changing bond type 15 character map 11 charges specifications 192 symbols drawing 90 192 check structure overview 32 checking chemistry 32 Chem amp Bio 3D 77 78 Chem amp Bio 3D preview 78 Chem amp Bio 3D preview options 77 Chem amp Bio 3D launching 78 Chem amp Bio Draw Chem amp Bio Draw 12 0 221 User G
335. olled separately by CambridgeSoft Corporation CS CS is a distributor and not a publisher of information supplied by third parties Accordingly CS has no editorial control over such information Database Suppliers Supplier individually own all right title and interest including copyright in their database and retain all such rights in providing information to Customers The materials contained in The Merck Index are protected by copyright laws and international copy right treaties as well as other intellectual property laws and treaties Copyright in the materials con tained on the CD and internet subscription products including but not limited to the textual material chemical structures representations artwork photographs computer software audio and visual elements is owned or controlled separately by the Merck amp Co Inc Merck and CambridgeSoft Corporation CS 2 Limitations on Use Except as expressly provided by copyright law copying redistribution or publication whether for commercial or non commercial purposes must be with the express permis sion of CS and or Merck In any copying redistribution or publication of copyrighted material any changes to or deletion of author attribution or copyright notice or any other proprietary notice of CS Merck or other Database producer are prohibited 3 Grant of License CD DVD Databases CambridgeSoft Software Products are licensed not sold Ca
336. om Properties Go to Structure gt Atom Properties Press the Hotkey 3 In the Atom Properties dialog box select the properties to associate with the selected atom s 4 Click OK Query Indicators Query indicators display the atom properties that you assign to a structure as the figure below illustrates If more than one property is assigned a character for each property appears adjacent to the atom x3 T 2HS S Figure 10 1 This structure illustrates a variety of possible atom properties that can be assigned The icons in the structure are described throughout this guide The list below describes the query property for each indicator For more information see Query Indicators on page 121 Substituents Free Sites followed by the number of free sites U Substituents Up to followed by the maxi mum number of substituents X Substituents Exactly followed by the number of substituents H Implicit Hydrogens R Ring Bond Count S Unsaturation C Reaction Change T Reaction Stereo L Translation none Abnormal Valence Viewing indicators for an atom or bond Except for the substituents query properties the characters indicate that a given property is applied but not the value of that property To find the value of a query property setting 1 Select the atom 2 Doone of the following Right click point to an atom and point to the appropriate property Chem a
337. on while protecting intellectual property with digital signatures and 21CFR Part 11 and 37 CFR compliance e Chem Bio Draw draw and annotate molecules reactions and biological pathways ChemACX find and purchase reagents Inventory store and track reagents and samples Registration record newly made compounds BioAssay model complex protocols and record results from biological testing BioSAR generate reports linking activity with structure BioViz analyze biological results Virtually every aspect of discovery process from synthesis planning library enumeration reagent selection primary and secondary screening in vivo testing through to analysis of results and the reporting of data is covered by the integrated E Notebook solution Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Replace Shared Drives with Oracle DMPK Screening Biology Genetics and Microscopy LIMS Method Execution 21 CFR Part 11 GxP Development and Testing CambridgeSoft s Enterprise E Notebook meets the needs of ever expanding research and development communities that rely on data sharing across scientific disciplines and campuses as globaliza tion has increased demands E Notebook allows custom integration of a large array of modules in ho
338. on 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com LABORATORY Workflow LIMS Visual LIMS Lab Automation Service Request Workflow allows scientists to communicate as they work Direct Communication from F Nofebook to create tasks and send results Method Execution Framework to enable standard operation procedures and compliance Applied Technologies and Benefits Workflow management enables discovery teams to rapidly trial new procedures capture best practices and scale successful designs from a manual prototype right up to a fully automated high throughput lab But discovery and research by its very nature demands that processes be flexible and that workflow execution rapidly adapt to new techniques and equipment Conventional laboratory information workflow applications can not meet this requirement because of their heavyweight configu ration needs their lack of adaptability and the cost and complex ity of integrating them with rapidly changing lab technology Workflow LIMS addresses these problems by providing a visual easy to use environment for describing processes and building workflows out of those processes enabling scientists to rapidly trial new procedures and by offering a rapid development tool kit for equipment integration which supports gradual automati
339. on is illustrated below OH abs OH OH orl amp 1 To add stereochemical notation to a structure go to Structure gt Enhanced Stereochemistry The power of this notation becomes clear when you draw complex enantiomers For example beta cypermethrin is a mixture of four distinct stereoisomers consisting of two enantiomeric 88 Chemistry Features Chapter 8 pairs However drawing this requires only one structure c Figure 8 3 beta Cypermethrin Two stereo centers have the amp 1 designation because of their fixed relative configuration when one is R the other must be S As a result they form a group The third stereo center varies independently and is designated amp 2 Group numbers are incremented automati cally To see all the beta cypermethrin stereoi somers go to File gt Open Samples gt b Cypermethrin To indicate stereochemistry for a group 1 Select all atoms in the group using Shift click 2 Go to Structure gt Enhanced Stereochemistry and select a stereochemistry marker See Displaying Stereochemistry Indicators on page 86 for information on showing and hiding indicators You can save enhanced stereochemistry nota tion in any of these formats CDX CDXML MOL V3000 RXN V3000 SKC TGF NOTE Mol V3000 SKC and TGF are avail able in ChemBioDraw Ultra Chem amp Bio Draw 12 0 Ultra and Chem amp Bio Draw 12 0 Pro only When saving to SKC or TGF form
340. on to minimize up front costs and ongoing risk CambridgeSoft s Workflow LIMS simplifies even manual lab pro cedures by managing the breakdown of a procedure into tasks and by automating the majority of data capture and transfer tasks but by capturing process as well as data Pathways reduces the costs and risks of implementing discovery techniques and enables companies to accelerate the entire discovery process EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com INFORMATICS Compliant DB amp Oracle Cartridge Compliant Storage and Chemical Data Management Compliant DB CambridgeSoft s Compliant DB is the industry s enterprise content management system developed by a large pharmaceutical company It serves as an electronic library that collects organizes warehouses indexes and safely archives all your structured and unstructured electronic records From raw data and laboratory reports to compliance records Compliant DB also will support any of CambridgeSoft s workflow solutions including E Notebook BioAssay and Inventory As its name implies Compliant DB is fully compliant with the requirements of 21 CFR Part 11 for electronic records and electronic signatures Compliant DB can be used directly over your company s intranet extranet or over the Internet with a simple web browser Complaint DB gives your organization a secure 21 CFR Part 11 compliant centralized electronic library for all e
341. ond attached to the selected atoms Must be Finds compounds that have at present least one multiple bond double triple or aromatic attached to the selected atoms Reaction Change The Reaction Change property specifies whether a change occurs at selected atoms after a reaction This property is meaningful only when searching a database that contains chemical reactions In ChemFinder only the product atom is checked The stereo designa tion 1s ignored on reactants NOTE The reaction change property is avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Option Search Result May be Default Finds all reactions anything regardless of any change to selected atoms after a reaction Must be as Finds all reactions that are specified changed at the selected atoms exactly as specified by the reac tion center property in the Atom Properties dialog box Br R Br Ro on Rn NH2 lt N Ri Ri Figure 10 4 The reaction change indicator is circled in the figure above Free Sites A free site query lets you specify the maximum number of substituents a result can have How ever it also requires that the bonds in the results appear exactly as they appear in the query structure NOTE The Free Sites feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To increase the number of free sites 1 To dis
342. one or more attachment points that connect it to the main structure Attachment points must be single bonds For nicknames with two or more attachment points the numbering sequence of the attach ment points determines the order in which other parts of the structure are attached For example if you expand the structure H Leu OH the hydrogen is bonded to the first attach ment point in leucine and the hydroxyl group to the second Defining attachment order When you define your own nickname you first draw the functional group structure and then indicate the attachment points The numbering order of the attachment points for structures that have two is determined by which bond you draw first For example when the leucine nickname was created the bond for the amino attachment point was drawn first Therefore it is numbered first NOTE If you don t know which attachment point was drawn first select the attachment point you want labeled 1 and go to Object Bring to Front Then define the nick name For more information see Using Nicknames on page 18 To define a new nickname 1 Create a structure containing the functional group to define as a nickname 2 Select the functional group You must indicate the connection point for the functional group by selecting the new fragment Chem amp Bio Draw 12 0 75 User Guide without the bond connected to the attachment point Figure 6 22 Adding a nickname
343. or save data as an image file for use in journal article submission Draw Biological Pathways EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com INFORMATICS BIoSAR amp BioDraw Data Mining and Pathway Drawing BioSAR BioSAR Enterprise a strategic must for any discovery organization interested in serious data mining is a data dictionary driven structure activity analysis program Users may choose among assays registered in the dictionary or search for assays of interest The power of BioSAR lies in the researcher s freedom from dependence on IT support for dynamically working with all avail able scientific data For example once an assay is registered into the data dictionary it is automatically included in the powerful analysis framework By reducing the time between question and answer BioSAR gives researchers the ability to explore new ideas and avoids this issue by placing SAR report creation in the researcher s control BioSAR Enterprise allows the researcher to create custom reports and views of their data You decide what is displayed and BioSAR takes care of the rest While most SAR tools provide only a table based interface BioSAR provides both a form view and table view and connects to BioViz for high dimensional analysis BioSAR merges the sophisti cation of a
344. ored using the foreground color are changed to match the foreground color in the destina tion document PASTING TO AN EMPTY DOCUMENT If you paste a Chem amp Bio Draw 12 0 drawing into an empty document and the settings between the documents are different the Change Settings dialog box appears 150 Sharing Information Chapter 11 To change the settings in the destination docu ment to match the settings in the source docu ment click Change Settings All of the settings in the destination document are changed to match those of the source docu ment All of the colors in the Color palette of the destination document are changed to those specified in the source document To scale the objects from the source document to the settings in the destination document click Don t Change Settings The settings from the source document are scaled to those in the destination document using the ratios given above NOTE If the source document was created in a ChemDraw version earlier than 3 0 the name of the document appears as Unknown in the dialog box Embedding Objects Windows Chem amp Bio Draw 12 0 supports the Object Linking and Embedding OLE protocol on Windows This lets you edit structures that are pasted in other types of documents Chem amp Bio Draw 12 0 is an OLE server which means it can create OLE objects that can you can copy and paste into other OLE client applica tions When you transfer drawing f
345. orksheet go to ChemOffice12 gt New ChemOffice Worksheet When a worksheet is active ChemDraw Excel appears in the title bar and the Chem amp Bio Draw 12 0 toolbar is active Importing Tables ChemDraw Excel lets you import from MDL SDFiles Imports all records in the file Each structure is given the name stored in the SD file MDL SDFiles are supported only in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Chem amp Bio Draw 12 0 databases Imports all fields stored in the main form Molecular weight and formula fields are not imported because ChemDraw Excel calculates them Each structure is named Structure lt n gt where n is a unique number NOTE To import CFW files into Excel save them with the allow CAL OLE Automation access security setting checked See Setting Security Options in Chapter 3 of the Chem Finder manual for details When you import a table structure data are transformed into structure drawings in the first column and all other fields are imported in separate columns To import a table 1 In Excel select the cell where you want the import to start The upper left corner of the import is at this cell Data is filled down and to the right 2 Go to ChemOffice12 gt Import Export gt Import Table The Import Table dialog box appears Chem amp Bio Draw 12 0 103 User Guide 3 Type or select the file name to import and click Open All records are
346. oth ultra high volume laboratories and lower throughput set tings BioAssay includes support for laboratory automation calcu lation and statistics and also complicated low and medium throughput assays such as animal models and in vivo experiments modeling in vivo experiments BioAssay is designed to tackle the needs of high and low through put screening biologists alike by providing an application flexible enough to model any assay regardless of complexity through an easy to use interface for importing storing and analyzing the data The software supports the quick set up of biological models auto mated calculations and curve fitting data validation and the cre ation of customized structure activity reports BioAssay Extends E Notebook BioAssay Enterprise is a scalable flexible biological screening solu tion utilizing Oracle s role based security and the Oracle Cartridge When used as part of ChemOffice Enterprise BioAssay is integrat ed with E Notebook for experimental data Inventory Enterprise for plate tracking and management Registration Enterprise for the reg istration of new compounds and BioSAR Enterprise for customized reporting BioAssay Ultra is designed to deliver much of the functionality of our enterprise level applications without a widespread roll out BioAssay Ultra coupled with BioViz offers a user friendly inter face for importing viewing validating and plotting your biolog ical assay dat
347. otocol InChI is a trademark of the International Union of Pure and Applied Chemistry InChI Material in Chem amp Bio Draw 12 0 is 9 IUPAC 2005 To copy structures as InChI strings to other documents 1 Select the structure 2 Go to Edit gt Copy As gt InChl You may copy only legitimate InChI struc tures If you attempt to copy a structure not supported by the InChI protocol a warning informs you that the structure is not supported Creating InChIKey strings Chem amp Bio Draw 12 0 supports Standard InchIKey available in InChI 1 02 An InChIKey string is a condensed digital repre sentation of an InChI string All InChiKey strings are the same length whereas InChl strings are not This standard makes InChIKey strings useful for Web searching and database indexing To copy a structure as an InChIKey string to other documents 1 Select the structure 2 Go to Edit gt Copy As gt InChiKey For more information on InChITM and InChIKey see www iupac org inchi Drag and Drop You can use drag and drop to copy objects to other documents To use this feature in other applications they must support drag and drop The object 1s transferred as a Chem amp Bio Draw 12 0 object and can be edited Scrap and clipping Files You can use clipping files Macintosh and scrap files Windows to copying parts of a drawing to other applications without having to save the file in Chem amp Bio Draw 12 0
348. our database uses 190 Chemical Interpretation Appendix C Bond Conventions The following table describes the chemical conventions Chem amp Bio Draw 12 0 recog nizes Bond Description Single bond unspecified stereo chemistry Single bond down stereochem wuni 1Stry into the plane of the paper away from the viewer from the first drawn atom to the second drawn atom Single bond up stereochemistry out of the plane of the paper toward the viewer from the first drawn atom fo the second drawn atom Li Single bond mixture of up and down stereochemistries in some unspecified proportion Dative bond Often used to indicate polar bonds such as the N O bond in pyridine N oxide Double bond with cis trans stere Ochemistry as drawn Double bond with cis trans stere ochemistry unknown bond either single or double according to rules of tautomerism Aromatic bond part of a delocal ized resonance system Triple bond Quadruple Bond A single bond near a closed circle is recog nized as aromatic Atom Labels A simple atom label may contain any of the following 1 A single element An element and some number of hydrogen H atoms Ps A nickname Ala LA CX Repeating units within OICH2u4CHs parentheses O CH 4 C
349. over 200 000 molecules studied by the National Cancer Institute ChemReact and ChemSynth These reaction database collections from InfoChem GmbH com prising essential information on chemical reactions published in the literature between 1974 and 2001 The largest is ChemReact500 with almost 500 000 reactions selected with an eye toward synthetic utility ChemSynth is a subset of the reac tions found in ChemReact500 chosen because they have greater than 50 yield and have been sited in leading journals more than once ChemReact68 has 68 000 reactions that have greater than 50 yield and have appeared in more than five example reactions EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com DATABASES ChemACX amp Sigma Aldrich MSDS Available Chemicals and Material Safety Data Sheets ChemACX Database Sifting through chemical catalogs is a poor use of time for any researcher ChemACX database solves this problem by offering a complete tool for research chemical sourcing and purchasing With an emphasis on up to date information of high quality ChemACX allows you to purchase chemicals fast efficiently and without worry or cumbersome paper catalogs The database can be accessed from both desktop and enterprise environments and boasts nearly 500 catalogs from major suppliers from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds in between Sigma Aldrich MSDS Environmental Heath and Safety EH amp S
350. overy process EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com INFORMATICS Compliant DB amp Oracle Cartridge Compliant Storage and Chemical Data Management Compliant DB CambridgeSoft s Compliant DB is the industry s enterprise content management system developed by a large pharmaceutical company It serves as an electronic library that collects organizes warehouses indexes and safely archives all your structured and unstructured electronic records From raw data and laboratory reports to compliance records Compliant DB also will support any of CambridgeSoft s workflow solutions including E Notebook BioAssay and Inventory As its name implies Compliant DB is fully compliant with the requirements of 21 CFR Part 11 for electronic records and electronic signatures Compliant DB can be used directly over your company s intranet extranet or over the Internet with a simple web browser Complaint DB gives your organization a secure 21 CFR Part 11 compliant centralized electronic library for all electronic data files Not only can machine readable instrument data files be stored but also images multimedia files presentations human readable word processing and Adobe PDF documents spreadsheets and hundreds of other formats This data can serve as source data instrument data to BioAssay and also repository Although Compliant DB can operate as a stand alone application only CambridgeSoft provi
351. p Bio Draw 12 0 For more on drawing biological structures see BioDraw on page 35 More Versatile Nicknames Nicknames have long been a useful feature in Chem amp Bio Draw With new enhancements for version 12 0 the nickname library includes structures that can have an unlimited number of connec tion points or no connection points at all ChemScript Support You can now execute ChemScript scripts in ChemBioDraw Ultra 12 0 Use any of the sample scripts that are provide or create your own See ChemScript on page 78 Customize NMR Data Chem amp Bio Draw 12 0 lets you supplement the ChemNMR data for proton found in Chem amp Bio Draw 12 0 with your own data 2 What s New Introduction Designed for scientists students and scientific authors Chem amp Bio Draw 12 0 is a powerful yet easy to use tool for producing a nearly unlimited variety of biological and chemical drawings You can create your own drawings or use those provided in the vast library of available templates Having completed a draw ing you can export it to a desktop publishing program post it on a Web page or store itin a database You can use Chem amp Bio Draw 12 0 with other CambridgeSoft products ChemBioFinder amp BioViz 12 0 Chem amp Bio 3D 12 0 Chem amp Bio Draw 12 0 Excel Chem amp Bio Office 2009 The ChemDraw Series CambridgeSoft is proud to offer ChemDraw a series of applications designed to help you
352. p ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Track amp Barcode Samples Create Any Report from Database Full Audit Trail Sample Login E Notebook is able to easily configure sample logins registration of sample assignment of barcode label and initiation of sample tracking by incorporating CambridgeSoft s Inventory application Through E Notebook forms can be created to keep track of newly synthesized or acquired compounds tracking their physical prop erties and tests and assigning unique identifiers New compounds are entered directly via the E Notebook form and chemical along with non chemical data is kept alongside the sample When a proprietary compound is registered if desired it is compared for uniqueness via a configurable stereoselective duplicate check and assigned a registry number Sample Tracking Iracking samples requesting analysis and establishing chain of custody can all be simply managed within the E Notebook inter face E Notebook serves as a repository for analytical data and experiments linking such data directly to the sample ID and it acts as a communication portal with which scientists and analysts communicate with each other during the service request lifecycle Scientists create and send service requests directly to an analyst with the click of a button Paper is eliminated when results are obtained the analyst can send the images and chromatograms directly back to
353. p Software to Enterprise Solutions KNOWLEDGE CHEMICAL LABORATORY amp SCIENTIFIC MANAGEMENT BIOLOGICAL MANUFACTURING DATABASES BioAssay amp BioViz Enterprise Research Discovery Development Trials amp Manufacturing Enterprise Solutions include Chem amp Bio Office with Oracle Cartridge and Chem amp Bio Office Workgroup based on SQL Server to help organizations from small workgroups to large enterprises collaborate and share information more effectively Knowledge Management with Notebook including Reaction Explorer CombiChem E Signatures for intellectual property protection and 27 CFR11 Compliance streamlines daily record keeping with rigorous security and efficient archiving Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant SDMS for storage of your data Biological Informatics scientists use BioDraw BioAssay BioSAR and BioViz to set up biological models and visualize information generate spreadsheets correlating structure and activity search by structure and draw and annotate pathways Chemical Informatics including Registration organizes new compound information Inventory provides complete management of chemical and biological inventories including GxP Validation DocManager indexes chemical structures in documents Manufacturing Informatics include Inventory to meet the chemical reagent sample and compound tracking needs of large multi site chemical
354. parts of any Paid Subscription Services and databases at any time 8 Representations and Warranties The User shall indemnify defend and hold CS Merck and or other Supplier harmless from any damages expenses and costs including reasonable attorneys fees arising out of any breach or alleged breach of these Terms and Conditions representations and or warranties herein by the User or any third party to whom User shares her his password or otherwise makes available this Subscription Service The User shall cooperate in the defense of any claim brought against CambridgeSoft Merck and or other Database Suppliers In no event shall CS Merck and or other Supplier be liable for any indirect special or consequential damages such as but not limited to loss of anticipated profits or other economic loss in connection with or arising out of the use of the software by you or the services provided for in this agreement even if CS Merck and or other Supplier has been advised of the possibility of such damages CS and or Merck s entire liability and your exclusive remedy shall be at CS s discretion a return of any pro rata portion of the subscription fee The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to per form any such term or condition by the other party This Agreement shall be
355. plate struc ture Customizing Templates You can modifying any of the template pal ettes and creating your own palette Creating templates and palettes When you create a palette a set of empty tem plate panes appear above the document win dow The templates you draw for your palette appear in these panes After you save your pal ette it will contain the templates you have drawn You can then select your palette from the palette list in the Templates tool To create a template palette 1 Go to File gt Open Style Sheets gt New Tem plates 2 Click in a template pane 3 In the document window draw a new struc ture This will become a template in the new palette 4 Click another template pane and draw another structure as desired 5 After you draw all the templates in your palette go to File gt Save NOTE Save your palette in the Chem amp Bio Draw 12 0 Items folder to ensure that it appears in the Main toolbar 74 Advanced Drawing Techniques Chapter 6 6 In any drawing select the Template tool on the Main toolbar to use you palette Modifying templates and palettes MODIFYING A TEMPLATE 1 Go to File gt Open Templates and choose the palette from the list 2 To modify a template click in its template pane and modify it in the document window as desired ADDING AND DELETING ROWS AND COLUMNS 1 in the palette click in a pane where to add the new column or row or select the one to delete
356. play the Query tools go to View gt Other Toolbars gt Query Tools or click the Query Tools icon on the Main Tool pal ette 2 Click the Free Site tool on the Query tools palette 3 Click the atom to which you want to apply free sites 4 Continue to click the atom to increase the free site number To reduce the number of free sites hold the Alt or Option key while clicking the atom You can also change the free sites using the Atom Properties dialog box or the shortcut menu See Atom Properties on page 120 Reaction Stereo The Reaction Stereo property specifies that the selected atoms are stereocenters in a reaction This property is only meaningful when search ing a database containing chemical reactions Br R Re Rxn Rn NH cl Cl N Ri 1 Figure 10 5 The reaction stereo indicator is circled in this example Option Search Result Any Default Finds all compounds regardless of the stereochemistry at the selected atoms Inversion Finds compounds in which the selected atoms have an inverted stereo configuration after a reac tion Chem amp Bio Draw 12 0 125 User Guide Option Search Result Retention Finds compounds whose selected atoms have an unchanged stereo configuration after a reaction Translation The Translation property specifies what is required to match in the structure query and possible database hits in a Markush DARC query Opt
357. ppears as soon as you add a bond 2 Click again to add a horizontal bond in the opposite direction 3 Repeat steps 1 and 2 with each successive Chemical Warning box until all horizontal bonds are added Figure 5 8 Adding horizontal bonds to the backbone Add labels to the first and last carbon atoms 1 Select the Text tool 2 Click the uppermost carbon atom to create a text box and type CHO 3 Click the lower most carbon atom and type 2 CHO CHOH Figure 5 9 Adding atom labels Chem amp Bio Draw 12 0 49 User Guide Add the repeating labels for the hydrogens and hydroxyls 1 Click the atom shown in A below and type the letter H 2 Double click each of the other atoms labeled as hydrogen in B A B CHO CHO H H H H H CHOH HOH Figure 5 10 Adding repeating atom labels TIP Double clicking with the text tool repeats the last label 3 Click one of the remaining atoms and type 0 0000 4 Double click the remaining atoms to repeat the label A B CHO CHO H OH H OH HO H H OH H OH CHOH HOH Figure 5 11 Completing the drawing 50 Tutorials Chapter 5 View the basic properties of the structure and paste the information into your document 1 Click a selection tool to select the last struc ture drawn If the structure is not selected double click the structure 2 Go to View gt Show Analysis Window 3 In the Analysis window click Paste The analysis information app
358. ppears in the ChemDraw document window ChemScript ChemScript is the cheminformatics Software Development Kit SDK a library of the chemical intelligence programming scripts that are prevalent throughout CambridgeSoft products ChemBioDraw Ultra lets you run these scripts on the drawing in the active win dow You can use the scripts that are provided with ChemBioDraw Ultra customize them or create your own For more information on ChemScript see the ChemScript section in the ChemBioOffice Desktop documentation To run a script on the current drawing 1 Go to File gt Run ChemScript 2 In the Open dialog box select the script and click Open 3 Optional To run the script again go to File gt Re run Previously Selected Chem Script ChemBioDraw Ultra also includes a library of sample scripts for you to use Go to File gt Chem Scripts and select an option Naming Structures Chem amp Bio Draw 12 0 incudes two features to help you generate structures and chemical names Name gt Struct and Struct Name These two features provide unprecedented ability and convenience to create and name structures Collectively these features are called Struct Name Struct gt Name generates systematic names for chemical structures using the Cahn Ingold Prelog rules for stereochemistry Using this option you can generate the name of structures you have drawn Name gt Struct is a comprehensive algorithm for converting E
359. pplication allows users to reformat plates and create daughter plates as well as integrate with liquid dispensers handlers for plate reformatting from pipette log files Compliance Handling FDA regulations in an organization is an area that lends itself to automation Thus systems must be carefully implement ed in order to meet the letter and spirit of FDA guidelines Underlying the system are the controls expected by systems in reg ulated environments audit tables security and validated develop ment methods All transactions on all containers in the system are tracked and audits are customizable for simple presentation Document Management To manage the myriad of documents that get generated in research and regulated environments CambridgeSoft stores documents securely in Oracle where they are indexed by chemistry and text and managed by database security Storing the associated docu ments in Oracle preserves system integrity such that you can back up to a known point and be assured that the documents and data are entirely in sync with each other It also provides tight docu ment security reduces IT overhead associated with file shares and attaches directly to Inventory containers 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP 2 2 2 H E E E 8 X denm ChemBio0ffice i E q Rf de INL
360. process using CambridgeSoft s E Notebook in each subsequent stage adds increasing scientific and economic value by providing workflow automation and knowledge sharing Research and Discovery E Notebook Enterprise is capable of providing knowledge manage ment chemical and biological focused solutions in virtually all areas of discovery Researchers can record and share their experi mental information while protecting intellectual property with digital signatures and 21CFR Part 11 and 37 CFR compliance e Chem Bio Draw draw and annotate molecules reactions and biological pathways ChemACX find and purchase reagents Inventory store and track reagents and samples Registration record newly made compounds BioAssay model complex protocols and record results from biological testing BioSAR generate reports linking activity with structure BioViz analyze biological results Virtually every aspect of discovery process from synthesis planning library enumeration reagent selection primary and secondary screening in vivo testing through to analysis of results and the reporting of data is covered by the integrated E Notebook solution Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Replace Shared Drives with Oracle DMPK Screen
361. ption Services and the Subscriber and any third party to any other applicable civil or criminal penalties under copyright or other laws In the case of an authorized site license a Subscriber shall cause any employee agent or other third party which the Subscriber allows to use the Paid Subscription Service materials to abide by all of the terms and conditions of this Agreement In all other cases only the Subscriber is permitted to access the Paid Subscription Service materials Should CambridgeSoft become aware of any use that might cause revocation of the license they shall notify the Subscriber The Subscriber shall have 90 days from date of notice to correct such violation before any action will be taken 11 Confidentiality The Software contains trade secrets and proprietary know how that belong to CS and are being made available to you in strict confidence ANY USE OR DISCLOSURE OF THE SOFT WARE OR USE OF ITS ALGORITHMS PROTOCOLS OR INTERFACES OTHER THAN IN STRICT ACCORDANCE WITH THIS LICENSE AGREEMENT MAY BE ACTIONABLE AS A VIOLATION OF OUR TRADE SECRET RIGHTS CS Limited Warranty Software Limited Warranty CS s sole warranty with respect to the Software 1s that it shall be free of errors in program logic or documentation attributable to CS which prevent the performance of the principal computing functions of the Software CS warrants this for a period of thirty 30 days from the date of receipt CS s Liability In no event
362. r Menu bar oc BioDraw toolbar d magnification controls Figure 2 1 ChemBioDraw Ultra work area Toolbars To display or hide a toolbar select it in the View menu A check mark appears next to the toolbar name when it is visible The Main Toolbar Most common tools are on the main toolbar These include all tools necessary to draw and edit structures reactions and shapes Go to View gt Show Main Toolbar 8 Getting Started Chapter 2 367 d iy 9 18 h e e a AQ e document window f Main toolbar g status bar Tearing Off Toolbars The main toolbar has other toolbars extending from it You can tear off these smaller tool bars and place them anywhere on your screen To tear off a toolbar 1 Click the arrow on the lower right of a tool in the main toolbar 2 While holding the mouse button down point to the title bar and release the button Docking and Floating You can dock or float any of the standard tool bars When you dock a toolbar it becomes attached to the drawing window Whereas floating toolbars appear in front of the docu ment window and you can move them where you want To dock a toolbar do one of the following Click and drag the toolbar to any edge out side the drawing window Right click the toolbar and select Dock Toolbar To float a toolbar do one of the following Click and drag the docked toolbar into the drawing wi
363. r grid line and align it to the first You can also move selected objects in small increments to align them with the Crosshair using the arrow keys available on some key boards To move 1 point select the objects and press an arrow key To move in 10pt increments hold down the Alt key Windows or the Option key Macintosh while you press the arrow key Chemical Interpretation Chem amp Bio Draw 12 0 converts lines charac ters and other symbols into chemically mean ingful figures as you work This occurs in the background but you can also choose to view this chemical data Chem amp Bio Draw 12 0 uses the data when exporting to file formats that support only a subset of the notations that Chem amp Bio Draw 12 0 does This section describes how Chem amp Bio Draw 12 0 interprets what you draw Chemical Intelligence Chem amp Bio Draw 12 0 was designed as a tool to aid in chemical communication Most chem ists would understand AcOo CgH4COOH immediately whether or not they recognized it as aspirin Most computer programs however require what is known as a complete connec tion table in this case a collection of 21 atoms connected by 5 double bonds and 16 sin gle bonds in a specific pattern Chem amp Bio Draw 12 0 takes what makes sense to a chemist and converts it into what makes sense to another application This chemical intelligence can be used as a sophisticated spelling checker for chemica
364. r modules such as E Notebook to track batch records in manufacturing or to look up reagents from stockroom when planning a synthesis BioAssay when sup porting a high throughput screening environment Registration for tracking proprietary compounds DocManager for linking certifi cates of analyzes analytical reports or other documents associat ed with samples and ChemACX available chemicals database for sourcing new compounds Inventory Enterprise includes plate handling and interfaces to liquid handlers for HTS environments freezer rack layout and targeting for managing biologicals full chain of custody audit trails for GxP compliance request disbursement workflow for use in both manufacturing and pre clinical settings and features tailored to specific material domains e Reagent handling and stockroom reporting e Request disbursement workflow for stockroom and GxP environments EH amp S module and links for MSDS data sheets e Freezer rack layout for biological materials Extensive plate handling for HTS and uHTS settings Inventory is also available in two other editions Workgroup and Desktop Inventory Workgroup is a rich client SQL Server based product geared at managing stockrooms and reagents Inventory Ultra is a desktop edition based on the Workgroup product and includes the ChemACX database us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 7
365. r of atoms When this function is called with just a cell ref erence it displays the total number of atoms in the structure When this function is called with a cell reference and an atomic symbol it dis plays the number of atoms of the given ele ment in the structure Functions CHEM NUM ATOMS cell ref CHEM NUM ATOMS cell ref atomic symbol Examples In cell NUM ATOMS A2 Result 27 In cell NUM ATOMS A2 C Result 12 Number of hydrogen bond acceptors Displays the number of hydrogen bond accep tors based on topology Function CHEM NUM HBACCEPTORS cell ref Example In cell CHEM NUM HBACCEPTORS 2 Result 1 Number of hydrogen bond donors Displays the number of hydrogen bond donors based on topology Function CHEM NUM HBDONORS cell ref Example In cell NUM HBDONORS 2 Result 0 SMILES string Displays the SMILES string for the structure Function CHEM SMILES cell ref Example In cell CHEM SMILES 2 Result O C C CC C1 Cc2c1cccc2 Formal charge Displays the net charge on the molecule Function CHEMPROPSTD FORMAL CHARGE cell ref Example In cell CHEMPROPSTD FORMAL CHARGE A2 Result 1 Does cell have a structure drawing Returns TRUE if the cell has a ChemOffice Excel structure drawing including reaction drawings returns FALSE otherwise Function ISS
366. r partial name view struc ture drawings or use the ChemDraw ActiveX Plugin for structure and substructure searches in formation over 1 617 588 9390 EMAIL info cambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP BioAssay BioViz BioDraw Biological Assay Visualization and Pathways BioAssay Ultra BioAssay Ultra the cornerstone of BioOffice provides flexible storge retrieval and analysis of biological data BioAssay easily manages both high and low throughput biological screening data Designed for complex lead optimization experiments the soft ware supports quick set up of biological protocols automated calculations and curve fitting and the creation of customized structure activity reports BioAssay brings all of this functionality to your desktop BioAssay Ultra compatible with the MSDE database offers a user friendly interface for importing viewing validating and plotting your biological assay data BioViz Combining biological data with chemical structures is of the utmost importance in any drug discovery environment BioViz allows you to visually analyze and perform statistical analysis on structure related data combined with biological data in ChemFinder Users can search over structural and biological data and construct various plots such as scatterplots or histograms The plots are interactive allowing you to select subsets of your data perform statistical analysis filter p
367. ra structures and annotations on the same page StructZ Name contains the leading comprehensive methods for converting chemical structures into chemical names and names to structures It can be used for many types of com pounds including charged compounds and salts highly symmet ric structures and many other types of inorganic and organometallics Struct Name is available in two forms batch application and an interactive version that is also available in ChemDraw Ultra ChemDraw Excel allows the user to create chemically knowledgeable spreadsheets within the familiar Microsoft Excel environment You can build and manipulate chemical structures compute chemical properties and perform database searches us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA e ChemDraw s improved Struct Name feature produces names for more types of compounds Live ChemDraw window embedded in Chem3D application allows simultaneous 2D and 3D editing Chem3D brings workstation quality molecular graphics and rigorous computational methods to your desktop ChemNMR be used to accurately estimate 13C and 1H chemical shifts The structure and the spectrum app
368. rable Architecture The E Notebook architecture is designed to provide organizations with an unparalleled level of flexibility A powerful configuration layer is provided to make it possible to modify substantially the look and feel of the application in order to meet very diverse work flows Detailed workflow support in the same application is pro vided for researchers in early stage discovery through early clinical development even though the requirements for these groups are totallydifferent Beyond configuration a rich API is provided for custom development and system integration E Notebook is also in production with integrated inventory sys tems including CambridgeSoft s Inventory manager as well as in house systems analytical data capturing systems and com pound registration systems E Notebook supports limiting access to certain information at the project or group level if desired as secu rity is granular Information can be shared or secured as desired throughout the framework RESEARCH amp CHEMISTRY APPLIED ANALYTICAL SAMPLE DEVELOPMENT RESEARCH BIOLOGY SERVICES MANAGEMENT E Notebook Drug Safety amp Configured to Comprehensive Toxicology Individual Function Integrated Corporate Workflow Knowledge Development Ed Compliance Requirements Management amp Testing Execution for Development for Research amp _ Trials amp Discovery Trials amp KAFARA Lifecycle Manufacturing 228 Ese
369. rademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Validated for GxP Environments with Audit Trails Container History Store Datafiles with Samples such as Batch and Certificates of Analysis Allows for Flexible Reporting Electronic Data Files In addition to storing moving and disposing containers the application allows users to reformat plates and create daughter plates as well as integrate with liquid dispensers handlers for plate reformatting from pipette log files Compliance Handling FDA regulations in an organization is an area that lends itself to automation Thus systems must be carefully implement ed in order to meet the letter and spirit of FDA guidelines Underlying the system are the controls expected by systems in reg ulated environments audit tables security and validated develop ment methods All transactions on all containers in the system are tracked and audits are customizable for simple presentation Document Management To manage the myriad of documents that get generated in research and regulated environments CambridgeSoft stores documents securely in Oracle where they are indexed by chemistry and text and managed by database security Storing the associated docu ments in Oracle preserves system integrity such that you can back up to a known point and be assured that the documents and data are entirely in s
370. re page is visible in the document window To view the entire drawing area in a document window at once go to View gt Show Document The Magnification control shows the reduction in magnification that was required to have the entire page appear on the screen The Magnification Control Where the magnify and reduce commands let you quickly increase or decrease the magnifi cation the magnification control lets you be more precise using a numeric value To use the magnification controls in Windows select a value from the dropdown list or type a value To use the Magnification controls in the Mac intosh do one of the following Select a value from the drop down list Select Other from the drop down list In the dialog box that appears type a value and click OK Rulers Use the rulers to position objects a measured distance away from a reference point or create objects of an approximate size To set the ruler units go to File gt Preferences and select the General tab Displaying Rulers To toggle rulers on and off go to View gt Show Rulers The rulers appear along the top and left edges of the document window As you move the pointer ruler guides appear on each ruler indicating the position of the pointer Figure B 4 How rulers indicate position A The cursor B Ruler guides indicating vertical and hori zontal location of the cursor When you select an object two guides appear in each ruler The four
371. records Create litter records 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com KNOWLEDGE Analytical Services amp Electronic Journal and Record Keeping Formulation and Validation E Notebook s formulation module is designed to support the dual workflows and regulatory compliance needs of formulation engi neers The flexibility allows any number of formulations to be created and security allows only designated administrators to create a new formulation Analytical amp Quality Control Analytical and Quality Control Laboratories must execute defined procedures to test material that may be administered during pre clinical and clinical trials This work must also be compliant with both GxP and 21 CFR Part 11 Templates for standard analytical tests are provided and analytical procedures are implemented as E Notebook forms which are easily designed and controlled Equally important Votebook provides workflow enforcement that monitors data entry and ensures that the forms are complet ed in sequence for proper method execution For example rules can be configured such that the Day 3 form of a multi day process will not accept any entries unless all required fields on the Day 2 form are first completed The forms can contain automatic calculations to compute totals averages differences and muc
372. resentations enclose only part ofa structure within brackets One or more bonds cross each of the enclosing brackets The crossing bonds match up making the polymer structure more explicit You create a structure based polymer represen tation by enclosing a portion of a structure in brackets with a bracket type of SRU n The subscript n is recommended by IUPAC to denote structure based representations of unknown size but you can edit the text using the text tool A structure based representation of poly vinyl chloride is shown in below CI n You can also use the bracket usage types Crosslink xl Graft grf and Modifica tion mod to represent specific types of repeating units in a structure based representa tion Source based Polymers Source based polymer representations enclose an entire discrete chemical substance in brack ets The mode of polymerization may be obvi ous from context or it might be unknown Source based representations are useful when describing processes where the starting materi 132 Query Structures Chapter 10 als are known but the exact structure of the reaction product is not You can create a source based representation by enclosing a structure in Monomer mon brackets A source based representation of poly vinyl chloride is shown in below Cl Z mon You can use Mer mer brackets for compo nents of a copolymer where those indiv
373. right Bu Figure 6 17 Dragging an arrow 4 Point to the arrow Adjustment handles appear at the ends and in the middle 5 Drag the center up to decrease the curve You may also drag the ends or the point 72 Advanced Drawing Techniques Chapter 6 width adjustment handles to adjust the arrow as necessary NT S 7 f t s Figure 6 18 Adjusting an arrow Create the remaining arrows 1 Select the Draw Curve tool 2 Click just to the right of the O atom label and drag to draw the arrow Release the mouse button x 0 i gt 09 Figure 6 19 Drawing custom arrows o ah Refine the shape of the arrow 1 If the arrow isn t exactly how you want it select the Edit curve tool to change its shape and position When you use the Edit curve tool to select a curve control handles appear that let you change the shape of the curve 2 Click and drag a terminal control handle at the end of the dotted line to change the shape of the curve at a particular location 3 Click and drag a midpoint control handle at the middle of the dotted line to move a particular point in the curve Pi g E B AN Figure 6 20 Adjusting a curve 4 To add an arrow head go to Curves gt Full Arrow at End 5 Press Esc when you are finished 6 Create the remaining arrow as described above to complete the intermediate as shown below 7 o 7 Templates Chem amp Bio Draw 12 0
374. riority rules The CIP rules are designed to order ligands by their priority and determine a descriptor based on the orientation of the ordered ligands in space A ligand is an entity attached to a stereocenter For example a tetrahedral carbon has four ligands corresponding to its four substituents When a tetrahedral carbon is in a ring it still has four ligands the two ligands outside the ring a third consisting of the ring unpeeled clockwise and a fourth consisting of the ring unpeeled counterclockwise Five rules used to determine the priority of ligands are summarized below in simplified form For more detailed information see the references They are checked sequentially as follows Rule 1 Higher atomic number precedes lower Rule 2 Higher atomic mass precedes lower Rule 3 cis precedes trans Rule 4 Like pairs of descriptors precede unlike pairs R S Cahn C K Ingold and V Prelog Specification of Molecular Chirality Angew Chem Int Ed Engl 1966 5 385 414 errata 1966 5 511 Angew Chem 1966 78 413 447 V Prelog and G Helmchen Basic Principals of the CIP System and Proposals for a Revi sion Angew Chem 1982 94 614 631 Angew Chem Int Ed Engl 1982 21 567 583 P Mata A M Lobo C Marshall and A P Johnson The CIP Sequence Rules Analy sis and Proposal for a Revision Tetrahe dron Asymmetry 1993 4 657 668 Rule 5 R precedes S Chem
375. rious individ uals E Notebook can generate customized reports that meaning fully summarize the process in real time These reports are navigable clicking on each step will bring you to the corresponding experiment v Database Structure d 4134 001 Specia E ler BUTOH CAREDNTLL FRDLINE Compou Solvent Temper Time Yield Remarks ih AnPreps A134001 MS Esca Spreadsheet E Yeldirtemaion Ey sospes nd ature Hr 20 scars PEL Bo DMsoF 5 4 D Sarele Shes au J Bo n B eu ena lue Comm 5 cs tomo Boe piso 236 70 2 equis TMG Ens las D DMSO 25 18 89 2 equiv TMG Gama laf 5 4 62 CHA st eD DMSO 40 40 78 CHA sat ear DMSO 50 48 62 2eqdv TMG DOHA sak continuous estrscton with Boe 25 25 80 Regu TMG as Boe l DMSO 40 72 n Bo 25 TB Calo as henihydrate tez Fes Mansa Us 1800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP MAIL CambridgeSoft Corporation 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 Chemical Synthesis Scale up and Analytical DMPK Screening Biology Genetics and Microscopy LIMS Method Execution 21 CFR Part 11 and GxP Assay amp Screen
376. rm Signatures mem 1 Compliant p Bc Em IP Protection Compliance zum p Bc I Enterprise E73 Research Discovery Development Trials Manufacturing Enterprise Solutions include Chem amp Bio Office with Oracle Cartridge and Chem amp Bio Office Workgroup based on SQL Server to help organizations from small workgroups to large enterprises collaborate and share information more effectively Knowledge Management with E Norebook including Reaction Explorer CombiChem E Signatures for intellectual property protection and 27 CFR11 Compliance streamlines daily record keeping with rigorous security and efficient archiving Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant DB for storage of your data Biological Informatics scientists use BioDraw BioAssay BioSAR and BioViz to set up biological models and visualize information generate spreadsheets correlating structure and activity search by structure and draw and annotate pathways Chemical Informatics including Registration organizes new compound information Inventory provides complete management of chemical and biological inventories including GxP Validation DocManager indexes chemical structures in documents Manufacturing Informatics include zzz z to meet the chemical reagent sample and compound tracking needs of large multi site chemical and pharmaceutical laboratories and E Notebook for manufacturing compliance management Des
377. rnative groups feature is avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Alternative groups sometimes called R Groups or G Groups Generic Groups are shown below F 9 NH OH OH F Defining Alternative Groups You can create alternative group definitions R G etc that represent a set of substituents each of which is used in the query To define an alternative group 1 Go to View gt Other Toolbars gt Query Tools to open the Query toolbar 2 Click the Alternative Group query tool and drag with the tool to create an area large enough to draw the alternative groups 3 Type a title such as Rj in the Alternative Group Title box then draw the substructure fragments in the Alternative Group box Figure 10 11 Defining an alternative group Specify where the fragments should bond to the parent structure on the alternative group label by defining Attachment Points 1 Doone of the following Select the diamond shaped Attachment Point tool on the Chemical Symbols palette View gt Other Toolbars gt Chemical Symbols and click a substructure fragment where you want to place the attachment point Point to a substructure fragment where you want to place the attachment point and press the Hotkey period An attachment point symbol appears Chem amp Bio Draw 12 0 135 User Guide 2 Repeat for all fragments Figure 10 12 Adding atta
378. rocess We deliver what you need on time and within budget without surprises Product Development Development Consulting With custom development CambridgeSoft works collaboratively with your team to create a system that meets your needs while execut ing our quality driven software development process We meet your needs on time and within budget without surprises Systems Integration Process improvement often requires integrating systems designed for focused areas of work CambridgeSoft has integrated various E Notebook registration inventory and biological assay systems in a variety of settings Whether these are CambridgeSoft a third party product or an in house developed solution CambridgeSoft has the expertise to unite these systems in order to they improve business processes laboratory efficiency and decision making Application Configuration Your organization will see the benefit from implementing a CambridgeSoft application but would like to customize it for a unique environment Our professional services teams provide those specific features by developing market add ins or other modifications that are supported in the future Systems Deployment Installation and Configuration CambridgeSoft has a tested methodology for system deployment that consists of an IT architectural review a business workflow and process review as relates to specific scientific areas a process integration review and maintenance guideline
379. rojection In this step you will use the Orbital tool to draw the hollow circle that is particular to Newman Projections 1 Click the Orbital tool and select the s Open orbital 2 Point to the left center carbon and drag out ward The size of the orbital is constrained just like bonds are The constraint is based on a percent age of the Fixed Length setting in the Drawing tab of the Document settings dialog box Figure 5 19 Adding an orbital NOTE Orbitals are not automatically grouped with the closest structure To group the orbital with the existing structure so you can move them as a unit go to Object Group Move part of the structure to the front to over lap the orbital 1 Click the Marquee tool The orbital is selected Click in the worksheet to deselect it 2 Point above the structure and drag around the upper fragment to select the three bonds Do not select the bond connecting the two fragments You can Shifttclick on each bond separately if that is easier Rotate the selection 1 Double click the rotation handle to open the Rotate Objects dialog box 2 Type 180 in the Angle text box and click Rotate Figure 5 20 After rotation With the rotated bonds still selected change the layering of the structure so that the selec tion is in front 3 Go to Object gt Bring to Front there is no vis ible change when you do this Move the front part of the structure to create a
380. rom Chem amp Bio Draw 12 0 into another document type that supports OLE you can open the drawing and edit it from within the client application For example to edit a drawing inserted into Microsoft Word for Windows version 6 0 or later do one of the following n Word select the drawing and go to Edit gt CS ChemDraw Drawing Object Double click the drawing The Chem amp Bio Draw 12 0 tools and menus replace those of Word Use the tools to edit the drawing When you have finished making changes click in another area of the Word document The Word tools and menus are restored Edit Graphic Object Macintosh Chem amp Bio Draw 12 0 supports the Edit Graphic Object EGO protocol for editing structures pasted into other types of docu ments When you drag an object from Chem amp Bio Draw 12 0 into another type of document that supports the EGO protocol or copy it with the clipboard you can double click the object and it appears in a Chem amp Bio Draw 12 0 document window When you close the docu ment window any changes you made are reflected in the other document NOTE As ofthis writing versions of Microsoft Word after 5 0 do not support EGO Transferring PostScript Macintosh To obtain the highest quality drawings possible on a PostScript printer Chem amp Bio Draw 12 0 creates a screen representation and a Post Script representation of your drawing For best print quality under all circum
381. round a point If more than one point is selected the exclu sion sphere is around the first selected point and the subse quent points are allowed within the exclusion sphere when the query is evaluated Indicated as a range in A beginning at 0 Defines the normal from a defined plane in the direction of a point Normal Point Defines a point positioned at a specified distance from a first point in the direction of a sec ond point in order or in the direction of the normal Centroid Defines a point positioned at the average position of all other points selected All constraint values can be edited with the text tool Only exclusion spheres show the change visually When you create a point a dialog box is dis played Specify the distance from the first selected point to the calculated point The dis tance may be specified as an absolute value in or as a percentage of the distance between the selected points Negative values indicate that the calculated point is further from the sec ond point than the first point 1s rather than being between them Geometry and constraint objects update dynamically when you change the structure Chem amp Bio Draw 12 0 143 User Guide they cannot be moved independently They may be used with CDX MOL SKC and TGF E ud ISIS Mol Rxn files full read write compatibility they are Do edi not compatible with other formats They can Allowed X X X ho
382. roup the new color is applied and the original shading is ignored A Figure 6 24 A The mitochondrion structure in its default color B The structure colored blue as a group C The structure colored blue as an integral group The new color applies to all structures in the group even if the original colors of the objects in the group are not the same Labels You can use labels to represent atoms and define nicknames that help you draw struc 60 Advanced Drawing Techniques Chapter 6 tures For example you can use the label Ph to represent a phenyl functional group rather than having to draw it Labels are useful for drawing structures quickly or emphasizing a part of your structure NOTE Youcan define nicknames in ChemBio Draw Ultra Chem amp Bio Draw 12 0 Ultra and Chem amp Bio Draw 12 0 Pro only You first add a label to part of your structure You can then expand the label to show the part of the structure the label represents or reduce it back to the label Expanding Labels If your structures contain defined nicknames long atom labels or contracted labels you can restore your structures to the expanded form Contracted Ph CH CHCH CH3 Expanded CH3 When you expand a label that contains a diva lent nickname for example H Ala OH the first attachment is to the character to the left of the nickname H The second attachment is to the character to the right of the nick
383. rs Application Data CambridgeSoftNChemOffice2010 ChemDrawNChemNMR 3 Open a DOS prompt In Windows XP go to Start gt Run and enter cmd in the Run window Click OK In Windows Vista go to Start and enter cmd in the search field Press the Enter key 4 at the DOS prompt navigate to the Chem NMR directory in step 2 5 Enter the command MakeChemNMRUserDB exe lt input file gt lt resource directory gt lt output directory gt where lt input file gt is the full path and filename of the SDF file that contains the correction data resource directory gt and output direc tory are the full path to the ChemNMR directory 6 Restart Chem amp Bio Draw Restoring Default NMR Data If you want to stop using your own data you can restore Chem amp Bio Draw to its original settings To restore the original settings 1 Exit Chem amp Bio Draw 2 Locate the ChemNMR directory Chem amp Bio Draw 12 0 97 User Guide 3 Delete the files Ushiftdb5H1 txt and Example supplementary data Usimilvecx hl The example below represents an SDF file that 4 Restart Chem amp Bio Draw includes supplementary NMR data for two structures The supplementary data follows the structure data and is shaded gray for clarity ACD Labs07190711112D 1414 0 0 0 0 0 0 0 15 V2000 5 7578 1 9992 0 0000C 0 0 0 5 7578 3 3267 0 0000C 0 0 4 6062 1 327
384. rsonal files such as nicknames and standard templates To add a path to a ChemDraw Items folder 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Directories tab 3 Click Add New browse to a location and click OK A new path is added to the list 4 To rearrange the search order click Move Up and Move Down 5 To delete a path click Remove To delete all added paths click Default Paths Accessing Documents Quickly If have a file that you always want readily available to you whenever you launch Chem amp Bio Draw 12 0 save the file in the ChemDraw Items directory Files in this directory appear in the Templates list By default the directory is at C Documents and Settings All Users Application Data CambridgeSoft ChemOffice2010N ChemDraw ChemDraw Items Whenever you need to open the file go to File gt Open Templates and select the file name from the list Customizing Toolbars The look and arrangement of toolbars are defined by a set of XML files If you are famil iar with editing XML files your can modify the toolbar for the way you work You can remove rename and resize buttons change button icons or move them from one toolbar to another You can also create or delete toolbars The toolbar schema The Toolbars xsd file located in the Toolbars directory contains the schema definitions for all the toolbars These include definitions but Chem amp Bio Draw 12 0 159
385. rties from an atom 1 Select the atom 2 Go to Structure gt Atom Properties 3 Click Use Defaults To remove specific properties from an atom do one of the following Right click the atom In the context menu select Atom Properties and choose the prop erties to remove Go to Structure gt Atom Properties and click the atom properties to remove With query indicators shown click the appropriate query indicator with the eraser tool Atom Property Options The properties you can assign to atoms are described below NOTE These features are available in Chem BioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Substituents A substituent is defined as a non hydrogen atom connected by a bond of any order The substituents properties specify the number of substituents that may be bonded to the selected atoms For example in the figure below the carbonyl carbon B has a substituents count of two the alpha carbon A and the aldehyde oxygen hydrogen atoms are not counted The alde hyde oxygen has only one substituent Figure 10 2 Substituent count The substituent count atom property lets you specify the number of bonds to an atom in the target structure This includes bonds already drawn in the query structure The various substituent options are described below Unspecified This is the default The target base determines the search Some databases find compounds with an
386. ry or directly from E Notebook As compounds are registered regardless of whether through the web user interface E Notebook or from a batch file they are com pared for uniqueness via a configurable stereoselective duplicate check and assigned a registry number All information about the compound including its test data and other syntheses is tracked by the registry number and this is used to link data throughout ChemOffice Enterprise Registration Enterprise is the only true n tiered application of its kind that is designed around thin clients and thin servers with interfaces directly to Inventory batch file registration and E Notebook Oracle is supported on a variety of platforms and operating systems Using Oracle secures your pro prietary data through the use of Oracle s role based security and allows all chemical and non chemical data to be stored directly in the Oracle tables EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com INFORMATICS DocManager amp ChemFinder GxP Registration and Enterprise Infrastructure Formulations amp Mixtures Formulation scientists face different challenges from those work ing with individual molecules yet many of the tools they are forced to use emerge from the drug discovery world where single molecule research is the norm Take an essential task such as com pound registration and you will find that most systems are designed for registration of single
387. ry Pro Inventory Pro contains the same features as CambridgeSoft s Inventory Ultra application except without CambridgeSoft s ChemACX database Us 1800 315 7300 INT L EU 00 800 875 20000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 1617 588 9390 EMAIL 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Inventory manages the chemical and reagent tracking needs of laboratories and research centers Inventory maintains its own internal chemical structure database with advanced duplicate checking E Notebook stores Microsoft Office documents ChemDraw structures reaction drawings and related data in a convenient searchable format E Notebook Ultra E Notebook Ultra is an efficient accurate way to store lab note book information It stores Microsoft Office documents ChemDraw structures reaction drawings and related data in an electronic notebook that is searchable by text or chemical struc ture You can organize pages by project experiment or in your own style with the MSDE database CombiChem Excel builds combinatorial libraries E Notebook is configured exactly like a chemist would like his or her own notebook to be Reactions can be easily drawn into the reaction template by either selecting from the generous list of preloaded reagen
388. s 138 Expand Generic Structures 138 R Logic Queries seee 139 Atom to Atom Mapping 140 Stereochemical Symbols 142 SD Propertie S etiri 142 Export Compatibility 144 Chapter 11 Sharing Information 147 The C einst ocn Ra 147 Text Line Notation esses 147 Drag and Drop esee 149 Transferring Objects 149 Embedding Objects Windows 150 pasce Minos 151 TOLD uo scie 152 ISIS compatibility 153 Graphics export border preference 153 File Formats sse 153 iv Contents Transferring Across Platforms 154 Macintosh to Windows sues 155 Windows to 155 Appendix A Preferences and Settings 157 Theme OptlOns suee s conn entrer 157 libcr e 157 Setting Preferences 157 Setting the Default Tool 158 158 New Lines and Closing Text Boxes 158 Highlight Box Tolerance 159 The ChemDraw Items Folder 159 Accessing Documents Quickly 159 Customizing Toolbars 159 The toolbar schem
389. s 4 Click OK These settings affect all new captions or atom labels in the current document To use these settings in new documents save them in a style sheet Windows or stationery pad Macin tosh For more information see Saving Cus tomized Styles on page 161 Formatting a Caption or Label You can set the text format for an individual caption or atom label before you type The for mat change is applied to the current text only To set the text format before you type 1 Select the Text tool and click in the docu ment window A text box appears 2 To set the text format do one of the follow ing Go to Text gt Font Style or Size Set the format options on the Style toolbar 3 Type the text in the text box The format is applied to the typed text Any subsequent text you type is formatted accord ing to the default document settings for the current document 166 Preferences and Settings Appendix A Changing Text Spacing You can change the text settings for a specific caption or atom label The setting change is applied to the selected object only You can also choose whether to have the settings applied to the selected text and to all subse quent text you type To change the text settings for a specific cap tion or atom label 1 Select the text to change with a selection tool 2 Set the appropriate options on the Text menu To change only part of a single caption select the part yo
390. s By care fully following this proven methodology CambridgeSoft installs and configures systems that are easy to maintain and have the flex ibility to accommodate variations in the science or business work flow that come from extensive experience in these areas EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com SERVICES Training amp Support Educational Training and Technical Support Systems Optimization CambridgeSoft s systems deployment team will work with you to make sure that your computing environment has been optimized for high performance Your systems networks applications and databases are assessed and designed to deliver maximum achieve ment Beta and Pre Release Programs Committed to maximizing your productivity through the use of our products as well as exposing you to the newest technologies our beta and pre release programs provide you with first hand product knowledge and allows CambridgeSoft to improve appli cations with your feedback Pilot Software Evaluations It makes sense to pilot an application before a major commitment to an enterprise wide implementation is made CambridgeSoft will work closely with you to plan the evaluation deploy the application and gather feedback regarding systems design APT s and technology specifications Training Effective user administrator and help desk training is often an afterthought in many systems deployments However the produc t
391. s all copies shall bear CambridgeSoft s copyright and proprietary notices You may not make copies of any accompa nying written materials 4 Assignment Restrictions for CD DVD databases You may not rent lease or otherwise sublet the Software or any part thereof You may transfer on a permanent basis the rights granted under this license provided you transfer this Agreement and all copies of the Software including prior versions and all accompanying materials The recipient must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft 5 Revocation of Subscription Access Any use which is commercial and or non personal is strictly prohibited and may subject the Subscriber making such uses to revocation of access to this Paid Sub scription Service as well as any other applicable civil or criminal penalties Similarly sharing a Sub scriber password with a non Subscriber or otherwise making this Paid Subscription Service available to third parties other than the Authorized User as defined above is strictly prohibited and may sub ject the Subscriber participating in such activities to revocation of access to the Paid Subscription Services and the Subscriber and any third party to any other applicable civil or criminal penalties under copyright or other laws In the case of an authorized site license a Subscriber shall cause any employee agent or other third party which the Subscriber allows to us
392. s always a solid or dashed bond NOTE If you click a tautomeric bond solid dashed a second time with the dashed bond tool you create an aromatic double bond dashed dashed Chem amp Bio Draw 12 0 15 User Guide Aligning Double Bonds Double bonds can have one of three align ments relative to other bonds above below and centered Above m uw Below Pis n ud Centered 1 Click the bond tool used to create the exist ing double bond 2 To change the alignment do one of the fol lowing Click the center of the double bond Right click point to Bond Position on the context menu and choose the alignment Moving Atoms 1 Click a selection tool 2 Point to the atom to move A highlight box appears over the atom 3 Shiftt drag the atom Reducing Ring Size To reduce the number of atoms in a ring shift drag one atom on top of another atom For example you can convert cyclohexane to cyclopentane 1 Using a bond tool point to an atom and Shift drag 16 Basic Drawings Chapter 3 2 Release when one atom is on top of the other The bond between the atoms disap pears NOTE You can also move atoms using a selec tion tool See Moving Objects on page 107 Bond Crossing When one bond crosses another you can indi cate which bond is in front 1 Select the object to move to the front 2 Go to Object gt Bring to Front The selected object now appears in fron
393. s in the File menu and then select Amino Acids in the Open Tem plates submenu 4 Introduction Chapter 1 TEXT The manual also uses formatting for different types of information NOTE Notes such as this highlight important information TIP Tips supply useful nice to know infor mation supplemental to the main text CAUTION These indicate important information that if ignored may lead to data loss or other serious problems FEATURE An asterisk indicates that a feature is avail able in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only A note indicates which features are available in ChemBioDraw Ultra 12 0 BioDraw Ultra 12 0 and BioDraw Pro 12 0 only Features not identified with a note or asterisk are available in all versions SHORTCUT KEYS When a shortcut key sequence is given the Windows OS sequence is listed first followed by the Macintosh OS sequence example Use Shift Ctrl G or Shift Command G to ungroup objects Additional Information These resources are available to help you get started with Chem amp Bio Draw 12 0 QUICK REFERENCE CARD The QRCs summarize commands and features The cards are in the back of the Chem amp Bio Draw 12 0 printed manual ONLINE HELP In Chem amp Bio Draw 12 0 press F1 or go to Help gt Contents TOOL TIPS This is the name or a short description of a tool To see a tool tip point to a tool STATUS BAR
394. s and posters ChemDraw Pro will boost your productivity more than ever Draw quality publications with structures reactions chemical queries polymers relative stereochemistry generic structures TLC plate depictions and a biological sequence tool Publish on the web using the ChemDraw Plug in Create precise database queries by specifying atom and bond properties and stereochem istry Display spectra structures and annotations on the same page StructZ Name contains the leading comprehensive methods for converting chemical structures into chemical names and names to structures It can be used for many types of com pounds including charged compounds and salts highly symmet ric structures and many other types of inorganic and organometallics Struct Name is available in two forms batch application and an interactive version that is also available in ChemDraw Ultra ChemDraw Excel allows the user to create chemically knowledgeable spreadsheets within the familiar Microsoft Excel environment You can build and manipulate chemical structures compute chemical properties and perform database searches us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts
395. s color font size and style 1 Select the text object with a selection tool 2 Go to Object gt Object Settings The object dialog box opens 3 Click the Captions or Atom Labels tab 4 Select or modify the settings and click OK 5 The change affects only the selected cap tion or atom label Coloring text You can color some or all captions and atom labels before or after you type them 1 Select the Text tool 2 Click where to place the text 3 Choose a color from the Color menu 4 Type the caption or atom label You can also color one or more captions or labels or selected parts of them 1 Select the text to color 2 Choose a color from the Color menu Caption width To edit the width of a caption 1 Seta caption using the Text tool A resize handle appears on the right side of the cap tion 2 Drag the resize handle to change the width of the caption Deleting Labels To delete an atom label leaving the underlying bonds unchanged do one of the following Select the Eraser tool and click the atom label Chem amp Bio Draw 12 0 17 User Guide Witha selection bond or ring tool selected point to the atom label and press the space bar Backspace or Delete key About Fonts Chem amp Bio Draw 12 0 uses the fonts installed on your computer If you open a document that uses fonts that are not installed the missing fonts are replaced with the installed fonts Hotkeys and Nicknames
396. s diffi cult to manipulate without utilizing special software and Oracle data cartridges define new recognized data types CambridgeSoft s Oracle Cartridge utilizes this technology making it possible to manipulate chemical structure and reaction data from within Oracle improving portability and consistency in applications Since the Oracle Cartridge is accessed through native Oracle SQL programmers can interact with chemical structure data directly in the database The CambridgeSoft Oracle Cartridge supports CDX CDXML MolFile MolFile v 3000 RXN and SMILES formats making it flexible enough to be included with both new and legacy data applications without the need for file conversion Chemical infor mation can originate from either ChemDraw or ISIS Draw E Notebook Inventory or Registration Oracle Cartridge has extensive support for stereochemistry relative stereochemistry tautomers and structure normalization There is also a built in structure enu merator for nonspecific structures basic property predictors nomenclature algorithms names struct and dynamic utilities for molecular file format conversions 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com BioAssay For complicated supporting an ultra HTS platform BioAssay has become the lead ing choice for managing biological experimental data It is the only application of its kind to provide a best of breed solution for b
397. s of potential receptor ligands To create a 3D query you add geome tries lines planes etc and constraints speci fied as ranges to a query structure For example you might specify that two atoms must be between 4 and 5 apart or that two planes must be separated by 80 100 degrees NOTE The 3D Properties feature is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only To assign 3D properties to a structure 1 Select the structure or substructure NOTE Because some 3D properties specify an order use Shift Click to select them in the order you want 2 Go to Structure gt Add 3D Property and select an option from the table below NOTE In the table points may be atoms centroids or points Lines may be lines or normals Option Search Result Angle Defines an angle constraint between three points in order Indicated as a range Defines a dihedral torsional angle constraint among four points in order between two lines or two planes Indicated as a range Dihedral Defines a distance constraint between two points a point and a line or a point and a plane Indicated as a range in Ang stroms Distance Line Defines the best fit line for the selected points Option Search Result Plane Defines the best fit plane for the selected points or for a point and a line Exclusion Defines an exclusion sphere Sphere a
398. s racks plate man agement proprietary compounds and stockroom are just some of the areas where Inventory has been deployed The system manages data associated with both commercially pro cured and internally produced chemical substances from procure ment or initial production through depletion and disposal Inventory Enterprise is an Oracle based ChemOffice Enterprise product and can be used with other modules such as E Notebook to track batch records in manufacturing or to look up reagents from stockroom when planning a synthesis BioAssay when sup porting a high throughput screening environment Registration for tracking proprietary compounds DocManager for linking certifi cates of analyzes analytical reports or other documents associat ed with samples and ChemACX available chemicals database for sourcing new compounds Inventory Enterprise includes plate handling and interfaces to liquid handlers for HTS environments freezer rack layout and targeting for managing biologicals full chain of custody audit trails for GxP compliance request disbursement workflow for use in both manufacturing and pre clinical settings and features tailored to specific material domains e Reagent handling and stockroom reporting e Request disbursement workflow for stockroom and GxP environments EH amp S module and links for MSDS data sheets e Freezer rack layout for biological materials Extensive plate handling for HTS and uHTS set
399. ser across multiple bonds to make multiple deletions Add a bond 1 Click the Solid Bond tool 2 Point to an atom as shown in Figure 6 14 3 Click to add a bond Ure Figure 6 14 Adding a bond Add second and third bonds 4 Point to the same atom as in Step 2 shown in Figure 6 15 and click twice slowly to add two more bonds AA AK Figure 6 15 Adding two bonds to an atom Create a double bond 5 Point to a bond as shown in Figure 6 16 and click The double bond will initially form to the inside Click twice more to move it to the out side as shown in Figure 6 16 B Figure 6 16 Creating a double bond Add an atom label using a hotkey 6 Point to the atom to label shown in figure A below and type the letter o SS 7 Without moving the cursor type a minus The OH label changes to O 99 SS Complete the intermediate structure by adding another OH Chem amp Bio Draw 12 0 71 User Guide 1 Point to the atom shown in Figure A below A B OH SS SS 2 Do one of the following Type the letter o Double click the atom to open a text box and type OH The next step is to add arrows to indicate elec tron flow Y ou add the first arrow using the adjustable Arrows tool and the others using the Draw Curve tool 1 Choose an upward curved arrow from the Arrows palette 2 Point near the double bond where to indi cate the start of electron flow 3 Drag to the
400. ss pro vides a baseline for the future development and deployment of a tailored solution Users gain valuable first hand knowledge in experiencing how the system can help achieve individual and workgroup goals Legacy System Migration Legacy systems with private data structures and architecture can be barriers for migrating systems to new technologies Our con sultants have significant experience with these systems and can successfully migrate chemical and biologial data business work flow and other aspects of legacy informatics technologies 21 CFR Part 11 Compliance and GxP Validation As an integral part in creating 21 CFR Part 11 and GxP validated applications CambridgeSoft offers services to Audit the software and process Create conforming systems design specifications Create IQ OQ PQ documentation Generate test plans and validation matrices Insure systems compliance with functional guidelines Us 1800 315 7300 INT L EU 00 800 875 20000 UK 1 617 588 9300 FAX 44 1223 464900 JP 1 617 588 9390 0120 146 700 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com With custom development CambridgeSoft works collaboratively with your team to create a system that meets your needs while executing our quality driven software development p
401. stances you will want to leave the Include PostScript and Include ChemDraw Laser Prep preferences selected default when you copy and paste to other applications If you never plan to print to a PostScript printer or never plan to give your document to some one who uses a PostScript printer you can turn the preferences off To deselect the PostScript preferences 1 Go to File gt Preferences 2 Deselect Include PostScript and Include ChemDraw LaserPrep To transfer only a few drawings to another document select Include PostScript and Include ChemDraw Laser Prep in the Preferences dialog box The PostScript commands and the ChemDraw Laser Prep are transferred with each drawing The transferred drawings can be printed inde pendently of Chem amp Bio Draw 12 0 If you do not check the Include PostScript check box when printing to a PostScript printer Chem amp Bio Draw 12 0 sends QuickDraw commands to the printer For more informa tion see Printing Background Color on page 171 NOTE You can also transfer drawings to a document in a remote location whose printer cannot be initialized To print to a non PostScript printer deselect Include PostScript and Include ChemDraw Laser Prep on the General tab of the Preferences dia log box Exporting You can export Chem amp Bio Draw 12 0 draw ings in various file formats and open them in other applications Conversely Chem amp Bio Draw 12 0 recognizes a v
402. string paste the string in a document window When the SMILES string is on the Clipboard you can transfer it to another application that can interpret SMILES strings If you copy more than one structure from Chem amp Bio Draw 12 0 to the Clipboard the SMILES string are separated by a period SMILES supports an alternate notation for aro matic structures using lowercase letters Chem amp Bio Draw 12 0 generates this type of SMILES string for any structure drawn with explicit aromatic bonds either by using the Aromatic bond type in the Atom Properties dialog box or by placing a circle within any ring structure 1 1 Figure 11 2 Aromatic SMILES notation cl1cececl 148 Sharing Information Chapter 11 Pasting SMILES You can convert that text string into a struc ture To paste a SMILES string as a structure 1 In the source file where the SMILES string is located select the SMILES string and press Ctrl C 2 In Chem amp Bio Draw 12 0 go to Edit gt Paste Special gt SMILES Creating SLN Strings You can copy a structure to the Clipboard as an SLN string for export to a Tripos application To copy a structure as an SLN string 1 Select a structure 2 Go to Edit gt Copy As gt SLN The Structure is copied to the clipboard as an SLN String C 1 CCCCC21 Figure 11 3 SLN strings Creating InChI Strings Chem amp Bio Draw 12 0 supports the IUPAC International Chemical Identifier InChITM pr
403. synthesis 67 Drawing Reactions cose rotto 67 The Reaction Interpreter ss 70 Drawing an Intermediate 70 73 Selecting a template suus 73 New Drawings esee 73 Fusing a Template sss 74 Customizing Templates 74 Defining Nicknames 75 Attachment points sss 75 Deleting Nicknames sss 76 Troubleshooting Nicknames 76 aD VIGO 77 3D Maodel sss 77 Chem amp Bio 3D Preview options 77 1 78 Chapter 7 Naming Structures eese 79 Struct Name 79 Unsupported structures esses 79 Supported Structures esses 79 Auto Update 81 Name Struct D 82 Converting Names to Structures 82 Chapter 8 Chemistry 85 Chemical Analysis ssaiscsnuseserrsdssadseueciuse 85 ChemBioFinder HotLink 86 Using the ChemBioFinder HotLink 86 Stereochemistry MN NNNM 86 Displaying Stereochemistry Indicators 86 Relative Stereochemistry 88 Chemical Annotations 89 5
404. t The serial number is under the license name MACINTOSH In Chem amp Bio Draw 12 0 for Macintosh choose About CS ChemDraw in the Apple menu The serial number appears at the bottom left Chem amp Bio Draw 12 0 205 User Guide 206 Technical Support Appendix F Shortcuts and Hotkeys Hotkeys are organized into atom labels bond types and functions such as adding a charge or displaying a bond Shortcuts are organized by the menu on which the command is found Nicknames are listed alphabetically by abbre viation in two tables Each listing is a link to a page that displays the structure and full name A navigation bar at the bottom of the page lets you step through the section or return to the listings NOTE You can modify Hotkeys and Nick names The tables in this section refer to the default values Atom Keys Use atom keys to insert atoms in a drawing using your keyboard For example place your mouse over an atom and press 3 to add a tert butyl group A a F f Ph Por4 Ac Aor5 H h Q q Br b I i R n Bu 1 K k S S s Bu p Me m Si S t Bu 3 N n TMS t C c Na N X X Chem amp Bio Draw 12 0 207 User Guide Cl Corl o COOCH3 E D d OTs T CH20H 6 Et e P p B B Bond Hotkeys To modify a bond place your mouse over the bond and select a key listed belo
405. t atom labels 164 text 163 formula command description 85 using 163 fractional character widths 166 framing objects 27 free energy calculation 202 definition 91 free sites drawing 125 226 Index in queries 123 freezing point calculation 202 fusing a template 74 G groups 134 generic groups 134 generic nicknames 119 120 generic structures expanding 138 165 201 202 get ChemDraw Excel list 104 getting started tutorial 45 Gibbs free energy definition 91 Gibbs free energy 112 grouping objects 31 69 groups integral 31 guidelines 70 H hash spacing description 162 H Dot and H Dash 194 specification 194 headers creating 184 heat of formation definition 92 Henry s Law constant 113 Henry s Law 201 Henry s law definition 91 hiding atom numbers 64 hiding palettes 8 hiding query indicators 122 high resolution non PostScript printing 161 high resolution printing 171 highlight box selecting 28 highlight box tolerance 159 home page CambridgeSoft 216 Hotkeys 159 creating 167 hotkeys xml file 167 hotkeys xml file 168 hot linked properties 81 how to use this guide 4 hybrid orbitals drawing 89 hydrogens implicit 123 hyphens font submenu 163 I Draw 157 implicit hydrogens 123 imported objects selecting 28 importing using file formats 151 importing hitlists 104 importing tables 103 importing tables to ChemDraw Excel 103 in Chem amp Bio 3D preview 78 InChl strings copy as 147 InChIKey strings copy
406. t Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com ChemACX is fully structure searchable with more than 1 million products from nearly 500 catalogs ChemACX and the Sigma Aldrich MSDS are updated semi annually to meet the needs of scientists Search by name synonym partial name formula and other criteria to be aware of their proper handling storage disposal and emer gency procedures Helping to fulfill these diverse needs is the Sigma Aldrich MSDS collection The database contains over 130 000 MSDSs for the products of the Sigma Aldrich family of catalogs Sigma Aldrich Fluka Supelco Riedel de Ha n in HTML format With a click of a hyperlink users will be able to view the Sigma Aldrich MSDS in their preferred browser This information is smoothly integrated with the ChemACX database and other enterprise applications Drugs Synonyms and Properties Drugs Synonyms and Properties from Ashgate provides compre hensive coverage of the 8 000 drugs currently in common use worldwide A key component of this reference is the extensive cov erage given to synonyms The electronic version adds almost 70 000 synonyms and trade names that did not fit into the print version This information is also available as an SD file to facilitate in silico research Nanogen Inde
407. t Finds compounds with no allowed additional hydrogen atoms attached to the selected atoms Ring Bond Count The Ring Bond Count specifies the number of bonds attached to an atom that are part of rings of any size For simple cases this also speci Chem amp Bio Draw 12 0 123 User Guide fies the maximum number of rings in which an atom can reside Option Search Result Any Default Finds compounds in which the selected atoms can bea member of any type of ring or a member of no ring at all No ring Finds compounds in which the bonds selected atoms are acyclic As drawn Finds compounds in which the selected atoms reside in the same type and number of rings as drawn Simple ring Finds compounds in which the selected atoms is a member of only one ring the atom has two ring bonds Fusion Spiro or higher Finds compounds in which the selected atoms lies at ring fusions the atom has three ring bonds Finds compounds in which the selected atoms is a member of a spiro or higher linkage the atom has four or more ring bonds 124 Query Structures Chapter 10 Unsaturation The Unsaturation property specifies whether a multiple bond is attached to the selected atoms Option Search Result Unspecified Default Finds compounds regardless of whether a multiple bond is attached to the selected atoms Must be Finds compounds that do not absent have a multiple b
408. t box closing 158 creating new line 158 text conventions 4 text line notation 147 text settings captions font size and style 166 changing defaults 161 text spacing changing 166 theme options 157 TLC 93 234 Index TLC spots crescent 95 custom about 95 custom adding 94 display or set Rf 94 enlarged 95 resizing 95 Rf about 95 tails 95 wide 95 tolerance effect on highlight box 159 tool tips 5 toolbar schema 159 toolbar XML files 160 toolbars customizing 159 icons editing 160 tearing off 8 tools acyclic chain 22 alternative group 135 arc 26 attachment point 135 BioDraw 9 bold bond 13 bold wedge bond 13 bond 13 bracket 26 cyclohexane chair 21 cyclohexane ring 46 51 70 cyclooctane ring 21 cyclopentadiene ring 21 cyclopropane ring 21 dashed bond 13 dative bond 13 dissociation 67 hashed bond 13 hashed wedge bond 13 hollow wedge bond 13 lasso 28 Marquee 28 mass fragmentation 66 67 reaction atom to atom mapping 140 retrosynthesis 67 setting the default tool 158 structure perspective 65 wavy bond 13 topological index 115 topological polar surface area 202 topology 129 total connectivity 117 total valence connectivity 117 trackball tool 65 transferring across platforms 154 transferring information across platforms 154 keeping in scale 149 transferring objects 149 transferring PostScript Macintosh 151 translation 126 translation query property 126 triple bonds drawing 14 tRNA 3 38 troubleshoot
409. t in a single applicationplatform E Notebook both lowers the total investment required to meet these needs and provides a sub stantial increase in productivity due to a far more integratedenvi ronment for scientists and technical staff E Notebook Architecture CambridgeSoft s E Notebook provides a comprehensive easy to use interface designed to replace paper laboratorynotebooks in a variety of settings Underneath is a fullyconfigurable secure sys tem for organizing the flow ofinformation generated by your organization Scientists can enter chemical reactions Microsoft documents Word Excel PowerPoint spectra biological data and images and other types of information and documents It also allows you to search by text chemical substructure metadata tags organizational hierarchy or other keys KNOWLEDGE Overview amp E Notebook s Flexible Architecture E Notebook Architecture E Notebook Enterprise edition is a globally deployable Oracle based application designed for everyone from small research groups to global organizations Oracle Cartridge manages chemical structures and reactions in a common data repository layered with detailed security and is 21CFR Part 11 Compliant audit trails digital signatures The enterprise edition works with procurement databases and services including ChemACX database and Inventory management systems to save time locating chemicals and entering structures Flexible and Configu
410. t of all other objects Similarly go to Object gt Send to Back to position the bond behind other objects NOTE For bonds with 3D coordinates those coordinates determine the visible bond cross ings Bring To Front and Send To Back have no effect Captions and Atom labels You can annotate simple hydrocarbon struc tures using captions and atom labels using the text tool For example you can add the atom label OH and the caption Phenol to a drawing of toluene to create OH Phenol 1 Using the Benzene tool click in the docu ment window A benzene ring appears 2 Using the Solid Bond tool click one of the benzene carbons to create toluene 3 Using the Text tool click the end carbon on the methyl group of toluene A text box appears 4 In the text box type OH 5 Click outside the text box 6 Using the Text tool click below the draw ing and type Phenol in the text box 7 Click outside the text box To edit the caption or atom label click in the text box with the text tool and begin typing Repeating atom labels You can repeat an atom label using the text bond or ring tools 1 Click the Text tool 2 Labela single atom 3 Do one of the following Using the Text tool double click another atom Using a bond ring or acyclic chain tool triple click another atom Formatting captions and labels You can change a variety of text properties such a
411. t of the dative bond g Interpreted ISIS as unspecified cis trans stereochemistry h Converted to Double i Converted to S D j Only M X Q A others written as aliases k Truncated to the first 5 elements 1 Converted to single m An RG file will be created automatically n Converted to non anonymous alternative groups o Lists of greater than 5 elements converted to alternative groups p the low end of the repeat range is always treated as 1 Sharing Information Chem amp Bio Draw 12 0 includes many of the standard system commands for transferring information within and between documents and between Chem amp Bio Draw 12 0 and doc uments created using other applications You can transfer information using the Clipboard drag and drop file formats When you drag and drop Chem amp Bio Draw 12 0 information or use the clipboard the object you are copying can be edited The Clipboard You can use the clipboard to transfer part or all information within an active document win dow between applications on the same com puter or on a network Use the standard copy and paste or cut and paste tools to transfer information to any application that supports these tools The information is transferred as a drawing object Double click the object to edit it in Chem amp Bio Draw 12 0 You may also use the Copy As tool to translate a selected structure to a SMILES SLN or InChI strin
412. t will disassemble the ring into acyclic substructures ChemNMR views remaining parts of the mole cule as substituents of a substructure Each substituent adds to or subtracts from the base shift of the substructure to which it is attached Additivity rules determine the increment of each contribution If an increment for a substit uent cannot be determined ChemNMR uses embedded substituents smaller structural units with the same neighboring atoms Or it will use increments of identical or embedded substituents of a corresponding substructure by assuming that the effects of the substituents are of the same magnitude ChemNMR provides a detailed protocol of the estimation process applied It gives substruc tures as names compound classes in most cases substituents in form of a linear code respectively The data set for the 1H NMR Shift tool cur rently contains 700 base values and about 2000 increments The 13C NMR Shift tool is based on 4000 parameters It also implements models for ethylenes cis trans and cyclohexanes equatorial axial ChemNMR Limitations The program handles the following elements H D He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm m Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg 1 Pb Bi P
413. t0 ibid 291 Baily vo much les sol in ether benzen water 28 mg 100 ml at 25 Us 1800 315 7300 INT L EU 0080087520000 UK MAIL CambridgeSoft Corporation 1 617 588 9300 FAX 44 1223 464900 JP 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 2009 WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA DocManager parses Word Excel and PowerPoint documents including free text and structures e ChemfFinder is tightly integrated with BioSAR BioViz and Oracle Support for advanced form layout and design DocManager Enterprise DocManager parses Microsoft Word Excel and PowerPoint documents including free text and structures DocManager has a web based interface and a file drop folder for quick submissions Oracle Cartridge is compatible with Linux Solaris AIX and Windows and includes structure searching property predictions and nomenclature Web browser based DocManager Enterprise extends the capability of standard search engines to include full free text searching and chemically intelligent structure searching of electronic documents including Text Microsoft Word Excel PowerPoint and Adobe PDE The DocManager Enterprise interface allows users to easily submit documents through a series of simple to navigate web forms When a new document is submitted DocManager builds a free text
414. te a tRNA structure or create virtually any other biological drawing Then just as in the Chem amp Bio Draw 12 0 series you can export your BioDraw series drawings to your presenta tions grant proposals and publications Chem amp Bio Draw 12 0 3 User Guide About This Manual This manual describes all the drawing features in Chem amp Bio Draw 12 0 and how to use them The chapters are organized by task are intended to help you familiarize yourself with Chem amp Bio Draw so that you can start using it as quickly as possible If you are a new user you may want to first read Getting Started on page 7 Then con tinue with Tutorials on page 45 This section demonstrates most of the features of Chem amp Bio Draw 12 0 Some of the material in this manual describes tasks that must be performed in conjunction with other software For example instructions for the ChemDraw Excel describes tasks that must be performed in conjunction with Microsoft Excel For assistance consult the Excel online help or user s guide Conventions for this guide This guide uses several basic conventions to help you quickly learn Chem amp Bio Draw 12 0 INSTRUCTIONS Instructions are designed to help you navigate through menus and screens Items on screen appear in bold For example to open a new drawing template 1 Go to File gt Open Templates gt Amino Acids This step asks you to select the File menu select Open Template
415. tends the capability of standard search engines to include full free text searching and chemically intelligent structure searching of electronic documents including Text Microsoft Word Excel PowerPoint and Adobe PDE The DocManager Enterprise interface allows users to easily submit documents through a series of simple to navigate web forms When a new document is submitted DocManager builds a free text index of the document and extracts chemical informa tion into a chemically aware substructure searchable database Chemical information can originate from either ChemDraw or ISIS Draw DocManager Enterprise includes a batch loading utility for admin istration level users to load multiple documents at one time The system can be configured to submit a batch of documents as one event or as a reoccurring submission to be executed daily The administrator specifies a time for the submission to take place and the location of the files DocManager Enterprise utilizes the search ing intelligence of the ChemOffice Enterprise suite 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com MANUFACTURING Reference Standards Inventory Enterprise CambridgeSoft s Inventory Enterprise application is designed to manage the chemical reagent sample and compound tracking needs of large multi site chemical and pharmaceutical laboratories Inventory Enterprise is Oracle based ChemOffice Enterprise product t
416. ter with a plus sign indicates that you are in the duplication mode of a selection tool 3 Drag the selection rectangle to the right and release the mouse button Figure 6 10 Duplicating a structure NOTE To keep the copy aligned with the orig inal hold Shift while dragging Modify the duplicate structure 1 Select the Solid Bond tool 2 Click the far right bond of the copied struc ture Figure A 3 Point to a terminal carbon shown in A below 4 Click the carbon atom until three bonds appear allowing a pause between each click NOTE If you click too fast the click is inter preted either as a double click which opens a text box or a triple click which duplicates your last atom label A B 0507 Figure 6 11 Adding multiple bonds to an atom 5 Point to a terminal carbon atom shown in Figure A below 6 Type capital OH A B OH Figure 6 12 Adding an atom label Replace the product caption 1 To update the product s caption select the caption with the Text tool and type 4 hydroxy 4 methyl 2 pentanone press the Enter or Return key and type 1 mole 2 Using the Text tool add 2 Mole to the cap tion for the reactant If the captions are not aligned properly under their structures move them using a selection tool Adding a frame To complete the drawing add a shadowed box around it 1 Click the Drawing Elements tool 2 In the Drawing Elements toolbar select
417. the CS License Agreement grants to you personally a license to use one copy of the enclosed Software in accordance with the terms of this Agreement In this case the CS License Agreement does not permit commercial use of the Software nor does it permit you to allow any other person to use the Software 8 Modification of Databases Web sites or Subscription Services CS reserves the right to change modify suspend or discontinue any or all parts of any Paid Subscription Services and databases at any time 9 Termination You may terminate the license at any time by destroying all copies of the Software and documentation in your possession Without prejudice to any other rights CS may terminate this Agreement if you fail to comply with its terms and conditions In such event you must destroy all copies of the Software Product and all of its component parts 10 Revocation of Subscription Access Any use which is commercial and or non personal is strictly prohibited and may subject the Subscriber making such uses to revocation of access to this Paid Sub scription Service as well as any other applicable civil or criminal penalties Similarly sharing a Sub scriber password with a non Subscriber or otherwise making this Paid Subscription Service available to third parties other than the Authorized User as defined above is strictly prohibited and may sub ject the Subscriber participating in such activities to revocation of access to the Paid Subscri
418. the follow ing Select a keyword Select Add New Keyword 4 In the Content text box enter the notes to apply to the object or drawing 5 Click OK Deleting a keyword When you delete a keyword all the notes for that keyword are also deleted 1 In the Annotate dialog box select from the Keyword list the keyword 20 Basic Drawings Chapter 3 2 Click Delete Keyword 3 Click OK Setting Preferences You can specify how the captions and labels look each time you use Chem amp Bio Draw 12 0 Go to File gt Preferences and click the Building Display tab Then choose from these options Automatic Atom Label Alignment when this feature 1s selected the alignment of atom labels will adjust according to the positions of any bonds attached to the atom labels For example CH3 at the left end of a horizontal bond changes to H3C Automatically Rectify Hydrogens in Atom Labels When this feature is selected hydro gens are added or removed from atom labels to preserve standard valences when you change your drawing For example if you increase the bond order in ethane to make ethylene the CH3 changes to CH7 NOTE The Automatically Rectify Hydrogens in Atom Labels feature does not affect Hotkeys To add a substructure press a hotkey To change how many hydrogens are added to the substruc ture select the hotkey again Formatting Atom Labels To set the default character style for
419. the grid 1 Select the Text tool and click where to enter the data Reactants Formula MW Limiting Equivalents Sample Mass Weight Molarity Density Volume Reactant Moles Reactant Mass Figure 8 5 Entering data in the Grid 2 Set the limiting compound If the default setting is incorrect right click or control click the word No in the limiting row and select Set Limiting from the context menu 3 Enter values for all reactants as applicable If you are using units other than the defaults type in the units along with the values no space required Value Comments Limiting Indicates the limiting reactant Only one reactant may be speci fied as limiting Sample Mass Mass ofreactant Default units g Weight Reactant purity Defaults to 100 Volume Default units ml Requires either a molarity or a density to also be entered Molarity Default units M Density Default units g ml After you enter the minimum amount of infor mation required the values are calculated As you continue entering information or edit inputs the values are recalculated NOTE Entered values are in bold face calcu lated values are in normal font Reactants Products Formula C3H602S C2H40 Formula C5H 1903S MW 106 14 44 05 MW 150 20 Limiting Yes No Equivalents Equivalents Expected Mass 114 26g Sample Mass Entered values Expected Moles 760 76mmol Weig
420. this agreement even if CS Merck and or other Supplier has been advised of the possibility of such damages CS and or Merck s entire liability and your exclusive remedy shall be at CS s discretion a return of any pro rata portion of the subscription fee The failure of either party to assert a right hereunder or to insist upon compli ance with any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term or condition by the other party NO OTHER WARRANTIES CS DISCLAIMS OTHER IMPLIED WARRANTIES INCLUDING BUT NOT LIM ITED TO IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE AND IMPLIED WARRANTIES ARISING BY USAGE OF TRADE COURSE OF DEALING OR COURSE OF PERFORMANCE NOTWITHSTANDING THE ABOVE WHERE APPLICABLE IF YOU QUALIFY AS A CONSUMER UNDER THE MAGNUSONMOSS WARRANTY ACT THEN YOU MAY BE ENTITLED TO ANY IMPLIED WARRANTIES ALLOWED BY LAW FOR THE PERIOD OF THE EXPRESS WARRANTY AS SET FORTH ABOVE SOME STATES DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES SO THE ABOVE LIMITATION MIGHT NOT APPLY TO YOU THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE No Waiver The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent fa
421. ting 140 displaying structures 108 dissociation tool 67 distributing objects 32 disulfide bridges 43 document location default 157 posters 184 setting up multi paged 183 document and object settings 160 document settings 172 Adv Synth Catal 174 J Mol Mod 175 new document 176 new slide 176 overview 160 phytomedicine 177 RSC document 178 Science of Synthesis 179 Synthesis Synlett document 180 Verlag Helvetica Chimica Acta 180 Wiley document 181 document setup multiple paged documents 183 posters 184 document window drawing area 183 enlarging 183 reducing 183 documentation web page 215 documents creating 9 saving 10 Does cell have a reaction drawing 111 Does cell have a structure drawing 111 d orbitals drawing 90 DOS prompt 97 double bond changing type 15 drawing 14 orientation 16 double either bonds drawing 14 drawing acyclic chains 22 arcs 26 arrows 67 benzene and cyclopentadiene rings 22 charge symbols 90 192 curves 27 daggers 26 database conventions 189 d orbitals 90 double bonds 14 double either bonds 14 dz2 orbitals 90 fixed angle bonds 13 free sites 125 hybrid orbitals 89 mirror images 59 nonlinear sequences 41 p orbitals 89 quadruple bonds 14 radicals 90 reaction intermediates 70 reactions 67 resonance delocalized rings 22 rings with fixed length 21 sequences 40 sigma orbitals 89 single bonds 13 single lobe orbitals 89 s orbitals 89 stereochemical symbols 142 struc
422. tings Inventory is also available in two other editions Workgroup and Desktop Inventory Workgroup is a rich client SQL Server based product geared at managing stockrooms and reagents Inventory Ultra is a desktop edition based on the Workgroup product and includes the ChemACX database us 1 800 315 7300 INT L 1 617 588 9300 FAX EU 00 800 875 20000 UK 44 1223 464900 JP 1 617 588 9390 0120 146 700 ChemOffice ChemDraw BioOffice BioDraw amp ChemBioFinder are trademarks of CambridgeSoft Corporation 92009 WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA Register and Track Chemicals amp Biologicals throughout the enterprise Freezer Rack Plate Handling Targeting Workflow and HTS Support Supports Barcoding Report Generation amp Audit Trails Registration Enterprise Registration Enterprise is built around robust data model for pure compounds batches salt management automatic duplicate checking and unique ID assignments Built on the Oracle Cartridge it handles stereochemistry including advances in rela tive stereochemistry tautomerization and structure normaliza tion for duplicate checking Using ChemScript it also can enforce drawing business rules such as orientation around a scaffold and functional group normalization Compounds may be entered individually through a user friendly web form through the use of a batch loader from Invento
423. tion CambrideSoft s E Notebook meets these requirements under Good Laboratory and Manufacturing Processes GxP and provides the basis to manage materials and records during clinical trials CambridgeSoft www cambridgesoft com 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA KNOWLEDGE Chemistry amp Electronic Journal and Record Keeping Chemistry Under the R amp D value chain chemistry can be further divided into three separate stages synthetic chemistry research discovery analytical chemistry pre clinical and process chemistry development The flexibility and configura bility of E Notebook enables a successful data repository analysis sharing reporting and searching efficiently and paper free Synthetic Chemistry Synthetic Chemists take advantage of many features tied into a smooth interface within CambridgeSoft s Enterprise E Notebook Reactions are drawn with in place editing stoichiometry grid dynamically fills with the formulas molecular weights and chem ical names Reagents can also be imported from other systems such as available chemicals from the ChemACX database or Registration system CombiChem is one important aspect of library generation for Synthetic Chemists For some E Notebook serves as the complete CombiChem solution taking advantage of features such as the enu
424. tion 91 critical volume 112 crosshair displaying 187 moving 188 using to align objects 188 curved arrows 68 curves 27 autoscaling 150 custom shift correction data 97 customized settings saving 161 customizing ChemDraw 157 saving document settings 161 customizing colors 169 customizing toolbars 159 cycloalkane rings converting to delocal ized rings 22 cyclohexane chair ring tool 21 cyclohexane ring tool 46 51 70 cyclopentadiene ring tool 21 cyclopentadiene ring changing orientation Chem amp Bio Draw 12 0 223 User Guide 22 cyclopentadiene rings drawing 22 cyclopropane ring tool 21 D daggers 26 data Sgroup support for 153 database conventions 189 database conventions in structure drawings 189 dative bonds drawing 15 default atom properties resetting 122 bond properties resetting 128 changing 161 document location 157 file format 157 stationery pad 170 default document location 157 default file format 158 default format changing 165 default open file format 157 default save file format 158 default styles 160 defining alternative groups 135 defining nicknames 75 deleting delete key 30 nicknames 76 objects 30 rows and columns 74 delocalized rings drawing 22 deselecting objects 28 29 deselecting one object 29 detecting errors check structure command 32 error checking 33 disable chemical warnings 33 45 displaying 224 Index cross hairs 187 rulers 187 displaying and prin
425. tion to it To show or hide a window select it in the View menu Windows cannot be docked Three commonly used windows are described 10 Getting Started Chapter 2 below Other windows are described through out this guide The Info Window This window shows the size and position ofthe pointer and anything you have selected To show or hide the window go to View gt Show Info Window Pointer X and Y display the current mouse coordinates dX and dY indicate the change in X and Y of a moved selection Selection X and Y display the position of a selection W and H are the width and height Other Angle is the angle of a bond or rotation of a selection Dist 1s the bond length or the distance a selection has moved When resizing an object indicates the current percentage of the original size Periodic Table Use the periodic table to insert atoms into structures Go to View gt Show Periodic Table Window Click a symbol to highlight the atom and acti vate the Text tool Drag across the table to highlight each atom TO ADD AN ATOM Select it in the periodic table and click an empty space in the document The atom appears in its chemically neutral form For example carbon appears as CH4 and hydrogen appears as H TO LABEL AN ATOM Click an existing unlabeled atom TO CHANGE THE OXIDATION STATE Using the symbol for the atom click the atom in the document window TO CHANGE TO A DIFFERENT ATOM Select the new atom
426. tists with Tel Fax Computers Email Information on new releases Purchase Date Serial No Please copy serial number from CS Installation Instructions 1 Product you are registering check one L Chem amp Bio OfPce Chem amp Blo Draw I BioO ffice 2 BioDraw 2 Chem amp Bio Office Enterprise 2 System running CS software check one J Microsoft Windows A Apple Macintosh 3 Please check one that best describes you Commercial Academic Student 4 Your discipline J Analytical Chem J Physical Chem J Proteomics Inorganic Chem 2 Organic Chem 2 Genomics US 1 617 588 9300 FAX EU 00 800 875 20000 FAX 44 1223 464990 Japan 03 3502 7800 FAX 03 3502 7890 MAIL 100 CambridgePark Drive Cambridge MA 02140 USA 1 Gov t Non Profit Biochemistry Pharmacology A Information Thank You Enjoy your software 1617 588 9390 Web EMAIL www cambridgesoft com info cambridgesoft com QUESTIONNAIRE CPTIONAL Chem amp Bio 3D 2 Inventory I BioAssay 2 EN otebook 2 Chem amp Bio ffice W orkgroup 2 Other Q Other Q Other 2 Chemical Engineering Biology 2 Other CambridgeSoft www cambridgesoft
427. tom label font size is set to 14 points When the atom label is pasted into the destination docu Chem amp Bio Draw 12 0 149 User Guide ment the font size is scaled by a factor of 0 5 to give a final atom label font size of 7 points CAPTIONS Chem amp Bio Draw 12 0 autoscales captions using the ratio of the fixed length in the desti nation document to the fixed length in the source document times the caption font size The font size of the caption can be any size and is not related to the setting in the Settings dia log box This assures that captions are always in proportion to the bonds with which they are pasted For example if the source document has a fixed length of 1 0 cm and the destination doc ument has a fixed length of 2 0 cm and the caption you are pasting is 12 points then the resulting caption size after autoscaling is 2 0 cm 1 0 cm x 12 points 24 points NON BOND OBJECTS AND COLOR All objects that are not affected by settings in the Document Settings dialog boxes such as arrows and boxes are scaled to maintain the same proportions to bonds that were present in the source document With the exception of the foreground and background color the colors present in the selection to be pasted are added to the destina tion document s Color palette if they are not already present up to a maximum of 20 total colors The background color in the destina tion document is unchanged and all objects col
428. tool 2 Click and drag in the document window in the direction you want the chain to grow The number at the end of the chain indi cates how many atoms you have drawn Changing Chain Direction To change the direction as you draw press the Ctrl or Command key while drawing in the direction you want NOTE Release the mouse button before you release the Ctrl or Command key Figure 3 4 Reversing chain direction NOTE If Fixed Lengths is off use Ctrl Alt or Command Option fo reverse chain direction Fixed Angles must be on to reverse direction FIXED LENGTH When Fixed Lengths is on you can drag the pointer on the acyclic chain tool to make any angle relative to the X axis At a constant chain length the positions of the first bond and all subsequent odd numbered atoms depend on the direction you drag Before releasing the mouse button you can change this position by dragging in the opposite direction FIXED ANGLE When Fixed Angles is on the angle the acyclic chain makes relative to the X axis is con strained to 15 degree increments Adding chains to structures To add an acyclic chain to an existing struc ture click an atom in the structure Click and drag in the direction you want to draw the chain Specifying chain length To specify the exact length of a chain before you draw it 1 Select the Acyclic Chain tool 2 Click an existing atom or an empty area ina document window The Add Chain dialo
429. ts Search by name synonym partial name formula and other criteria to be aware of their proper handling storage disposal and emer gency procedures Helping to fulfill these diverse needs is the Sigma Aldrich MSDS collection The database contains over 130 000 MSDSs for the products of the Sigma Aldrich family of catalogs Sigma Aldrich Fluka Supelco Riedel de Ha n in HTML format With a click of a hyperlink users will be able to view the Sigma Aldrich MSDS in their preferred browser This information is smoothly integrated with the ChemACX database and other enterprise applications Drugs Synonyms and Properties Drugs Synonyms and Properties from Ashgate provides compre hensive coverage of the 8 000 drugs currently in common use worldwide A key component of this reference is the extensive cov erage given to synonyms The electronic version adds almost 70 000 synonyms and trade names that did not fit into the print version This information is also available as an SD file to facilitate in silico research Nanogen Index The Nanogen Index contains data on over 1 000 pesticides and other environmental contaminants The database is the up to date and authoritative source for information on all pesticides and agri cultural chemicals in world wide use those which are currently under development in R amp D pipelines and compounds which were once marketed or reached a development status Data fields include chemical struct
430. ts This is s status message only This named Displayed for any Alternative alternative Group Box whose contained The stereocenter Displayedfor any asymmetric group contains structures have varying has no stereo center without attached fragments with numbers of attachment bonds specified wedged hashed dashed or inconsistent points Since all structures bold bonds This is a status valences within an Alternative Group message only and appears Box are to be used inter only when Show Stereochem changeably they must have istry is tuned on and there is at the same number of attach least one other wedged ments This is a status hashed dashed or bold bond message only in the structure This named Displayed for any Alternative There is a Displayed for any alternative Group Box that is empty This valence and odd membered ring drawn as group contains 15 a status message only charge error a delocalized system with a no fragment somewhere in circle in the middle where Part of a mole cule is outside of the alternative group definition Displayed for any Alternative Group Box whose border crosses part of a structure This is a status message only 198 Chemical Interpretation Appendix C this aromatic System there is no corresponding associated charge For example a delocalized repre sentation of cyclopentadiene must include either a negative charge or a multicenter attachment
431. ts on the page 1 Select the object 2 Go to Object gt Center on Page The selected objects move so that the center of the Selection rectangle is positioned at the cen ter of the page 32 Basic Drawings Chapter 3 Aligning Objects You can align objects vertically and horizon tally along their centers or edges NOTE Objects are aligned with the selected object that appears highest on the page To align two or more objects 1 Select the objects 2 Go to Object gt Align NOTE Ifyou select only part of a structure or group with a selection tool only that part is used for the alignment operation but the entire structure or group is moved Distributing Objects Use the distribute commands to position three or more objects an equal distance apart To distribute objects 1 Select the objects For reactants and prod ucts with different shapes select the parts of the objects to distribute 2 Go to Object gt Distribute and choose Verti cally or Horizontally Check Structure You can check structures for errors in valences atom labels and defined nicknames 1 Select a structure part of a structure or caption 2 Go to Structure gt Check Structure If a structure is incorrect a message win dow appears Possible Error in Drawing There are too many bonds to tus unlabeled Carbon 3 To continue checking the structure click Ignore To ignore all subsequent errors click Ignor
432. ts counting down after the first change is made Default File Format 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Open Save tab 3 Click the checkbox next to Use Default File Format in the Saving Files section and choose a format from the list New Lines and Closing Text Boxes The default way to create a new line in a cap tion text box is with the Enter or Return key The default way to create a new line in an atom 158 Preferences and Settings Appendix A label 15 with Alt Enter or Option Return close the text box click outside the text box or select another tool To change the default 1 Go to File gt Preferences TIP In Macintosh OS X the Preferences dia log box is on the ChemDraw menu 2 Choose the appropriate option on the Build ing Display tab To change the Select default for Atom Label text Require Alt Enter or Option Return to Cre ate New Line in Atom Labels Caption text Require Alt Enter or Option Return to Cre ate New Line in Cap tions 3 Click OK Bitmap Fonts Macintosh When text appears in a document on the screen it can appear using either a bitmap or a TrueType font To use bitmap fonts 1f they are available 1 Go to File gt Preferences 2 Select Use Bitmap Fonts When Available Text drawn using Bitmap fonts looks better and appears more quickly than text drawn using TrueType fonts However the size a
433. ts or by entering or drawing one s own chemicals Commonly used reagents can be stored in a separate folder for easy access Another fantastic feature is the pro cedural section This section contains pre written procedural sen tences with the ability to easily drop in the specific names of reagent chemicals present in the reaction One can also easily add other data to the notebook page such as spectra and Microsoft Word or Excel documents CombiChem Excel CambridgeSoft provides you with the tools to effectively plan combinatorial chemistry experiments in Excel The CombiChem Excel add in introduces additional functionality for handling combinatorial chemistry Users can generate products from a reaction and lists of reagents you can view all the products arising from a given reagent or all the reagents of a given product and you can lay out reagent and reaction plates info cambridgesoft com CambridgeSoft www cambridgesoft com SCIENTIFIC The Merck Index NCI AIDS Scientific Reference Chemical Reactions and Patents ChemBioFinder Gateway ChemBioFinder Gateway allows searching of the complete CambridgeSoft reference collection of databases with a single query Search such databases as The Merck Index R amp D Insight for Chemists and Traditional Chinese Medicines with only one click of a search button All results federate back to the spe cific databases for complete information The Merck Index Known for its
434. ture automatically from name 82 triple bonds 14 drawing a structure tutorial 45 drawing area 183 drawing elements autoscaling 150 color 25 fill patterns 25 drawing settings changing defaults 161 margin width effect on atom labels 167 margin width effect on bond crossing 162 duplicating objects 30 Dz2 orbitals drawing 90 E edit 11 editing atom numbers 65 bond type 15 bonds 15 embedded objects 150 generic nickname file 120 query indicators 122 element recognized 193 element lists 130 element Not lists 130 elemental analysis caption 85 description 85 embedding objects 150 empirical formulas 192 enantiomers describing 88 enlarge document window 183 page size 185 error checking 33 error messages 104 197 exact mass caption 85 definition 85 Excel tables exporting 104 expanding labels 60 expanding 60 export compatibility 142 exporting compatibility 144 mapping 142 Chem amp Bio Draw 12 0 225 User Guide query properties 144 query structures 144 using file formats 151 exporting reaction mapping 142 FAQs online accessing 215 technical support 205 file formats CDX 10 MDL MolFile V3000 153 native 10 file formats table 153 Fischer projections tutorial 48 fixed angle bonds 13 fixed lengths description 162 scaling 32 flatten command 66 flip type 134 flush left justification 164 flush right justification 164 font imaging speed 158 new captions 166 footers creating 184 formal charge 111 forma
435. u store the CDS file in the ChemDraw Items folder it appears in the Open Templates menu under the File menu To save a document s setting as a Style Sheet or Stationery Pad 1 Go to File gt Save As The Save As dialog box appears 2 Name the file and change the type in OS X format to CD Style Sheet cds or ChemDraw Stationery pad 3 To save the file in the ChemDraw items folder click Go To ChemDraw Items 4 Click Save Settings From Other Documents To apply document settings to the active win dow that are contained in a different document go to File gt Apply Document Settings from and choose the document from which to apply the settings The settings in the active document window change to those found in the style sheet or sta tionery pad that you choose NOTE Applied settings are for the current document only To make them the default set tings for all documents you open go to File Open Style Sheets To apply the document settings from a docu ment or style sheet not listed in the menu 1 Go to File gt Apply Document Settings from gt Other The select document dialog box appears 2 Open the appropriate folder and select a document or Style Sheet Stationery Pad 3 Click Open Applying Object Settings You can apply settings from another document to selected objects in the current document You can apply the chosen settings to the selected objects only or to all new objects drawn in the
436. u want to change with the Text tool To specify a font and size for selected text do one of the following Choose the font and size from the Text menu Right click and choose the font and size from the right click menu Select the font and size from the drop down menus on the Style Toolbar Fractional Character Widths On the Macintosh you can choose to have the spacing between characters as close to propor tional as possible If you are printing to a Post Script printer this option improves the font appearance To set fractional widths 1 Go to File gt Document Settings 2 Click the Hdr Ftr tab in the Document Set tings dialog box 3 Click Fractional Widths Specifying the Margin Width You can adjust the white space surrounding the atom label so that some of the attached bond is hidden C P d 0278 in 0978 in To adjust the white space 1 Go to File gt Document Settings The Docu ment Settings dialog box appears 2 Click the Drawing tab 3 Type a new Margin Width value 4 Click OK The margin width is applied to all subsequent drawings in the current document Customizing Hotkeys If you are familiar with XML you can custom ize the set of Chem amp Bio Draw Hotkeys You can modify the existing Hotkeys and even cre ate your own To customize Hotkeys you must open the Chem amp Bio Draw Hotkeys text file hot keys xml in a text editor By default this file is
437. ubstructures that match the one you define in the search dialog box 1 Select a cell containing the label Structure 2 Go to ChemOffice12 Search Normal 3 The ChemDraw for Excel dialog box appears 4 Select the Search Tab 5 Click in the empty window and draw the structure for which you want to search 6 Select the Normal tab at the bottom of the dialog box 7 For Search Type select either Full Structure or Sub Structure 8 For Filter Type select to either include or exclude hits 9 Enter a formula query 10 Click Search The hit list is displayed in a column named Match Items matching the search criteria are labeled as TRUE Similarity Searches Perform a similarity search to find structures with features corresponding to a structure of your choosing For more information about similarity searching see the ChemFinder User s Guide To search for similarity 1 Selecta cell containing the label Structure 2 Go to ChemOffice12 gt Search gt Similarity The ChemDraw for Excel dialog box appears 3 Select the Search Tab 4 Click in the empty window and draw the structure for which you want to search 5 Select the Similarity tab 6 Select the Search Type 7 Select the Sort Results order 8 Select the Similarity Percent value 9 Click Search The hit list is displayed in a column named Similarity Items matching the search criteria are labeled as TRUE R Group Analysis An R group analysis
438. uct and includes the CZez4CX database with over 450 cat alogs of chemical reagents The three primary entities in an Inventory system are locations containers and substances Users or administrators con figure a network of locations which represent locations within an organization Containers are created to represent actual containers in your facility Each container is assigned a unique barcode which can be printed using a customized template from the Inventory interface Each container stores a substance Additional text fields are avail able to track other chemical contents such as the solvent Custom fields may also be defined To keep track of substances the system maintains its own internal chemical structure database containing unique substances that can be associated with inventory contain ers Advanced duplicate checking is incorporated in the system Every field in a record including the chemical structure molecu lar formula and molecular weight are searchable The application includes a number of specially designed invento ry search forms Search results are returned in list form and can be exported into a document PDF HTML using the report engine The nventory interface allows for printing labels as well as generating reports Inventory uses a report application that incor porates wizards that allow for the quick creation of simple reports and label templates that can be shared across an organization Invento
439. ucture gt Properties On the Bond Properties tab select the desired properties from the drop down lists and click OK Point to bond and press the Hotkey The Bond Properties dialog box appears In the Bond Properties dialog box select the properties to associate with the selected atoms Click OK The character that appears depends on which query properties have been assigned If more than one property is assigned more than one indicator appears adjacent to the atoms See Query Indicators on page 121 The indicators are Indicator Bond Query Property Any Bond Types Any S D Bond Types Single Double D A Bond Types Double Aromatic Chem amp Bio Draw 12 0 127 User Guide Indicator Bond Query Property S A Bond Types Single Aromatic Rng Topology Ring Chn Topology Chain R C Topology Ring or Chain Rxn Reaction Center Viewing Bond Properties The descriptor for the Reaction Center query property indicates that the property is applied but not the value of the property To find the value of a query bond property set ting 1 Select the bond 2 Doone of the following Right click point to Bond Properties and select to a property Go to Structure gt Bond Properties 128 Query Structures Chapter 10 Removing Bond Properties To remove all query properties from one or more bonds 1 Select the bonds 2 Go to Structure Bond Properties 3 Click
440. uctures 1 Enter the names into cells 2 Select the cells to convert NOTE Optional To keep the original text copy and paste it elsewhere This command can also convert names generated from Excel for mulas 3 Select ChemOffice12 gt Convert gt Name To Molecule Chem amp Bio Draw 12 0 105 User Guide If the cell contains a name supported by Name Struct the structure appears with the given name as the name of the cell 4 To show the structure select the cell and choose ChemOffice12 gt Picture gt Show Saving Structures You can save a chemical structure to a separate file 1 In the spreadsheet select the cell containing the structure 2 Go to ChemOffice12 gt Molecule gt Save The Save to File dialog box appears 3 Select an existing file or enter a new file name and click Save Searching You can search for structures based on the cri teria and search function you use ChemDraw Excel offers three basic search functions Normal search Similarity search R Group Analysis Opening a database Before searching you must open the structure database 1 In Excel go to ChemOffice12 gt New ChemOffice Worksheet 2 Go to ChemOffice12 gt Import Export gt Import Table or Import ChemFinder list and select the file to import After you open a database you can search for structures 106 ChemDraw Excel Chapter 9 Normal Searches Use a normal search to find full structures and s
441. uide SDK 78 Chem 3D 78 ChemBioFinder hotlink 86 ChemBioFinder com 216 ChemClub com 215 ChemDraw customizing 157 Hotkeys file 167 ChemDraw Items folder location 159 ChemDraw items folder description 159 isotope table 126 scripts 161 templates 73 ChemDraw laser prep 171 ChemDraw Excel 103 adding structure files 105 adding structures 105 adding structures as SMILES 105 adding structures by name 105 aligning structures 108 converting old worksheets 104 exporting to SDFiles 104 functions 108 get ChemDraw list command 104 import hit list error messages 104 importing tables 103 naming structures 107 searching 106 starting 103 chemical composition 109 chemical formula 109 chemical intelligence 189 chemical interpretation 189 chemical name structure from 82 chemical properties 92 boiling point 202 chemical properties 91 CLogP 202 CMR 202 222 Index critical temperature 202 critical volume 202 freezing point 202 Gibbs free energy 202 heat of formation 202 Henry s Law 201 ideal gas thermal capacity 202 LogP 201 molar refractivity 202 thermal capacity 202 TPSA 202 using 91 chemical symbols rotating 91 chemical syntax checking 33 chemical warnings 33 disabling 45 suppressing 33 chemically significant text 192 chemicals purchasing online 216 chemistry of ChemDraw 189 chemistry checking 32 ChemNews Com 216 ChemNMR example supplementary data 95 98 NMR shifts 95 using 95 ChemNMR database 97 Che
442. umber See Editing Atom Numbers on page 65 Showing Atom Numbers 1 Select one or more atoms to number 2 While pointing to the selected atoms or structure do one of the following Right click or Control click point to Atom on the context menu and click Show Atom Number Type the HotKey single quote 3 For a single atom do one of the following Right click and click Show Atom Number from the context menu Type the HotKey single quote Hiding atom numbers 1 Select the atoms or structure 2 Right click or Control click point to Atom and deselect Show Atom Number To remove an atom number indicator do one of the following Click the indicator with the Eraser tool Point to the indicator with the Marquee or Lasso tool and type Backspace or Delete Editing Atom Numbers To edit the atom number text and style 1 Select the Text tool 2 Select the atom number indicator and type the changes 2 Click the appropriate position option and enter a value To position Type a value for Position from the atom or bond by angle or by center to the indicator clock center NOTE When you type in a new indicator you reset the counter for that structure to a new style You may then continue numbering in that style with the standard means For example if you type a in a text box then point to another atom and use the context menu or HotKey the atom will be l
443. up Settings You can save page setup settings in a style sheet or stationary pad Whenever you open a style sheet or stationery pad these settings are used The settings are saved in addition to the text settings drawing settings and the color palette 35mm Slide Boundary Guides If you make 35mm slides from a hard copy ofa document or from a screen shot you can dis play boundary lines that appear on your screen positioned at 7 inches and 10 5 inches to match the 2 3 ratio for the 35 mm slide format These guides help you keep your drawing within this region to maintain the proper ratio but are not printed The drawing area of the page must be at least 7 x 10 5 inches for these boundary lines to be visible Chem amp Bio Draw 12 0 185 User Guide To display the 35mm slide boundary lines 1 Go to File gt Preferences 2 Select the Building Display tab 3 Select the Show 35mm Slide Boundary Guides check box 4 Click OK Two 35mm Slide Boundary Guides appear in the same orientation you have chosen in the Page Setup dialog box These guides appear in every document Viewing Drawings You can use a close up view of objects in your reaction scheme to make sure they are properly positioned At times you may want to reduce your view so that you can move groups of objects around the page You can change the magnification to perform these functions using the Magnify and Reduce commands in the View menu the Zoom tool
444. ure Data file SD YES YES Galactic Industries SPC YES NO Windows Metafile YES YES EMF WMF TIFF file TIF YES YES a available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Transferring Across Platforms Use the following procedures to transfer between Macintosh and Windows From the following table determine the versions of the Chem amp Bio Draw 12 0 software between which you want to transfer documents and fol low the appropriate instructions When you transfer files across platforms fonts are not transferred If font in the transferred document is not available Chem amp Bio Draw 12 0 substitutes fonts for those that are avail able on the new platform Macintosh to Windows To open a Chem amp Bio Draw 12 0 file in Win dows that was created on a Macintosh follow the instructions for the appropriate versions shown in the table below Windows to Macintosh To open a Chem amp Bio Draw 12 0 file ona Macintosh that was created in Windows fol low the instructions for the appropriate ver sions shown in th e table below From Macintosh Version To Windows Version Instructions 24 0 24 0 Save as ChemDraw and add cdx to the file name Save as ChemDraw 3 x and add chm to the file name From Windows To Instructions Version Macintosh Version 24 0 24 0 Save as the default ChemDraw lt 3
445. ures and SMILES strings names CAS IUPAC trade the various registration codes assigned to the com pounds RTECS EINECS ELINCS CAS US EPA CA DPR Tarrifs etc Hazard and Safety codes the developing company and use EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com PROFESSIONAL Development Deployment Custom Development and System Deployment When processes and technologies are disjointed organizations lose efficiency and decision making capability Our Professional Services use technology to bring business processes together integrate systems and assist with strategic informatics planning Informatics Planning Strategic and Operational Planning A formal review of the discovery and development process and human system interfaces is mapped to form the basis of a roadmap for successful technology utilization Analysis of the current laboratory and technology workflows An analysis of the current state of the science technology environment including architecture operational processes A view of strategic goals and the barriers to achievement The delivery of a phased technology transition plan Requirements Analysis amp Proof of Concept With years of experience meeting the needs of the scientific com munity CambridgeSoft understands the user The prototyping process allows definition and testing of the functional and techni cal feasibility of potential technology solutions The proce
446. ures for trade or common names NOTE Because the syntax of German is simi lar to that of English Name Struct can also interpret many German names Converting Names to Structures To place a structure into the document window using the structure name you can either type the name or paste the name from the clipboard converting typed names To type the name and convert it to its structure 1 Go to Structure gt Convert Name to Structure The Insert Structure dialog box appears 2 Type the name example 2 bromobenzoic acid NOTE You can also copy a name to the clip board and type Crtl V or Command V to paste the name into the dialog box 3 To place the name below the structure select Paste name below structure 4 Click OK Converting Clipboard names To paste a name on the clipboard as a struc ture 1 Click in the document window 2 Go to Edit gt Paste Special gt Name as Struc ture The structure appears in your docu ment Converting captions You can convert a caption in the drawing area to a structure 1 Select the caption 2 Go to Structure gt Convert Name to Structure Supported Structures Struct Name can name compounds in the fol lowing classes of structures Principal groups in rings and chains Hydrazines S Se and Te Acid Halides Hydroperoxides S Se and Te Acids Ketones and chalcogen S Se and Te analogs Esters Acid Halides Amide derivativ
447. use applications lab instruments and back end data storage to provide a true end to end solution for development and testing Designing workflows and calculations is much faster and requires far less programming using the E Notebook than existing lab infor mation systems End users include scientists and process chemists who scale up and design manufacturing procedures toxicologists who determine the metabolic fate of drug candidates formulation scientists who determine drug dosing and delivery systems as well as many others Trials and Manvfacturing A suitable drug candidate has the desired activity to provide dis ease therapy while still meeting safety requirements can be man ufactured in a cost effective fashion under 21 CFR Part 11 and GMP and is stable formulation conditions The handling of guidelines under normal and storage materials including chain of custody requirements material documentation material workflow such as availability states and recertification dates are tracked and handled by the E Notebook application CambrideSoft s E Notebook meets these requirements under Good Laboratory and Manufacturing Processes GxP and provides the basis to manage materials and records during clinical trials CambridgeSoft www cambridgesoft com 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge Massachusetts 02140 USA KNO
448. usly including check in out move retire delete and update For instance if a request is made of the system that is fulfilled by another user such as dispensing the requester can automatically receive e mail notification of the progress Likewise users can be alerted to pending requests in the system EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com INFORMATICS Inventory amp GxP Document Storage Batch Records Conflict Resolution The Conflict Resolution processes and duplicates in the system automatically You may also search for duplicates at any time If a conflict is found the screen identifies the conflicting field s by highlighting it in red The user has the option to select the existing substance and edit the con flicting substance or create a duplicate substance and resolve the conflict later flags corrects Printed Reports amp Labels The Jnventory interface allows for printing labels and can generate elaborate reports Inventory Desktop and Workgroup use a report engine that incorporates wizards that allow for the quick creation of simple report label templates that can be shared across an organization A user has the ability to design a label based on tem plates for a number of commercially available label sheets e g Avery Dennison The Inventory manager makes extensive use of barcodes and w
449. ute value you choose in the units specified for your document Fixed Length Constrain the bonds drawn to the length you specify This also adjusts the preferred bond length when you use the Clean Up Structure command See Drawing fixed length bond on page 13 and Clean Up Structure on page 62 Bold Width Set the width of the line used when bold and wedge bonds are drawn The 162 Preferences and Settings Appendix A Bold Width setting must be greater than the Line Width setting The end of a wedge is 1 5 times the bold width Line Width Set the width of all bonds lines and arrowheads in the drawing Margin Width Change the amount of space surrounding all atom labels that will erase por tions of the bonds to which they are attached The margin width also determines the amount of white space surrounding the front bonds in a bond crossing See Bond Crossing on page 16 Hash Spacing Set the spacing between the hashed lines used when wedged hashed bonds hashed bonds dashed bonds dashed arrows or dashed curves are drawn 2pt Apt Spt M N SC Units Set the units used in the Object Settings dialog box to centimeters inches points or picas Atom and Bond Indicators Set which indica tors to display See Atom Numbering on page 64 and Stereochemistry on page 86 Configuring Documents 1 Go to File gt Document Settings 2 Click the Drawing tab and configure the s
450. values calculated automatically or prices in a catalog and BioViz will generate an interactive window showing a scatterplot histogram or other useful data graphic The Plot Window the key to data visualization in BioViz is able to show two variables plotted against each other in a scatterplot with each point representing a structure from the current hit list If you for example modify the list by performing a search the plot updates to show the new set of points You can drag a rectan gle around a set of points to select them or zoom in to see them more closely 1 617 588 9390 EMAIL infoGcambridgesoft com WWW www cambridgesoft com 100 CambridgePark Drive Cambridge Massachusetts 02140 USA CambridgeSoft www cambridgesoft com CHEMICAL Inventory Registration Chemical and Biological Inventory Freezer Management Chemicals and Biologicals Inventory is an application designed to manage the chemical and biological reagent tracking needs of laboratories and research cen ters in multiple contexts lab reagents freezers racks plate man agement proprietary compounds and stockroom are just some of the areas where Inventory has been deployed The system manages data associated with both commercially pro cured and internally produced chemical substances from procure ment or initial production through depletion and disposal Inventory Enterprise is an Oracle based ChemOffice Enterprise product and can be used with othe
451. ver you may also use the Software on a porta ble or home computer provided that you use the software on only one computer at a time You may not a electronically transfer the Software from one computer to another b distribute copies of the Software to others or c modify or translate the Software without the prior written consent of CS d place the software on a server so that it is accessible via a public network such as the Internet e sublicense rent lease or lend any portion of the Software or Documentation f modify or adapt the Software or merge it into another program g modify or circumvent the software activation or h reverse engineer the software activation so as to circumvent it The Software may be placed on a file or disk server connected to a network provided that a license has been purchased for every computer with access to that server You may make only those copies of the Software which are necessary to install and use it as permitted by this agreement or are for purposes of backup and archival records all copies shall bear CS s copyright and proprietary notices You may not make copies of any accom panying written materials With a fixed license the software cannot be installed on more than the number of computers equiva lent to the number of fixed licenses purchased For example a 10 user fixed license means the soft ware can be installed on no more than 10 different computers A fixed license cannot be insta
452. vide necessary background about chemicals their prop erties and reactions Development PROFESSIONAL SERVICES Training amp Support CambridgeSoft s scientific staff has the industry experience and the chemical and biological knowledge to maximize the effectiveness of your information systems ENTERPRISE amp Chem amp Bio Office Enterprise Integrated Research Discovery Development Desktop to Enterprise Since the company s founding CambridgeSoft s desktop soft ware starting with its industry leading Chem amp Bio Draw has been the cornerstone application for scientists who draw and annotate molecules reactions and pathways This suite of enter prise applications has developed and now provides solutions in all areas of discovery Research and Discovery Researchers record and share their experimental information using E Notebook while protecting intellectual prop erty with digital signatures and 21 CFR Part 11 compliance They can design both single experiments or design combinatorial libraries of compounds They can find and purchase reagents in ChemACX database store and use them from Inventory record newly made compounds within a proprietary Registration system record the results in BioAssay analyze the results with BioViz and generate reports linking activity and structure with BioSAR can Virtually every aspect of discovery from synthesis planning library enumeration reagent selection pr
453. vidual object within a group move the selection tool over an object until it is highlighted and click once The object is selected not the group To select grouped objects move the selection tool over an object until it is highlighted and double click it Ungrouping Objects To ungroup objects 1 Select a group 2 Go to Object gt Ungroup or right click the group and select Group gt Ungroup Integral Groups To create a group so that individual objects cannot be accessed 1 Select the objects 2 Go to Object gt Group 3 Right click the group and select Group Integral Chem amp Bio Draw 12 0 3l User Guide To restore an integral group to a regular group 1 Select the integral group 2 Right click the group and deselect Group Integral Scaling Objects To resize objects 1 Select the object s 2 Doone of the following Go to Object gt Scale Double click a resize handle The Scale Objects dialog box appears 3 Do one of the following Select the first option to resize the object so that the bonds are the default length Select the second option to resize the object so that the bonds are the length specified in the text box you must enter a value Select the third option to resize the object to a percentage of the current size A value greater than 100 enlarges it a value less than 100 reduces it 4 Click Scale Centering Objects To center an object or group of objec
454. w Change to single bond 1 Change to dashed bond d Change to double bond 2 Change to wavy bond y Change to triple bond 3 Position a double bond to the 1 left Change to quadruple bond 4 Center a double bond Change to bold bond b 208 Shortcuts and Hotkeys Appendix G Position a double bond to the r right Change to wedged bond Ww Bring bond to front f Change to hashed bond H Open a bond properties text box slash or Change to hashed wedged bond h Function Hotkeys Add an attachment point period Add an atom number single quote Add a negative charge Add a positive charge Sprout one bond Sprout two bonds 9 Sprout three bonds 8 Display the Atom Properties dialog box slash or Display the Choose Nickname dialog box equals Open an atom label Enter text box Remove an atom lt Backspace gt label lt Delete gt or lt space gt Shortcuts Below is a list of key combinations for a vari ety of common tasks File Create a new document Ctrl n Open a document Ctrl o Save a document Ctrl s Save a document as Shift Ctrl s Print a document Ctrl p Page setup Shift Ctrl p Close a document Ctrl w Exit Chem amp Bio Draw Alt F4 Edit Cut Ctrl x Copy Ctrl c Paste
455. want a corner of the bracket 3 Drag from one corner of the box diagonally to the opposite corner Daggers To draw a dagger 1 Select a dagger tool from the Brackets pal ette 2 Click in the drawing window NOTE To change the size of the dagger size edit the Atom Label font size in the Text Settings dialog box Framing Objects You can enclose your drawings or group struc tures with a rectangle brackets parentheses or braces To enclose your object 1 Select the drawing to enclose 2 Go to Object gt Add Frame Pen Tools The pen tools are useful for drawing freehand curves and shapes To draw a curve select the Draw curve tool on the Main toolbar or go to View gt Other Toolbars gt Pen Tools Then click and drag your cursor across the drawing win dow NOTE The pen tools are available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Editing curves To edit a curve click it using the Edit Curve tool To change the shape click and drag a handle You can also change its size and color Freehand Shapes To create a closed freehand shape draw a curve and go to Curves gt Closed To add curve properties select Filled Faded or Shaded under the Curve menu To add color select a color in the Color menu CA e d Figure 3 6 freehand curve with different proper ties applied A A simple curve B enclosed C filled D faded E shaded Sel
456. wever be saved in print only formats such as TIFF Ring Bond Count Export Compatibility Any X X X Because query properties are useful only in a No tins bond chemical database you must transfer your A MES X X structures from Chem amp Bio Draw 12 0 into DUC S your search system Not all file formats sup port the same query properties and not all Simple ring X X X chemical databases support the same file for mats Consult the documentation for your data Fusion X X X base to see which file formats are supported The following table lists the query properties Spiroorhigher x X X that Chem amp Bio Draw 12 0 writes to SKC TGF and Clipboard file formats The CDX is Unsaturation the preferred format to use to retain all query properties in a drawing Unspecified X X X Must be absent Exported Query ISIS Mol Rxn Properties Must be present x X X Atom Properties Reaction Change Substituents May be any X X thing U ified X X X nspecifie x Must PESE m T Free Sites b b b specified Upto Reaction Stereo Any X X Exactly Xc Xc Xc Inversion X X Implicit Hydrogens Retention Not allowed X X X a Translation 144 Query Structures Chapter 10 Exported Query Properties Equal Broad Any Narrow Abnormal Valence Not Allowed Allowed Bond Properties Bond Type Single Dashed Hashed Wedged Hashed Bold Wedged Wavy Hollow Wedged Dative Double Double Either
457. wever you can place unattached symbol anywhere and resize them H dot and H dash To represent a hydrogen atom that is coming out of the plane toward you along the Z axis use the H dot symbol To represent a hydrogen atom that is directed backwards into the plane away from you along the Z axis use the H dot symbol To insert H dots and H dashes click an atom 90 Chemistry Features Chapter 8 Lone Pair Use the lone pair symbol to indicate a lone pair of electrons common in Lewis structures 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the lone pair from the palette 2 Click and drag the atom to where you want the lone pair The lone pair is offset from the atom at a fixed position Radical Use the radical symbol to indicate a single non bonded electron 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the radical from the palette 2 Click and drag the atom to where you want the radical symbol Radical Cation and Radical Anion Use the charge radical symbols to represent radicals that are charged 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the symbol from the palette 2 Chck and drag the atom to where you want the symbol To add a radical cation or radical anion symbol in a horizontal orientation click an atom Charge Symbols To draw a charge and associate it with a struc ture 1 Hold down the mouse
458. x The Nanogen Index contains data on over 1 000 pesticides and other environmental contaminants The database is the up to date and authoritative source for information on all pesticides and agri cultural chemicals in world wide use those which are currently under development in R amp D pipelines and compounds which were once marketed or reached a development status Data fields include chemical structures and SMILES strings names CAS IUPAC trade the various registration codes assigned to the com pounds RTECS EINECS ELINCS CAS US EPA CA DPR Tarrifs etc Hazard and Safety codes the developing company and use EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com PROFESSIONAL Development Deployment Custom Development and System Deployment When processes and technologies are disjointed organizations lose efficiency and decision making capability Our Professional Services use technology to bring business processes together integrate systems and assist with strategic informatics planning Informatics Planning Strategic and Operational Planning A formal review of the discovery and development process and human system interfaces is mapped to form the basis of a roadmap for successful technology utilization Analysis of the current laboratory and technology workflows An analysis of the current state of the science technology environment including architecture operational processes A v
459. xample if the command is LABELTEXT the value is the label that appears If the command is BONDDISPLA Y the value corresponds to the bond display type Chem amp Bio Draw 12 0 167 User Guide To create a hotkey that switches to a particular tool choose TOOLMODE for a command and use any of these command names for a value LASSO MARQUEE 3DTRACKBALL MASSFRAG ERASER TEXT SOLIDBOND MULTIBOND DASHEDBOND PEN HASHEDBOND ARROW HASHEDWEDGEDBOND ORBITAL BOLDBOND DRAWINGELEMENTS WEDGEDBOND BRACKET HOLLOWWEDGEDBOND CHEMICALSYMBOLS WAVYBOND ARC TABLE QUERY ACYCLICCHAIN SNAKINGCHAIN TEMPLATE CYCLOPROPANE CYCLOBUTANE CYCLOPENTANE 168 Preferences and Settings Appendix A CYCLOHEXANE CYCLOHEPTANE CYCLOOCTANE CYCLOHEXANECHAIRI CYCLOHEXANECHAIR2 CYCLOPENTADIENE BENZENE TLCPLATE NOTE The features that are available depends on the level of Chem amp Bio Draw 12 0 you are using description This text is useful for whenever you edit the hotkey xml file The tool description explains what each Hotkey does Editing the hotkeys xml file To customize Chem amp Bio Draw Hotkeys 1 Determine whether you want to create or edit an Atom Bond or Generic Hotkey type 2 Open the hotkeys xml file in a text editor 3 Navigate to the appropriate Hotkey list in the hotkeys xm1 file 4 Either add or a new
460. xporting 142 manual 141 reaction 140 margin width adjusting 162 description 162 effect on bond crossings 162 setting 167 specifying 167 margin width specifying 167 Marquee tool 27 28 mass fragmentation tool 66 67 mass charge displaying 85 maximize objects 186 melting point definition 91 messages analysis 197 status 197 mirror images creating 59 modifying a template 74 modifying templates and palettes 74 molar refractivity 202 molar refractivity 113 molecular mass definition 85 228 Index molecular weight caption 85 definition 85 moving atoms 16 30 crosshair 188 objects 30 multi attached atom labels command 61 multi center attachments 63 194 multi center attachments see also variable attachments 63 multi center bonds 63 multiple atoms 61 multiple atoms adding a label of 62 multiple attachment points 136 multiple paged documents setup 183 name inserting as structure 82 of structure inserting 79 name to structure see Name Struct 82 name automatic structure from 82 Name Struct 82 converting 82 limitations 82 naming structures 107 native file format 10 new document 176 new drawings 73 new lines in captions 158 new slide 176 Newman projections tutorial 54 nicknames 18 207 defining 75 defining peptides 43 deleting 76 troubleshooting 76 NMR data restoring default 97 NMR see ChemNMR spectra 95 nonlinear sequences 41 non PostScript printing high resolution 161 Macintosh 151 non r
461. y substitution at this atom other databases including DARC find only compounds with substitution exactly as drawn Free Sites Finds compounds in which the selected atoms may contain a range of substitu ents up to the number specified plus the num ber of bonds as drawn A value of zero finds a substituent count as drawn You can also use the Free Sites symbol in the Query toolbar to apply free sites Up to Finds compounds in which the selected atoms may contain a range of substituents up to the number specified Exactly Finds compounds in which the selected atoms contain the exact number of substituents as specified up to 15 substituents Implicit Hydrogens An implicit hydrogen is a hydrogen atom in which it or its bond 1s implied but is not visi ble An explicit hydrogen and its bond are visi ble A B z Z I NH 27 NN Figure 10 3 A examples of implicit hydrogens B an explicit hydrogen The Implicit Hydrogens property specifies whether additional implicit hydrogen atoms may be attached to the selected atoms If implicit hydrogen atoms are not allowed all valences to that atom must be filled by bonds to non hydrogen atoms NOTE The implicit hydrogens property is available in ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 only Option Search Result Allowed Default Finds compounds regardless of whether hydrogen atoms are attached to the selected atoms No
462. ync with each other It also provides tight docu ment security reduces IT overhead associated with file shares and attaches directly to Inventory containers 1 617 588 9390 EMAIL infoGcambridgesoft com CambridgeSoft www cambridgesoft com DESKTOP 2 2 2 H E E E 8 X denm ChemBio0ffice i E q Rf de INL e En 6 ChemDrow Uira WwinMa 8 e amp Fri Win Wan ChemDraw Sid n Mac LI L L ChenDeaw E E i E ChemBic3D Uro Wa ChemBiesD ActiveX Pro We E Li L ChimBiisl Pus Wee Chief Skl Win L 0 Chemffinder Pro LEE Chenfinder Std We Li tiros 19 BioAssay Pro We a L Ive l dE OE d d del E ded Yhynnkey Free We a ma LNokback BE CNetcbook Pro We LI L Li E ChemDraw Excel We a E Cli NAAR amp Chop Winn a P Hollis tink Winn a Strudure Clean Up a a jajajaja 8 Stokhiomery Grid a s Mose Tool Win Mac s a E Polymer Draw Win Mac m 2 E Sepan lind Wins L Clase sipil Wi
463. you can edit it in its native application from within the drawing window Files When you insert a file the file becomes part of the drawing You can edit it only if it is ina Chem amp Bio Draw 12 0 format To insert a file 1 Go to Edit Insert File 2 In the Open dialog box select the file type from the drop down menu 3 Select the file and click Open The file is embedded in the drawing To insert an object 1 Go to Edit gt Insert Object 2 In the Insert Object dialog box click Create from File 3 Browse to the file you want to insert and click OK NOTE If you select file type All files and choose a file type that Chem amp Bio Draw 12 0 does not support such as TXT you will get an error message and the file will not be embed ded To create a new object 1 Go to Edit gt Insert Object 1 Click Create New 2 Select the Object Type 3 Click OK ISIS compatibility ChemBioDraw Ultra 12 0 ChemDraw Ultra 12 0 and ChemDraw Pro 12 0 support ISIS Sketch including R Logic and leaving groups Attached Data Chem amp Bio Draw 12 0 supports associating text fields with objects such as atoms and bonds by defining a field name The feature is compatible with the Data SGroup in MDL formats and will be converted to Data SGroups when saved in MDL formats if a field name is specified and it is attached to acollection of atoms and bonds or asingle set of brackets
464. ytical Services Sample Management Workflow LIMS Compliant DB Oracle Cartridge BioAssay Enterprise BioDraw BioSAR amp BioViz Registration Enterprise ChemBioFinder Enterprise Compliance E Notebook DocManager Enterprise Enterprise KNOWLEDGE MANAGEMENT Research organizations thrive when information is easily captured well organized and readily avail able Nofebook Enterprise streamlines record keeping with rigorous security and efficient archiv ing and facilitates text and structure searching Nofebook provides organizations with a powerful mechanism to transfer mission criticalwork product from shared drives to a well organized compli ant and searchable Oracle application MS Office chemical structures and workflow support modules are provided for the full range of research and development activities LABORATORY INFORMATICS Laboratory Informatics includes Workflow LIMS for instrumentation automation Compliant DB for stor age of your data and the Oracle Cartridge which is the industry s only enterprise content manage ment system developed by a large pharmaceutical company BIOLOGICAL INFORMATICS Finding structural determinants of biological activity requires processing masses of biological assay data Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models and visualize information The BioViz application allows you to create graphical representations of data

Chem & Bio Draw 12.0 for Windows and Macintosh

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Chem &amp; Bio Draw 12.0 for Windows and Macintosh

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Chem & Bio Draw 12.0 for Windows and Macintosh