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ChemBioDraw v14 User Guide - Welcome

1. Products Formula MV Equivalents FoCompletion Expected Mass 2 76kg 1 09kg Expected Moles 30 00mal 30 0 mol Measured Mass Purity Product Mass Product Moles Co Yield 4 Note Entered values are in bold face calculated values are in normal font You can show or hide rows or columns in the grid To hide a row right click the row and select Hide Row from the context menu Chapter 9 Advanced Drawing Techniques 135 of 315 hemBioD 14 f EMBO AE PerkinElmer For the Better Reactants Products Formula Formula MW MW Limiting mine eo Equivalents Equivalents Hide column oCampletion sample Maf Show All Expected Mass 2 7 Gkg 1 09kg Yo Weight EEM Expected Moles 30 00mol 30 00mol Molarity A Mh ao nici Measured Mass Dansity Purity an tate Volume ee Product Mass Colors Reactant Mirer EREE AT 30 00ma Product Moles Reactant Mass 4 00kg 7 Yield To hide acolumn right click the column and select Hide Column from the context menu To display hidden rows or columns select Show All from the context menu To change the color of the text select Color from the context menu Templates ChemBioDraw includes a library of templates You can use a template as a starting point for a new drawing or to add to an existing drawing A palette is a set of templates The templates you define are not limited to atoms and bonds Templates can also contain captions
2. a b Figure 6 4 a Horizontal orientation b Vertical orientation Chapter 6 Basic Drawings 68 of 315 ChemBioDraw 14 0 i Perkin For the Better 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 key and drag or click in the document window Resonance Structures You can draw cyclopentadiene or benzene in multiple versions The double bonds in the cyclopentadiene or benzene ring tools can be drawn in either of two forms Normally the first bond drawn is a double bond This is the orientation indicated on the cyclopentadiene and benzene Ring tool pointers To draw click in the document window with either the cyclopentadiene or benzene drawing tool To shift the orientation so the first bond drawn is a single bond do one of the following a lt Shift gt drag from the beginning of the first single bond to the end of the single bond a lt Shift gt click ina document window to draw the bond with a fixed length Chains You can draw hydrocarbon chains using either the Acyclic chain tool or Snaking chain tool Use the Acyclic chain tool to draw straight hydrocarbon chains 1 Select the Acyclic chain tool Chapter 6 Basic Drawings 69 of 315 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 indicates how many
3. 2 22 22 c cece cece e ccc cece cece cece eee e eee e cece eee eee e eee ecee cece eceeceeeeeeeeeeeeeees 46 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved i ChemBioDraw 14 0 i Perkin For the Better OIE CUS apa ot odeote ose bt ese bea E sem A E E O 47 INC IONICS ccs axotctenecsca ne edetiveneeeeded nen ounen baheaa neces eun acca sone dane wonsdeanaeeiatesisciese NER 50 Chapter 6 Basic Drawings 00000000000000000000000 cc cee cee cece cece cece cee oaao aooaa raana nonoo anonn 52 BONOS ces pee ae ec ge te ned apes es ees act ee nian ante see retlnc aeewacee secon asoeeen nes ceaeuessaredecsete 52 AO aa A E E E E E A E 57 G PIONS eee e E E E E E eae eee eee 58 Drown i c 9 eee er EE EE ere ae 67 0 0 9 e E E E A ee ee Ene 69 IDOC Ae ee ae al ae are eee 71 Clean Up Structure 2 00 0 ccccc cece ec cece cece nce e cece eee ceeceeceeceecceeceeceeteeceecceeceeceeceeceeees 88 Checking Structures 2 00 2 c occ c ccc cece cece cece cece cece cee cececeeeceeecececceeceeeceeeceeceeecsceceeeeeeeees 89 Chemical WarningS 2 02 cece eee cece cece cece eceec cee ceeceeceeceecceeceeceececcceeceeceeceeceeceeeteeceeees 89 Chapter 7 BioDraw Ultra feature only 0 0 0 02 c ccc c ccc cece eee c cece ec cceceececccecceeceeceecees 92 BioDraw Templates _ 02 2 2 e cece cece cece ec ee cee cece eee e cece cece cee ceeceeeereeceeceececceceeceecer
4. Control well Empty Well E Compound Well Viewing related structures After enumerating an experiment you may view which reactants went into a product or which products arose from a given reactant Chapter 12 ChemDraw Excel and CombiChem 218 of 315 W P l To view the related structures 1 Select a row on an Experiment Reactant or Experiment Product sheet 2 Goto ChemOffice14 gt CombiChem gt Highlight Related Records The related records on the Experiment Reactant and Experiment Product sheet are displayed in color 3 Optional To remove the highlighting from all rows go to ChemOffice14 gt CombiChem gt Highlight gt Unhighlight All Setting preferences Combichem provides several options for you to choose how and whether certain information appears on each work sheet Go to ChemOffice14 gt CombiChem gt Preferencesand select from these options By default row 1 of each Combichem worksheet contains instructions Select deselect this option to display or remove them from each new sheet you create By default the reaction arrow and products appear on each Experiment worksheet Select this option to display the full reaction on each new Experiment sheet Assign rows and columns in plates Choose Left to Right to assign well numbers by row 1 1 1 2 1 3 etc Choose Top to Bottom to assign well numbers by column 1 1 2 1 3 1 etc Assign numeric or alphabetic labels to plate columns Assign numeric or alph
5. Normal Use this for standard text Superscript Reduces the text size by about 25 percent and raises its baseline Subscript Reduces the text size by about 25 percent and lowers the baseline Formula Formats in a way that is appropriate for most chemical formulas that is numbers are subscripted You must however manually capitalize You can also apply multiple styles to different portions of a single caption Chapter 4 Preferences and Settings 27 of 315 ChemBioDraw 14 0 i ean Perkin For the Better Style Indicators Select any text in the document window and navigate to Text gt Style to view the styles that have been applied A check indicates the style applies to all the selected text A hyphen indicates the style applies to some of the selected text Specifying Line Spacing You can specify these types of line spacing Automatic Consistently spaced lines of text based on the height of the tallest character in the caption This is the default line spacing 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 spacing that you specify Aligning Text You can align 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 settings in the Object Settings dialog To open the object settings dialog 1 Select a caption or atom la
6. 3 From the Atom Labels tab check the Show Labels on Terminal Carbons check box To add or remove a terminal carbon label right click the atom and select or deselect Show Terminal Carbon Labels Chemical Significance By default captions are considered to be chemically significant if possible If you create a label for example CH30H you are able to attach bonds to it and it is modified appropriately even though you may have intended it to be alabel not a molecule Moreover it s values are included in the Analysis window The labels with incorrect valences are marked with a red box To remove the red box 1 Select the label with the Selection tool 2 Right click and deselect Interpret Chemically in the context menu 3 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 the values update as you modify the structure For more information about Auto update see Auto Update on page 147 Chapter 6 Basic Drawings 66 of 315 To add analysis data to a caption 1 Right click the structure and select Analysis from the context menu 2 Choose the properties to add Chemical Formula C H C1O Molecular Weight 128 56 Drawing Rings The Main Tools palette contains the following ring tools that enable you to draw ring sizes and types a p gt Orf h See g c 0O O d _ a
7. 3 Select a color and click OK Note The modified colors are saved when you exit ChemBioDraw To apply a color to a structure 1 Select the structure 2 Navigate to Color gt By Element Chapter 4 Preferences and Settings 36 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 L Note The atom colors are not dynamically set hence changing the label does not reset the color The Color Palette Use the 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 You can use style sheets 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 Document and Object Settings on page 23 Note If you Select an object or group that contains multiple colors a check mark appears next to each of the col ors inthe Color menu The check mark alerts you that a change would affect more than one color To change the color palette in the current document 1 Navigate to File gt Document Settings The Document Settings dialog appears 2 Click the Colors tab 3 Click the color to change either background or foreground and select Other The Color dialog opens 4 Click the new color in the Basic Colors or the Custom Colors section 5 Click OK The color changes to the new color and
8. Navigate to Structure gt Bond Properties Removing Bond Properties To remove all query properties from one or more bonds 1 Select the bonds 2 Navigate to Structure gt Bond Properties Chapter 14 Query Structures 240 of 315 W P 3 Click Use Defaults To remove specific bond properties 1 Select the bond 2 Doone of the following Right click to open a context menu point to the appropriate property and click the property to remove Navigate 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 corresponds to the current type of the bond single double and so on as drawn Single all and Dative Finds compounds with the bond type you select for the selected bonds Double or Double Bold Finds compounds whose selected bonds are double Double Either Finds compounds whose selected bonds are double bonds and have either cis trans stereochemical configuration 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 any compound regardless of the bond type of the selected bonds S D Finds compounds whose sel
9. OMe OPh M B OCH OH x SE Figure 14 17 Anonymous alternative groups To create anonymous alternative groups Chapter 14 Query Structures 254 of 315 1 Open an atom label text box 2 Type an open bracket followed by a list of elements fragments nicknames or generic nicknames separated by commas followed by a close bracket T Expand Generic Structures You can generate multiple structures from an abbreviated combinatorial structure with the Expand Generic Structure tool The tool is limited to 500 generated structures For large combinatorial expansions use CombiChem for Excel Four kinds of abbreviated combinatorial definitions may be used Definition Example Alternative Groups and R tables OMe OH NH Anonymous Alternative Groups l Br Cl F Element Lists Variable Attachment Chapter 14 Query Structures 255 of 315 W P l Definition Example Definitions are expanded into multiple complete molecules If more than one site is present in the selection the expan sion includes all permutations of substitutions Expansions are generated in a new document To expand a generic structure 1 Select one or more generic structures to expand _ Note For alternative group R tables you must select the alternative group label and the table must be selected If the label is selected but not the table the label will not change in the expansion and will app
10. m ChemDraw XML a CML Connection Table a ISIS TGF a SIS Reactions MDL MolFile m Accelrys MolFile SMD Other format options are noted in format descriptions Importing You can import graphics or documents from other applications into ChemBioDraw Objects Inserted objects are OLE files and can be resized and rotated but not flipped You also can edit it in its native applic ation from within the drawing window Files Files that you insert become part of the drawing You can edit a file only if it is in a ChemBioDraw format To insert a file 1 Navigate to Edit gt Insert File 2 Inthe Open dialog select the file type from the drop down list 3 Select the file and click Open The file is embedded in the drawing To insert an object 1 Navigate to Edit gt Insert Object 2 Inthe Insert Object dialog click Create from File 3 Browse to the object file and click OK 7 Note You will get an error message if you choose a file type that ChemBioDraw does not support such as TXT To create an object 1 Navigate to Edit gt Insert Object 2 Click Create New 3 Select the Object Type Chapter 15 Sharing Information 272 of 315 W P l 4 Click OK ISIS Compatibility ChemBioDraw Ultra and ChemDraw Pro support ISIS Sketch including R Logic and leaving groups Attached Data Using field names you can attach text to objects such as atoms and bonds The feature is compatible with the Data SGroup
11. 2 Select a color from the Color menu 3 From the context menu choose either Filled Faded or Shaded Drawing Elements Drawing elements are simple shapes such as circles and rectangles Drawing Elements T Oren 7 ea were Sia eo 120 160 On GEO na ae i Oi MONS 3 1 To group drawing elements with a structure navigate to Object gt Group See Grouping Objects on page 85 2 To move an object select it and click and drag it with a Selection tool See Moving Objects on page 83 Circles and Ovals To draw a circle or an oval 1 Select one of the Circle or Oval tools 2 Point where you want the center of the circle or oval 3 Drag outward from the center Resizing and Rotating You can resize and reshape ovals and rectangles for both length and width Circles have only a radius adjustment Rectangles also have corner handles that proportionately adjust length and width Figure 6 6 A rectangle corner handles 1 Point to a shape with its drawing tool or a selection tool to display adjustment handles 2 Click and drag to modify the shape Lines Lines look similar to bonds but behave differently Lines are not included in chemical interpretation a Lines that cross appear solid bonds do not To draw aline Chapter 6 Basic Drawings 75 of 315 W P l 1 Inthe Drawing Elements toolbar select a line tool 2 Click and drag in the drawing window where you want the line Arcs You can
12. CH COOH Deuterium and Tritium appear as one letter symbols Chapter 16 Chemical Interpretation 282 of 315 o 1 CD OD Radicals 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 valence in addition to any charge effects Two examples are Ph Ph gt c er we Ph a Note The lone pair s ymbol is interpreted as a diradical when it is placed next to an unlabeled carbon atom H Dot H Dash H Dot and H Dash symbols from the Chemical Symbols palette indicate the stereochemistry of a single hydrogen atom These symbols are most common in fused systems such as below H H 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 interaction is with a dative bond from the electron pair donor to the acceptor Using a plain bond instead of the dative bond will cause a valence error The dative bond more accurately 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 Prop erties dialog Multi center Attachments Multi center attachments are meaningful
13. Chapter 15 Sharing Information 269 of 315 ChemBioDraw 14 0 i aa Perkin For the Better To create a scrap or clipping file 1 Select an object in a document 2 Drag the selection out of the document window 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 This section explains behaviors of certain features in ChemBioDraw when you transfer objects using the clipboard or drag and drop from one document to another Autoscaling Objects that you transfer are scaled to match the settings of the destination document Bonds When you copy or move a structure to another document the structure adopts the new document s fixed length value but 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 assume 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 to 200 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 assume 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
14. The Toolbar XML Files The Toolbars directory at C Documents and Settings All Users Application Data Cam bridgeSoft Chemoffice2014 ChemDraw GUI Common XML Toolbars contains the subdirectory 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 toolbars The XML file when launched validates itself against the Tool bars xsd file stored online Editing the XML Files You can edit the files using any xml or text editor After you save the files exit and restart ChemBioDraw Your changes will take effect Create a backup of all XML files you intend to edit _ Note All images files you use as icons must be in png format Document and Object Settings You can apply document and object settings to the current document The changes you specify in the document set tings are applicable only within the document and are not applicable throughout the application The changes you spe cify in the object settings are specific to the selected object Settings include Drawing settings Set drawing options such as the fixed length used to draw bonds 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 Chapter 4 Preferences and Settings 23 of 315 ChemBioDraw 14 0 PerkinElmer For the Better Prin
15. Warning Description Stereobond between l A stereobond connects two stereocenters Chiral Atoms An unlabeled atom is attached to exactly two identical bonds that create a 180 degree angle Linear Atom Chapter 6 Basic Drawings 91 of 315 W P l BioDraw Ultra feature only ChemBioDraw includes a variety of tools for drawing metabolic pathways such as enzymes and receptors To dis play the BioDraw toolbars navigate to View gt Show BioDraw Toolbar You can also include standard shapes such as circles ellipses and arrows using the Drawing Elements tool palette or the Arrows tool palette You can also create custom shapes using the Curve tool You can change the color of an object change its line and fill properties and rotate it To create a BioDraw object either click or drag on the page where you want it to appear Clicking gives you the default size and shape dragging lets you not only scale the object but also distort it by dragging on the X and Y axes Linear objects elongate in the direction they are dragged The membrane and protein tools DNA and helix add more sub units as they are dragged and display the subunit count You can also ungroup an object and move or remove unwanted parts and retain only those parts of the object that you require To ungroup an object 1 From the context menu navigate to Group gt Integral 2 Select Group gt Ungroup The object is ungrouped and you can move each object indep
16. in MDL formats and is converted to Data SGroups when saved in MDL formats if a field name is specified and it is attached to a collection of atoms and bonds orsingle set of brackets When attached to a collection of atoms and bonds and a set of brackets a field name is converted to two different Data SGroups To attach data to an object 1 Select the object 2 Navigate to Object gt Attach Data The Attach Data dialog box appears 3 Enter the field name and click OK 4 Enter the data in the text box under the object Note You cannot edit field names in ChemBioDraw While ChemBioDraw allows any field name length MDL formats have their own restrictions Likewise ChemBioDraw allows data to be attached to any object When sav ing to MDL formats data is lost unless the object meets the conditions noted above Modifying Attached Data Two additional commands appear on the context menu when you select attached data Select Linked Objects Changes the selection to include all of the objects associated with the data Position Lets you position the data relative to the associated structure Note Positioning information is lost whenever you save to MDL formats Graphics Export Border Preference You can specify the border size when exporting pictures This preference affects the output of all graphical formats such as WMF PICT EPS TIFF GIF BMP and PNG It applies to the clipboard and saved files The default val
17. m Links to ChemSpider database Names and synonyms m Chemical identifiers such as CAS Registry Numbers and ChemACX IDs The HotLink information and the data itself are continually updated The HotLink displays information for the structure in the document window To open the ChemBioFinder HotLink 1 Select a structure 2 Go to View gt Show ChemBioFinder HotLink Window _ Note To access ChemSpider database click on the value of either InchiKey or Std InchiKey in the Properties table in the ChemBioFinder Hotlink window Chapter 11 Chemistry Features 150 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Stereochemistry ChemBioDraw calculates the absolute stereochemistry according to the Cahn Ingold Prelog CIP priority rules For more information see Cahn Ingold Prelog on page 284 Only tetrahedral and double bond stereochemistry are supported and only non racemic stereochemistry is inter preted Stereochemical indicators for aromatic bonds are not displayed ChemBioDraw uses this notation R S Standard tetrahedral stereochemistry r s Tetrahedral stereochemistry determined by other stereochemical centers For example cis decalin and myo inositol E Z Standard double bond stereochemistry Stereochemistry Indicators ChemBioDraw updates stereochemistry indicators as you change your drawing To include stereochemistry indicators in your drawing 1 Select the structure 2 Right click and sele
18. 100 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 Atom Label Size 10 pt Caption Font Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 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 39 of 315 ChemBioDraw 14 0 J Mol Mod 1 column New Document Chapter 4 Preferences and Settings P gt Perkin For the Better Bond Spacing of length 20 Atom Label Font Atom Label Size 12 pt Caption Font Caption Size 12 pt Drawing Area Width x Height 693 pt x 918 pt Page Size US Letter Reduction 80 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 Times New Roman Atom Label Size 10 pt Caption Font Times New Roman 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 100 Fixed 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 Atom Label Size 10 pt Caption Font Cap
19. H q n 1 is the cyclomatic number of molecular graph nis the number of atoms in the molecular graph S is the sum of all entries in the it row or column of the topological distance matrix of the molecule The distance matrix stores the shortest path between all pairs of atoms Boiling point The boiling point is report in Kelvin A solution boils at a slightly higher temperature than the pure solvent The change in boiling point is calculated using the formula AT Kpm Where K is the molal boiling point constant m is the concentration of the solute expressed as molality and AT is the change in temperature Cluster count Is the number of paths of a given length in the distance matrix Connolly accessible area This is the locus of the center of a spherical probe representing the solvent as it is rolled over the molecular model Connolly molecular surface area The contact surface created when a spherical probe representing the solvent is rolled over the molecular model Units Angstroms2 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 Connolly solvent excluded volume This is the volume of space bounded by the solvent accessible molecular surface Chapter 12 ChemDraw Excel and CombiChem 204 of 315 Critical pressure Reported in bars this is the least applied pressure required at the critica
20. Option Action Show size The current value of the band appears above it The value is always shown on top of the band and is always bound to it If you drag it to another position a tether appears between the band and the text 81 kDa You can move the marker label by pressing the ALT key Set Size A dialog box prompting for the new mass size of the band appears The band will be automatically moved according to its new value You can locate the bands that fall out of range and are hidden Style Specify the style for the selected band There are four pos sible style options available Filled Not filled dashed bold and doubled filled bands The styles can also be combined Set Custom A dialog box prompting you to select a graphic file to be dis Band played as the selected band appears Chapter 11 Chemistry Features 172 of 315 ChemBioDraw 14 0 J PerkinElmer For the Better Option Action Duplicate Band To duplicate a band select a band and CTRL drag Remove Cus The custom band setting is removed for the selec tom Band ted band and the band appears in its default style Delete Band Deletes a band from the lane You can also delete the bands in a lane by hovering over them and pressing Delete Ei Note You can have empty lanes ChemNMR Ultra Feature Using ChemNMR you can estimate and display proton and Carbon 13 chemical shifts for a selected molecule As with ChemBioDraw you can also use ChemBio3D to
21. To change the text settings for a selected caption or atom label 1 Select the text to change with a selection tool 2 Set the appropriate options on the Text menu To change part of a caption select the part you want to change using 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 m Right click and choose the font and size from the context menu Select the font and font size from the drop down list on the Style Toolbar Biopolymer settings You can specify how the sequences and residues appear in either the entire document or for a specific sequence as follows For the entire document go to File gt Document Settings and select the Biopolymer Display tab Foran object use the Object Settings dialog box In the biopolymer Display tab select from these options Residues per line specify the number of residues to be displayed in each line of the sequence Residue per block specify the number of residues to be displayed in each block of the sequence Amino acid Termini Set either NH2 COOH or H OH as the termini in the sequence 7 Note When the termini are displayed using the NH2 COOH style the underlying atoms are actually H and OH The labels are intended to convey whether the N or C terminus is present Since this can be confusing or ambigu ous this display is not recommended and is provided only for compatibility with other produc
22. and down stereochemistries in some unspecified proportion ae Dative bond Often used to indicate polar bonds such as the N O bond in pyridine N oxide _ gt Double bond with cis trans stereochemistry as drawn Double bond with cis trans stereochemistry unknown Tautomeric bond either single or double according to rules of tautomerism Aromatic bond part of a delocalized resonance system Triple bond Quadruple Bond A single bond near a closed circle is recognized as aromatic Chapter 16 Chemical Interpretation 278 of 315 Atom Labels A simple atom label may contain any of the following A single element Cl a An element and some number of hydrogen atoms CHs a A nickname Me Ala AON Repeating units within parentheses CH COOCIOPh A series of any combination of the above ChemBioDraw 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 H CO instead OCH 3 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 atta
23. ethane 1 propane 1 n butane 2 Shape attribute The shape attribute kappa measures the branching of a molecule and is scaled so as to fall between the minimum and maximum values possible for the given order The first order shape attribute counts the number of one bond paths The second order attribute counts the number of two bond paths and so on The first three orders 1 3 are available Shape coefficient The shape coefficient is given by I D R R Where the diameter D is the maximum such value for all atoms and is held by the most outlying atom s The radius R is the minimum such value and is held by the most central atom s Examples values for D methane 0 ethane 1 propane 2 n butane 3 Example values for R Radius methane 0 ethane 1 propane 1 n butane 2 Sum Of degrees Is the sum of degrees of every atom An atom s degree is the number of nonhydrogen atoms to which it is bonded Sum of valence degrees Is the sum of degrees of every atom An atom s valence degree is equal to the sum of its adjacent bonds orders including hydrogens Chapter 12 ChemDraw Excel and CombiChem 209 of 315 W P Topological diameter Is the longest dimension of a molecule Total connectivity Is the connectivity considered over all the heteroatoms Total Valence Connectivity Is the valence connectivity considered over all the heteroatoms Vapor pressure Is the pressure exerted by
24. tion Type and Other Info You can also add your own keywords To annotate a document 1 Navigate to File gt Document Annotations The Annotate dialog opens 2 Select a keyword from the keyword list or add your own keyword 3 To adda keyword a Select Add New Annotation from the keyword list The Add New Annotation dialog appears b Enter a keyword in the New Keyword text field c Inthe New Content text field enter the notes to apply to the document and click Add 4 Click OK Deleting a Keyword When you delete a keyword the annotation for that keyword is also deleted 1 Inthe Annotate dialog box select the keyword from the Keyword list 2 Click Delete Keyword Click Yes when prompted for confirmation 3 Click OK Discarding Changes To retrieve the last saved version of a file navigate to File gt Revert Chapter 2 Getting Started 7 of 315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better Undo Redo and Repeat ChemBioDraw tracks your actions To undo redo or repeat your last action select the appropriate option in the Edit menu The number of actions tracked is limited by the amount of memory RAM and virtual memory available Note ChemBioDraw tracks only those actions you have performed since you last saved the document Saving Documents Navigate to File gt Save Choose a folder in which to store the file Type a file name in the Save As text field Select a file format Click Save
25. 0 6354 in de d r Selection TH s x 32236 in HH Y 1 0856 in Wes 1 4752 in H 1 3901 in Other Angle Dist oi 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 is the bond length or the distance a selection has moved When resizing an object indicates the current percentage of the original size Mirror Images You can reflect structures through planes perpendicular to the X axis or Y axis By copying a structure you can create its mirror image to create stereoisomers To create a mirror image 1 Draw a structure with defined stereochemistry for example wedged bonds 2 lt control gt drag the structure to copy it 3 With the copy still selected navigate to Object gt Flip Horizontal or Flip Vertical You can also use the Flip Hori zontally or Flip Vertically tools on the Object toolbar Chapter 6 Basic Drawings 84 of 315 Deleting Objects To delete selected objects do one of the following Press the lt delete gt key m Navigate to Edit gt Clear Use the Eraser tool Joining Structures To join two structures so that they share a bond 1 Select a bond in the first structure 2 lt Shift gt click to select the bond in the second structure 3 Navigat
26. ChemBioDraw 14 0 i aa Perkin For the Better Wiener index Function MOLECULAR TOPOLOGY WIENER INDEX cell ref Example In cell MOLECULAR TOPOLOGY WIENER INDEX A2 Result 249 MOLECULAR_NETWORKS_LOGP The partition coefficient is a ratio of concentrations of un ionized compound between two solutions The logarithm of the ratio of the concentrations of the un ionized solute in the solvents is called LogP Function MOLECULAR NETWORKS LOGP cell ref Example In cell MOLECULAR NETWORKS LOGP A4 Result 3 019 MOLECULAR_NETWORKS_LOGS MOLECULAR_NETWORKS LogS determines the solubility of a substance measured in mol liter Function MOLECULAR NETWORKS LOGS cell ref Example In cell MOLECULAR NETWORKS LOGS A4 Result 2 029 MOLECULAR_NETWORKS_PKa MOLECULAR_NETWORKS PkKais the negative log of the acid dissociation constant Ka It describes the tendency of compounds or ions to dissociate in solution Function MOLECULAR NETWORKS PKa Cell ref Example In cell MOLECULAR NETWORKS PKa A4 Result 14 834000 Predicting druglikeness Using ChemDraw Excel functions you can create calculators to determine the druglikneness of a structure You can calculate values for the Lipinski rule of five Ghose and Congreve rule of three Chapter 12 ChemDraw Excel and CombiChem 200 of 315 1 The Lipinski rule of five 2 The Ghose modifications 3 The Congreve Rule of Three Lipinski rule of five The Lipinski rul
27. Click in the drawing window where you want the plasmid map The Insert Plasmid Map dialog appears Chapter 7 BioDraw Ultra feature only 98 of 315 3 Inthe Insert Plasmid Map dialog enter the number of base pairs in the map and click OK The plasmid map is drawn Adding Regions Regions represent the fragments in the plasmid You can add as many regions you want to your map To add regions 1 Right click the plasmid map and select Regions in the context menu 2 Inthe Regions dialog enter the base pairs numbers for the start and end of the fragment into their respective fields For example if a fragment includes all base pairs from 1 to 1000 type 1 and 1000 in the text fields 3 For the Start and End base pair numbers for the fragment to appear in the drawing select Add Markers At Region Ends 4 Click Add 5 To add additional regions repeat steps 2 4 6 Click OK Adding Markers Markers let you annotate base pairs in the plasmid map For example to label a base pair or fragment add a marker to it To add a marker 1 Right click the plasmid map and select Markers in the context menu 2 Inthe Markers dialog box enter the number of the base pair for which you want to add a marker in the Position box 3 Inthe Label text box enter the text to identify the marker 4 Click Add 5 Click OK Moving Markers To move a marker label click and drag the label You can also edit the value in the label Resizing Regi
28. F Check Pike imera When Leag M U replete Darg er GLE Dbm Drbe in Other apara Lis Defi Uir Hi 2 To restore the default settings click Use Defaults Theme Options The theme defines the appearance of the ChemBioDraw GUI but does not affect functions By default ChemBioDraw displays the ChemDraw theme The theme ChemDraw Large has larger versions of the icons which are more read able but will require larger screen real estate However other themes such as Draw are also available To change themes 1 Navigate to File gt Preferences and select the General tab 2 Select atheme in the Theme drop down list 3 Click OK Chapter 4 Preferences and Settings 20 of 315 W P Draw The I Draw theme changes the look of the Main toolbar However besides changing the toolbar you can select the l Draw mode to activate two other helpful features Sprout rings as opposed to spiro rings a The default style sheet is changed to I Draw Styles cds To activate the I Draw mode navigate to File gt Preferences and click I Draw Mode Default Document Location You can set the default file directory for each time you open a file To set the default file directory 1 Navigate to File gt Preferences The Preferences dialog 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
29. In Figure b there is more than one attachment point on a single atom in a nickname Chapter 9 Advanced Drawing Techniques 140 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Incorrect Correct n gp man ol 9 l ChemScript ChemScript is the cheminformatics Software Development Kit SDK It contains the programming algorithms com mon throughout PerkinElmer Informatics products With enough knowledge writing software code you can apply ChemScript to create your own scripts to use with ChemBioOffice applications ChemBioDraw Ultra also includes a library of sample scripts for you to use Navigate to File gt ChemScripts and select an option Torun a script on the current drawing 1 Navigate to File gt Run ChemScript 2 Inthe Open dialog select the script and click Open 3 Optional To run the script again navigate to File gt Re run Previously Selected ChemScript ChemScript Integration _ Note ChemScript is an advanced feature intended for users with some programming experience ChemScript lets you add custom functions to ChemBioDraw Custom scripts can be launched from the application and the results of the script are returned to anew ChemBioDraw document Scripts must be written using either PYTHON or NET You use custom scripts to Chapter 9 Advanced Drawing Techniques 141 of 315 m Apply custom drawing rules using ChemScript Launch external applications from ChemBioDraw Automate workflow from C
30. O FP W N gt 7 Note ChemBioDraw uses the CDX file format by default Some other formats store a picture of your drawing but may not store the chemical data associated with a structure in its entirety For example if you save a ChemBioDraw drawing in the eps file format you will store only a picture of the structure without storing the chem ical significance of the connections between atoms and bonds ChemBioDraw lets you add comments or descriptions to the document you save To enable disable document comments 1 Navigate to File gt Preferences The Preferences dialog appears 2 Click the Open Save tab 3 Check the Prompt for Comment check box To add document comments 1 Click Save The Set Document Comment dialog appears Set Document Comment Comment ceel 2 Enter the description and click OK Autosave You can configure ChemBioDraw to periodically save an open document Chapter 2 Getting Started 8 of 315 P gt Perkin For the Better ChemBioDraw 14 0 1 Navigate to File gt Preferences The Preferences dialog appears 2 Click the Open Save tab 3 Check the Autosave Every check box and enter a time frame in minutes for example 5 minutes The time starts after you make your first change to the document Default File Format 1 Navigate to File gt Preferences The Preferences dialog appears 2 Click the Open Save tab 3 Check the Use Default File Format check box in the Saving Files sec
31. Setting preferences You can specify how the captions and labels appear each time you use ChemBioDraw The changes you specify are available throughout the application Navigate to File gt Preferences and click the Building Display tab Then choose from these options Automatic Atom Label Alignment The alignment of atom labels adjusts according to the positions of any bonds attached to the atom labels For example CH at the left end of a horizontal bond changes to AAC 3 Chapter 6 Basic Drawings 65 of 315 Automatically Rectify Hydrogens in Atom Labels Adds or removes hydrogens 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 CH 3 2 Setting Default Atom Label Styles To set the default character style for atom labels navigate to File gt Document Settings and click Atom Labels You changes to CH can modify the font style baseline style and whether terminal carbons and implied hydrogens appear CH c HC CH A c a b To set the default atom label style for a document 1 Navigate to File gt Documents and Settings 2 From the Atoms Labels tab check the Show Labels on Terminal Carbons check box 3 Click OK To set the default atom label style 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 appears
32. Struct Name Ultra Feature 0 00 0 0 0 o lec c cece eee c cece ee ceeceeccecceeceeceecees 143 IC INAIN sate terc ants tote een nine gnacewaceeesanecsuuse cose acauietnusew sue E EEE E 143 NaMe SUCI acca eet eee ee anaes eases se O E EEE ENERE 147 Chapter 11 Chemistry Features 0 00 0 o occ cece eee cece cee cee cece ccc ceeceecceceeccccceceeeceeceeee 149 SUMIG URS AALY SIS sicwcnscncrconeras escencetedeenamdssmuacdtemmice AEE E AAEE AAS NE 149 ChemBioFinder hotlink _ 2 00000 00 022 e occ e eee eee eens 150 Stereochemistry 2 020c06d52icdnanswandedecdeciesend lawccowacedoedaescbodedivdwssscudacesdSoue tesauenddooseenseatdduaes 151 Chemical Annotations cas cela eee eee cete ene ae enenceecuae setae senda seein io geeieeceesseetesane 154 Chemical Properties 2 22 c cece e eee e cece cee cece e cece cece cee ceeceececceceeceececeecceceeseesercesersereeres 158 SD VIEWING rs cesses eer an ace obese Aedes eres in Uae tactanunea eae a semencaseteceobeueenseencscntuse mace 165 sce reese sees E ese cose an cece seen eseeutaeeeanensineeunesaseucotaassonseaunse sec esara seco 168 ChemNMR Ultra Feature 22 20 0002 c cece cee eee ccc e cece cee ceeceeceeccccceeceeceecececeeteeeeeees 173 Chapter 12 ChemDraw Excel and CombiChem _ 2 2 2 22 o eco cece cece eee ec cece eeeccereeeeees 180 Setting Up ChemDraw Excel 20 cece cece eee eee cece ccc ee cee cceccecceccecccecceccecceceeeseeceeces 180 ITEM CASS eae
33. colors boxes arcs orbitals arrows reaction mechanism symbols and curves You can paste pictures from other applications into a template pane You can download templates from the PerkinElmer Informatics web site and use them For more information on available templates and user download able templates see ChemBioDraw template files and BioDraw templates To open a template do one of the following Select a template toolbar from the Main toolbar Navigate to View gt Templates and select a template toolbar from the list To add to a drawing using a template 1 Select the required template from the template toolbar 2 Inthe document window click and drag the mouse until the template is oriented the way you need Tip To modify the template size press the lt ALT gt key while drawing it You can also use the templates to add structural features to existing drawings To add structural features to existing drawings 1 Select the required template from the template toolbar 2 Click an atom or bond in the existing drawing to add the template structure Chapter 9 Advanced Drawing Techniques 136 of 315 Customizing Templates You can modify a template palette to create your own palette When you create a palette a set of empty template panes appear above the document window After you save your palette it contains the templates you have drawn You can then select your palette from the palette list in the Templates tool Y
34. 1 Hotkeys that sets the label for the single letter amino acids DNA Hotkeys that sets the label for the DNA sequence RNA Hotkeys that sets the label for the RNA sequence m Generic Hotkeys that 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 is the keyboard key that invokes the command You can assign the same key to different functions as long as the functions are defined for 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 _ Note Hotkeys are case sensitve For example you can define the hotkeys S and s to different functions within an object type 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 pre cedence Chapter 4 Preferences and Settings 33 of 315 P gt Perkin For the Better ChemBioDraw 14 0 Command Command is any one of the predefined command names All available commands are described in the hotkeys xml file The command ID s are defined based on the object types as follows Object Type Command ID Description Atom LABELTEXT Sets
35. 210 COMIC GI aoaea ee ater cecte sae mae cen eee ey seen cenes ceemeeseueeemee itd toe EE A 212 Chapter 13 ChemScript aaan anaana ccc eee ee cee cece cece cece eee eceeceecceeceeceeceecceceeeeeeseesees 220 Why use ChemScript 2 20 0 ccc cece cece ee cece cece cece cece ceecceecececececcecceecceecececeeceeeeeeeceeecs 220 How ChemScript works _ 222 2 c cece ccc c cece ccc ccc cece ec eeceeceeceeeeceeceeceececceceeceeceecereeseeseeeees 221 Getting Started 20 2 cece cece eee cee eee eee e eee e eee cence eee ee cece seeeeeeeceeeeeeseeeeeeeees 221 EE CITIAG SCM OUS casts ree creaacs conocer aauccamusacdaccacataetacseucsaudedcacuads r EEO EE EEEE 222 Introducing the ChemScript API 0 2 0 02 ccc ccc cee cee cece cece ee ceeceececccceceeceeceeceeeceeceesees 223 TUONA eaae ge ee eee ee ee 224 Useful References bai tr ventencivadiocucsunauasededcue aeusameieecmene eae ucexdenaeaten eel caeseacerooeeseueeamoeeeeend 227 Chapter 14 Query Structures _ 2 00 0 0 o oo ccc cece cece cece cece cece cee ceeeceeeccecccecceeceeeteeeeeeeees 228 SEACA EIMMMMAUOM Ss 25 Secchi oranda seed ee eee e e r e e ae a ea 228 Generic Labels aaa iste sks sees e ae ese ieeseeese asa one aeneee te sce onaceee eo sbaeeeecseee Eien setae 228 Atom a 56 231 Bond Properties 22 2 2 c cece cece cece ccc cee cece cece cee ceceeceeceececeeceecceceececceseeceececcereeseeseecees 239 FIST aes te se ee ee ee ee ee ee ees ae cee aes epat
36. 3 4 aminophenyl 2 phenylacrylic acid To increase the number of free sites 1 To display the query tools navigate to View gt Other Toolbars gt Query Tools or click the Query Tools icon on the Main Tool palette 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 press lt Alt gt key while clicking the atom You can also change the free sites using the Atom Properties dialog or the shortcut menu See Atom Properties on page 231 Translation The Translation property specifies what is required to match in the structure query and possible database hits ina Markush DARC query Equal Default Matches specific to specific or generic to generic terms Broad Translates specific query atoms to corresponding superatoms in the database Chapter 14 Query Structures 238 of 315 W P l 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 distinguish different isotopic compounds for example between mono and hexa deuterobenzene by specifying a nuclide at any location 7 Note The isotopic abundance property is available in ChemBioDraw Ultra ChemDraw Ultra and C
37. A dialog box appears 3 Select Search Directly to import an SD file to search _ Note SDfiles have the extension sdf 4 Enter the file path in the Database field or click Browse to locate the file 5 Click OK Records in the file that match the generic reaction are returned To search for reactants using ChemBioFinder 1 Goto ChemOffice14 gt CombiChem gt Reactants gt Search for Reactants 2 Inthe dialog box select Search in ChemFinder 3 Inthe Database field enter the path to the ChemBioFinder form to be used to search the ChemBioFinder data base E Note ChemBioFinder form files have the extension cfx or cfw 4 Click OK ChemBioFinder launches Chapter 12 ChemDraw Excel and CombiChem 214 0f 315 After launching ChemBioFinder uses the form you entered to search its corresponding database for records that match the generic reactant You can browse the search results in ChemBioFinder before importing them into the Excel reactant worksheet Tip To omit a record from the search results navigate to the record in ChemBioFinder and go to Record gt Omit from List in the ChemBioFinder main menu 5 In Excel go to ChemOffice14 gt CombiChem gt Reactants gt Import ChemBioFinder Hitlist Alternatively you can copy and paste the query structure into ChemBioFinder to perform a search In Excel select the cell that contains the generic reactant Click the Copy Molecule icon on the ChemOffice toolbar In ChemBioFinder op
38. A j e O Oi Figure 6 3 a cyclopropane b cyclopentane c cycloheptane d cyclohexane chair 1 e cyclopentadiene f cyc lobutane g cyclohexane h cyclooctane i cyclohexane chair 2 j benzene To draw a ring 1 From the Main toolbar select a ring tool 2 Click and drag in the document 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 You can also use hotkeys to fuse rings For more information see Bond Hotkeys on page 45 You can also reduce the size of the rings For more information see Reducing Ring Size on page 55 Spiro and Sprout Rings By default clicking an atom in a ring using a ring tool forms a spiro link However if you click an atom while pressing the lt Alt gt key on your keyboard it will sprout the ring Chapter 6 Basic Drawings 67 of 315 You can change this behavior so that a sprout bond appears instead of a spiro ring 1 Navigate to File gt Preferences 2 From the Building Display tab check the Sprout Rings Instead of Spiro When Clicking check box Cyclohexane Chair Rings You can draw cyclohexane chair rings in two orientations horizontal and vertical When you draw a cyclohexane chair ring by clicking the chair is drawn in a horizontal orientation To orient a cyclohexane chair ring to a vertical orientation 1 Click one of the Cyclohexane Chair Ring tools 2 Click drag in the structure to the orientation you want
39. AT Is the change in temperature Critical Pressure Reported in bars this is the least applied pressure required at the critical temperature to liquefy a gas Critical Temperature Reported in Kelvin this is the temperature above which a gas cannot be liquefied regardless of the pressure applied Critical Volume Reported in cm mol this is the volume occupied by one mole of a substance at the critical temperature and pres sure CLogP CMR Use CLogP to calculate n octanol water partition coefficient log Pow LogP values based on literature rather than cal culations are included in the report file Use CMR to calculate Molar Refractivity MR values based on literature rather than calculations are included in the report file 7 Note CLogP and CMR values appear only in ChemBioDraw Ultra and ChemDraw Ultra Gibbs Free Energy Gibbs free energy is defined as G p T U pV TS Which is same as G p T H TS Chapter 11 Chemistry Features 160 of 315 W Where m U is the internal energy SI unit Joule pis pressure SI unit Pascal Vis volume SI unit m3 T is the temperature SI unit Kelvin m Sis the entropy SI unit joule per Kelvin H is the enthalpy SI unit Joule 7 Note H and S are thermodynamic values found at standard temperature and pressure Heat of Formation Reported in KJ mole the heat of formation is the increase in enthalpy resulting from the formation of one mole of a sub stan
40. Background color The color of the document window By default the background is white Foreground color The color of objects that you draw By default the foreground is black Chapter 4 Preferences and Settings 35 of 315 hemBioD 14 j ChemBioDraw 14 0 PerkinElmer For the Better Individual objects You can assign colors to objects to help then stand out from other objects Individual elements You can assign colors to specific atoms or elements in a structure To change the background and foreground colors 1 Navigate to File gt Document Settings and select the Colors tab 2 Select the background and foreground colors 3 Click OK Color by Element You can now color atom labels using colors associated with their atomic symbols You can assign colors to elements in the periodic table Whenever you use a particular element in your drawing the element appears in same color you assigned to it in the periodic table To assign different colors to elements in a periodic table 1 Navigate to View gt Show Periodic Table Window The periodic table appears Periodit NA E EAREN F j e afs e Pae fealSc 1 oP Ifo JME a ce ae fa Sr zr Nb Mo Te Ru Rh Pd g Cd In Sn Sb Te 1 xe Cs Ba La HF Ta w Re Os Ir Pt Jau Hg TI Pb Bi Po Jat Rn Fr Ra Ac RF Db 5 Bh Hs Mt Ds Ra fen Ww age iT Pa fee fru fen res Fu le 2 Double click an element The color palette appears
41. C NET Just a few of the many books and Web sites are listed below Books Python Beginning Python From Novice to Professional by Magnus Lie Hetland Dive into Python by Mark Pilgrim Learning Python by Mark Lutz amp David Ascher This is a beginner intermediate learning manual and reference a Python in a Nutshell by Alex Martelli This book is a brief introduction and good reference to Python C NET C ina Nutshell by Peter Drayton Ben Albahari and Ted Neward Pro C with NET 3 0 by Andrew Troelsen C Essentials by Ben Albahari Peter Drayton and Brad Merrill C 3 0 Cookbook by Jay Hilyard and Stephen Teilhet Web Sites Python You can find more information on Python at http www python org This is the official Python programming language site NET For information on _NET see http msdn microsoft com Chapter 13 ChemScript 227 of 315 Query Structures A query is 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 A query structure is a parameter you use to search a chemical database 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 Below are two query structure examples Figure 14 1 Two example structure queries A The results include any connec
42. CDXML YES YES ChemDraw 3 5 CHM YES YES ChemDraw 2 0 and ChemDraw 2 1 CHM YES NO ChemDraw Template CTP YES YES ChemDraw Template Style Sheet CTS YES YES ChemDraw Style Sheets CDS YES YES Connection Table CT YES YES Chemical Markup Language CML YES YES Bitmap BMP YES YES PostScript EPS NO YES Graphic Image Format GIF YES YES ISIS SKC TGF RXN YES YES JCAMP JDX DX YES NO JPEG JPG JPEG YES YES MDL MolFile MOL YES YES MDL RGFile MOL YES YES MDL V3000 MolFile MOL YES YES Chapter 15 Sharing Information 275 of 315 ChemBioDraw 14 0 i Perkin For the Better Format Import Export MSI ChemNote MSM YES YES Portable Network Graphics PNG YES YES Standard Molecular Data SMD YES YES Structure Data file SDF YES YES Galactic Spectra SPC YES NO Windows Metafile YES YES EMF WMF Scalable Vector Graphics SVG NO YES Portable Document Format PDF YES YES Tagged Image File TIF TIFF YES YES Transferring Across Platforms You can can open cdx files in either ChemBioDraw for Macintosh or Windows When you transfer files across plat forms fonts are not transferred If a font in the transferred document is not available ChemBioDraw substitutes fonts for those that are available on the new platform Chapter 15 Sharing Information 276 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 Chemical Interpretation ChemBioDraw converts lines characters and other symbols into chem
43. CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved viii P gt ChemBioDraw 14 0 PerkinElmer For the Better Copy Structure to MS Word from ChemDraw Excel Lets you copy structures from ChemDraw Excel worksheets to Microsoft Word through a setting in the General Prefer ences dialog See General Preferences on page 210 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved Introduction Designed for scientists students and scientific authors ChemBioDraw is a powerful yet easy to use tool for pro ducing chemical and biological drawings You can create your own drawings or use those provided in the library of available templates Technical Support The online menu link Technical Support opens the Technical Support Web page Here you can find desktop support resources including the PerkinElmer Informatics Knowledge Base product downloads FAQ and documentation To reach the PerkinElmer Informatics Technical Support Web page 1 Navigate to Online gt Browse PerkinElmer Technical Support The Technical Support Web page opens 2 Click Desktop Support About this Guide This guide describes the features in ChemBioDraw Some tasks described in this guide must be performed in con junction with other software For example instructions for ChemDraw Excel describe tasks that require Microsoft Excel For assistance consult the Microsoft Excel onl
44. ChemBioDraw by selecting the appropriate option in the Search menu Registering Online To activate any ChemBioOffice application register with the PerkinElmer Informatics Web site to receive a regis tration code Upon filling out a registration form you will receive a registration code by e mail this does not apply to site licenses If your serial number is invalid or you do not have an Internet connection contact PerkinElmer Informatics Support to receive a registration code You may use your ChemBioOffice 2014 applications a limited number of times while waiting for the registration pro cess to finish 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 ChemACX com and the e mail edition of ChemBioNews To register online navigate to Search gt Register Online The user registration Web page opens in your browser User s Guide The Search menu also lets you find current and previous versions of the documentation To access the doc umentation page navigate to Search gt Browse PerkinElmer Documentation The Desktop gt gt Support Documentation Web page appears Select the Manuals link 7 Note If you do not have a PerkinElmer Informatics user account you will first be directed to a sign up page Technical Support The Search menu link Browse PerkinElmer Technical Support opens the Technical Sup
45. D Ala Arg Asn Asp cys Gin Glu Gly His Ile A R H D C 9 E G H Leu Lys Met Phe Pro Ser Thr Trp Tyr Val L K M F P 5 T Wi W A C G T A C G U Using the biopolymer editor you can create a sequence by explicitly specifying the residue name instead of the IUPAC code When you enter a letter the auto completion feature suggests a match with a known residue in the lib rary For example when you enter a the residue Ala is suggested To accept the suggestion press lt SPACE gt or lt ENTER gt key Press TAB to move the caret to the end of the selected label To enter 8 amino acids type a nickname such as bAla The b is converted to the 8 symbol You can also create 8 amino acids using the 8 amino acid button in the biopolymer editor 8 amino acids always display using three letter codes Glycine does not have a beta carbon and so there is no beta version To enter D amino acids specify d before the residue name Glycine is also achiral and so does not have a D ver sion _ amp Note Use the D amino acid and 3 amino acid buttons simultaneously to produce D 8 amino acids Chapter 8 Drawing Biopolymers 102 of 315 W P l You can also overwrite and replace the sequence atoms using the residue replacement button in the biopolymer editor For more information see Replacing Residues on page 109 Toggle Amino Acids Toggle Amino Acid Style AA1 lt gt AA3 option lets you change the amino acid representation from si
46. FASTA Peptide command or by using the Biopolymer toolbar to build each chain To build intra sequence disulfide bridge 1 Select the single bond tool 2 Draw a bond between the C 6 and C 11 residues in the A chain as shown below tc OT H G I E Q C C T 8 1 C 8 L Y Q L E N Y C N OH To build inter sequence disulfide bridges 1 Select the bond tool and draw a bond between the C 7 in A chain and C 7 in B chain 2 Draw another bond between the C 20 in A chain and C 19 in B chain as shown below TC ti lt rd H G V E Q C C T S 1 C L Y Q L E N Y C N OH H F V N Q H L C G S H L V E A L Y L V C G E R G F F Y T P K T OH Lactam Bridges You can draw lactam bridges between Lys Asp and Lys Glu residues The residues connect via amide bonds between side chains You can also mix disulfide and lactam bridges To draw a lactam bridge 1 Draw asequence that contains Lys and either Asp or Glu 2 Using solid bond tool draw a bond from Lys to the other residue An example is shown below H G E E K S OH Chapter 8 Drawing Biopolymers 116 of 315 hemBioD 14 i A j PerkinElmer For the Better IZ Chapter 8 Drawing Biopolymers 117 of 315 Advanced Drawing Techniques The advanced features help you save time or perform functions that cannot be accomplished using the basic tools For example you can view your drawing as 3D models or create stereoisomer
47. General tab select or type the tolerance This change affects all documents The ChemDraw Items Folder The folder contains the preferences hotkeys nicknames and isotopes files scripts and the generic nicknames file It also contains template documents and template Stationery Pads You can have multiple ChemDraw Items folders This is useful in corporate installations for maintaining personal files such as nicknames and standard templates The location of the ChemDraw Items folder is based on your operating system If you are using ChemOffice 2014 the folder is at C ProgramData CambridgeSoft ChemOffice2014 ChemDraw ChemDraw Items To add a path to a ChemDraw Items folder Navigate to File gt Preferences The Preferences dialog appears Click the Directories tab Click Add New browse to a location and click OK A new path is added to the list Torearrange the search order click Move Up and Move Down O fF WwW N gt To delete a path click Remove To delete all added paths click Default Paths Default Styles ChemBioDraw saves default styles as a style sheet When you launch ChemBioDraw the last style sheet you use opens as the default If you choose different one that file becomes the default You can set a default that is not changed 1 Navigate to File gt Preferences 2 On the Open Save tab browse to the default style sheet 3 Deselect Opening Any Style Sheet Changes Default 4 Click OK To view the d
48. P a Function CHEMPROPPRO VAPOR PRESSURE cell ref Example In cell CHEMPROPPRO VAPOR PRESSURE A2 Result 47 57999897 Critical pressure The minimum pressure that must be applied to liquefy the structure at the critical temperature Units bar Function CHEMPROPPRO CRITICAL PRESSURE cell ref Example 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 Function CHEMPROPPRO CRITICAL TEMPERATURE cell ref Examples In cell CHEMPROPPRO CRITICAL TEMPERATURE A2 Result 615 351 Critical volume The volume occupied at the compound s critical temperature and pressure Units cm mole Function CHEMPROPPRO CRITICAL VOLUME cell ref Chapter 12 ChemDraw Excel and CombiChem 193 of 315 ChemBioDraw 14 0 Example 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 Function CHEMPROPPRO GIBBS FREE ENERGY Cell ref Example In cell CHEMPROPPRO GIBBS FREE ENERGY A2 Result 84 77 Heat of formation The heat of formation for the structure at 298 15 K and 1 atm Units kcals mole Function CHEMPROPPRO HEAT OF FORMATION Cell ref Examples In cell CHEMPROPPRO HEAT OF FORMATION A2 Result 105 73 Ideal gas thermal capacity The constant p
49. a ae ee aces esas sie a Geena eee ates See ee eee ae 180 Importing hit listS 2 0 2 0c ec ccc cee cee cece cece cece nce e cece cee ceeceeceecececeeceeceeceuceeeceeteeceeeee 181 Exporting tables toc ots seectss pe rrcrndoceeenetinacseesueai be eot map neeueaubwinshe bed ctemsiateneesecla ceased beceuaieeceeeseentbes 181 Synchronizing Tables 0 eee cece ccc cece cece cece ec eececcececeeceeceeccecceeceeceeceeceeeceeceeceeeees 182 Adding structures as snc ce ageetsauececeecoecsqnsenauuse a seoteeeoee since chee orooro orooro eorn saenaceeteceaisassonate 183 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved iii ChemBioDraw 14 0 i Perkin For the Better CAN AIG oi 6 cceengsincenemocben acca cet taunts aeehbecaaderncedeenauocde e dade naceedueanbuahessenauseseuaeueusechsseuconceties 184 R Group analysis go ccec oucdscreSecehorscvasacgebave shcdiwtatecleaecewelenestdbedentadactsdsyeecsedeaetenwsdhaneesauswceth 185 Working with Structures 1 2 0 0 2 oo ccc cece cece eee c cece cece cece cee ceeeceeeceeeeeeeceecceecececeeeeeeeeeeceeeeee 186 ChemDraw Excel Functions 2 00 02 0 o elec ccc cece eee eee eee ene ence eee eee enn e eee een e ee eeeees 188 Chemical Properties 2 22 c cece cece cece cece cece cece eee eeceeeeeceeeceeceecceceeceeeceeseeceereereeeeeeeeeees 202 General Preferences 2 22 2 i occ eee eee ee ee eee ee ee ee nee cen cee e ene e ene e eens
50. a structure 2 Doone of the following Right click to open a context menu point to Bond point to the property you want and choose the desired options Chapter 14 Query Structures 239 of 315 Navigate to Structure gt Bond Properties On the Bond Properties tab select the properties from the drop down list and click OK Point to bond and press the hotkey The Bond Properties dialog appears 3 Inthe Bond Properties dialog select the properties to associate with the selected atoms Click OK For more information see Query Indicators on page 232 The indicators are Indicator Bond Query Property Any Bond Types on page 241 Any S D Bond Types on page 241 Single or Double D A Bond Types on page 241 Double or Aromatic S A Bond Types on page 241 Single or Aromatic Rng Topology on page 241 The bond must be part of a ring Chn Topology on page 241 The bond must be part of a chain and not part of a ring R C Topology on page 241 The bond may be part of a ring or chain Rxn Reaction Center on page 241 The bond must be part of a reaction center Viewing Bond Properties The descriptor for the Reaction Center query property indicates the property is applied but not the value of the prop erty To find the value of a query bond property setting 1 Select the bond 2 Doone of the following Right click to open a context menu point to Bond Properties and select to a property
51. after you enter a dialog prompts you to specify the attachment point Double click on atom to select new attachment point You can expand and contract protected residues just as any other residues Pasting Sequences You can paste sequences in FASTA format Since only single letter IUPAC codes are present in the FASTA format you must indicate whether this corresponds to a peptide DNA or RNA biopolymer sequence You can paste ALL IUPAC symbols for residues with the exception of those characters indicating spaces or omissions To paste a sequence 1 Right click and navigate to the Paste Special sub menu Chapter 8 Drawing Biopolymers 104 of 315 hemBioD 14 i Ea j PerkinElmer For the Better Edit View Object Structure Text Curve Undo not available Ctrl 7 Redo not available Shitt Ctrl 2 Cut Ctril A Copy Ctr c Paste Ctrl V Clear Del Select All Ctrl A Repeat not available Ctri Copy As Paste Special z SMILES Alt Ctrl P Name as Structure InChI CDXML Text MOL Text Alt Shitt Ctrl F Biopolymer FASTA Peptide FASTA DNA FASTA RNA 2 Select one of three options to paste FASTA Peptide FASTA RNA FASTA DNA gt gil 52421 b AAD44166 1 cytochrome b Elephas maximus maximus LCLYTHIGRNIY YOSYLYSETWNTGIMLLLITMATAFMGY VLPWGOOMSFWGOATVITNLFSAIPYIGTNLY EWIWOOPFSVDKATLNREFFAPHEFILPFTMVALAGVHLTFLUETOSNSPLOLTSDSDEIPFHPY YTIKDI LG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEW YFLFAYAILRSVP
52. and click OK To print a document from Explorer Chapter 3 Page Layout 12 of 315 W P l 1 Select the document to print 2 Navigate to File gt Print ChemBioDraw opens and the Print dialog appears 3 Make your selections in the Print dialog and click OK Print Options Select Printer This window lists all printers connected to your computer You can use the default printer or select another printer Print to File The document is saved as a prn file and includes your printer preferences The document can then be sent later to a printer Find Printer Click to map to a printer not listed in the Select Printer window Page Range Select the pages to print To print parts of your document select the parts and choose Selection in the Print Options dialog Number of copies By default only one copy is printed Scaling With some printers you can reduce or enlarge your drawings by a variable percentage 25 400 This option scales all objects and text in the document window The size changes relative to the paper size margins and orientation The enlarge or reduce option is useful for changing the size of the drawing area while keeping the image size If your document fills the page on one printer and you use another printer that requires larger margins the drawing may dis appear off the edge of the document window You can reduce the drawing size with the reduce option to fit in the doc ument window Saving Page Set
53. appearing in the product worksheet Chapter 12 ChemDraw Excel and CombiChem 216 0f 315 ChemBioDraw 14 0 f i PerkinElmer For the Better Ei Note Whenever you create a new experiment existing experiment worksheets are retained If you want to delete them right click each experiment tab and select Delete or use the experiments floating form Combi Option s gt Experiment gt Delete Go to Combi Options gt Experiment gt Toggle to hide unhide all the experiment worksheets in the workbook Configuring plates After you create an experiment you can assign your products to product wells and your experiment reactants to react ant block plates This is useful if you are going to use a robotic synthesizer You can configure plates of up to 50 rows and 50 columns To set up assignments 1 Open either an Experiment Reactant or Experiment Product worksheet 2 Goto ChemOffice14 gt CombiChem gt Plates gt Configure Plates The Configure Plates dialog box appears 3 Inthe Configuration of drop down list select either Product Plates or Reactant Block Plates 4 Enter the number of rows and columns to assign to the plate The numbered buttons represent wells in the plate you chose Configure Plates Configuration OF aiislallasigElt Rows 2 Column 8 Control Well Empty Well E Compound Well 5 Designate which wells you want to use as controls synthesized compounds and left empty Click a well to change its designa
54. appears on the Color menu To add a customized color Esec colors nl bel See ire E LE EG ER REE BREE EEE EEE EE ee Eag tee fi Figure 4 2 Setting custom colors A Color refiner box B Luminosity box 6 Click acolor in the Color Refiner box to set the hue and saturation The pointer turns into a cross hair when you click You can drag to a different region to change the hue and sat uration Chapter 4 Preferences and Settings 37 of 315 W P l 7 Click inthe Luminosity box to set the color brightness 8 If necessary change the hue saturation luminosity and RGB components by typing the values in the text boxes 9 Click Add to Custom Colors 10 Click OK Templates and Color The background and foreground colors in a template from the template pop up palette are not used when the template is drawn in a document window However other colors in the template are added to the color palette of the document if they are not already present For more information see Autoscaling on page 270 Saving Color Palette Settings You can save the color palette in a style sheet The color palette is saved with other document settings such as page setup settings text settings and drawing settings Printing Background Color To change whether the background color is printed 1 Navigate to File gt Preferences 2 Select or de select Print Background Color on the General tab 3 Click OK Document Settings ChemBi
55. apply object settings 1 Select the object 2 Goto Object gt Apply Object Settings from and choose the document from which to apply the settings A dialog box appears 3 Doone of the following To selected object only click No To selected object and any new objects you draw click Yes Chapter 4 Preferences and Settings 32 of 315 W P l Customizing Hotkeys If you are familiar with XML you can edit the ChemBioDraw Hotkeys or create your own To customize Hotkeys open the Hotkeys xml file in a text editor There are two paths depending on whether this is a default installation or a custom installation The preferred method is to edit this file from a custom installation loc ation e If a Default Installation the path is Go gt Applications gt Right click on ChemBioDraw gt Choose Show Package Contents gt Con tents gt Resources gt SpecialPurpose gt ChemDraw Items gt Hotkeys xml e fa Custom Installation the path is Custom location folder gt ChemDraw Items gt Hotkeys xml Note It is safest to edit the Hotkeys xml file from a custom installation location rather than from the default install ation location Since when editing the Hotkeys xml from the default installation location this can affect the whole ChemBioDraw package content The Hotkeys within the file are organized by object type a Atom Hotkeys that modify atoms Bond Hotkeys that modify bonds m AA
56. atom label size for the document determines font and size for stereochemical flags To draw a stereochemical flag Chapter 14 Query Structures 260 of 315 1 To display the Query tools navigate to View gt Other Toolbars gt Query Tools or click the Query Tools icon on the Main Tool palette 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 useful in pharmacophore searching when looking for a 3D relationship among atoms and bonds for example in a series of potential receptor ligands To create a 3D query you add geometries lines planes and so on and constraints specified as ranges to a query structure For example you can specify that two atoms must be between 4 and 5 A apart or that two planes must be separated by 80 100 degrees To assign 3D properties to a structure 1 Select the structure or substructure E Note Because some 3D properties specify an order use SHIFT Click to select them in the order you want 2 Navigate to Structure gt Add 3D Property and select an option from the table below E Note In the table points may be atoms centroids or points Lines may be lines or normals Angle Defines an angle constraint between three points in order Indicated as a range Dihedral Defines a dihedral torsional angle constraint among four points in order between two lines or two planes In
57. bonds For substructures with two or more attachment points the attach ment point numbering sequence determines the order in which other parts of the structure are attached For example LA substructure can be any part of a drawn structure Chapter 9 Advanced Drawing Techniques 138 of 315 if you expand the structure H Leu OH the hydrogen is bonded to the first attachment point in leucine and the hydroxyl group to the second For more information see Using Nicknames on page 62 To define a new nickname In the example below a b alanine structure is used 1 Draw the b alanine structure On ae OH HN 2 Draw a bond to the NH2 group 3 Delete the label on the OH group aa 4 Using the Attachment Point tool add an attachment to the N terminus 5 Add an attachment to the C terminus O 6 Select the structure and navigate to Structure gt Define Nickname 7 Type a short name for the nickname Tip To avoid possible conflicts with elements specify names with more than two characters 8 Click OK 7 Note The attachment point order is determined by the order in which you add the attachment points to the struc ture You can also define nicknames from a structure containing a single radical Attachment points are added at the site of the radical Chapter 9 Advanced Drawing Techniques 139 of 315 Nicknames can also be defined by carving a substructure out of a structure Nicknames and A
58. can modify arrows with a context menu command Some of these commands are also found on the Curves menu Use the context menu to create arrows for which there are no tools such as bold dashed or dipole Chapter 6 Basic Drawings 72 of315 ChemBioDraw 14 0 i cae Perkin For the Better iM j w Plain Dashed Bold Full Arrow ak Start Full Arrow ak End Half Arrow ak Start Left Half Arrow at Start Right Half Arrow at End Left Half Arrow ak End Right s Solid Arrowhead Hollow Arrowhead Angled Arrowhead Mo Go Cross Mo Go Hash Dipole Object Settings Annotate Colors 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 point ing For example to 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 lt shift gt key The adjustment handle changes to a small highlighted rectangle and the cursor changes to the symbol 3 While pressing the lt shift gt key 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 Chapter 6 Basic Drawings 73 of 315 ChemBioDraw 14 0 i aa Perkin For the Be
59. click the bond again to flip its orientation The final structure is CHsOH OH Tutorial 5 Newman projections This tutorial demonstrates how to draw a Newman projection of ethane Chapter 19 Tutorials 308 of 315 Draw ethane 1 Click the Solid Bond tool 2 Inthe document window click drag downward to create the first bond 3 Click the atom at the bottom of the bond to add a second bond 4 Click the bottom atom again to add a third bond ILA 5 Hover the mouse over the end of each bond without clicking and type H to add the hydrogen atoms Duplicate the structure 1 Click a selection tool The last structure you drew is selected 2 To create a duplicate hold down the CTRL key while dragging the selection rectangle upward to the right of the ori ginal The selection box disappears while you are dragging 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 other tertiary carbon 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 Chapter 19 Tutorials 309 of 315 P gt Perkin For the Better ChemBioDraw 14 0 Drawing the Newman projection In this step you draw the hollow circle that is particular to Newman projections 1 Click the Orbital to
60. dialog box 1 Navigate to File gt Preferences The Preferences dialog appears 2 Click the Open Save tab 3 Click Use Default File Format in the Opening Files section and choose the file format Setting the Default Tool You can choose which tool is selected when you open documents 1 Navigate to File gt Preferences The Preferences dialog appears 2 Click the Open Save tab 3 Under Opening Files select a tool New Lines and Closing Text Boxes To create a new line in a caption text box press either lt Enter gt or lt Return gt To create a new line in an atom label press lt Alt gt lt Enter gt To close the text box click outside the text box or select another tool To change the default 1 Navigate to File gt Preferences 2 Choose the appropriate option on the Building Display tab to change the default for a Atom Label Text Require lt Alt gt lt Enter gt to create new line in Atom labels Caption Text Require lt Alt gt lt Enter gt to create new line in Captions 3 Click OK Chapter 4 Preferences and Settings 21 of 315 Highlight Box Tolerance Tolerance determines the size of the highlight box and how close you move the cursor to an object to activate it The default setting for the Tolerance is 5 pixels At this setting 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 Navigate to File gt Preferences 2 On the
61. document settings for subsequent drawings in the current document m Choosing a new format for an individual caption or label from the Text menu or toolbar before you type Selecting text and applying a new format to an individual label after you type To specify the text settings for new captions and atom labels in the current document 1 Navigate to File gt Document Settings The Document Settings dialog appears 2 Select Text Captions or Atom Labels category 3 Select the appropriate options 4 Click OK These settings affect all new captions or atom labels in the current document You can set the text format for an individual caption or atom label before you begin typing To set the text format before you type 1 Click the Text tool and click in the document window A text field appears 2 Set the text format in one of the following ways From the Text menu choose the format options From the Style toolbar choose the format options 3 Type the text in the text box 7 Note The format change is applied to the current text only Any subsequent text you type is formatted according to the default document settings for the current document To specify a font style 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 context menu From the Style Toolbar select the font and size from the drop down menus Cha
62. drawing area 5 Create Headers and Footers as described in Headers and Footers on page 11 6 Click OK A new document 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 ChemBioDraw calculates the num ber 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 1 Navigate to File gt Document Settings 2 On the Layout tab click Poster Chapter 3 Page Layout 10 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 3 Enter the Height Width and Page Overlap 4 Select whether to Print Registration Marks 5 Create Headers and Footers 6 Click OK Headers and Footers For posters only one header and footer appear for the entire document To create a header and footer Navigate to File gt Document Settings Click Header Footer category Enter the position from the edge of the page for the header or footer to appear Type the text to appear in the header or footer O A O N gt Type additional information in the Text box from the following a filename amp f page number amp p date printed amp d time printed amp t 6 Position the text horizonta
63. i AL For the Better NH gt 3 With the Text tool selected click the atom shown below and then type OH in the text box that appears IA NH Displaying stereochemical markers We now display the stereochemical markers R and S for the two isomers To add the markers 1 Select the entire structure with the Lasso or Marquee tool 2 Goto Object gt Show Stereochemistry The S marker appears NH 3 Select the structure and go to Object gt Flip Horizontal The R marker appears 4 With the structure selected go to Object gt Rotate 180 Vertical You can also use the object toolbar to rotate the structure Chapter 19 Tutorials 313 of 315 ChemBioDraw 14 0 i Perkin For the Better I FJ HO 7 O The Wedged bond becomes hashed and the R stereochemistry is preserved Tutorial 7 Templates ChemBioDraw comes with an extensive template library of pre drawn structures and images You can use a template to either start a new drawing or to modify one that already exists In this tutorial we use the phenanthrene template to create peroxydibenzene The template and final drawing are shown below peroxydibenzene To add the template for phenanthrene 1 Goto File gt Open Style Sheets gt New Document 2 Inthe Main toolbar select the template tool The list of template palettes appears 3 Inthe Aromatics palette select the phenanthrene template 4 Click in the document window Phenant
64. i cman Perkin For the Better Labels Meaning CYC Cyclic CYH Cyclic or H CBC Carbocyclic CBH Carbocyclic or H ARY Aryl ARH Aryl or H CAL Cycloalkyl CAH Cycloalkyl or H CEL Cycloalkenyl CEH Cycloalkenyl or H CHC Heterocyclic CHH Heterocyclic or H HAR Hetero aryl HAH Hetero aryl or H CXX No carbon CXH No carbon or H Atom Properties Atom properties determine the structural features 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 attachments have no attachments or perhaps be a specific iso tope 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 do one of the following m Right click select Atom Properties Navigate to Structure gt Atom Properties Press the hotkey 3 Inthe Atom Properties dialog select the properties to associate with the selected atom s 4 Click OK Chapter 14 Query Structures 231 of 315 W P Query Indicators Query indicators display the atom properties you assign to a structure as shown below If more than one property is assigned an indicator for each property appears adjacent to the atom Figure 14 2 This structure illustrates several possible atom properties that can be assigned The list below describes each indicator Substituents Free Sites Followed by the number of fre
65. in RNA context not T in DNA context N any base A U G C In RNA context A T G C in DNA con text Chapter 8 Drawing Biopolymers Cys Asp Glu Phe Gly His lle Lys Leu Met Asn Pro Gin Arg Ser Thr Val P gt Perkin For the Better Cysteine Aspartic Acid Glutamic Acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Proline Glutamine Arginine Serine Threonine Valine 112 of 315 ChemBioDraw 14 0 i ora Perkin For the Better W Trp Tryptophan Y Tyr Tyrosine The tables below list the three letter codes for non specific and non proteinogenic amino acids IUPAC Amino Three Non specific Amino Acid Acid Code Letter Code B ASX asparagine or aspartic acid Z Glix glutamic acid or glutamine J Xle leucine or isoleucine X Xaa Any amino acid no nickname IUPAC Amino Three Non proteinogenic Amino Acid Code Letter Acid Code O Pyl Pyrrolysine U Sec Selenocysteine Aib Q Aminoisobutyric acid Abz 2 Aminobenzoic acid Nle Norleucine Cyclic Crosslinked and Branched Peptides You can create cyclic peptides by bonding together the terminal residues in a peptide sequence A looped bond indic ates the peptide is cyclic An example of cyclic peptide is shown below Chapter 8 Drawing Biopolymers 113 of 315 ChemBioDraw 14 0 i ae Perkin For the Better You can create a crosslinked peptide such as insulin using the biopolymer tool and bo
66. in the target structures Element NOT Lists The element not list specifies that the elements in the list are not allowed in the search results Commas must sep arate 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 you can replace the word NOT with a minus sign For example NOTIF Br NOT F Br F Br Figure 14 5 Element NOT lists Note An element not list may contain only atomic elements plus D deuterium and T tritium To create an element NOT list 1 Open an atom label text box 2 Type an open bracket the word NOT and a space for example NOT followed by a list of elements sep arated by commas Cl Br followed by a close bracket T for example NOT Cl Br I Polymers You can indicate polymers using either brackets parentheses or braces that enclose repeating structures or struc tural fragments The bracket properties lets you specify the context and orientation of the repeating units For example NH F TH Chapter 14 Query Structures 243 of 315 W P l To enclose structures with brackets 1 Todisplay the Bracket toolbar navigate to View gt Other Toolbars gt Bracket 2 On the Bracket toolbar select one of the double bracket tools 3 To draw the brackets click and drag across the structure to enclose This gives default valu
67. labels You can use the repeating bond label technique in Tutorial 4 or use hotkeys For the Hotkey method just point and type the letter o The Text tool method is repeated here with a slight variation 1 Select the Solid Bond tool point to the atom shown in the figure below and double click to open a text box 2 Type OH Chapter 19 Tutorials 306 of 315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better Sai Figure 19 8 Adding the OH labels 3 Move the pointer to the other atoms as shown and triple click to repeat the atom label Tip If the drawing is too small to place the labels go to View gt Magnify to enlarge it Add the CH OH label 1 Triple click the upper atom of C5 2 Press ENTER to open the atom label text box Type CH2 before the OH Change the type of the front bonds 1 Click the Bold Bond tool Chapter 19 Tutorials 307 of 315 hemBioD 14 f ChemBioDraw 0 PerkinElmer For the Better 2 Click the bond shown in the figure 3 The cursor changes to a bold arrow as you point to the bond 4 Click the Wedge bond tool 5 Click each ring bond 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 O Tip If you move the pointer too far the highlight box disappears If placing the pointer is difficult go to View gt Mag nify 7 Note If the wedge is pointed in the wrong direction
68. letters to the atoms in your structure You can add Numbers 1 2 3 and so on Text ending with a number atom1 Greek letters for alpha beta and so on Letters a b c and so on The default indicator is numbers T A Tip To use text instead of numbers number an atom and then edit the number See Formatting Atom Numbers below 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 and select Atom gt Show Atom number in the context menu Type the hotkey single quote To hide atom numbers 1 Select the atoms or structure 2 Right click point to Atom and deselect Show Atom Number Note To remove an atom number indicator click the indicator with the Eraser tool Formatting Atom Numbers To edit the atom number text and style 1 Select the Text tool 2 Select the atom number and type the new text Chapter 9 Advanced Drawing Techniques 124 of 315 ChemBioDraw 14 0 gt PerkinElmer For the Better Note When you type a new indicator the counter resets to the new style and you can continue numbering in that style with the standard means For example if you type ain a text box then point to another atom and use the context menu or hotkey the atom is labeled B Switching to another structure resets the counter 3 To edit the atom number style select the atom number with the Text
69. limit the rotation to the X or Y axes only You can also select part of a complex molecule and rotate it around a particular bond _ Note You cannot apply structure perspective to orbitals To remove the Structure Perspective Tool effect 1 Select the structure with the Marquee or Lasso Tool 2 Navigate to Object gt Flatten _ Note Flattening the structure removes its z coordinate information but does not change its appearance Mass Fragmentation Mass fragmentation mimics the molecular fragmentation in a mass spectrometer When you apply the mass frag mentation tool to a structure you cut through the structure severing its bonds and creating fragments from the ori ginal structure This is not a predictive tool you must specify what bonds are to be broken To fragment a structure use the Mass Fragmentation Tool to drag the cursor across one or more bonds When you release the mouse button bonds that you cross are broken 1 i Te Chemical Formula CHg Exact Mass 42 05 i Chemical Formula C3 le Exact Mass 42 05 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 lt ALT gt key while drawing When the line crosses a bond the formula and exact mass for the fragments on either side of the bond appear as if the bond were homolytically broken That is a single bond turns into a monoradical on each fragment a double bo
70. of 0 5 Assume that the destination document has an atom label font size set to 14 points If you paste the atom label into the destination document the font size is scaled by a factor of 0 5 to give a final atom label font size of 7 points Captions ChemBioDraw autoscales captions using the ratio of the fixed length in the destination 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 dialog This ensures 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 document 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 The document settings do not affect all objects Objects such as arrows and boxes are scaled to maintain the same proportions to bonds that were in the source document Except for the foreground and background color the colors present in the selection to be pasted are added to the des tination document s Color palette if they are not already up to 20 total colors The background color in the destination document remains and all objects colored using the foreground color are changed to match the foreground color in the destination document Pasting to an
71. or the object is entirely within selection rectangle To set one selection tool to behave like the other click either one of the tools while pressing lt Alt gt To toggle a selection tool and the last drawing tool used press lt Control gt lt Alt gt lt Tab gt Selecting Entire Structures To select an entire chemical structure double 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 Marquee tool 2 Point to an object in a document window A highlight box appears over the pointed object 3 Click the object The selected objects appear within the selection rectangle and the cursor changes to a hand _ Note You can also select the individual objects in a group See Grouping Objects on page 85 Selecting Multiple Objects When you select multiple objects each object displays a selection box To add more objects to the selection press lt shift gt and select the other objects To select all objects navigate to Edit gt Select All Deselecting All Objects To deselect all objects do one of the following Click an empty area outside the selection rectangle m Press lt esc gt Select a different tool Select another object without holding down the lt shift gt key Deselecting One Object To deselect one of several selected objects hold down the lt shift gt
72. peptide appears as H Ala Phe Arg Met Val OH H Phe Gin Gly If the residues does not have leaving groups that can be automatically found the Modify nickname dialog appears and you need to manually define the third attachment point Consider the following example 1 Draw two biopolymer chains as shown below H Ala Phe Gly Asp Met Val OH H Phe Thr Gin Met OH 2 Using the solid bond tool drag from the lower chain s Met 4 to the upper chain s Met 5 Since neither of these residues have defined leaving groups the Modify Nickname dialog appears twice once for each residue Modify Nickname Cancel aa ema HI Undo Double click on atom to select new attachment point 3 Define new attachment points The resulting structure is H Ala Phe Gly Asp Met Val OH H Phe Thr Gin Met OH Disulfide Bridges You can build disulfide bridges either between Cys residues within the same structure or between residues in two dif ferent structures For example consider the endocrine hormone Insulin Chapter 8 Drawing Biopolymers 115 of 315 ChemBioDraw 14 0 i a Perkin For the Better Insulin consists of two chains an A chain and a B chain connected by disulfide bridges A Chain GIVEQCCTSICSLYQLENYCN B Chain FVNQHLCGSHLVEALYLVCGERGFFYTPKT You can build these chains either by copying and pasting the above text using the Paste Special gt
73. predict NMR ChemBio3D includes several interfaces to computational chemistry packages which predict NMR Some packages predict IR spectra and other spectra as well For more information on ChemBio3D packages which have NMR predictions and their available parameters see the Chem amp Bio 3D User Guide Setting Parameters Values in ChemNMR Use the ChemNMR option in Preferences dialog to set the parameter values in ChemNMR See the example below Ping EnH ies se CEE rihi Lis kirg es 3 aragi Opera har REAM Seay ave i e Frequency 30 Miu b Appi reem wuppded eager data i appi ue ped primana data Gpions hor I AR M anny eythane agarrar a data Use Delme rues Mode kx Cancel Solvent The solvent is not user definable in ChemNMR except by adding new custom shift correction data Most spectra in the default ChemNMR database are run in deuterated chloroform but the database is intended to be solvent free In ChemBioDraw you can set either deuterated chloroform or deuterated dimethyl sulfoxide as solvent from the Prefer ences dialog Spectral shifts which depend on the solvent are generally indicated as rough predictions Chapter 11 Chemistry Features 173 of 315 W P l Spectrometer Frequency ChemNMR s default for estimating proton NMR is a spectrometer frequency of 300 MHz To change the default fre quency either set the new frequency using the Preferences dialog or hold the lt Alt gt key while sel
74. string to a variable Type the following line and press lt Enter gt myMol Mol LoadData CLCCCCCI1C This message appears Open molecule successfully chemical x smiles Reporting a Chemical Name You can now use the variable to report the chemical name For example at the command prompt type the line below and press Enter myMol chemicalName The line methyl cyclohexane Is returned Counting Atoms To count the atoms in the string type the following line and press lt Enter gt myMol CountAtoms The command returns the atom count for the structure defined with the chemical x smiles format for C1CCCCC1C which is 7 Exiting IDLE To exit type this line and press lt Enter gt exit Confirm any prompts to complete the exit command Python IDLE exits Getting Started Guide ChemScript includes a Getting Started guide to help you begin developing and using your own scripts To open the guide go to Start gt All Programs gt ChemBioOffice2014 gt ChemScript 14 0 gt Getting Started The document includes notes on the ChemScript objects and functionality Python and an overview of examples installed Editing Scripts Using IDLE or another development environment you can either edit the scripts provided with ChemBioOffice or cre ate your own Regardless of how you develop a script it must include these commands Chapter 13 ChemScript 222 of 315 from sys import from os import from os path import f
75. the document window Drag downward to draw the first bond 3 Point to the lower atom and drag downward again to draw the second bond P gt PerkinElmer For the Better The red wavy box appears because Show Chemical Warnings is selected We will keep it selected for now 4 Repeat step 3 there are five bonds A B C aana beana B ee La bls Fa Figure 19 3 Drawing the backbone Chapter 19 Tutorials paaa i yg aa i 3 Fih Fih 302 of 315 7 Note When you drag the pointer along the length of the bonds the pointer alternates between an arrow and a cross The arrow indicates 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 horizontal bond point to the uppermost Chemical Warning box and click it Note that the red wavy box disappears when you add a bond 2 Click again to add a horizontal bond in the opposite direction 3 Repeat steps 1 and 2 with each Chemical Warning box until all horizontal bonds are added Figure 19 4 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 CH20OH CHO CHOH Figure 19 5 Adding atom labels Add the repeating labels for the hydrogens and
76. 00 1 3275 0 00000000000000000 1210000 101110000 Chapter 11 Chemistry Features 177 of 315 ChemBioDraw 14 0 i pau Perkin For the Better 101210000 121320000 121410000 M ZZC 15 M ZZC 2 6 M ZZC 34 M ZZC 4 1 M ZZC 53 M ZZC 6 2 MCHG2718 1 M ZZC 79 M ZZC 8 13 M ZZC 9 10 M ZZC 107 M ZZC 118 M ZZC 12 11 M ZZC 13 12 M END gt lt D gt i gt lt solvent gt d6 DMSO gt lt SHIFT1 gt 2 9 61 0 0 gt lt SHIFT2 gt 3 8 92 0 0 gt lt SHIFT3 gt 6 9 01 0 0 gt lt SHIFT4 gt 10 3 11 0 0 gt lt SHIFT5 gt 11 1 16 0 0 gt lt SHIFTS gt 5 TH gt lt solvent gt d6 DMSO gt lt SHIFT1 gt 2 9 6 0 0 gt lt SHIFT2 gt 3 8 91 0 0 gt lt SHIFT3 gt 6 9 11 0 0 gt lt SHIFT4 gt 10 2 75 0 0 gt lt SHIFT5 gt 11 1 17 0 0 gt lt SHIFT6 gt 12 2 41 0 0 gt lt SHIFTS gt 6 ACD Labs07190711112D 151500000000 16 V2000 7 1683 1 9521 0 0000 CO000 00000000 7 1683 3 2484 0 0000 CO0000000000 0 6 0438 1 2962 0 0000 C 000000000000 6 0438 3 8887 0 0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4 9194 1 9521 0 0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4 9194 3 2484 0 0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 2927 1 2962 0 0000 N030000000 0009 4171 1 9521 0 00000050000000000 8 2927 0 0000 0 0000 O 0000000000000 3 7950 1 2962 0 0000 C0 0000000 0000 3 7950 0 0000 0 0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 2489 2 1708 0 0000 C0000 0 0 0 0000 0 1 1401 1 5149 0 0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0 0000 2 1552 0 0000 O 000000000000 1 1401 0 2186 0 0000 00000000000001210000132
77. 000017100002420000351000046100005620000510100007 8100007920000101110000101210000121310000131420000 13 1510000M ZZC 1 5M ZZC 2 6M ZZC 3 4M ZZC 4 1M ZZC 5 3M ZZC 6 2M CHG 2718 1M ZZC 7 9M ZZC 8 14M ZZC 9 10M ZZC 10 7M ZZC 11 8M ZZC 12 11M ZZC 13 12M ZZC 14 13M END gt lt ID gt 2 gt lt solvent gt d6 DMSO gt lt SHIFT1 gt 2 9 6 0 0 gt lt SHIFT2 gt 3 8 91 0 0 gt Chapter 11 Chemistry Features 178 of 315 lt SHIFT3 gt 6 9 11 0 0 gt lt SHIFT4 gt 10 2 75 0 0 gt lt SHIFT5 gt 11 1 17 0 0 gt lt SHIFT6 gt 12 2 41 0 0 gt lt SHIFTS gt 6 ChemNMR Limitations The program handles the following elements and isotopes 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 Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Nep Pu Am Cm Bk Cf Es Fm Md No Lr Functional groups are expanded automatically Inthe case of 1H 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 solvents may strongly increase these deviations It does not estimate shifts of hydrogen atoms bonded to heteroatoms because they are significantly affected by solvents concentration impurities and Steric effects Incase of 13C NMR it es
78. 0a a aa Daa DAAD DAADAA DDALL DLDP LLDD DDAL LLa Laa D Laora naani 267 Transferring Objects a00a000000000000000000 00000 cece oaoa aoao ceecececeeceeceeceeccceceeceeceeceecceeceeeeesees 2 70 Embedding Objects oes cette trasne near ensyssaaeses ce daorenseraaeacecueneneecaaccumenese nr seneuaeatess 2 1 ORIN coc c ere sees ses ection ae on ese peta oe ees Bae ra erence dest EE EEEE 211 ADONI e E E A AER ES 2 2 Transferring Across Platforms 0 0 0 00 ccc cece cece cee cee cee cece cece ee ccecceccecccecceccecceccecceeceeseecees 2 6 Chapter 16 Chemical Interpretation _ 2 2 02 2 o eee e ccc cece cece cece cece eeceeceeceeeceeceeceeeeene 277 Database Conventions 0 c cece cece cece cece ee ee cen riae n ene eennaceeaeeeecnuacecavacceasaseuarasscasasene 2 7 Chapter 17 Property Calculations _ 0 0 00 0 llc ccc eee cece cc ee cece cecceeeeecceceeceeeceeceeees 290 Chapter 18 ChemBioDraw Web Resources 2 22 22 02 cee eee ec ee cee cece cece ee ceeccecceccecceeceecees 293 Registering Online 0 eee c cece cece cece ec eee cece eet eeceecececcecceceeceececceeeceuceeceeceeeteeceecees 293 SO SUNOS E ha see aed aoe tae EEE cae A tee E E AEE 293 Technica SUD DON neice cess eekeeesiee tice tens sect E udertete cuss ciseu diem alesse eeadeeeeaeedetecacenetetesecee 293 Querying SciFinder with ChemBioDraw Ultra Feature 2 0 2 2 ccc e cece cece ec eee eee cecceeceeceeces 295 Chapter 19 Tu
79. 14 f PARNER teed PerkinElmer For the Better Gel Electrophoresis Tool Gel electrophoresis separates molecules using an electric field applied to a gel matrix The gel electrophoresis tool in ChemBioDraw 14 0 works much like the TLC tool and lets you easily draw and mark bands based on weight or dis tance For more information see TLC on page 168 TLC Plate Enhancements Lets you copy and drag spots between lanes For more information see TLC on page 168 Polymer Bead Enhancements Lets you re size polymer beads For more information on polymer beads and other attachment points see Attach ment Points on page 122 New Toolbars ChemBioDraw 14 0 introduces several new toolbars including Structure Curves Windows and Biopolymer tool bars You access these toolbars from the View menu Color by Element Lets you color atom labels using colors associated with their atomic symbols as shown in the example below For more information see Color by Element on page 36 New Property Predictions Incorporates new calculations from Molecular Networks for predicting pKa LogS and LogP See Property Pre dictions in ChemBioDraw on page 158 JPEG JPG file export Lets you export files of type JPEG Copy As Paste Special CDXML and MOL files as text Lets you save CDXML and MOL files to the clipboard as text and then paste in other applications as text See Creat ing CDXML or MOL Text on page 269 Copyright 1998 2014
80. 15 P gt Perkin For the Better ChemBioDraw 14 0 To copy a structure 1 Select the 2 propanone structure and its caption 2 Press and hold the lt CTRL gt key The hand pointer 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 7 Note To keep the copy aligned with the original press the lt SHIFT gt key while dragging Modify the duplicate structure 1 Select the Solid Bond tool 2 Click the far right bond of the copied structure Figure below 3 Point to a terminal carbon 4 Click the carbon atom until three bonds appear allowing a pause between each click _ Note If you click too fast the click is interpreted either as a double click which opens a text box or a triple click which duplicates your last atom label A B O O 5 Point to a terminal carbon atom 6 Type OH A B O O A L k a oT wA OH Chapter 9 Advanced Drawing Techniques 129 of 315 Replace the product caption 1 Select the caption with the Text tool and type 4 hydroxy 4 methyl 2 pentanone press the lt ENTER gt key and type 1 mole 2 Using the Text tool add 2 Mole to the caption for the reactant Clean Up Reactions After you draw a reaction you can clean the reaction using the Clean Up Reaction command under the Structure menu When you apply the Clean Up Reaction command the spacing between the reaction compon
81. 2 e eee e cece cece DPL eeeseeeeeeeeceeseereees 13 35mm Slide Boundary Guides _ 2 22 22 oie cece e cee cece eee cece eee cece cece ee ceeeeeeeeeeeeeeeseeseeseeee 13 Viewing DrawingS 2 22 e cece eee cece cece cece eee e cece cece eee ee cece cence eee eeeeeeeceeeeeeeeseeeeerseeseesees 14 TOS siete recs ie pe ee ee bee esa eect a ae ee ee ee 16 Chapter 4 Preferences and Settings _ 0 22 0 2 22 2 coco cece cc ccc cece ccc e cee eee e cece ceeeeeseeseeeeeees 20 Setting Preferences _ 2 22 2 occ ccc ccc cece eee e cece e eee cece cece cece cee cent eee ceeeeeeeeeesecetserseenees 20 Customizing Toolbars ec 23 Document and Object Settings 22 22 22 o occ ccecccce eee eee e cee 002D oao oron nan 23 CUSTOMIZING OK CYS cic hereeet tec ehd eon ed Laut uete tan doidcunenduhereusicswutesde dae chews dbeetucdeeeteel aiuee ves 33 Working with Color _ 2 2 0 0 2 occ c cece cece cece eee eee e cece cee cece cece eee ee eee ceeeeeeceeeeeseeseeseerseeseesees 35 Document Settings 2 220 022 cle ccc cc cece eee c eee nce e eee e cence eee ece cece cece cceesceceeecececceeseceeses 38 Chapter 5 Shortcuts and Hotkeys _ 22 202 02 2 ooo cc ccc cece ee ec e cc ee cee cece eeseeeeeeseeseees 44 Atom KeyS oes ene ae eee esis oes Seren shan acini ddan eeee D DLLD seen ceeseotes ase cnaasee 44 Bond Hotkeys 2 22 02 cece cece eee eee eee cece cece eee e cece cece cece ceeeeeecececececccecceeeceeeeeeeeeees 45 Function HotkeyS
82. 4 Inthe final structure there is 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 the other double bond Figure 19 1 To change the bond order type 7 5 To create the double bond in the second ring either hover the mouse over the bond and type 2 or click it 6 Using the bond tool click the carbon atoms circled in the figure below Three new bonds will appear 7 Hover your mouse over one of the bond shown below and type 2 Do the same for the other bond Chapter 19 Tutorials 300 of 315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better 8 Hover the mouse over the right most terminal carbon and type the letter o to create the ketone functional group 9 Toconnect the left terminal carbons select the solid bond tool and click drag a bond from one carbon to the other The structure is complete Tutorial 3 Fischer projections This tutorial demonstrates how to create a Fischer projection of glucose Chapter 19 Tutorials 301 of 315 ChemBioDraw 14 0 CHO I OH HO Hi Hi OH Hi OH CH OH Chemical Formula CaHi20x Exact Mass 180 06 Molecular Weight 180 16 mz 180 06 100 0 181 07 6 0 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 33 29 Figure 19 2 Fischer projections To draw the first bond 1 Click the Solid Bond tool 2 Point in
83. BOND CYCLOHEXANE DASHEDBOND CYCLOPENTANE PEN CYCLOBUTANE HASHEDBOND CYCLOPROPANE ARROW TEMPLATE HASHEDWEDGEDBOND SNAKINGCHAIN ORBITAL ACYCLICCHAIN BOLDBOND QUERY DRAWINGELEMENTS TABLE WEDGEDBOND ARC BRACKET WAVYBOND HOLLOWWEDGEDBOND CHEMICALSYMBOLS 7 Note The features that are available depends on the level of ChemBioDraw you have Description The tool description explains what each hotkey does Editing the Hotkeys xml file To edit ChemBioDraw hotkeys Open the hotkeys xml file in a text editor Navigate to the appropriate hotkey list inthe hotkeys xm1 file 1 2 3 Either add a new hotkey entry using the appropriate format and values or edit an existing hotkey in the list 4 Save the hotkeys xml file 5 Exit and restart ChemBioDraw i Caution Exercise caution when editing hotkeys xml file since if the formatting is incorrect it will not be read and some functions of ChemBioDraw may cease to work correctly Make a back up the original copy of the file prior to making any changes 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 up to 16 million colors but the number of colors may be limited by your monitor and dis play card What You Can Color In ChemBioDraw you can change the color of the background foreground or individual objects and elements
84. C NH e H Aad OFmoc ArgiTrt Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights vi reserved Cyclic and branched peptides Lets you create cyclic peptides by bonding together the terminal residues in a pep tide sequence A looped bond indicates that the peptide is cyclic You can create branched peptides using the sequence builder and bond tools For more information see Cyclic Crosslinked and Branched Peptides on page 113 Lactam bridges Lets you form lactam bridges between residues with available amino and carboxylic acid leaving groups such as Lys Asp and Lys Glu For more information see Lactam Bridges on page 116 Merging sequences Lets you merge multiple sequences into one sequence by bonding together their terminal residues Hybrid biopolymers Lets you create hybrid also called chimeric biopolymers containing peptide nucleotide and linker residues using the Biopolymer toolbar For more information see Hybrid Biopolymers on page 110 Pasting sequences Lets you paste sequences in the FASTA format You can also copy a text string describing a biopolymer as a series of single or multi letter residues with valid separators Space tab dash and paste it as a sequence The text string can be generated within or outside of ChemBioDraw See Pasting Sequences on page 104 Displaying expanded residues Expanded residues can appear in either linear m
85. CHEMPROPSTD CONNOLLY ACCESSIBLE AREA Cell ref Example In cell CHEMPROPSTD CONNOLLY ACCESSIBLE AREA 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 AREA cell ref Example In cell CHEMPROPSTD CONNOLLY MOLECULAR AREA A2 Result 212 294 _ Note The default probe radius used in the calculations is 1 4 angstroms Note The surface area calculation is performed with Michael Connolly s program for computing molecular surface areas and volume M L Connolly The Molecular Surface Package J Mol Graphics 1993 11 Connolly solvent excluded volume The volume contained within the contact molecular surface Units Angstroms Function CHEMPROPSTD CONNOLLY SOLVENT EXCLUDED VOLUME Cell ref Example In cell CHEMPROPSTD CONNOLLY SOLVENT EXCLUDED VOLUME A2 Result 170 277 _ Note The volume calculation is performed with Michael Connolly s program for computing molecular surface areas and volume M L Connolly The Molecular Surface Package J Mol Graphics 1993 11 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 Comp
86. ChemBioDraw tools ChemBioDraw User Interface By default the user interface displays commonly used toolbars the main menu and document status bar The user interface appears below Chapter 2 Getting Started 4of 315 ChemBioDraw 14 0 i a PerkinE 3 For the Better ChemBioDraw Ultra Untitled Document 1 o eE jJ File Edit View Object Structure Text Curves Colors Search Window Help x B nB o i far QO Jimestew Roman 2 H BI U mx O A ae y fy S ee SciFinder Tool peut Magnification Controls _ 2 t Q db P 388 Q O e Text Formatting Tools amp A w 4 BioDraw Toolbar My gt amp Main Toolbar x Document Window Saves the document ChemBioDraw Ultra windows user interface Toolbars In ChemBioDraw several new toolbars are introduced such as Structure Curves Windows and Biopolymer tool bars 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 You can also hide the toolbar by clicking on the X icon on the upper right corner of the toolbar The Main Toolbar The main toolbar includes the tools most commonly used for drawing structures These include all selection and bond tools You can open other toolbars from the main toolbar Navigate to View gt Show Main Toolbar Tearing off Toolbars Some tools on the main toolbar have other toolbars associated with them T
87. Elmer For the Better Annotate Keyword Name Content T 3 Specify anew name for the template in the Content text box 4 Click OK 5 Click Save The annotation appears as a tooltip when you point to the annotated template Deleting a Template 1 Select the template pane for the template to delete 2 Inthe document window select the entire drawing 3 Navigate to Edit gt Clear 4 Navigate to File gt Save Orienting Templates To make templates 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 Template panel If necessary first click and drag the resize handle Defining Nicknames A nickname is an alphanumeric abbreviation that represents a substructure Nicknames are useful for drawing large structures or structures that repeatedly use similar features Contracted labels are similar to nicknames but they are for one time use only in the current document ChemBioDraw includes a library of nicknames of common functional groups and monomers For example if you typ ically draw protein structures you may consider using amino acid nicknames in your drawings rather than drawing each amino acid The substructure that a nickname represents connects to the rest of the structure using one or more attachment points Attachment points must be single
88. Empty Document If you paste a ChemBioDraw drawing into an empty document that has different settings the Change Settings dialog appears To change the settings in the destination document to match the settings in the source document click Change Set tings Chapter 15 Sharing Information 270 of 315 W P All of the settings in the destination document are changed to match those of the source document 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 Set tings 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 ChemBioDraw supports the Object Linking and Embedding OLE protocol on Windows This lets you edit structures that are pasted in other types of documents ChemBioDraw is an OLE server which means it can create OLE objects that you can copy and paste into other OLE client applications When you transfer drawing from ChemBioDraw to another document type that supports OLE you can open and edit the drawing within the new application For example to edit a drawing inserted into Microsoft Word 2003 or later do on
89. HUMAN HEALTH ENVIRONMENTAL HEALTH ChemBioDraw 14 0 User Guide p gt PerkinElmer For the Better ChemBioDraw 14 0 i Perkin For the Better Table of Contents Recent Additions ciseais ec es cacesantee nae sents bigs a eee Ren eh bina aad aera bees euteee amen eea eee weew ee Aues vi Chapter 1 Introduction __ 20 2 aoaaa aoaaa aoaaa aoaaa ece ec eeceeeeeeee eee cece eee ee cee eeeeeceeeeeeeseeeeeee 1 About this Guide 2 2 5 0 cc ccc ceca cee ee cece eee cccesceescceusaevaccuceueccccccasceccteaccascuceusesscuversnceteuseacs 1 Chapter 2 Getting Started 82 22 ccc cc ccc ccc eee ee eee e cece cence eceeeeeseeeeeeeeeseeeees 4 About ChemBioDraw Tutorials 2 2 002022 eee eeeeeeeeeeeeeeeee eee ee eeeeeeee 4 ChemBioDraw User Interface _ 2 2 2 0 cece eee eee eee eee eee eee reran 4 TODS psec eas oe os ate ata ae ene nates one atee teases aceaansa nes awes bese cess E E yaceseascee 5 OC CTS aerer E E E E E E 6 Chapter 3 Page Layout 22 00000 aa aoaaa aoaaa a oaaao a0 e eee e eee cece cece eee seesceeteereeereees 10 The Drawing Area __ 222 22 2 eee c ccc eee ccc ec ee cee cece cece ence ec eee cee cee eee ceeceeeececeeececceseeeeeetceseerees 10 The Document Type 022 22 e eee cece e cece cece cece eee eee e cece cence eee cece eee eeeeeeeeeeeeceeeeeeseeseeseees 10 PAMINO crepe ect eons ese ew eon ain pte reece A eid create eestor ihe A we alee nee eee oe ee 12 Saving Page Setup Settings 2 022
90. Harmonic Zero Point Energy Heat Capacity Heat of Formation Henry s Law Constant Mol Weight Molecular Mass Molecular Surfaces Molecular Topological Index Molecular Volume Mulliken Charges Mulliken Populations Spin Density Sum Of Degrees Sum of Valence Degrees T Thermodynamic Energy Topological Dia meter Total Connectivity 163 of 315 ChemBioDraw 14 0 Connolly Accessible Area Connolly Molecular Area Connolly Solvent Excluded Volume Critical Pressure Critical Temperature Critical Volume D Dipole E Electron Density Electrostatic Potential Elemental Analysis Enthalpy Entropy Exact Mass F Formal Charge Frequencies Hyper Polarizability m z Hyperfine Coupling N Constants I Num Rotatable Bonds Ideal Gas Thermal O Capacity Internal Energy Ovality Ionization Potential P K Kinetic Energy Partition Coefficient pKa L Polar Surface Area LogP Polarizability LogS Potential Energy Lowdin Charges Principal Moment Lowdin Populations R M Radius Mass RMS Force Melting Point S Mol Formula SCF Energy Mol Formula HTML Mol Refractivity Shape Attribute Shape Coefficient P gt Perkin For the Better Total Energy Total Valence Con nectivity V Vapor Pressure W Water Solubility Wiener Index Z Zero Point Energy ChemBioFinder Properties The properties listed below can be calculated in ChemBioFinder Ultra for ChemBioOffice For more info
91. Hold down the lt SHIFT gt key to select more than one 2 Navigate to Structure gt Expand Label When you expand a residue into its structure the label appears below the structure Contracting Labels To collapse the structure back to its label in the sequence 1 Double click the label to select the structure 2 Navigate to Structure gt Contract Label If you edit the label prior to contracting the structure the new label text is incorporated into the contracted structure For example if you modify a residue and change its name from Ala to Ala on contraction the sequence contains the string Ala Clean Up Biopolymers After you contract the labels you can use the Clean Up Biopolymer command to clean the sequence This com mand re arranges the sequence so that the residues are aligned and wrapped To specify the number of residues per line and the number of residues per block in a biopolymer select the biopolymer and navigate to Object gt Object Settings gt Biopolymer Display tab Chapter 8 Drawing Biopolymers 106 of 315 hemBioD 14 i ChemBioDraw 0 Perkin For the Better Modifying Sequence Residues Note When you modify a residue structure in your drawing you must define a new nickname to ensure that the contracted label includes your changes To modify a sequence residue 1 If the residue in the sequence is contracted right click the residue and select Expand Label 2 Modify the re
92. If you add atoms or bonds to a grouped structure the new atoms and bonds are part of the group To group objects 1 Select the objects using a selection tool 2 Navigate to Object gt Group To select an individual object within a group move the selection tool over the object until it is highlighted and click once Chapter 6 Basic Drawings 85 of 315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better To select grouped objects move the selection tool over an object in the group until it is highlighted and double click it Ungrouping Objects To ungroup objects 1 Select a group 2 Navigate to Object gt Ungroup or right click the group and select Group gt Ungroup To create a group so that individual objects cannot be selected integral group 1 Select the objects 2 Navigate to Object gt Group 3 Right click the group and select Group gt lIntegral To restore an integral group to a regular group 1 Select the integral group 2 Right click the group and deselect Group gt lIntegral 7 Note Many of the shapes and drawings within the template documents are integral groups However they can be ungrouped and edited Scaling objects To scale one or more objects to a different size 1 Select the object s 2 Doone of the following Goto Object gt Scale Double click a resize handle The Scale Objects dialog appears Scale Objects m Scale selected objects so that median bond is Fixed Leng
93. Import Export gt Import Table or Import ChemFinder list and select the file to import Normal searches Use anormal search to find full structures and substructures that match the one you define in the search dialog box Select a cell containing the label Structure Goto ChemOffice14 gt Search gt Normal The ChemDraw for Excel dialog box appears Select the Search Tab Click in the empty window and draw the structure for which you want to search Select the Normal tab at the bottom of the dialog box For Search Type select either Full Structure or SubStructure For Filter Type select to either include or exclude hits Enter a formula query O CON OO FPF W N 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 Select a cell containing the label Structure Goto ChemOffice14 gt Search gt Similarity The ChemDraw for Excel dialog box appears Select the Search Tab Click in the empty window and draw the structure for which you want to search Select the Similarity tab For Search Type select either Full Structure or Sub Structure Select the Sort Results order Select the Similarity Perce
94. K 1 in SI units The thermal capacity at constant pressure of an ideal gas is _ 6 2 Cae 37 p 1 Nk Where H is the enthalpy of the gas calculated as H U pV MOLECULAR_NETWORKS_LOGP The partition coefficient is a ratio of concentrations of un ionized compound between two solutions To measure the partition coefficient of ionizable solutes the pH of the aqueous phase is adjusted so that the predominant form of the compound is un ionized The logarithm of the ratio of the concentrations of the un ionized solute in the solvents is called LogP Normally one of the solvents chosen is water the second is hydrophobic such as octanol MOLECULAR_NETWORKS_LOGS MOLECULAR_NETWORKS _LogS determines the solubility of a substance measured in mol liter The aqueous sol ubility of a compound is known to significantly affect absorption and distribution characteristics of that compound MOLECULAR_NETWORKS_PKa MOLECULAR_NETWORKS PkKais the negative log of the acid dissociation constant Ka It describes the tendency of compounds or ions to dissociate in solution Mass This is the mass of one molecule of a substance relative to the unified atomic mass unit u equal to 1 12 the mass of one atom of 12C Also called molecular mass Melting point Is the temperature at which a solid becomes a liquid at standard atmospheric pressure At the melting point the solid and liquid phase exist in equilibrium The formula to calc
95. NELGOVLALFLSIVIL GOLMPFLHTSKRURSMSAILRPLSOALFWTLIMDLLTLTWIGSOPVEYPYTIHIOOMASILY TF SILAPFPLPIAGX IENY When you hover your mouse over the residue a description of the residue and sequence data appears WL P W G O M S F W G T N V E W 1 W G G F 5 _D K A T L N R F F A F H F 41 P F T M V A L A G V H L T F L H E T G 9 H N P L G L T S 0 S 0 K 1 P F H P T K 0 F L 6 L_ L L l L L L L L A L L P 0 M L G Chapter 8 Drawing Biopolymers 105 of 315 W P l Paste Text Strings You can also paste text strings with valid separators Space tab and dash are considered as valid separators The text string you copy can be generated within or outside of ChemBioDraw The text strings must contain valid residue names nicknames optionally including termini If no termini are explicitly defined then default termini is assigned To paste a text string 1 Copy the text string for example H Ala Gly Pro NH2 and right click in an empty space 2 From the context menu select Paste Special gt Biopolymer The text string is pasted as a sequence 1 2 3 H Ala Gly Pro NH _ Note The labels in the text string must correspond to explicit nicknames Expanding Sequences After creating a Sequence you can expand the whole sequence or just specific labels To expand a sequence 1 Select one or more labels in the sequence using lasso tool or marque tool
96. Preferences To select which types of chemical warnings to display 1 Navigate to File gt Preferences 2 Click the Warnings tab 3 Select the types of warnings and click OK The types of warnings are listed below Warning Description An Object drawn has an improper valence or charge For example when positive and neg Valence and Charge ative charges have been assigned to the same element charges have been assigned in Errors more than one way or a charge has been assigned to a nickname generic nickname or alternative group name Unbalanced Par Parentheses are not matched into nested open close pairs entheses Generated for invalid isotopes For example this warning is generated for every label that Invalid Isotopes has anumeric superscript immediately preceding an atomic symbol where the super scripted number does not correspond to a recognized isotope For example 4CH Isolated Bonds An unlabeled single bond is not attached to other bonds Atoms Near Other Bonds An atom is close to a bond but not attached to it Unspecified Stereo l EDO An asymmetric center is without attached wedged hashed dashed or bold bonds A stereocenter where the absolute stereochemistry cannot be determined from the struc ture as drawn For example this warning would be generated for a carbon atom attached by bold bonds to four different ligands Chapter 6 Basic Drawings 90 of 315 ChemBioDraw 14 0 i Perkin For the Better
97. Reaction Stereo property specifies that the selected atoms are stereocenters in a reaction This property is mean ingful when only searching a database containing chemical reactions Br Br Fri aTi MIH gt h cl i k Chapter 14 Query Structures 236 of 315 Figure 14 4 The reaction stereo indicator circled 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 reaction Retention Finds compounds whose selected atoms have an unchanged stereo configuration after a reaction Free Sites Using free sites you can specify the maximum number of substituents a result can have However it also requires that the bonds in the results appear exactly as they appear in the query structure ChemDraw uses the following nota tions for free sites 0 Zero free sites a 1 One free sites a 2 Two free sites a 3 15 Three through fifteen free sites For example assume you want to use the query structure below to search for as many as two substitutions on the vinyl carbon atom while maintaining the bond pattern Your query structure would look something like this H N Some of the results can include H N Figure 14 1 E 3 4 aminophenyl acrylic acid Chapter 14 Query Structures 237 of 315 HN Figure 14 2 4 cyclohexylidenemethyl aniline NH Figure 14 3 E
98. Sheet ChemOffice2014 ChemDraw Chem Draw tems New Document cds Browse tists menieiiditees 2 Customize the options found in the General Preferences dialog based on your work needs The options dis play under three categories Molecules amp Structures Import Export and Misc Molecules amp Structures e Double Click To Add Molecule Launches ChemDraw when you double click a cell e Ask Before Adding Molecule Prompts a message when you double click a cell to add a molecule e Use Filename in Load Molecule Displays file name instead of chemical formula below the molecule after loading the molecule e Align Structure Specifies how the structure is aligned in a cell You can choose to reduce the column width row height or both Import Export e Import Table Specifies whether to overwrite the table or to append records to the existing table e Automatically generate structures while importing a table Generates structure pictures for each record while importing a table using the Import Table command Disabling this option can speed up the import pro cess Only structure and table data are imported and no pictures are generated Select the structure cells and use Show Picture to display the pictures e Ask If Record Import Count Exceeds Prompts a message when the table being imported contains more records than the count number specified e SDF Export Version Specifies the Structure Data File SDF version expo
99. The method of replacing residues is demonstrated for tetraglycine sequence below 1 Draw a tetraglycine sequence H Gly Gly Gly Gly OH 2 Select Bioploymer Editor in the Biopolymer toolbar 3 Inthe tetraglycine sequence click on the 4th Gly residue An orange chevron indicates the position where the next residue will be inserted H Gly Sly Gly Gly gt OH 4 Select Replace current residue mode in the biopolymer toolbar The Gly text is selected 5 Type Ala or click the Ala button to replace Gly H Gly Gly Gly Ala2 OH To change the form of a residue 1 On the tetrapeptide sequence above click on the 2nd Gly residue 2 Click and select both the L amino acid and the Beta amino acid 3 Click Cys button to replace Gly with beta Cys as shown H Gly pCys Gly Ala OH Adding Residues You can add one or more residues to an existing sequence To add a residue Chapter 8 Drawing Biopolymers 109 of 315 1 Choose the appropriate biopolymer tool 2 Click a residue you want the new residue to be adjacent to An orange chevron indicates the insertion point 3 Type the new residue The new label is added to the right of the existing residue Note To prepend or insert at the beginning of a sequence select the terminus atom select the amino group pro tein sequence or 3 group DNA RNA sequence Numbering Residues You can display the residue ID above any residue To display t
100. Three letter D amino acids have the prefix D Chapter 8 Drawing Biopolymers 101 of 315 W P Note The lt SHIFT gt key acts as a toggle Hence to enter D amino acids press lt SHIFT gt while entering a single letter sequence while in L mode Alternatively to enter L amino acids while in D mode press lt SHIFT gt while enter ing a single letter sequence _ Note You can enter three letter amino acids using the Biopolymer Editor on page 102 and you can use either the keyboard or toolbar to enter residues 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 where you want to start the sequence A text box appears 3 Inthe text box enter the single letter label for the residue Note For a list of residue labels see IUPAC Codes on page 111 4 Repeat step 2 for each residue 5 When your chain is complete press lt ENTER gt or lt Esc gt By default when creating a Sequence new residues are inserted after the current active residue The insertion point is indicated by an orange chevron You can overwrite or replace a sequence atom using the residue replacement button You can also replace a sequence atom by hovering over a residue and pressing a hotkey when no active residue is present Biopolymer Editor The Biopolymers toolbar contains a tool called Biopolymer Editor Biopolymers J x PA AA DNA RNA B L
101. Up Structure command See Chains on page 69 and Attachment Points on page 122 Units Set the units used in the Object Settings dialog box to centimeters inches points or picas Atom and Bond Indicators Set which indicators to display See Atom Numbering on page 124 Configuring Documents 1 Navigate to File gt Document Settings 2 Click the Drawing category and configure the settings 3 Click OK Terminal Carbon Labels By default ChemBioDraw does not display terminal carbons To display terminal carbon labels 1 Navigate to File gt Document Settings Chapter 4 Preferences and Settings 25 of 315 ChemBioDraw 14 0 PerkinElmer For the Better 2 Select the Atom Labels category 3 Select Show Labels On Terminal Carbons See figure below Er es Text Effects Line Spacing Underline Automatic 7 fe variable C Fixed at Qin Configuring Objects To configure the drawing settings for a selected object 1 Select the object 2 Navigate 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 into your drawing You can also rename these properties when desired For instance you may consider renaming Molecular Weight to MW to save room on the page The changes you make apply only to the properties you paste in your drawing The names in the Ana
102. You can type or paste chemical names into cells and convert the names to structures 1 Enter the names into cells 2 Select the cells to convert Tip You can also convert names generated from Excel formulas 3 Select ChemOffice14 gt Convert gt Name To Molecule If the cell contains a name that Name Struct supports the structure appears with the given name as the name of the cell Saving structures You can save a chemical structure to a separate file 1 Inthe worksheet select the cell containing the structure 2 Goto ChemOffice14 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 The following formats are supported ChemBioDraw cdx Connection Table ct ChemBioDraw XML cdxml MSI Molfile msm ChemDraw 3 5 chm SMD 4 2 smd ChemBio3D XML c3xml Metafile wmf MDL Molfile mol GIF gif MDL Sketch skc TIFF tif MDL Rxn rxn PNG png MDL Graphic tgf Bitmap bmp PostScript eps Searching You can search for structures based on the criteria 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 a structure database Chapter 12 ChemDraw Excel and CombiChem 184 of 315 1 In Excel go to ChemOffice14 gt New ChemOffice Worksheet 2 Goto ChemOffice14 gt
103. a vapor in equilibrium with its solid or liquid phase Vapor pressure measures the con centration of solvent molecules in the gas phase Vapor pressure can be calculated using Raoult s law The formula to calculate vapor pressure is Prot E X P X r Where p is vapor pressure i is a component index and y is a mole fraction Water solubility Is the maximum amount of a substance that can be dissolved in water at equilibrium at a given temperature and pres sure Water solubility is measured in mg L Wiener index Provides measure of branching defined as 24 W pa Where D are the off diagonal elements of the distance matrix General Preferences From the General Preferences dialog you can customize ChemDraw for Excel for your specific work needs To customize ChemDraw for Excel 1 Navigate to ChemOffice gt Options gt Preference The General Preferences dialog appears Chapter 12 ChemDraw Excel and CombiChem 210 0f 315 General Preferences 25 Molecule amp Structures Double Click To Add Molecule Overwnte existing table 7 Ask Before Adding Molecule E Use Filename in Load Molecule W Automatically generate structures while importing a table Ask lf Record Import Count Exceeds 300 Align Structure Pee Both column width and row height can be reduced ka a SESE EE v20 Misc W Ask Before Clearing Cells Copy Structures to MS Word As Bitmap Serer Default Style
104. abetic labels to plate rows Chapter 12 ChemDraw Excel and CombiChem 219 of 315 W P ChemScript ChemScript is the cheminformatics Software Development Kit SDK It contains the programming algorithms that are common throughout PerkinElmer products As a software developer you can apply ChemScript to create your own scripts to use with ChemBioOffice applications All example script files in the ChemScript library are available in Python and C NET If you are familiar with either of these languages you will find these scripts easy to understand However if you are new to either Python or C NET we suggest that you refer to the Web sites and books listed at the end of this chapter Although ChemScript is available in Python and C NET we will use Python in this guide to explain ChemScript Python is a non proprietary and widely used programming language Why use ChemScript ChemScript adds considerable versatility to how you manage your chemical data Using ChemScript you can modify view and transfer your data from one place to another using your own custom rules Here are just a few common uses Salt splitting and stripping Identify and remove salt fragments from a drawn structure and register the pure compound Canonical codes Generate canonical codes for a set of structures and use the codes to find duplicates in your data File format conversion Convert structure or reaction files from one format to another Genera
105. able Attachment command to draw different positional isomers of a compound using an abbreviated notation that retains chemical significance Chapter 9 Advanced Drawing Techniques 122 of 315 ChemBioDraw 14 0 i Perkin For the Better For example you can explicitly draw the three isomers of dibromobenzene as shown below Alternately you can express all three isomers as a single parent structure by using a variable attachment as shown below Br e Abbreviated notation for Er Br Figure 9 5 Isomers of dibromobenzene To add a variable attachment point to a structure 1 Select all or part of the structure 2 Navigate to Structure gt Add Variable Attachment 3 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 Note To draw the structure below you should only select the 5 rings atom that do not already have a bromine atom bound to them Selecting the entire molecule would cause a valence problem with the topmost carbon Tip If fixed lengths is enabled press lt ALT gt as you drag the bond Br Br Chapter 9 Advanced Drawing Techniques 123 of 315 W P l 7 Note After you draw a bond from an attachment point the asterisk disappears To view an attachment point pos ition the cursor over it with either a bond tool or a selection tool Atom Numbering You can add sequential numbers or
106. able dialog and click OK Insert Table Roms E Columns E Cancel The table appears in the document window Resizing Tables To resize rows or columns click and drag a border using the table tool Note To proportionally resize all rows and columns in the table click and drag the top and left border of the table Customizing Borders To customize the borders of the table 1 With the Table tool selected right click a border 2 Click Borders on the context menu The Table Borders dialog appears Chapter 3 Page Layout 16 of 315 hemBioD 14 f ChemBioDraw 14 0 PerkinElmer For the Better Table Borders Style Click on diagram below Dashed to apply borders Color Custom 3 Under Setting select a border setting 4 Under Style select the style color and width of the border to apply 5 For a custom border select the desired borders in the table diagram 6 Click OK The table tool includes commands to align cell contents fit add or delete cells and clear cells In general to change the table work with the right or bottom borders To change a row or column work with the left or top borders To resize a cell to fit its contents 1 Point to a border and right click 2 Choose Size To Fit Contents The cells resize to fit around the contents To add or delete rows or columns in the table 1 Point to the top or left border where you want to add or delete the row or column A border app
107. al data Template Based Product Generation Automatic generation of products from a set of reactants and a generically defined reaction For example reactions like those between amines and carboxylates Chapter 13 ChemScript 223 of 315 Substructure Identification and Mapping Atom by atom comparison of a molecule with a substructure Positive matching provides an atom by atom map of the substructure atoms to those in the molecule Salt Stripping Remove salts from a reaction based on a pre defined list of salt fragments Structure Orientation Enforce standard orientation of structures based on the established orientation of a common scaffold 2D Structure Generation and Cleanup Use ChemBioDraw based algorithms to generate structure from scratch or after modifying chemical data using a pro gram Canonical Codes Generate unique identifying codes from a chemical structure File Format Conversion Read and write file data using all PerkinElmer supported file formats CDX CDXML MOL CHM SKC SMILES etc Chemical Name and Structure Conversion Use the ChemBioDraw Struct Name feature to generate structures from chemical names and names from their struc tures Molecular Mechanics Optimize molecular structures using the MM2 force field The ChemScript API online PerkinElmer also provides the documentation of the API online You can find the API at sdk cambridgesoft com Tutorials We provide several sample scripts to illu
108. an upper case 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 as NCH This label has three tokens N C and H If you label C3 the tokens are placed from left to right because there are bonds to the left of the atom If you label C5 the tokens appear 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 prevents the label from flip ping when applied to the left side of a structure For example if you define the nickname CH n and label C5 with the combined label and nickname NCH 2 the final ori entation is CH N instead of HCN In this case the nickname CH is a token Chapter 4 Preferences and Settings 29 of 315 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 Changing Default Formats Each new caption or atom label uses default document settings for the font font size and style of captions and atom labels You can change the format by m Changing the document settings for subsequent drawings in the current document m Choosing a new format for an i
109. angle 2 Drag the rotation handle clockwise or counterclockwise 3 Torotate an atom label with a structure press the lt control gt key while dragging the structure Note Ifa single atom is unselected when a structure is rotated the structure rotates around the unselected atom as Shown in the example below To rotate a selected object by a specified angle 1 Do one of the following Navigate to Object gt Rotate Double click the rotation handle The Rotate Objects dialog appears 2 Enter a number and click either degrees CW for a clockwise rotation or degrees CCW for counterclockwise rota tion 3 Torotate the atom label text select Rotate Atom Labels 4 Click Rotate Objects are rotated around the center of the selection rectangle 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 Navigate 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 Chapter 6 Basic Drawings 82 of 315 1 Select the object A center of rotation indicator appears in the center of the object as shown in the figure Figure 6 8 A Center of rotation 2 While pressing the lt alt gt key click and d
110. aracter Map Window The character map is shown below Character Map zd JA alele mba il ona EE EE ofo fo fo fo jo fo fo fo jo fo fo fo fo fo fo eale hle Hf Le ofiz ja a siel7 lels f felli 4 l lo r t ofa v feole ft Y efele le Z r LITT TUT OU UT AN fi jo The character map is active only when a text field 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 field 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 field The eight most recently used characters appear at the top of the window A character may appear more than once in this section if the versions use different fonts Click the Back button to toggle among all the displayed characters Hotkeys Hotkeys are keys on your keyboard that are linked to specific atom labels Use ChemBioDraw hotkeys to quickly label atoms and apply atom properties The Hotkeys xml file in the ChemDraw Items folder contains the hotkeys provided with ChemBioDraw You can add or change hotkeys by editing this file in a text editor 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 curs
111. arbon atom must appear at the specified location Chapter 14 Query Structures 228 of 315 H N You can use other generic labels to indicate other types of query criteria The generic labels that ChemBio Office sup ports are listed below all are recognized as chemically significant m A Represents any non hydrogen M Represents a metal Q Represents an atom that is neither hydrogen nor carbon m X Represents any halide R Unrestricted represents one or more connected atoms of any kind To add a generic label to a structure do one of the following 1 Double click the atom to open a text box and type in the nickname 2 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 Customizing Hotkeys on page 33 Defining Generic Nicknames The generic nicknames recognized as chemically 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 displays because the structure contains variable substituents If you ignore this message th
112. ase for compounds that match the reactant query struc tures Once all the matching compounds are found CombiChem generates a list of reactions from the compounds that were found in the query The generic reaction you create must meet these criteria All generic atoms in the reactant s must be represented by R groups Solvents catalysts and other real world elements must not be included in the generic reaction m Multi step generic reactions are supported Entering a generic reaction To enter the generic reaction you must first create a reaction worksheet Goto ChemOffice14 gt CombiChem gt New Reaction A new worksheet named Reactions appears in your work book You then add the generic reaction to the reaction worksheet by either importing it or drawing it in ChemBioDraw To import the reaction 1 Place your cursor in the cell that contains the text Reaction Double click to edit 2 Either click the Load Molecule icon on the ChemOffice toolbar or go to ChemOffice14 gt Molecule gt Load 3 Browse to the file that contains the generic reaction and click Open The reaction appears in the Reactions work sheet To draw the reaction in ChemBioDraw 1 Double click the cell that contains the text Reaction Double click to edit 2 When asked whether to add a new molecule click Yes ChemBioDraw launches Chapter 12 ChemDraw Excel and CombiChem 213 of 315 3 In ChemBioDraw draw the generic reac
113. ashed wedged bond Fuse 5 membered ring Fuse 6 membered ring Fuse 7 membered ring Fuse 8 membered ring Create chair form of cyclohexane with two different ori entations Function Hotkeys Function Key Add an attachment point period Add an atom number single quote Add a negative charge Add a positive charge Sprout one bond 0 Sprout two bonds 9 Sprout three bonds 8 Display the Atom Properties dia Slash or log box Display the Choose Nickname dia equals log box Chapter 5 Shortcuts and Hotkeys P gt Perkin For the Better Key slash or h 5 9or0 46 of 315 ChemBioDraw 14 0 Function Key Open an atom label text box lt Enter gt Remove an atom label Shortcuts lt Backspace gt lt Delete gt or lt space gt Below is alist of key combinations for common tasks File Command Create a new doc ument Open a document Save a document Save a document as Print a document Page setup Close a document Exit ChemBioDraw Edit Command Cut Copy Paste Select all Undo Redo Repeat last command Key Combination CTRL N CTRL O CTRL S SHIFT CTRL S CTRL P SHIFT CTRL P CTRL W ALT F4 Key Combination CTRL X CTRL C CTRL V CTRL A CTRL Z SHIFT CTRL Z CTRL Y Chapter 5 Shortcuts and Hotkeys P gt Perkin For the Better 47 of 315 ChemBioDraw 14 0 Command Clear View Command Actual size Reduce Magnif
114. assigned to nucleic and amino acids You can expand contract or remove labels to complete the drawing To display the Biopolymer toolbar navigate to View gt Show Biopolymer Toolbar The Biopolymers toolbar appears Biopolymers x fa AA DNA RNA B fy D Ala Arg As Asp cys Gin Glu Gly His Ile A R H D C 9 E G H Leu Lys Met Phe Pro Ser Thr Trp Tyr Val L K M F P 5 T WW W A C G T A C G U The Biopolymers toolbar includes the following options Biopolymer Editor Enables all the nucleic and amino acids Single Letter Amino Acid Enables all the amino acids Beta Amino Acids L Amino Acids D amino Acids Enables addition of Beta L and D amino acids DNA Sequence Enables the deoxyribonucleotides that can be used to create a DNA molecule RNA Sequence Enables the ribonucleotides that can be used to create a RNA molecule To draw a sequence 1 Select one of these tools from the Biopolymer toolbar AA1 tool Single letter amino acid tool Create a polypeptide chain using a one letter label to represent each amino acid You can create the sequences by typing the IUPAC code for the standard amino acids or by pressing the icons on the toolbar By default L amino acids are created Single letter sequences are drawn with a fixed separation so that residues align with residues in adjacent rows You can create D amino acids using the D amino acid stereochemistry option Single letter D amino acids are displayed in lower case
115. atoms you have drawn Changing Chain Direction To change the direction as you draw use the Snaking chain tool or press the lt Control gt key with Acyclic tool selec ted while drawing in the direction you want Note Release the mouse button before you release the lt Control gt key Applying Fixed Lengths Applying fixed lengths and fixed angles enables you to create structures with consistent bond lengths and angles The fixed length dimension is set in the Drawing Settings dialog The fixed angle dimension increments angles by 15 degrees Fixed length is used to constrain the length of the bonds drawn to the length you specify when the Fixed Lengths command in the Object menu is enabled with a check mark This also adjusts the preferred bond length for struc tures modified by the Clean Up Structure command When Fixed Lengths is enabled the pointer on the Acyclic chain can be dragged 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 change this position by dragging in the opposite direction lf Fixed Lengths is disabled hold down the lt Control gt lt ALT gt keys to reverse chain direction Fixed Angles must be enabled to reverse direction Fixed Angles When Fixed Angles is enabled the angle the Acyclic chain makes relative to the X axis is constrained to 15 degree inc
116. bel 2 Navigate to Object gt Object Settings The Object Settings dialog appears Captions You specify the caption justification and line spacing on the Text Captions tab of the Object Settings dialog All text in a single caption must have the same justification and line Spacing There are four available justifications Alignment Flush Left Flush Left Center Flush Right Justified Flush Left Creates left justified 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 Chapter 4 Preferences and Settings 28 of 315 Note When using Stacked Above justification enter the tokens from top to bottom using lt alt gt lt enter gt to go toa new line If you change the justification after the label is entered waming may appear Examples of the atom label justifications are shown below fl H l o C C D N CH gt cH Olle OMe a E bi Z CC B RNH Figure 4 1 Atom label justification A stacked above B centered C flush left D flush right Automatic Alignment When you justify atom labels automatically ChemBioDraw breaks the label into tokens A token consists of
117. bols 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 Indicating an attachment point is useful in polymer bound combinatorial synthesis protein chemistry and other situ ations The Chemical Symbols toolbar includes attachment point drawing tools that indicate a point of attachment while maintaining chemical meaning Chapter 11 Chemistry Features 157 of 315 ChemBioDraw 14 0 i aa Perkin For the Better _ ia The bead tools are intended to indicate attachment to a resin Any of these tools may be used for variable attach ments in queries see Attachment Points on page 122 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 _ Note You can resize a polymer bead by selecting it with a marque tool and dragging the resize drag handles 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 example the radical cation symbol is rotated and resized from the charge The Info window shows the angle that one of the ends of a symbol makes with the X axis as you rotate To rotate a chemical symbol 1 Select the chemical symbol 2 Drag the rotation han
118. ce from its constituent elements at constant pressure Henry s Law Constant A unitless value Henry s Law Constant can be expressed as kH pe 7 Where p is the partial pressure of the solute in the gas above the solution c is the concentration of the solute and K e is a constant with the dimensions of pressure divided by concentration The constant known as the Henry s law constant depends on the solute solvent and temperature LogP The partition coefficient is a ratio of concentrations of un ionized compound between two solutions To measure the partition coefficient of ionizable solutes the pH of the aqueous phase is adjusted so that the predominant form of the compound is un ionized The logarithm of the ratio of the concentrations of the un ionized solute in the solvents is called LogP Normally one of the solvents chosen is water the second is hydrophobic such as octanol The formula to calculate LogP is solute I log P _ lee he octfwat toite a c patente LogS LogS determines the solubility of a substance measured in mol liter The aqueous solubility of a compound is known to significantly affect absorption and distribution characteristics of that compound Chapter 11 Chemistry Features 161 of 315 ChemBioDraw 14 0 i aaa Perkin For the Better _ Note LogS calculations are available only in Microsoft Windows version of ChemBioDraw Melting point Is the temperature at which a solid becomes a liq
119. cel and CombiChem 205 of 315 W Where m U is the internal energy SI unit Joule pis pressure SI unit Pascal m Vis volume SI unit m3 a T is the temperature SI unit Kelvin Sis the entropy SI unit joule per Kelvin H is the enthalpy SI unit Joule 7 Note H and S are thermodynamic values found at standard temperature and pressure Heat of formation Reported in KJ mole the heat of formation is the increase in enthalpy resulting from the formation of one mole of a sub stance from its constituent elements at constant pressure Henry s Law constant A unitless value Henry s Law Constant can be expressed as KH pe E Where p is the partial pressure of the solute in the gas above the solution c is the concentration of the solute and kK m is a constant with the dimensions of pressure divided by concentration The constant known as the Henry s law constant depends on the solute solvent and temperature Ideal gas thermal capacity The thermal capacity at constant volume of an ideal gas is d p SF T epika i uR Lum Where m Cj is a constant dependent on temperature m U is the internal energy a T is the absolute temperature a Vis the volume nis the amount of substance of the gas Ris the gas constant 8 314 J K 1mol 1 in SI units Chapter 12 ChemDraw Excel and CombiChem 206 of 315 N is the number of gas particles J Kp is the Boltzmann constant 1 381x10 23J
120. ch it is attached Additivity rules determine the increment of each contribution If an increment for a substituent cannot be determined ChemNMR uses embedded substituents smal ler 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 substructures as names com pound classes in most cases substituents in the form of a linear code respectively It also implements models for ethylenes cis trans and cyclohexanes equatorial axial To view 1H or 19C NMR information 1 Select a structure 2 Navigate to Structure gt Predict 1H NMR Shifts or Predict 13C NMR Shifts ChemNMR redraws the molecule with the estimated shifts and displays the information and line spectrum in a new window Modifying NMR Frequency You can change the default NMR frequency of 300 Mhz in ChemDraw Proton NMR predictions To change the frequency Chapter 11 Chemistry Features 174 of 315 hemBioD 14 i ChemBioDraw 0 PerkinE For the Better 1 Navigate to File gt Preferences The Preferences dialog appears 2 Select ChemNMR option Preferences x ira rni E ir Tepls arin Oper for 1HE kigh Tet peka DEN een e bW Appi iban guppied experimental dts b App uer pappia aaperimenta data piora f
121. ched 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 Chapter 16 Chemical Interpretation 279 of 315 A multi attached label that is parsed from left to right O CH CCHa A multi attached label that is parsed from right to left HaCCH C A bond attached to the open parenthesis of a repeating CH3 40H group is treated as if bonded to the first of those groups CH2 CHy 0H A bond attached to the close parenthesis or repeat count of CHo a repeating group is treated as if bonded to the last of those ij groups CHalGHs gt CH Multiple fragments within a single label can be specified Implicitly using standard valence rules COO Na Explicitly using a Space period unsuperscripted or unsub ne scripted bullet or combination COoc Na CO0 Nat COO Na An unsuperscripted unsubscripted integer at the start of a frag CHOC h Na F E nore ment is recognized as a stoichiometric multiplier and is treated as CHOO hNatNatNat if the appropriate number of fragments were drawn explicitly Chemically Significant Text Often it is simpler to write a chemical formula like MeOH or H 50 than to draw an atoms and bonds structure ChemBioDraw interprets any unamb
122. ck the attachment points with the Attachment Point tool Hiding 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 To hide the attachment rank indicators and remove the numbers from the attachment points 1 Navigate to File gt Preferences 2 Inthe Preferences dialog click Building Display 3 Deselect Show Attachment Rank Indicators This change affects all documents Chapter 14 Query Structures 252 of 315 ChemBioDraw 14 0 i Perkin For the Better The figure below shows an alternative group definition and a parent structure with the attachment rank indicators hid den Figure 14 14 Hidden attachment indicators R group reaction queries You can search and store reactions In a reaction one or Several compounds reactants are transformed into other compounds products Individual reactants or products are separated from each other with plus signs The react ants are separated from the products with an arrow You can also search for chemical reactions containing r groups An example of a chemical reaction containing r groups is shown below Searching for reactants Searching for reactants is useful if you have a known starting material and you are interested in learning more about what substances it can produce A reactants query is v
123. ct Object Settings from the context menu 3 From the Drawing tab under Atom Indicators and Bond Indicators select Show Stereochemistry The stereo centers are marked as shown in this example Chapter 11 Chemistry Features 151 of 315 i 14 i ChemBioDraw 0 PerkinElmer For the Better cholesterol Hiding Indicators 1 Select the indicator you want to hide 2 Right click and select Hide Indicator from the context menu Formatting Indicators To change the font style 1 Select the indicator you want to manipulate 2 Right click and select the Style from the context menu Applying Parenthesis To apply parentheses to stereochemistry indicators 1 Navigate to File gt Preferences 2 From the Preferences dialog under the Building Display tab select Include Parentheses When Showing Ste reochemistry Removing Indicators To remove an indicator click on it using the Eraser tool Positioning Indicators You can position a query indicator by either dragging it or entering a numeric value for the new location To indicate an exact location Chapter 11 Chemistry Features 152 of 315 1 Select the indicator you want to re position 2 Right click and choose Position from the context menu The Position Indicator dialog appears 3 Click the appropriate option and type a value as described in the table below To Position Type a Value for the Position by From the atom or bond center Angle in degrees to indicator c
124. cules by using a constrained least squares technique This method works with a standard deviation 1 27 cm mol and can handle molecules containing hydro gen oxygen nitrogen sulfur and halogens Method Two Is an extension of method one that includes 120 atomic contributions evaluated from 538 molecules by using a constrained least squares analysis technique In addition to the atoms introduced for method one this method can handle molecules with phosphorus and selenium atoms This method works with a standard deviation of 0 77 cm mol Chapter 17 Property Calculations 290 of 315 W P i pKa CLogP and CMR Specific algorithms for calculating LogP and molar refractivity from fragment based methods developed by the Medicinal Chemistry Project and BioByte For more information see http www biobyte com blqsar index html LogP and CLogP estimate the Octanol Water Partition Coefficient but use different methods CLogP and CMR are calculated as part of the Chemical Properties window Several other sources exist for LogP data however The ChemBioDraw Report Window for LogP Prediction The Chemical Properties window shows averaged LogP and MR values Via the Report button you can see the original values from each applicable estimation method The estimation methods are Crippen s fragmentation Viswanadhan s fragmentation and Broto s method The ChemBioDraw Report Window for LogP Empirical Data For selected substances the Ch
125. d Above a Below Chapter 6 Basic Drawings 54 of 315 Centered p nA 1 Click the bond tool used to create the existing double bond 2 To change the alignment do one of the following Click the center of the double bond Right click point to Bond Position on the context menu and choose the alignment Moving Atoms To move an atom ina structure click and drag it using a selection tool To move two bonded atoms in a structure click and drag the bond between them To move individual atoms 1 Click a selection tool 2 Point to the atom you want to move A highlight box appears over the atom 3 lt SHIFT gt drag the atom _ Note You can also move atoms using a selection tool See Moving Objects on page 83 Reducing Ring Size You can reduce the number of atoms in a ring For example you can convert cyclohexane to cyclopentane To reduce the ring size do one of the following Using the selection tool click and drag m Using a bond tool point to an atom and lt SHIFT gt drag Release when one atom is on top of the other The bond between the atoms disappears Bond Crossing When one bond crosses another you can indicate which bond is in front The bond which is behind has a small sec tion cut out so you can clearly discern which bond is front most To move an object to the front position 1 Select the object to move to the front 2 Goto Object gt Bring to Front The selected object now appears in
126. d LA SMILES string is a line of text that represents the structure of a molecule A SMIRKS string describes chemical reac tions in text Chapter 15 Sharing Information 267 of 315 ChemBioDraw 14 0 i aa Perkin For the Better SMILES supports an alternate notation for aromatic structures using lowercase letters ChemBioDraw generates this type of SMILES string for any structure drawn with explicit aromatic bonds Cl CC CC C l Pasting SMILES To paste a SMILES string as a structure 1 Select the SMILES string in the source file and press CTRL C 2 From ChemBioDraw navigate 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 other applications To copy a structure as an SLN string 1 Select a structure 2 Navigate to Edit gt Copy As gt SLN The Structure is copied to the clipboard as an SLN String ciijccccc Creating InChI Strings ChemBioDraw supports IUPAC International Chemical Identifier InChI To copy structures as InChI strings to other documents 1 Select the structure 2 Navigate to Edit gt Copy As gt InChl You can copy only legitimate InChI structures If you attempt to copy a structure that the InChI protocol does not support a warning informs you that the structure is not supported Creating InChIKey Strings ChemBioDraw supports Standard InchlKey available in InChI 1 02 An InChIKey string is a c
127. d Drawing Techniques 000000000000000000000000000 cece cece ee ceececcceeceeceeceeceees 118 Coloring Objects asta ne eects ness acc nes ase se wees ats decease nc aca e ane suede saceneeoeeepeseaseteate 118 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved ji ChemBioDraw 14 0 i Perkin For the Better Be Lae eee nee ee See ve Lee ROE ee nn ve To Ee een eee eee eee ee 119 Attachment Points sec ce Sciticedh coc teenaeciecawhtbedenecoderadsubeoradnsarebeesenadeceuneustceetsadideesuveeaesdeteces 122 Atom Numbering 02 022 cc cece ccc c ccc cece cece ceecceecceecceeceeeceeeceeeeeeceeecccecceeceeeteesteeceeeeeees 124 Structure Perspective 0 2 occ cece ccc cee cece cece ccc e cc ec cee ceeccecceccecceeceecceccecceccecceecceceecces 125 Mass Fragmentation 0 02 c cece cece cece cece ccc e cece cee cee cee ceececccceceeceeceecceecceceeceeceeeeeeeees 126 Drawing Reactions 2 2 elec eee ec ce cece cece cece cece cece ceeceeeceeeceecccecccecceeceeeceeccceceeeceeeeeeeees 127 SOLCON G perpenre oe aceeesee ata eomeecee Sea E a 133 Templates ass 5 ae ees eas ee ee ote eee eet eeu ERARE 136 Defining Nicknames 22 c cece cece cece ccc cece cece ce ceecceeceeeceeecececeecceeceeecececeeceeeceeeceeeeeeees 138 ChemScript 02 0 o ec cee cece cece cece cece eee e cee eec eee eeceeeeeeeceeceeceeceseeseeceecerceseeceeeereerereees 141 Chapter 10
128. d drag your cursor across the drawing window Editing Curves You can edit a curve by selecting it and manipulating it with Edit Curve tool Chapter 6 Basic Drawings 77 of 315 ChemBioDraw 14 0 i aa Perkin For the Better To select an existing curve for editing 1 Select the Edit Curve tool from the Pen Tools palette on the Main toolbar 2 Point at the curve The cursor will change from a to an arrow when you are positioned correctly 3 Click to select the curve The curve is selected and adjustment handles appear along the curve as shown below The cursor appears as a hand with a sign inside However when the cursor is positioned exactly over the points on the curve the symbol disappears and the cursor appears as a hand Changing the Shape of a Curve Use the square handles at the end of the curve to increase or decrease the length of the curve Use the endpoints of the direction lines to change the direction of the curve To change the shape of a curve m Drag the direction lines to create the shape you want Chapter 6 Basic Drawings 78 of 315 W P Adding a Segment You can add a segment to an existing curve by selecting the curve with Edit Curve tool and clicking in the document window with the Edit Curve tool selected A segment is added to the end of the curve Freehand Shapes To create a closed freehand shape draw a curve and navigate to Curves gt Closed To add curve propertie
129. d 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 Based on 222 atomic contributions calculated from 1868 molecules by least squares analysis This method allows a calculation of logP with a standard deviation of 0 43 logP units and can handle molecules con taining hydrogen oxygen nitrogen sulfur halogens and phosphorus atoms If this method is applied to molecules with internal hydrogen bonds the standard deviation is 0 83 LogP units Henry s Law Two methods are used to predict Henry s Law constant Method One An approach based on the bond 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 chem icals This method estimates with a mean error of 0 30 units and a standard deviation of 0 45 units and can handle molecules containing carbon hydrogen oxygen nitrogen sulfur phosphorus and halogens Method Two Henry s Law constant is estimated from an equation found using linear regression Multifunctional compounds were omitted from this study This method should not be used for compounds where distant polar inter action is present Molar Refractivity Two fragmentation methods are used to estimate the molar refractivity value Method One Includes 93 atomic contributions evaluated from 504 mole
130. d to Back F3 Clean Up Biopolymer am Flip Selection Shift Ctrl H Linear Peptide Expand Label Rotate Selection Alt amp Shift4Ctrl H Contract Label Rotate Chri R Scale Ctrl K Object Settings Colors sles Toggle Amino Acid Style AA1 lt gt AA3 Abom b Toggle Amino Acid Stereo Le gt D Bond P Select Biopolymer Backbone Menge Sidechains With Residue Removing Residues When you remove a residue the bonds are automatically re created between the adjacent labels and any gaps closed To remove a residue 1 If the label is expanded contract the structure back to its label 2 Select the label or hover over it Chapter 8 Drawing Biopolymers 108 of 315 3 Press the lt DELETE gt key Replacing Residues The Biopolymer toolbar has two distinct modes of data entry Insertion mode and Replacement mode Insertion mode is the default mode In the Insertion mode an orange chevron indicates the position in which the next residue will be inserted For example the orange chevron in the sequence below indicates that the next residue will be inserted after the 4th Gly residue H Gly sly Gly Gly OH You can replace a residue in a Sequence using the Replace current residue button in the biopolymer toolbar In the replacement mode an orange rectangle indicates which residue is replaced For example the orange rectangle in the sequence shown below indicates that the 3rd G residue will be replaced H G G G OH
131. d using the dative bond tool Chapter 6 Basic Drawings 53 of 315 Wedged Bonds 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 Wedged bonds are drawn with a fixed orientation in a document window To change the orientation of the wedged bond Click the bond using the wedged bond tool 7 Note ChemBioDraw treats hashed wedged bonds with the narrow end in the plane of the screen and the wide end behind the plane Changing Bonds You can change bonds by Changing bond types Changing bond alignment and orientation m Moving atoms m Layering bonds Changing Bond Types Change a single bond from one type to another using one of the following methods Select a bond tool and click an existing bond Right click and select the new type from the context menu a With hotkeys See Shortcuts and Hotkeys on page 44 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 is always a solid or dashed bond 7 Note If you click a tautomeric bond solid dashed again with the dashed bond tool you create an aromatic double bond dashed dashed Aligning Double Bonds Double bonds can have one of three alignments relative to other bonds above below and centere
132. der table fields and their data in the ChemBioFinder table that are not in the MS Excel table are added to the MS Excel table 7 Note Changes you make in MS Excel do not affect the table in ChemBioFinder To synchronize a table Select the table Goto ChemOffice14 gt Sync Table with ChemFinder DB Select the ChemBioFinder table and click Open Select the fields to be used for matching a worksheet row with the database record and click OK O FP WwW N gt Select the fields to be updated To select multiple fields press lt Ctrl gt click each field Selecting fields marked New will add a column to your worksheet 6 Click OK Chapter 12 ChemDraw Excel and CombiChem 182 of 315 Adding structures You can add chemical structures to a worksheet from any file format that ChemBioDraw supports ChemDraw Excel assigns the chemical formula as structure name which can be changed by using the Name Molecule command The simplest way to insert a new structure in a cell is by double clicking a cell 1 Create a ChemOffice worksheet 2 Double click in a cell ChemDraw Excel displays a dialog asking you if you want to add a structure to the cell 3 Click Yes ChemBioDraw opens 4 Draw a structure and go to File gt Close or press lt Ctrl gt lt W gt to return to ChemDraw Excel Structure appears on the worksheet _ Note Double clicking a structure or cell containing a structure on a worksheet will start structure edi
133. des trans Rule 4 Like pairs of descriptors precede unlike pairs Rule 5 R precedes S ChemBioDraw 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 Stereocenter Indicator Double bond Z if the highest ranking ligand of each pair are on the same side of the bond otherwise E Tetrahedral atom When the lowest ranking ligand is located behind the central atom m R when remaining 3 ligands are arranged clockwise in descending order S when remaining 3 ligands are arranged counterclockwise 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 molecule as a whole considering the relationship between all stereo centers Stereochemical flags apply to the nearest structure if no structure is within the distance specified by the Fixed Length value the stereochemical flag is not assigned to any structure Chapter 16 Chemical Interpretation 285 of 315 hemBioD 14 f ChemBioDraw 0 PerkinElmer For the Better Abs COOH COOH Ho NH Figure 16 2 The Absolute flag indicates the exact stereoisomer as drawn Rel COOH NH H2 a iii NH gt Figure 16 3 The relative flag indicat
134. dicated as a range Distance Defines a distance constraint between two points a point and a line or a point and a plane Indicated as a range in angstroms Line Defines the best fit line for the selected points Plane Defines the best fit plane for the selected points or for a point and a line Exclusion Sphere Defines an exclusion sphere around a point If more than one point is selected the exclusion sphere is around the first selected point and the subsequent points are allowed within the exclusion sphere when the query is evaluated Indicated as a range in angstroms beginning at 0 Normal Defines the normal from a defined plane in the direction of a point Point Defines a point positioned at a specified distance from a first point in the direction of a second point in order or in the direction of the normal Centroid Defines a point positioned at the average position of all other points selected Note All constraint values can be edited with the text tool Only exclusion spheres show the change a When you create a point a dialog appears where you specify the distance from the first selected point to the cal culated point The distance may be an absolute value in or a percentage of the distance between the selected points Chapter 14 Query Structures 261 of 315 ChemBioDraw 14 0 i eae Perkin For the Better Negative values indicate that the calculated point is further from the second point than the first p
135. different lane Click the spot with the Eraser tool If you erase all spots in a lane the lane is deleted 1 Right click on a spot 2 Point to TLC Spots and take the appropriate action 3 To display R for all spots right click inthe plate and select Show Rf from the TLC Spots submenu 1 Right click a spot 2 Choose the style or color Note Keeping all styles unchecked creates a hollow spot 3 Tochange the style for all spots right click inthe plate and choose the style from the TLC Spots sub menu lt Shift gt drag the spot When you position the cursor on a spot and press lt Shift gt the cursor assumes one of three shapes depending on how it is positioned Cross arrows used to enlarge a spot Horizontal arrow used to widen a spot Vertical arrow used to elongate a spot or create a crescent Right click a spot and select Show Rf to indicate the spot s retention value By default the value of R is set to two decimal places Chapter 11 Chemistry Features 169 of 315 W P Moving the Tag Either click and drag the tag using a selection tool or Right click the tag and choose Position Edit the values in the Position Indicators box Editing the Rf Value Select the tag with the Text tool and edit the value f 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 Yo
136. ding associated charge For example a delocalized representation of cyclopentadiene must include either a negative charge or a multicenter attachment Displayed for any stereocenter tetrahedral atom asymmetric double bond etc where the absolute stereochemistry cannot be determined from the structure as drawn For example this message would be shown for a car bon atom attached by bold bonds to four different ligands This message is displayed only when Show Stereochemistry is also turned on Displayed for every label that has a numeric superscript immediately pre ceding an atomic symbol where the superscripted number does not cor respond to a recognized isotope For example 24CH s 289 of 315 ChemBioDraw 14 0 P gt Perkin For the Better Property Calculations You can calculate predicted values of selected physical and thermodynamic properties for structures of up to 200 heavy atoms This section describes how the values are determined LogP Three fragmentation methods are used to predict the logP values Method One Based on 94 atomic contributions 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 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 introduce
137. dle on the chemical symbol See Rotating Objects on page 82 Chemical Properties Chemical Property Prediction is a feature supported by ChemBioOffice It enables you to calculate values for a wide range of methodologies for example topological descriptors such as the Weiner index and Balaban index ther modynamic descriptors such as solubility melting and boiling points and partition coefficients such as CLogP prop erties related to the three dimensional shape and volume of a chemical such as the Connolly surface area and volume In total you can calculate more than 100 chemical properties for a given structure For a list of properties available in a specific application click the respective link below or visit the PerkinElmer Informatics website Property Predictions in ChemBioDraw on page 158 m Property Predictions in Chem3D on page 163 a Property Predictions in ChemDraw Excel on page 162 m ChemBioFinder Properties on page 164 Property Predictions in ChemBioDraw You can enter predicted values for the physical and thermodynamic properties of a chemical structure of up to 100 atoms Chapter 11 Chemistry Features 158 of 315 W P l 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 report is produced as a text file and the information in it can be cut and pasted to oth
138. draw solid or dashed arcs of different angles 90 120 180 and 270 To draw an arc 1 Do one of the following n ChemDraw Standard point to an Arc tool and drag in the palette to select the angle n other ChemBioDraw applications 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 curvature 4 Use a selection tool to change its size or orientation Navigate to View gt Show Info Window to display the info window The Info window indicates the distance between the ends of the arc and the angle the clockwise end makes with the X axis Info x Pointer a O 0521 in Y 0 6354 in ds d r Selection TH us Mt 3 2236 in HH Y 1 0856 in Wes 1 4752 in H 1 3901 in Other Angle Dist Syed When you drag the resize handle the Info window indicates the percentage as enlarged or reduced When you drag the Rotation handle the Info window indicates the degree rotated For more information about Info window see The Info Window on page 84 Chapter 6 Basic Drawings 76 0f 315 Brackets Brackets includes braces brackets and parentheses Bracke
139. 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 Bonds on page 56 and Attachment Points on page 122 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 proportional spacing if different bond lengths are used Chapter 4 Preferences and Settings 24 of 315 m An absolute value you choose in the units specified for your document Bold Width Set the width of the line used when bold and wedge bonds are drawn The 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 portions 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 55 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 Zpt Apt Spt y i ks i th A k a yt b in n Chain Angle Set the angle from 1 to 179 degrees between bonds created by the Acyclic chain tool or modified by the Clean
140. ds stored in the main form Chapter 12 ChemDraw Excel and CombiChem 180 of 315 W P Note To import CFW files into Excel save them with the allow CAL OLE Automation access security setting checked See Setting Security Options in the ChemBioFinder user guide for details 7 Note Structures saved as ChemFinder XML files can be imported into Excel using the add in 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 Goto ChemOffice14 gt Import Export gt Import Table The Import Table dialog box appears 3 Type or select the file name to import and click Open All records are added to your worksheet _ Note A progress dialog displays the import progress You can cancel the import process at any time by clicking Cancel On clicking Cancel you will be prompted either keep the records which were imported or cancel the import process or continue with importing _ Note You can only import a table into a new ChemOffice worksheet Importing hit lists You can search records in ChemBioFinder and import the hit list structures with data into Excel using the Import ChemFinder List command To import a hit list 1 Go to ChemOffice14 gt Import Ex
141. e Displayed when text is found that cannot be identified as an element nick name generic nickname or alternative group name 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 Group name Displayed for every label that contains a generic nickname an element list or an alternative group This is a status message only analysis continues as if the problematic label were not selected 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 regard less of how many captions are in the selection Displayed for any structure within an Alternative Group Box where the struc ture lacks an attachment point This is a status message only Displayed for any Alternative Group Box whose contained structures have varying numbers of attachment points Since all structures within an Altern ative Group Box are to be used interchangeably they must have the same number of attachments This is a status message only Displayed for any Alternative Group Box that is empty This is a status mes sage only 288 of 315 ChemBioDraw 14 0 Message Part of a molecu
142. e free site tool selected increments the substituent count upto 9 whereas lt Alt gt click decrements the count For example Does not find Chapter 14 Query Structures 234 of 315 Does not find Implicit Hydrogens An implicit hydrogen is a hydrogen atom in which it or its bond is implied but is not visible An explicit hydrogen and its bond are visible E I Figure 14 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 selec ted atoms If implicit hydrogen atoms are not allowed all valences to that atom must be filled by bonds to non hydro gen atoms Allowed Default Finds compounds regardless of whether hydrogen atoms are attached to the selected atoms Not allowed Finds compounds with no 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 specifies the maximum number of rings in which an atom can reside Chapter 14 Query Structures 235 of 315 Any Default Finds compounds in which the selected atoms can be a member of any type of ring or a member of no ring at all No ring bonds Finds compounds in which the selected atoms are acyclic As drawn Finds compounds in which the selected atoms reside in the same type and number o
143. e 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 CHEM MOLWEIGHT A2 Result 174 23896 In cell CHEMPROPSTD MOL WEIGHT A2 Result 174 238960 In cell CHEMPROPSTD MASS A2 Result 174 238960 Exact mass Displays the exact molecular mass of the molecule where atomic masses of each atom are based on the most com mon isotope for the element Units g mole Function CHEMPROPSTD EXACT MASS cell ref Example In cell CHEMPROPSTD EXACT MASS A2 Result 174 104465 Number of atoms When this function is called with just a cell reference it displays the total number of atoms in the structure When this function is called with a cell reference and an atomic symbol it displays the number of atoms of the given element in the structure Functions CHEM NUM ATOMS cell ref CHEM NUM ATOMS Cell ref atomic symbol Chapter 12 ChemDraw Excel and CombiChem 190 of 315 Examples In cell CHEM NUM ATOMS A2 Result 27 In cell CHEM NUM ATOMS A2 C Result 12 Number of hydrogen bond acceptors Displays the number of hydrogen bond acceptors based on topology Function CHEM NUM HBACCEPTORS cell ref Example In cell CHEM NUM HBACCEPTORS A2 Result 1 Number of hydrogen bond donors Displays the number of hydrogen bond donor
144. e 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 below Cl ni Chapter 14 Query Structures 244 of 315 ChemBioDraw 14 0 i an Perkin For the Better You can also use the bracket usage types Crosslink xl Graft grf and Modification mod to represent types of repeating units in a structure based representation Source based Polymers Source based polymer representations enclose a discrete chemical substance in brackets The mode of poly merization may be obvious from context or be unknown Source based representations are useful when describing processes where the starting materials 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 below Cl Pa man You can use Mer mer brackets for components of a copolymer where those individual components are known not to repeat themselves or they alternate with other components For example Go Copolymers represent substances with more than one repeating unit In general you can use bracket type Com ponent co You can also use Copolymer alternating alt Copolymer random ran and Copolymer block blk to represent different copolymer types in a sou
145. e d orbital is shown below oe D gt st s To draw ad 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 will be attached To draw a d_2 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 You can move any attached chemical symbol other than H dot and H dash any distance from its related atom The available chemical symbols are Figure 11 3 Chemical Symbols A Circle Plus B Plus C Radical cation D Lone pair E Electron Pushing F H dot G Attachment point H Polymer bead attachment point I Attachment point J Attachment point K H dash L Radical Pushing M Radical N Radical anion O Minus P Circle minus You can place unattached symbols anywhere within your document 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 dash symbol To insert H dots and H dashes click an atom Lone Pair Diradical Use the lone pair symbol to indicate a lone pair of electrons common in Lewis structures To use the lone pair symbo
146. e default This step resets the default to New Document Draw a ring 1 Click the Cyclohexane Ring tool 2 Click in an empty area of a document window A cyclohexane ring appears Rotate the ring 1 Go to Edit gt Select All or type CTRL A 2 Goto Object gt Rotate or type CTRL R 3 Inthe Rotate Objects dialog box enter 30 degrees for an angle and click Rotate The cyclohexane ring rotates Change cyclohexane to tetrahydropyran 1 Click outside the structure to deselect it 2 Point to the atom in the figure below and type the letter o Resize horizontally 1 Go to Edit gt Select All or typoeC TRL A 2 Using a selection tool click drag the right side handle to horizontally resize the ring Release the mouse button when the ring is stretched about 200 Chapter 19 Tutorials 305 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 201 0 Enlarge the ring 1 Go to Edit gt Select All or type CTRL A 2 Click drag the ring corner adjustment handle to 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 Click No Add vertical bonds 1 Click the Solid Bond tool 2 Point to the atom shown in the figure below and drag upward to create a bond 3 Point to the same atom and drag downward to create another bond 4 Repeat this procedure four more times adding the pairs of vertical bonds shown below Create OH
147. e for component order multiple group repeat count or single repeating unit label Setting Bracket Properties To set the Bracket Properties 1 Select a bracket 2 Navigate to Structure gt Bracket Properties The Bracket Properties dialog appears The Flip Type option appears only for ladder polymers See Flip Type on page 248 You can customize the text that appears to the bottom right of the bracket for these bracket types Component c the component order must be a non negative integer and is displayed as the letter c followed by an integer or c 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 in the document using the Text tool You cannot edit the text displayed for other bracket usage types Bracket Usage Polymer Representations are either structure based or source based The type of bracket you use depends on the type of representation Structure based Polymers Structure based representations enclose only part of a 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 represent a structure based polymer by enclosing a portion of a structure in brackets with a bracket type of SRU n IUPAC recommends the subscript n to denote structur
148. e fragments in the Alternative Group box Tip You can draw the box afterward to enclose the list of alternative groups Chapter 14 Query Structures 249 of 315 P gt ChemBioDraw 14 0 a Perkin For the Better Figure 14 9 Defining an alternative group Specify where the fragments should bond to the parent structure on the alternative group label by defining attachment Points 1 Do one 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 2 Repeat for all fragments Figure 14 10 Adding attachment points An attachment point symbol has been applied to the nitrogen atom When you create a structure that contains an alternative group an attachment point symbol appears next to the label The attachment point number matches that found in the definition Figure 14 11 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 on page 251 Chapter 14 Query Structures 250 of 315 ChemBioDraw 14 0 i cae Perkin For the Better Multiple Attachment Points You can use R groups that conta
149. e generic nicknames are ignored and the chemical formula mass etc are reported as if the atom label containing the generic nickname were not selected Reaxys Reaxys is a web based chemical search engine designed for synthetic and medical chemists The Reaxys database includes chemical properties structures reactions and experimental data Using ChemDraw for Reaxys with ChemDraw you can draw query structures to search the Reaxys database Chapter 14 Query Structures 229 of 315 ChemBioDraw 14 0 i eae Perkin For the Better _ Note For the Windows version you need both the Reaxys Structure Editor plug in and either the ChemDraw application or plugin installed on your system In addition to A M Q X and R Reaxys recognizes several other generic atoms To add a Reaxys generic label to a structure Right click an atom point to Insert Generic Label on the context menu point to Reaxys and click the label in the sub menu you wish to insert The table below lists the labels and their meaning Labels Meaning AH Any or H MH Metal or H QH Any except Carbon or H XH Halogen or H G Unspecified GH Unspecified or H G Unspecified ring closure allowed Unspecified ring closure allowed or H Acyclic Acyclic or H Carbacyclic Carbacyclic or H Alkynyl Alkynyl or H Alkyl Alkyl or H Alkenyl Alkenyl or H Hetero acyclic Hetero acyclic or H Alkoxy Alkoxy or H Chapter 14 Query Structures 230 of 315 ChemBioDraw 14 0
150. e of the following n Microsoft Word select the drawing and navigate to Edit gt CS ChemDraw Drawing Object Double click the drawing The ChemBioDraw tools and menus replace those of Word Use the tools to edit the drawing When you finish making changes click in another area of the Word document The Word tools and menus are restored Exporting You can export ChemBioDraw drawings in various file formats and open them in other applications Conversely ChemBioDraw recognizes a variety of file formats and can open documents from other applications To export a file 1 Navigate to File gt Save As 2 Inthe Save As dialog do the following a Type a name for the file and a location to save it to Click Go To ChemDraw Items to locate the ChemDraw Items folder b Select a file format c Click OK Some file formats do not support atom labels that contain nicknames or structural fragments When you save in these formats ChemBioDraw expands all atom labels and saves the file using the expanded form These formats do not support nicknames or structural fragments Connection Table MSI MolFile SMD Chapter 15 Sharing Information 271 0f 315 ChemBioDraw 14 0 i cman Perkin For the Better _ Note Some versions of ChemBioDraw 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 These text based formats can use the Text Options
151. e provides the reaction that defines the transformation The input sdf file contains all the structures that will be transformed O O J Vr R N s R NS N O oO Figure 13 2 The transform file defines how the transformation is applied to the source structures The script searches the input file for structures that contain a nitro group shown as a reactant in the transformation file If a structure is found the script transforms the nitro group to the form shown in the product and copies the entire structure to a new file The figure below shows one example B N 0 Chapter 13 ChemScript 226 of 315 W P Figure 13 3 A before the transformation is applied B after transformation Structures that don t meet the search criteria are ignored Example 8 Simple salt stripping The program reads an SD File identifies and removes salt components if any are present and outputs two SD files The output structure file contains the original structures without the salt component and the output salt file contains the salt components that were stripped along with a reference to the original structure See Example 008 script py _ Note This example uses a default set of salts that PerkinElmer provides However you can also define a cus tomized salt table that enables you to designate which chemicals are considered salts Useful References There are numerous resources available for learning Python and
152. e sites U Substituents Up to Followed by the maximum number of substituents X Substituents Exactly Followed by the number of substituents H Implicit Hydrogens See Implicit Hydrogens on page 235 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 Select the atom right click point to an atom and point to the appropriate property Navigate to Structure gt Properties and view the settings on the Atom Properties tab 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 Displaying Indicators for a Structure To display query indicators for a structure Chapter 14 Query Structures 232 of 315 W P l 1 Select the structure 2 Right click and navigate to Atom gt or Bond gt Show Query Indicator on the context menu Positioning Query Indicators You can position a query indicator by either dragging it or entering a numeric value for the new location 1 Right click the indicator and choose Position The Position Indicator dialog appears 2 Click the appropriate Position op
153. e to Object gt Join To join two structures so that they share an atom 1 Position the two chemical structures so that the atoms you want to fuse are near each other 2 Select the two atoms to be joined 3 Navigate to Object gt Join 7 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 information about front to back ordering of objects see Page Layout on page 10 Grouping Objects A group is a collection of objects that act as a single object You can select all grouped objects by double clicking on any of the contained objects with a selection tool When you 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 Objects within a non integral group can be selected individually and manipulated while still remaining part of the group You can change the position or orientation of grouped objects Individual objects within the group maintain their rel ative positions when the grouped objects are rotated 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
154. e uses five criteria to determine whether a substance is druglike The substance must have Five or fewer H bond donors Ten or fewer H bond acceptors A molecular weight under 500 daltons LogP lower than 5 Fewer than two violations of the above four rules To determine whether the substance meets the Lipinski rule requirement 1 Calculate the value of each of these functions CHEM NUM HBDONORS CHEM NUM HBACCEPTORS CHEM MOLWEIGHT CHEMPROPPRO LOGP 2 Verify that the value returned by the functions meets the lipinski rule criteria For example if the CHEM MOLWEIGHT returns a value lt 500 it satisfies lipinsky s third criteria 3 Calculate the number of criteria satisfied If the number of violations is less than two the Lipinsky rule is satisfied Ghose modifications The Ghose modifications use these criterias m Atom count between 20 and 70 Molar refractivity between 40 and 130 A molecular weight between 160 and 480 daltons LogP inthe range 0 4 to 5 6 Fewer than two violations of the above four rules To determine whether the substance meets the Ghose modification requirement 1 Calculate the value of each of these functions CHEM NUM ATOMS CHEMPROPPRO MOL REFRACTIVITY CHEM MOLWEIGHT CHEMPROPPRO LOGP Chapter 12 ChemDraw Excel and CombiChem 201 of 315 2 Verify that the value returned by the functions meets the Ghose modification criteria For example if the val
155. ear as a label in all gen erated structures 2 Navigate to Structure gt Expand Generic Structure The structures are generated in a new document 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 data base This is 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 combinations are based on a Boolean expression that you define To prepare an R Logic search nav igate to Structure gt R Logic Query to open the R Logic Query dialog To define a query select one or more R groups in your structure and how many times it must occur You can indicate that if the first R group condition is met another R group must also be found before the structure is returned as a res ult For example consider this query structure Chapter 14 Query Structures 256 of 315 W P l This structure indicates that both R sites must consist of either a fluorine or chlorine atom and that the R3 site must be either a bromine or iodine atom Assume you want to find all structures in your database that have either a F or CI atom at both R locations and either 1 Bror lat R3 1 Navigate to Structure gt R Logic Query 2 In the R Group drop down list select R 3 For Occurrence range select 2 This indicates that two instances of an R 4 group must occur in a structure fo
156. ears as shown below 2 Right click the border and select the appropriate option from the context menu To align all of the objects in a column or row point to a top or left border using the Table tool right click point to the Align command on the context menu and choose the alignment you want The cell contents shift and stay in a fixed position relative to the cell The default alignment is unaligned Chapter 3 Page Layout 17 of 315 W P l To align all objects in a table point to a bottom or right border right click point to Align and choose the alignment you want Using the Text Tool ChemBioDraw lets you create tables of text using the lt tab gt key with the Text tool Compound Formula Mol Wt Benzene C6H6 78 11 Toluene CVHS amp 97 14 To create the first row and establish the columns of a table Using the Text tool click ina document window where you want the table to start Type a caption Press lt tab gt A second caption box appears Type a second caption The second column appears 20 points to the right O FB WwW N gt Press lt tab gt again to create a third column and so on _ Note The style font and size that you set in each column are maintained in all the rows that follow To change the spacing between columns one point at a time while editing a caption 1 Select the caption 2 Move the caption with the arrow keys For more information on moving objects see Movi
157. ecause the isotope is in low abundance or because it includes many moderate abundance contributions are not taken into account Elemental Analysis The percent by weight of each element in the structure To open the analysis window 1 Select the entire structure or part of the structure If nothing is selected the analysis window displays value for the entire structure Chapter 11 Chemistry Features 149 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 2 Navigate to View gt Show Analysis Window The analysis windows displays values for the parts of the drawing you select or the entire drawing if nothing is selected 3 Optional Select Paste to add the analysis information to your drawing The information appears as a caption that you can edit glucose Chemical Formula Ca H120 Exact Mass 180 06 Molecular Weight 180 16 mz 180 06 100 0 18 1 07 6 9 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 53 29 Figure 11 1 Structural analysis The information updates as you edit the structure 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 PerkinElmer Informatics maintains a vast database of compounds and their properties ChemBioDraw provides a live Internet connection to a database that includes Links to available data resources such as the PerkinElmer Informatics Chemlndex
158. ected bonds are formed broken or undergo a change in bond order Not Center Finds compounds where the selected bonds are not part of the reaction center Not Modified Finds compounds where the selected bond s orders do not change but may or may not be part of the reaction center Unmapped Finds all compounds Element Lists An element list is alist of atoms allowed at a specified location For example the query structure below allows bro mobenzene lodobenzene or chlorobenzene to be returned An example of an element list is Br Cl Figure 14 4 An element list as an atom label The elements in the list must be separated by commas A space after each comma and brackets are optional 7 Note An element list may contain only atomic symbols plus D deuterium and T tritium To create an element list 1 Open an atom label text box 2 Type an open bracket followed by alist of elements separated by commas Cl Br followed by a close bracket for example CI Br I 3 Close the text box The figure below shows a query structure created to find compounds matching the following criteria Chapter 14 Query Structures 242 of 315 B A 7 C F A S2_1S Se Te A indicates that the atom must match any atom except hydrogen The Indicator B near the bond indicates that the bond must be single or double S D The element list C specifies that one of these elements must match
159. ected bonds are single or double D A Finds compounds whose selected bonds are double or aromatic S A Finds compounds whose selected bonds 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 environment of the selected bonds Unspecified Default Finds compounds regardless of topology Ring Finds compounds where the selected bonds are part of a ring Chain Finds compounds where the selected bonds are part of a chain but 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 meaningful only when searching a database containing chemical reactions Unspecified Default Finds compounds regardless of whether the selected bonds are affected by the reaction Chapter 14 Query Structures 241 of 315 W P l Center Finds compounds where the selected bonds are affected by a reaction but the type of change is unspecified Make Break Finds compounds where the selected bonds are either broken or created in a reaction Change Finds compounds where the bond order of the selected bonds changes in a reaction Make amp Change Finds compounds where the sel
160. ecting Predict 1H NMR Shifts and enter a frequency in MHz and run the spectrum The new frequency will apply until you reset it including after closing ChemBioDraw The spectrometer frequency parameter only applies to proton NMR For further information see m NMR Shifts on page 174 How to run NMR predictions in ChemDraw m Assigning Structures to Spectra on page 175 Re linking atoms to peaks a Viewing Spectral Assignments on page 175 Peaks associated with atoms Removing Spectral Assignments on page 175 Dissociating peaks from atoms m Custom Shift Correction Data on page 176 Adding new spectrum information m ChemNMR Limitations on page 179 Elements and standard deviations NMR References on page 179 Source citations NMR Shifts ChemNMR estimates chemical shifts for all hydrogen or carbon atoms for which additivity rules are available Fol lowing a hierarchical list it first identifies key substructures of a molecule A substructure provides the base value for the estimated shift For example benzene would be the key substructure of trinitrotoluene When a substructure is a ring system not available in the data ChemNMR approximates its base shift using embed ded rings and if necessary will disassemble the ring into acyclic substructures ChemNMR views remaining parts of the molecule as substituents of a substructure Each substituent adds to or sub tracts from the base shift of the substructure to whi
161. ed Value Limiting Sample Mass WWV eight Volume Comments Indicates the limiting reactant Only one reactant may be specified as limiting Mass of reactant Default units g Reactant purity Defaults to 100 Default units ml Requires either a molarity or a density to be entered Chapter 9 Advanced Drawing Techniques 134 of 315 ChemBioDraw 14 0 Value Molarity Density Default units M Default units g ml P gt PerkinElmer For the Better After you enter the minimum amount of information the values are calculated The values are automatically recalculated when you enter a new value edit input or modify the reaction To edit input click the input and enter the new value For example consider the following table Reactants Formula MW Limiting Equivalents Sample Mass Co Weight Molarity Density Volume Reactant Moles Reactant Mass 50 00mmel 6 67g Products Formula MW Equivalents Completion Expected Mass 4 61g 1 82g Expected Moles 50 00mmo 50 00mmal Measured Mass Purity Product Mass Product Moles fo Yield If you edit the value in the Reactant Moles field for the reactant in the table to 30 00 mol the rest of the table is updated Reactants Formula MW Limiting Equivalents Sample Mass Co Weight Molarity Density Volume Reactant Moles Reactant Mass 30 00 mol 1 51kg
162. eeese 242 POI VICI agate dec cee esas eee aoe edueeeueeciongsasuensedane seme eared een adeaosane nen duanesenecseseeeneeeecee 243 ETN IN OG CS saree eee heats cies Bes bees asec ce ee eee cede Siaueen ces Geek eases saunter ec E A 247 Alternative Groups 2 22 2 2 e cece cece eee cece ec eee e cece cece eee ecec ees eeceeceeeesceceececeeseeeeesercerceseeseeeees 248 Anonymous Alternative GroupS 0 2 2 cece eee e cee cee cee cece cece ee cee cee ceecececeeceeceeceeccueceeeeeceeceeees 254 Expand Generic Structures 2 0 2 2 cece cece ccc oaao cece ccc an0a ceeeeeceeceeceecceeceeseeseecceeeeeseereess 255 Atom to Atom Mapping 2 2 cc cece cece cece ccc cece cee cee cee ceececceeeceeceeceeceecceeceeceeceeceeeeeneees 257 Stereochemical Symbols 2 2 0 c cece eee ce ec cee cece cece ceecceccceecceecececeecceecceecceeceeeceeeeeeeeees 260 3D Properties l aa aaan 000000000000 aaa 0000o 00an a oaao 00a oDDD A LLDD LDD A LLDD DDALL DDALL a L aaoo orano oan 261 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved iv ChemBioDraw 14 0 i Perkin For the Better Export Compatibility 22 20 0000 2 lc ccc ccc cece cee cee cece cece ee ceeceecceeceeceeceecececeeteeceeceeeceeteesees 262 Chapter 15 Sharing Information _ 00 0 0 o occ cece ccc ee cece cee cect ccc eecccccecceecceceecceeceeceeees 267 The Clipboard oaaaaaaaaaaaaaaanaaa naano aa ooann an
163. eereeserseres 92 Customizable Objects once n uci cnadedacsadesswesadedias senanueesecase ede ooeedaedeeeioa dads oeednewedencageeseebacesaueds 95 Chapter 8 Drawing Biopolymers 2 22 22 cece ccc eee eee cece cece cece ec eeccceceeceeceececccecteeseecees 101 Biopolymer Editor 2 22 0 2 elec cece eee cee cece cece cece ee ceecceccecceeccecceccecceccceccecceccecceeceeeeeceees 102 Protecting Groups 22 5 2 cancoaeceGhSaboxeecarsereedabucsdheeeenseussGoilqendavevosetebvcanedceseeabaeeesemecssouaeee 103 Pasting SEQUENCES 1 2 lec e eee cee cee eee eee cece cece eee cece eee eeeeeee eee eeee cece roor orror roren 104 Expanding Sequences 2 2 2 eee cece eee cee cee cece cece ec eec eee ceeceeceececccceceeceeceeceeeeeeteeseeceeees 106 Contracting Labels 0 2 2 occ ccc cece cece cece ec cee cece eee cee cee ceececceceeeeceeceecececcuceuceeceeceeeeeees 106 Modifying Sequence Residues 2 22 22 eee eee eee eee eee eee e eben eee eeeen eens 107 Merging Sidechains with Residue 0 00 02 ccc eee eee cee cee cece ccc cee cee ceececccceceeceeceecececeeseeceees 107 Hybrid Biopolymers lt ot se sive desc cb nen cacunbSscuindsewcanseucdacewseedinabeus aged masunuebondiousuessereassaouss 110 UFAC ODES are eects wtnie saan E E scene E E data sanetataen ci EEE E E 111 Disulfide s1100 CNA 115 Lactam Bridges 2 cece 0000000000000000 oaao aaoo oaoa cee ceeceeeceeceeceeceecceeceeceeceeceueceeteeseeseeees 116 Chapter 9 Advance
164. efault style click the File menu The New menu item displays the name of the Style Sheet Saving Customized Styles Every new document you create uses a style sheet file for its document settings These files can also contain pre defined objects When you create a new document you actually create an untitled copy of the style sheet Changes you make to the copy do not affect the file Chapter 4 Preferences and Settings 22 of 315 You can create a style sheet with your own customized setting by saving it as a CDS file If you 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 1 Navigate to File gt Save As The Save As dialog appears 2 Name the file and change the type in OS X format to CD Style Sheet cds 3 Tosave the file in the ChemDraw items folder click Go To ChemDraw Items 4 Click Save Customizing Toolbars The look and arrangement of toolbars are defined by a set of XML files If you are familiar 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 contains the schema definitions for all the toolbars These include definitions but not the con tent for the toolbars the pop up text and the status bar text
165. emical Prop erties window s Report button includes a section Data from Database which includes measured values of the partition coefficient and pKa values at specified pH levels with source citations The ChemBioDraw ChemBioFinder Hotlink Window Several available databases include LogP and pKa information including ChemSpider from InChl link predicts several variations of LogP and LogD ChemINDEX Physical Properties section Environment Science Center database includes empirical pKa and LogP data ChemDraw Excel The ChemDraw add in module in Microsoft Excel predicts LogP function CHEMPROPPRO_LOGP CLogP function CLOGP_DRIVER_PARTITION COEFFICIENT MR function CHEMPROPPRO_MOL_REFRACTIVITY CMR function CLOGP_DRIVER_MOL_REFRACTIVITY ChemBioFinder ChemBioViz The Property Populator predicts LogP server ChemPropPro property LogP CLogP server CLogP driver property Partition_Coefficient MR server ChemPropPro property Mol Refractivity CMR server CLogP driver property Mol Refractivity ChemBio3D The Property Picker predicts LogP ChemPropPro LogP CLogP CLogP driver Partition Coefficient MR ChemPropPro Mol Refractivity CMR CLogP driver Mol Refractivity Chapter 17 Property Calculations 291 of 315 W P l The ChemBio3D MOPAC Interface Calculates the pKa of the most acidic hydrogen atom attached to an oxygen For more information see http www openmopac net
166. en the database to search Paste the generic reactant structure into a query form and run the search a ee N gt In the reactant worksheet in Excel go to ChemOffice14 gt CombiChem gt Reactants gt Import ChemBioFinder Hitlist to import the search results The search results appear in the reactant worksheet s Tip Use the Show Picture Hide Picture commands to toggle the display Recreating reactant worksheets You can edit the generic reaction at any time However you must then delete and recreate each reactant worksheet To recreate a reactant worksheet 1 Right click the reactant worksheet tab and select Delete 2 When prompted confirm that you want to delete the worksheet 3 Go to ChemOffice14 gt C ombiChem gt Reactants gt Make Reactant Worksheets 4 Goto ChemOffice14 gt CombiChem gt Reactants gt Search for Reactants For more information see Searching for reactants on page 214 If you try to create new reactant worksheets in a workbook that already contains reactant worksheets you will be asked whether you want to delete the existing worksheets When prompted choose one of these options Click Yes to replace the existing worksheet s The existing worksheet is permanently deleted Click No No new worksheet is created and the current worksheet s are kept To preserve the existing worksheets go to File gt Save As and save the workbook Then follow the steps above to recreate the reactant worksheet s When p
167. endently BioDraw Templates ChemBioDraw Ultra includes a variety of templates for illustrating biological systems in full color for publication 1 To open a template 2 Navigate to View gt Templates Select the template toolbar you want Some of the available BioDraw templates are shown below Chapter 7 BioDraw Ultra feature only 92 of 315 PerkinElmer For the Better ChemBioDraw 14 0 ed BioDraw Advanc HNO OH COC e 1 nly Chapter 7 BioDraw Ultra feature o gt ChemBioDraw 14 0 i PerkinElmer For the Better Animals al Arone f4 s al Chapter 7 BioDraw Ultra feature only 94 of 315 ChemBioDraw 14 0 For more information see Templates on page 136 Customizable Objects P gt Perkin For the Better The table below describes the BioDraw objects in the BioDraw toolbar which can be customized When customizing a BioDraw object you must use a selection tool or the same tool used to create it Tool Receptor G protein gamma subunit Helix P
168. enter or Clock in clock time From the atom or bond center Offset horizontal and vertical to bottom left of indicator baseline At specified coordinates Absolute horizontal and vertical Relative stereochemistry You can specify relationships between groups of stereocenters within a molecule This notation enables you to describe stereochemical properties and individual stereocenters rather than the entire molecule As a result you can illustrate properties of several enantiomers using only a few or just one structures The notation is illustrated below OH A OH OH orl ea 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 pairs However drawing this requires only one structure Chapter 11 Chemistry Features 153 of 315 ChemBioDraw 14 0 i ans Perkin For the Better cl Cl N Figure 11 2 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 stereocenter varies independently and is designated amp 2 Group numbers are incremented automatically To see all the beta cypermethrin stereoisomers go to File gt Open Samples gt b Cypermethrin To indicate stereoche
169. ents is mod ified the components are evenly distributed plus signs are inserted wherever necessary and the length of the arrow is adjusted To clean up a reaction 1 Select the reaction 2 Navigate to Structure gt Clean Up Reaction If the reaction is too wide for the document the reaction is wrapped to fill multiple lines as shown in the example below Figure 9 7 The reaction before applying the Clean Up Reaction command Chapter 9 Advanced Drawing Techniques 130 of 315 ChemBioDraw 14 0 i cman Perkin For the Better SS ss Figure 9 8 The reaction after applying the Clean Up Reaction command _ Note The Clean Up Reaction is available only for single step reactions _ Note The Clean Up Reaction command is available only for reactions with straight arrows In case of arrows with curvatures the Clean Up Reaction command is disabled The Reaction Interpreter The Reaction Interpreter parses reactions as drawn and breaks the reaction into the following distinct components m Reaction Scheme m Reaction Step m Reactants Products Conditions You can save the interpretation to disk by saving the file as CDXML This stored data is often important if reactions are to be stored in databases The reaction interpreter color codes the reactants products catalysts and annotations in a reaction when you hover over them with Show Reaction Interpretation selected This helps in determining whether the reacti
170. er documents like a word document A list of all the properties calculated is as follows B H P Boiling Point Heat of Formation pKa C Henry s Law Constant T Critical Pressure L tPSA Critical Temperature LogP Critical Volume LogS CLogP CMR M G Melting point Gibbs Free Energy MR About Molecular Networks MOSES pKa MOSES logS and MOSES logP for predicting acid dissociation constants aqueous solubility and octanol water distribution coefficients of chemical compounds are computational calculator modules based on Molecu lar Networks cheminformatics platform MOSES MOSES is developed maintained and owned by Molecular Net works GmbH Erlangen Germany For further information please visit www molecular networks com moses All rights reserved Molecular Networks GmbH Erlangen Germany www molecular networks com Limitations Only the following atom types and hybridization states are parameterized C 2 C 3 SP C C Sp aromatic Sp N 2 3 N N Sp amide aromatic O pS N P O 2 P 3 Sp Sp Sp p Ssp Ssulfoxide Ssulfone F Cl Br I Chapter 11 Chemistry Features 159 of 315 ChemBioDraw 14 0 i cae Perkin For the Better Boiling Point The boiling point is reported in Kelvin A solution boils at a slightly higher temperature than the pure solvent The change in boiling point is calculated using the formula AT Kpm Where K is the molal boiling point constant m is the concentration of the solute expressed as molality and
171. ere A is area V is Volume and O is Ovality The ovality of a helium atom is 1 0 and HC H 12 triple bonds is 1 7 equivalent to 1 7 24 Polar surface area The Polar Surface Area PSA is defined as the surface sum over all polar atoms Principal moment Of inertia This refers to the principal moments of inertia about the principal axes of a molecule The moments of inertia are com puted for a series of straight lines through the center of mass using the formula Chapter 12 ChemDraw Excel and CombiChem 208 of 315 2 I Nmd ill Distances are established along each line proportional to the reciprocal of the square root of on either side of the center of mass The locus of these distances forms an ellipsoidal surface The principal moments are associated with the principal axes of the ellipsoid lf all three moments are equal the molecule is considered to be a symmetrical top If no moments are equal the molecule is considered to be an asymmetrical top Radius The eccentricity of an atom is the largest value in its row or column of the distance matrix and represents how far away from the molecular center it resides The diameter D is the maximum such value for all atoms and is held by the most outlying atom s Examples Dia meter of methane 0 ethane 1 propane 2 n butane 3 The radius R is the minimum such value and is held by the most central atom s Examples Radius of methane 0
172. ertiary carbon click the same place as shown in step 4 above Changing Bond Order To create the double bond either hover over the center of the bond and type 2 or click on the bond Chapter 19 Tutorials 298 of 315 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 A 2 Type an uppercase O in the text box 3 Press the lt Esc gt key on your keyboard to close the text box or choosing another tool 4 An alternative is hover over the atom at the end of the double bond and hit the o key This is utilizing the Hotkey functionality of ChemDraw see Chapter 5 Shortcuts and Hotkeys Adding Captions To name the molecule 1 Using the Text tool click below and to the left of the structure A text box appears 2 Inthe text box type 2 propanone 3 Press the lt Esc gt key on your keyboard to close the text box or choose another tool Tutorial 2 Drawing rings In this tutorial you use rings to create this structure To create the ring system 1 Using the Benzene tool SHIFT click in an empty area of the document E Note Hold down the SHIFT key to change resonance structures when using the cyclopentadiene or benzene tools 2 Point to the center of the lower right bond in the benzene ring 3 Click to fuse another ring Chapter 19 Tutorials 299 of 315 hemBioD 14 i ChemBioDraw 14 0 PerkinElmer For the Better
173. ery similar to a reaction search except that there is nothing to the right of the arrow For example consider the query aa O 8104 Ra Chapter 14 Query Structures 253 of 315 Figure 14 15 Sample r group reactant query A likely hit for the above query is shown below Searching for products If you know the desired end product but not how to get there you can do a products query A products query is similar to areaction search except that there is nothing to the left of the arrow For example consider the query Cl 4 Jeon n Ra Figure 14 16 Sample r group product query Anonymous Alternative Groups Anonymous alternative groups are a cross between an element list and an alternative group Element lists comprise single elements but anonymous alternative groups can contain any structure that can be represented by text such as nicknames and generic nicknames Anonymous alternative groups are shortcut notations for regular alternative groups eliminating the need to specify a name such as R1 You can concisely define your search query using anonymous alternative groups By labeling an atom position as a list of substructures you specify that one of these substructures must match in the structure for which you are search ing Commas must separate the items in the anonymous alternative group A space after each comma and the brack ets are optional Examples of anonymous alternative groups are shown below
174. es the exact stereoisomer as drawn or its enantiomer Chapter 16 Chemical Interpretation 286 of 315 ChemBioDraw 14 0 i elaine Perkin For the Better Figure 16 4 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 fragments Bracket properties specify the orientation and context of the repeating units For an explanation of the bracket properties see Setting Bracket Properties on page 244 _ Note The polymer drawing feature is available only in ChemBioDraw Ultra and ChemDraw Pro References Graphic Representations Chemical Formulae 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 PurpleBook C 7 pdf Basic Definitions of Terms Relating to Polymers 19747 Pure Appl Chem 40 479 491 1974 Also available at http www iupac org reports 1996 681 2jenkins 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 fully analyzed two general types of messages are displayed Status messages that report a problem that may not affect the final analysis Critical mes
175. etter ChemBioDraw 14 0 Oo a D hs G E Fy F i f K e p OH 0 y Tey Tr hy G A PEG Phe Glu Met NH N P Ma po a o ie 4 i OH j e h m A Branched Biopolymers HN Residue labels typically have two attachment points However you can add attachment points so that the sequence branches For example Ala Leu Gly COOH R When you add an attachment point you specify the atom in the expanded label to which the bond will attach To bond from a sequence 1 Draw a bond starting at the label from which to create a branch The Modify Nickname dialog appears displaying the sequence structure you selected 2 Inthe Modify Nickname dialog double click the atom in the structure on which you want to add the attachment point A new attachment point appears 3 Click OK IUPAC Codes Use these codes to enter nucleotides or amino acids in your Sequence IUPAC Nuc Base IUPAC Amino Three Amino Acid leotide Code Acid Code Letter Code A Adenine A Ala Alanine Chapter 8 Drawing Biopolymers 111 0f 315 ChemBioDraw 14 0 C Cytosine G Guanine T or U Thymine or Uracil R A or G Either puRine Y C or T Either pYrimidine S G or C Three hydro gen bond Strong W A or T Two hydro gen bonds Weak K Gor T Keto group in base M A or C AMine group in base B CorGorT Not A B is letter after A D Aor Gor T Not C H AorC or T Not G V AorC or G Not U
176. ew window In the Document Window With the preview window open you can still change your drawing in the document window The preview window updates to reflect the changes In ChemBio3D Preview The preview window offers several options to view structures ChemBio 3D HotLink A B CpEFGH Figure 11 4 A Launch Chem3D B Display mode C Select D Translate E Rotate F Zoom G Spin H Rock Chapter 11 Chemistry Features 167 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Launch Chem 3D The structure will appear in ChemBio3D as a model that you can edit Display Mode Choose display options for the model wire frame stick ball amp stick cylindrical bonds and space filling Select Select the structure or parts of it Translate Move the structure Rotate Rotate the structure in three dimensions 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 ChemBio3D Preview close the preview window To edit the 3D model 1 Double click the 3D structure ChemBio3D opens 2 Edit the structure and close ChemBio3D The edited structure appears in the ChemBioDraw document window TLC The TLC Thin Layer Chromatography Tool lets you depict thin layer chromatography plates The tool creates a rect angula
177. experiments form Combi Option s gt Experiment gt New A dialog box appears asking whether you want to create the experiment with the selected number of reactants 7 Note Enumeration of a product library may take a long time especially if there are many reactants or you are using a slower processor CombiChem Excel saves your enumeration to a ChemFinder database file 3 When prompted save the experiments file EY Note When the enumeration is done CombiChem Excel imports your data to a worksheet Experiment worksheets After you create the experiment several sheets are added to your workbook Experiment Reactant sheets Contain lists of the reactants used in the experiment There is one Experiment React ant sheet for each reactant These sheets are named Experimentn Reactantm where nis the designates a spe cific experiment in case you create more than one and m is the reactant for the experiment Experiment Product sheet Contains the generic reaction and the enumerated products in the experiment based on the reactants you marked Y in the reactant worksheet s By default only the products are listed To list the complete enumerated reactions Go to ChemOffice14 gt CombiChem gt Preferences In the Combi Preferences dialog box select Show Full Reaction for each product Select a reactant worksheet gt oe yy Go to ChemOffice14 gt C ombiC hem gt Experiments gt New A new experiment is added with the full reactions
178. ext tool 2 Label a 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 Deleting Labels To delete an atom label do one of the following Select the Eraser tool and click the atom label a With a selection bond or ring tool selected point to the atom label and press the lt spacebar gt lt Backspace gt or lt Delete gt key Note that if an atom is labeled pressing the lt spacebar gt lt Backspace gt or lt Delete gt key will delete the label but not the atom To delete the atom as well press the lt Delete gt key a second time to delete the unlabeled atom Captions You can add and edit captions to your structures using the Text tool The following example adds the caption Phenol to a phenol structure To add the caption Phenol to a phenol structure 1 Draw the phenol structure 2 Using the Text tool click below the drawing and type Phenol in the text field 3 Click outside the text field aa Phenol To edit the caption click in the text field with the Text tool and begin typing For more information see New Lines and Closing Text Boxes on page 21 Chapter 6 Basic Drawings 58 of 315 W P Formatting Each new caption or atom label uses default document settings for font size and style of captions and atom labels You can change the format by Changing the
179. f 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 Finds compounds in which the selected atoms lies at ring fusions the atom has three ring bonds Spiro or higher Finds compounds in which the selected atoms is a member of a spiro or higher linkage the atom has four or more ring bonds Unsaturation The Unsaturation property specifies whether a multiple bond is attached to the selected atoms Unspecified Default Finds compounds regardless of whether a multiple bond is attached to the atom Must be absent Finds compounds that do not have a multiple bond attached to the selected atoms Must be present Finds compounds that have at 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 ChemBioFinder only the product atom is checked The stereo designation is ignored on reactants May be anything Default Finds all reactions regardless of any change to selected atoms after a reaction Must be as specified Finds all reactions that are changed at the selected atoms exactly as specified by the reaction center property in the Atom Properties dialog Br Br Fxi ari MH na cl N a Ry Reaction Stereo The
180. ffice SDK page contains documentation sample code and other resources for the Application Pro gramming Interfaces APIs Querying SciFinder with ChemBioDraw Ultra Feature SciFinder is a research discovery application created by CAS Chemical Abstract Services that provides integrated access to the world s most comprehensive and authoritative source of references substances and reactions in chem istry and related sciences ChemBioDraw provides an interface to search SciFinder with queries created on the desktop Send a ChemBioDraw structure or reaction query to SciFinder using one of the following methods Click the SciFinder icon on the main horizontal toolbar under menu bar m Navigate to Search gt Search SciFinder 7 Note The SciFinder icon and Search menu item will be grayed out unless the structure s being queried is selec ted The Search SciFinder dialog window opens If you have selected a structure or multiple structures you will see the following window Chapter 18 ChemBioDraw Web Resources 295 of 315 ChemBioDraw 14 0 PerkinElmer For the Better Search SciFinder SciFinder Substance Search Reaction Search Substructure C Substructure f Selected Structure s are Products OR Exact Structure C Selected Structure s are Reactants You can now choose whether you are interested in a substructure search or an exact search of the substances data base or if you want to
181. front of all other objects Similarly navigate to Object gt Send to Back to position the bond behind other objects Br Q LT Chapter 6 Basic Drawings 55 of 315 _ Note Some file formats store 3D coordinates for atoms while others only store 2D coordinates For bonds with 3D coordinates those coordinates determine the visible bond crossings Bring To Front and Send To Back have no effect For more details on converting bonds and structures into 3D view see 3D Viewing on page 165 Fixed Bonds By default ChemBioDraw draws structures with fixed bond lengths and bond angles The values of those lengths and angles is determined by the settings for the particular type of document For more information see Document Set tings on page 38 However you can modify the behavior so that you are not constrained to fixed bonds and angles _ Note To suppress fixed lengths and fixed angles press the ALT key as you drag the bond Drawing Fixed Length Bonds To draw bonds constrained to a fixed length 1 Navigate to Object gt Fixed Lengths and ensure a check mark appears next to Fixed Lengths 2 Draw a bond using any bond tool Drawing Fixed Angle Bonds Bond angles are generally either set to the default chain angle of 120 degrees or are constrained to angles of 15 degree increments To draw fixed angle bonds 1 Navigate to Object gt Fixed Angles and ensure a check mark appears next to Fixed Angles 2 Draw abond using any bond too
182. g 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 example in the following drawing you would point to the acyclic carbon adjacent to the ether oxygen 3 Drag from the reactant atom to the corresponding product atom The remaining atoms are mapped based on the manual mapping Chapter 14 Query Structures 259 of 315 hemBioD 14 i ChemBioDraw 0 PerkinE For the Better Figure 14 20 Finalized mapping You can set or change the mapping for other atoms in the reaction Clearing Reaction Mapping To clear reaction mapping 1 Select the structures whose mapping you want to clear 2 Navigate to Structure gt Clear Reaction Map Clicking and dragging from any atom to an empty space in the ChemDraw window using the Reaction Atom Atom Map tool will clear the mapping from that atom Exporting Reaction Mapping Reaction mapping and reaction center perception information are stored in the cdx file format You can open the file in ChemBioDraw for transfer to other applications that read atom mapping such as ChemBioFinder You can also copy mapped reactions to these same applications using the Clipboard Stereochemical Symbols There are three types of flags that indicate stereochemistry Racemic A racemic mixture Absolute A pure enantiomer of Known configuration Relative A pure enantiomer of unknown configuration The default
183. g techniques Each tutorial introduces new techniques or variations of tech niques from previous tutorials We therefore suggest that you follow the tutorials in order Before you begin review Conventions used in this Guide on page 1 to familiarize yourself with the terminology ChemBioDraw checks for correct chemical syntax as you draw If there is an error ared box appears around the erro neous object the red box does not print To disable the red box 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 this structure 2 propanone If you want the want the bond angles and lengths to be fixed navigate to Object gt Fixed Lengths and Fixed Angles This ensures that bond lengths and bond angles are consistent throughout the structure 7 Note The fixed length dimension is set in the Drawing tab of the Document Settings dialog The fixed angle dimen sion increments angles by 15 degrees To create bonds 1 Navigate to View gt Show Main Toolbar 2 Onthe Main toolbar select the Solid Bond tool 3 Click in the document window A bond appears 4 To adda second bond click the right end of the bond you just created The two bonds form a 120 degree angle _ Note The chain angle setting determines the angle between the two bonds To change the chain angle see Draw ing Settings on page 24 5 To create a t
184. gen analogs a Anhydrides a Aldehydes and chalcogen analogs Carbonic acids m Amides mides m Amines and Imines m Nitric acids Carboxylic Acids Peroxy acids Carboxylic Esters Salts Heteroatomic acid halides Sulfides and chalcogen analogs Heteroatomic acids P B As Sulfoxides and chalcogen analogs Heteroatomic esters Peroxides Hydrazides a S Seand Te Amides Hydrazines a S Se and Te Acid Halides Hydroperoxides S Se and Te Acids Ketones and chalcogen analogs a S Se and Te Esters m Nitriles Ringed Structures Bridged monocyclic structures Heteromonocyclic structures m Carbomonocyclic structures Ring fusions of only two rings Fused polycyclic trivially named structures Ring fusions of two multiple ring systems Other Compounds Boron compounds a Si Ge Sn and Pb compounds m Organometallic compounds Phosphorous and Arsenic compounds Name gt Struct recognizes most organic and inorganic nomenclature However some types are not supported Coordination complexes Polyboranes m Polymers Some highly bridged ring systems including fullerenes and porphyrins porphines Some stereochemistry designators D I dl endo exo syn anti r t c Chapter 10 Struct Name Ultra Feature 148 of 315 Chemistry Features Structure Analysis You can display the chemical formula exact mass molecular weight m z and elemental analysis for the entire doc
185. gned to that element A charge that does not follow an element is assigned to the next element NHa N H Charges that follow a monovalent element with a repeat count are NH assigned to the element before that element N Hg Charges that follow other repeating units are distributed among those Chapter 16 Chemical Interpretation 281 of 315 units CO gt co 0 Charges may be superscripted Multiple charges are recognized appropriately Fe Charges may have repeat counts as long as both the charge and the Fe repeat count are superscripted Fe A floating charge placed with the Chemical Symbols Tool is assigned to Fn the nearest atom If no atom is within the distance set as the Fixed Length II the charge is ignored and not assigned to any atom N Hs 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 provided by CRC Press Inc Iso topes are defined in the Isotopes Table file You can edit this file in any text editor to add new isotopes A super scripted number before the element symbol indicates isotope num Ll bers Isotopes can be included anywhere that regular elements can
186. h as MDL MOL may also be applied You can also force ChemScript to use specific file formats for reading and writing data Example 2 Create an SD file This example illustrates how you can create an SD file from existing CDXML files You can find the script at Example 002 script py We begin with a list of CDXML files that each contain a chemical structure The list of files is hard coded into the ChemScript script When executed the script uses the SDFileWriter method to create an SD file that includes all the structures Example 3 Create a list of CDXML files This example illustrates how to read an SD file and write a list of CDXML files You can find the source file at Example 003 script py Example 4 Filter an SD file This example uses the atomByAtomSearch method to demonstrate a simple application of the atom by atom sub structure search in ChemScript The program reads an SD file and filters structures into one of two output SD files structures that contain a phenyl group and structures that don t It also illustrates how you can read chemical data formatted as a SMILES string See Example 004 script py Example 5 Computing Canonical Codes This example script checks whether any structures appear in both of two SD files based on the structures canonical codes The output is a new SD file with the duplicate structures excluded See Example 005 script py Chapter 13 ChemScript 225 of 315 W P l This example first computes t
187. he canonical code for each structure Since the canonical code does not vary with dif ferent representations of the same chemical structure you can use it to determine whether two structures are chem ically equivalent This example also introduces the Python Dictionary which is an associative array The dictionary maps a key toa value The dictionary is used to determine whether a canonical code has been previously encountered This example uses an alternate looping construct to read an SD file Canonical codes should never be permanently stored because their representation can change among different versions of ChemScript Example 6 Structure Overlay This script introduces the ChemScript structure overlay feature It uses a scaffold structure file to superimpose two chemically similar structures The script first examines the structures in an SD file that contain a common scaffold substructure It then aligns these structures so that they have the same orientation with respect to the scaffold See Example 006 script py 7 Note The overlay functionality can also be used to align three dimensional structures Example 7 Reaction Transformation This example demonstrates reaction transformation This means that you can draw a reaction that defines a trans formation of a molecule and then apply that transformation to a set of structure files All the files necessary for this tutorial are in the Example 007 directory The transform1 cdxml fil
188. he magnification navigate to View gt Reduce To return the document to its actual size navigate to View gt Actual To display the whole document navigate to View gt Show Document Toset the magnification to a specific value select or enter a percentage enter Other between 1 999 in the General toolbar Rulers Use the rulers to position objects a measured distance 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 navigate to View gt Show Rulers As you move the pointer guides appear on each ruler indicating the position of the pointer Chapter 3 Page Layout 14 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Figure 3 1 How rulers indicate position A The cursor B Ruler guides indicating vertical and horizontal location of the cursor When you select an object two guides appear in each ruler The four guides together show the height and width of the selected object _ Note The rulers adopt the same units that were selected for the document settings The Crosshairs The crosshairs are helpful for positioning objects To toggle the crosshairs on and off navigate to View gt Show Crosshair To assist you in aligning objects the crosshairs include grid lines that extend from the major division marks on each axis You can also show the rulers with the crosshairs to v
189. he residue ID 1 Select the residue 2 Right click and select Show Residue ID from the context menu The residue ID appears above the residue Nonlinear Sequences Multi line Sequences Every sequence has a defined line size and a block size When a block size is reached an additional space is added to the sequence When a line size is reached subsequent residues are added on a new line However you can create sequence with irregular lines by selecting and dragging You can place a residue on a new line by selecting the residue in a Sequence tool mode and pressing lt ALT gt lt ENTER gt Subsequent residues are placed on a new line To add a new line as you are entering the sequence press lt ALT gt lt ENTER gt on your keyboard Subsequent residues are entered on a new line and the line size is set for that particular sequence H Pro Cys Leu His Lys Cys OH To create a multi line sequence 1 Draw the sequence 2 Use the sequencing tool to select the residue you want at the end of the first line Such as His in the example above 3 Press lt ALT gt lt ENTER gt on your keyboard Hybrid Biopolymers You can create mixed or hybrid biopolymers using the Biopolymer toolbar by combining the various Biopolymer tools Hence you can insert nucleic acid into amino acid sequences and vice versa and RNA and DNA can be used together Chapter 8 Drawing Biopolymers 110 of 315 P gt Perkin For the B
190. he second strand and spacing Coloring Residues After you draw a protein or DNA strand you can color each residue using any of the coloring tools shading fading or filled 1 Using the Marquee or Lasso tool select a residue to color 2 Select the desired color from the Color menu 3 Onthe Curves menu select either Filled Shaded or Faded tRNA To create a tRNA molecule 1 Select the tRNA tool from the BioDraw toolbar 2 Click and drag in the workspace until the tRNA object is the desired size Once you draw the tRNA molecule you can modify it accordingly Chapter 7 BioDraw Ultra feature only 97 of 315 ChemBioDraw 14 0 PerkinElmer For the Better Ribosomes To draw a Ribosome 1 On either the Ribosome or BioDraw toolbar select a Ribosome tool 2 Click and drag in the workspace until the Ribosome object is the desired size Once you draw 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 mark ers A simple pBI plasmid map is shown below Fagl 4353 Hpal 4193 Motl 4353 o Sall 4346 Narl 3989 f ii Narl Pstl S Stull l stul 459 Nhel 615 AatI1 3798 EC oR V 634 At i z a i Nool TTA 4410bp Apal 1189 Fspl 3008 Masel 1330 a BglII 1359 ri pBI plasmid map Creating a Plasmid Map 1 From the BioDraw Toolbar select the Plasmid Map tool 2
191. he 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 point of the dative bond g tInterpreted by ISIS as unspecified cis trans stereochemistry h Converted to double i Converted to aromatic j Only M X Q A others written as aliases k Truncated to the first 5 elements I Converted to single m An RG file will be created automatically Chapter 14 Query Structures 265 of 315 P gt ChemBioDraw 14 0 Perkin For the Better 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 Chapter 14 Query Structures 266 of 315 ChemBioDraw 14 0 i eae Perkin For the Better Sharing Information Many of the system commands you commonly use to transfer content from one place to another can also be used in ChemBioDraw Copy paste Import and export content files When you use the clipboard the objects you copy can be edited The Clipboard You can use the clipboard to transfer part or all information within an active document window between applications on the same computer or on a network Use the s
192. hemBioDraw The input data for the script consists of CDXML data from the currently active document in ChemDraw If you select a portion of the document only the selected part of the document is used as input to the script You can apply scripts to chemical structures and reactions You can place scripts in the Scripts directory for easy usage The Scripts directory is in the same directory as the ChemDraw items directory To launch a script do one of the following Navigate to File gt ChemScripts and select a script from the Scripts directory Navigate to File gt Run ChemScript and select a script from a directory other than the Scripts directory You can also use the sample scripts available in ChemDraw under File gt ChemScripts One example is given below 1 Draw a minimum of three structures in the document window 2 Navigate to File gt ChemScripts gt Layout Molecules in a Circle A new document window appears with the struc tures arranged in a circle Chapter 9 Advanced Drawing Techniques 142 of 315 ChemBioDraw 14 0 P gt Perkin For the Better Struct Name Ultra Feature ChemBioDraw includes two features for generating structures and chemical names Name gt Struct and Struct gt Name Collectively these features are called Struct Name Struct gt Name generates the names of chemical structures using the Cahn Ingold Prelog rules for stereochemistry Using this option you can generate the name of structures y
193. hemDraw Pro only Unspecified Default Any For ChemFinder the same as default Included for compatibility with other systems where the default may be different Natural Indicates an isotopically unmodified nuclide Enriched Indicates a mixture of isotopically substituted and isotopically 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 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 ChemBioDraw Items folder Note The Abnormal Valence atom property does not provide a visual indicator Not allowed Default Finds compounds where the selected atoms have only normal valences If the Check Struc ture When Copying to Clipboard or Exporting preference is turned on an error message warns of abnor mal valences Allowed Finds compounds with the specific valence drawn 7 Note If Abnormal Valence is allowed any Invalid Valence messages for those atoms are ignored by the Check Structure command Bond Properties An indicator appears next to a bond for each property you assign Assigning Bond Properties To define bond properties 1 Select one or more bonds in
194. hemDraw for Excel and ChemDrawExcel 14 functions are checked 4 Click OK ChemDraw Excel add in may also be disabled by some other third party product by programmatically changing registry values In this case you can enable it by resetting the value of LoadBehavior at HKEY LOCAL _ MACHINE SOFTWARE Microsoft Office Excel Addins ChemDrawExcelAddin14 ExcelAddIn and HKEY_ LOCAL _ MACHINE SOFTWARE Wow6432Node Microsoft Office Excel Addins C hemDrawExcelAddIn14 ExcelAddlIn for 64 bit system running 32 bit Microsoft Office Reset the value of LoadBehavior to 3 from 0 and re launch Excel To use ChemDraw Excel open a ChemOffice worksheet Go to ChemOffice14 gt New ChemOffice Worksheet When a worksheet is active ChemDraw Excel appears in the title bar To convert a normal Excel worksheet into a ChemDraw Excel worksheet go to ChemOffice14 gt Convert Work sheet ChemDraw for Excel appears in the Excel title bar Older ChemDraw Excel workbooks may be incompatible with the latest add in Therefore you may need to upgrade them To upgrade go to ChemOffice14 gt Upgrade Workbook Importing tables ChemDraw Excel lets you import from MDL SDFiles Imports all records in the file By default the name of the structure is its chemical formula However you can change the name by using Name Molecule command MDL SDFiles are supported only in ChemBioDraw Ultra and ChemDraw Pro only ChemBioFinder Databases CFW CFX Imports all fiel
195. hemical wamings are turned on a red warning box appears when you overlay the structure because the carbon atoms overlay the C C bond To turn off the chemical warning deselect Chemical Warnings in the View menu To disable this type of warning go to Preferences and deselect Atoms Near Other Bonds in the Warn ings tab 3 Release the mouse button and click outside the Selection Rectangle to deselect the structure Tutorial 6 Stereochemistry This tutorial demonstrates stereochemistry markers and the Flip command First we draw this structure O OH NH 2 amino 3 methylbutanoic acid To draw the structure 1 Click the Solid Bond tool 2 Inthe 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 Chapter 19 Tutorials 311 of 315 L S 5 Point to the atom shown below and click twice to create two bonds 6 Pointing to the bond shown below right click and select Double gt Plain from the context menu a 7 Click the Wedged Bond tool point to the atom below and then click Adding atom labels 1 With the Text tool selected click the atom shown below and then type NH2 in the text box that appears 2 With the Text tool selected click the atom shown below and then type O in the text box that appears Chapter 19 Tutorials 312 of 315 ChemBioDraw 14 0
196. hese are indicated by a small black tri angle in the lower right corner For example Chapter 2 Getting Started 5 of 315 W P You can tear off these smaller toolbars 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 _ Note If the toolbar does not open it is likely already open either docked or floating on the screen Docking and Floating You can dock or float any standard toolbar When you dock a toolbar it becomes attached to the drawing window The floating toolbars appear in front of the document window and you can move them around in the drawing window Double clicking the toolbar restores it to the last or default or docked position To dock a toolbar do one of the following Click and drag the toolbar to any edge outside the drawing window Right click the toolbar and select Dock Toolbar To float a toolbar do one of the following Double click the docked toolbar Click and drag the docked toolbar into the drawing window m Right click the toolbar and select Float Toolbar BioDraw Toolbar The BioDraw toolbar contains drawing tools for adding biological and biochemical elements to your drawings See BioDraw Ultra feature only on page 92 for more information Documents A document is a workspace where you create and ed
197. hotkeys see Hotkeys on page 61 and Shortcuts and Hotkeys on page 44 Periodic Table You can use the periodic table to insert atoms into structures Navigate to View gt Show Periodic Table Window Periodic Table Bhs asle E gandan a lt ea sr v er no oT ru entea fag cain sn fsb re tre cz es tar lra w reo ir Pe aula ni Pb ei Po ae fem F a ac RF bb or rs re os fraler Ww Elid Pa fu fen res Fm ul le Click a symbol in the periodic table to highlight the atom and activate the Text tool Move the mouse across the table to highlight each atom To add an atom Select the desired element 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 CH and hydrogen appears as H 4 2 To label an atom Click an existing unlabeled atom Chapter 6 Basic Drawings 57 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 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 in the periodic table and click the atom in the drawing you want to change To edit a label You can edit an atom label using the Text tool Highlight the text and click a symbol in the periodic table The highlighted text is replaced Repeating Atom Labels You can repeat an atom label using the text bond or ring tools 1 Click the T
198. how to subscribe Some of the advanced structure query creation capabilities of ChemBioDraw cannot be fully interpreted by SciFinder When your query contains spe cifications that SciFinder cannot handle it will try to simplify and interpret them to the best of its ability and will display a warning message The interpreted search structure will be displayed in the SciFinder sketcher for further manipulation as needed before starting the search If the results obtained are not appropriate please contact Cus tomer Support at CAS or PerkinElmer and they will try to address the issue and or propose an alternate query that might achieve the results you seek Some additional information about searching f you select a molecule within a reaction you can still specify a search of the substances database rather than a search of the reaction database You can select a portion of a molecule as your search entity It will be treated just like an entire molecule for exact or substructure searching If the selection consists of more than one fragment these will be treated as independent moieties all of which must be contained within the CAS record in order for it to be registered as a hit Multi step reactions or multiple reactions in a single search are not supported Each step in the reaction sequence must be searched separately Chapter 18 ChemBioDraw Web Resources 297 of 315 Tutorials The tutorials illustrate fundamental drawin
199. hree dimensions Two features in ChemBioDraw let you view struc tures in three dimensions 7 Note ChemBio3D must be installed on your computer to preview structures in three dimensions 3D Model Use a 3D model to paste a 3D version of the structure into your drawing 1 Select the structure 2 Navigate to Edit gt Get 3D Model The 3D structure appears in the document window Chapter 11 Chemistry Features 165 of 315 hemBioD 14 i ChemBioDraw 14 0 PerkinElmer For the Better OH To view the model in ChemBio3D double click on it _ Note 3D objects inserted in this way cannot be transferred between platforms For more information see File Formats on page 273 _ Note You can copy a model using Copy as CDX from ChemBio3D and paste into ChemBioDraw The result is a ChemDraw structure with 3D coordinates and it is possible to rotate this structure in 3D using the structure per spective tool ChemBio3D Preview Options The preview window displays structures you select in 3D and displays all structures if none are selected ChemBio 3D Preview works only for chemical structures To view navigate to View gt Show ChemBio3D Hotlink Window For example Chapter 11 Chemistry Features 166 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 ChemBio 3D HotLink lel kh Gel dees m With the preview window open you can change the structure s appearance in either the document window or the pre vi
200. hrene appears Now you must remove two bonds from the center ring of the structure and add two oxygen atoms To modify phenanthrene 1 Inthe Main toolbar select the Eraser tool Chapter 19 Tutorials 314 of 315 ChemBioDraw 14 0 i Perkin For the Better Click the bottom bond in the center ring Click the double bond at the top of the ring It is now a single bond Inthe Main toolbar select the Text tool Select one of the carbon atoms in the hydrocarbon chain what was the middle ring Type Oto change it to an oxygen atom N ODO OF fF W PND Select the other carbon atom and change it to an oxygen Peroxydibenzene is now shown Chapter 19 Tutorials 315 of 315
201. hydroxyl groups 1 Click the atom shown in A below and type the letter H Chapter 19 Tutorials 303 of 315 hemBioD 14 f ChemBioDraw 14 0 PerkinElmer For the Better 2 Double click each of the other atoms labeled as hydrogen in B A B CHO CHO H H H H H CHOH SHOH Figure 19 6 Adding repeating atom labels Tip Double click an atom with the text tool to repeat the last label 3 Click one of the remaining atoms and type O 4 Double click the remaining atoms to repeat the label A B CHO CHO H OH H OH HO H H OH HI OH CHOH CH 0H Figure 19 7 Completing the drawing View the basic properties of the structure and paste the information into your document 1 Click a selection tool to select the last structure drawn If the structure is not selected double click the structure 2 Goto View gt Show Analysis Window 3 Inthe Analysis window click Paste The analysis information appears as a caption below the structure Tutorial 4 Perspective Drawings In this tutorial we explain how to create a perspective drawing by creating a model of o D glucose as a Haworth pro jection Create a new document using the default style Chapter 19 Tutorials 304 of 315 P gt Perkin For the Better ChemBioDraw 14 0 Goto File gt Open Style Sheets gt New Document 7 Note If you are following the tutorials in order ChemBioDraw will remember your last drawing used the ACS style sheet and open it as th
202. ically meaningful figures as you work This occurs in the background but you can also choose to view this chemical data ChemBioDraw uses the data when exporting to file formats that support only a subset of the notations that ChemBioDraw does This section describes how ChemBioDraw interprets drawings 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 represented in at least four different ways in major data bases Ord Fe re lt O 0 A and three other isomers Merck Index Beilstein HC CH Figure 16 1 Representations of ferrocene Chapter 16 Chemical Interpretation 277 of 315 ChemBioDraw 14 0 i aa Perkin For the Better A successful search in one database might not produce results in another When in doubt consult the documentation for the conventions your database uses Bond Conventions The following table describes the chemical conventions ChemBioDraw recognizes Bond Description Single bond unspecified stereo chemistry Single bond down stereochemistry into the plane of the paper away from the viewer from maana 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 to the second drawn atom L a Single bond mixture of up
203. ickname Chapter 6 Basic Drawings 63 of 315 P gt Perkin For the Better ChemBioDraw 14 0 3 Select a nickname from the list Tip You can move within the nickname list by typing the first letter of the nickname rather than scrolling through the list 4 Click OK 7 Note Nicknames are tokens and do not flip orientation when applied to the left side of a structure when using Auto matic Justification For example in the absence of a defined nickname the label OTHP appears as PHTO However since the nickname THP is defined the label appears as THPO For more information see Aligning Text on page 28 Expanding Nicknames If your structures contain defined nicknames long atom labels or contracted labels ChemBioDraw can restore your structures to the fully expanded form While expanding a structure containing a defined nickname the nickname will be replaced by its expanded structure as shown below TFA F F a O For Biopolymers when you expand the nickname residue label appears below the expanded amino acid For example assume you have a chain of three amino acids glycine isoleucine and leucine Leu H N Gly COOH To select the amino acid double click the nickname as shown H N Leu NH Gly COOH a7 Chapter 6 Basic Drawings 64 of 315 ChemBioDraw 14 0 i eae Perkin For the Better To expand atom nicknames 1 Select the selection
204. iddle of an atom label creates bonds that are preferentially vertical Chapter 9 Advanced Drawing Techniques 121 of 315 Adding from the start of an atom label creates bonds that try to attain the chain angle setting in the Drawing Set tings dialog If that angle cannot be attained the next best angle is used Attachment Points You can draw polyhapto structures such as ferrocene Cp Fe or abbreviated notations for different positional iso mers of acompound using attachment points The procedure is similar and in both cases the structure retains chem ical significance You can generate all possible structures from an abbreviated combinatorial structure by using Expand Generic Structure feature For more information see Expand Generic Structures on page 255 Figure 9 4 Drawing a polyhapto structure Multi Center Attachments To add a multi center attachment point to a structure 1 Select all or part of the structure 2 Navigate to Structure gt Add Multi Center Attachment An asterisk indicates a multi center node To draw a bond to a multi center attachment point 1 Click the bond tool 2 Point to the asterisk and either click or drag to create a bond 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 Tip If fixed lengths is enabled press lt ALT gt as you drag the bond Variable Attachment Points You can use the Add Vari
205. iew the unit measurement associated with each division on the crosshair axes Moving the Crosshair 1 Position the cursor where the Crosshair axes intersect The cursor changes to an arrow near the center of the crosshair 2 Click and drag the crosshair To constrain crosshair to move in the X or Y direction lt shift gt drag the crosshair Positioning Objects To align two or more objects using the crosshairs do the following 1 Move the Crosshair axes and align it with the object 2 Select an object and drag it until it is aligned with either axis of the crosshair or a grid line 3 Select a second object Chapter 3 Page Layout 15 of 315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better 4 Drag the second object to the crosshair axis or 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 avail able on some keyboards To move 1 point select the objects and press an arrow key To move in 10pt increments press lt alt gt while you press the arrow key Tables After you create a table you can adjust its borders and color Creating Tables To create a table 1 Select the Table tool on the Main Tools toolbar 2 Do one of the following m Click and drag in the document window to create the table The table has two rows and two columns Click in the document window Type the numbers of rows and columns in the Insert T
206. iguous structural formula For example CH COCH CH 3 is recognized as Chapter 16 Chemical Interpretation 280 of 315 methyl ethyl ketone and MeOH is recognized as methanol On the other hand C H 6 might mean benzene or another isomer Generally empirical formulas C H 6 and H SO 4 are not recognized but structural formulas CH CH 3 and HOSO OH are Molecular weight and elemental analyses of empirical structures are possible but the Expand Label command does not work with them Empirical structures are discarded when they are transferred to other applications that require unambiguous structures Chemically significant text must be entirely in formula or for isotopes and charges superscript style ChemBioDraw does not recognize a chemical formula embedded within a larger block of text If you draw a bond add an atom label and then delete the bond you NH have a chemically meaningful text block whose font size and style match other atom labels If you create a caption with the text tool and set it to Formula style H O you have a chemically meaningful text block whose font size and 2 style match other captions Charges You can create charges as part of a atom label or with the appropriate symbol from the Chemical Symbols toolbar Charges are always assigned to a specific element in the atom label whose acceptable valences become those of the similar isoelectronic neutral element A charge following an element is assi
207. ij pentaleno 2 1 6 cde Jazulene is a fused ring system Bridged Fused Ring Systems ChemBioDraw supports bipodal both bivalent and polyvalent simple acyclic chained homogeneous atoms of only one element independent bridged fused ring systems For example Figure 10 3 The bridged fused ring system 9 10 epidiox yanthracene Chapter 10 Struct Name Ultra Feature 145 of 315 W P l Polymers Polymer structures cannot be expressed by SMILES However Struct gt Name supports many homopolymers copoly mers and alternating polymers For example A O mE Ha N OH O Figure 10 4 polyaziridine compound with sulfamic acid 1 1 Other Compounds m Phosphorous and Arsenic compounds m Si Ge Sn and Pb compounds Boron compounds Organometallic compounds Struct gt Name generates names with proper CIP stereochemistry descriptors Struct gt Name provides direct support for stoichoimetry specified as bracket properties including fractional stoi chiometry Also the manner in which the stoichiometry of 0 5 hemi and 1 5 Sesqui is handled is improved For example O o A H CI los HN OH Figure 10 5 2 aminooxy acetic acid hemihydrochloride Struct gt Name follows IUPAC rules as closely as possible when generating chemical names However while handling indicated hydrogens it conforms to CAS nomenclature recommendations For example the carbon atom between two oxygen atoms in 1 3 dio
208. in more than one attachment point for example For this type of R group you must indicate the attachment point order in your table If you have well defined multiple attachment points on your structure fragments you can search for specific materials This type of search is useful for finding similar structures that conform For example assume you want to find compounds in figure A below but not compounds in figure B Figure 14 12 Multiple attachment points By specifying the attachment point order you can exclude the unwanted compounds To specify the attachment points order 1 Draw the structure shown below Ry NH 2 Create an alternative group box labeled R1 Chapter 14 Query Structures 251 of 315 W P l 3 Draw the structure fragments and label them with attachment points When the alternative group definition is complete the attachment point symbols appear in the parent compound Figure 14 13 R groups with multi attachment points By numbering your attachment points you specify that the methyl group must be adjacent to the amine group The conformations that are not of interest are excluded Attachment Point Numbering Numbered attachment points let you specify how the structure fragments connect to your parent structure To set the order of the attachment points use the Attachment Point tool to click the ends of the bonds in the order you want To change attachment point order Cli
209. ine help or user s guide Conventions used in this Guide This guide uses several basic conventions to help you quickly learn ChemBioDraw Instructions Instructions are designed to help you navigate through menus and screens Menu items appear in bold For example to open a new drawing template 1 Goto File gt Open Templates gt Amino Acids This step asks you to select the File menu select Open Templates in the File menu and then select Amino Acids in the Open Templates sub menu Notes Tips and Cautions The guide uses particular icons for various types of information _ Note Notes highlight important information Tip Tips supply useful specific nice to know information supplemental to the main text i Caution Cautions indicate important information that if ignored may lead to data loss or other serious problems Additional Information These resources are available to help you get started with ChemBioDraw Online Help In ChemBioDraw press lt F1 gt or navigate to Help gt Contents Chapter 1 Introduction 1 of 315 Tool Tips This is the name or a short description of a tool To view a tool tip point to a tool A longer description of the tool tip is available in the status bar Status Bar See the lower left corner of the ChemBioDraw window for useful information as shown below ay ey A gt oO ee one oc Figure 1 1 Status bar displaying information about solid bond Serial Nu
210. it structures A document may contain multiple pages or a single page Creating Documents You can create a new document using either the default settings or a Style Sheet with customized settings To create a document navigate to File gt New Document Using Styles To create a new document using a different style sheet or stationery pad Chapter 2 Getting Started 6 of 315 W P 1 Navigate to File gt Open Style Sheets 2 Choose a Style Sheet from the list ChemBioDraw provides pre defined style sheets in the ChemDraw Items folder For example the ACS Document 1996 is configured to create documents set with the bond lengths bond width spacing and fonts used in the 2 column format of ACS journals For a list of the settings in these documents see Document Settings on page 38 Opening Documents To open a document do one of the following m Navigate to File gt Open From the Open dialog select the file name and location of the file and click Open From the File menu choose the document from the list at the bottom Selecting an Open Document The Window menu lists all open documents and templates The document you choose from the list becomes the act ive window Annotating Documents Annotations are useful for adding text information to help you identify documents in a database search Annotations are categorized using keywords and an associated data value There are several default keywords Name Descrip
211. ith the latest browsers on both Windows and Mac platforms is part of this process as well ChemDraw to SciFinder Interface Send ChemDraw structure and reaction queries directly to SciFinder to find useful information relevant to your com pound reaction For more information see Querying SciFinder with ChemBioDraw Ultra Feature on page 295 Biopolymer Builder Enhancements Single and multi letter amino acids Lets you create single letter amino acids and nucleotides either by entering the corresponding IUPAC code or by using the Biopolymer toolbar The Biopolymer Editor lets you create three letter or non standard amino acids by entering the residue name Toggle Amino Acid Style AA1 lt gt AA3 command Lets you change the amino acid representation from single to multi letter and vice versa For more information see Drawing Biopolymers on page 101 L and D amino acids Lets you create standard L or D amino acids by entering the relevant IUPAC code Toggle L and D amino acids The Toggle Amino Acid Stereo L lt gt D command lets you change the ste reochemistry of amino acids from L to D and vice versa Protecting groups Lets you add protecting groups such as Trt and Fmoc to amino acids containing additional NH or OH groups Arg Aad You can also expand and contract the protected residues For more information see Pro tecting Groups on page 103 H Aad OFmoc Arg Trt OH Fmoc O
212. ivity Shape Coefficient Boiling Point Freezing Point Molecular Formula Sum Of Degrees C G Molecular Weight Sum of Valence Chapter 11 Chemistry Features 162 of 315 ChemBioDraw 14 0 Cluster Count Critical Pressure Critical Temperature Critical Volume Connolly Accessible Area Gibbs Free Energy H Heat of Formation Henry s Law Constant I Connolly Molecular Surface Ideal Gas Thermal Area Connolly Solvent Access ible Surface Area Connolly Solvent Excluded Volume Exact Mass Capacity L LogP M Mass Property Predictions in Chem3D Number of Rotatable Bonds O Ovality p Principal Moments of Inertia X Y Z Polar Surface Area R Radius S P gt Perkin For the Better Degrees T Total Connectivity Topological Dia meter Topological Index Total Valence Con nectivity V Vapor Pressure W Water Solubility Wiener Index Chem3D lets you build analyze and compute properties very easily In addition to analyzing structures to calculate mass and formula predicting numerous physical properties you can also perform calculations for molecular topology A list of properties available in Chem3D is listed in the table below For more information on these properties see Chem3D online help or visit the PerkinElmer Informatics website Balaban Index Boiling Point C C V Cluster Count Chapter 11 Chemistry Features G Gibbs Free Energy H
213. ize A4 Reduction 100 43 of 315 ChemBioDraw 14 0 i Perkin For the Better 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 _ Note You can modify hotkeys and nicknames 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 lt 3 gt to add a tert butyl group Atom Label Key A a F f Ph Por4 Ac Aors H h Q q Br b i R r n Bu 1 K k S S s Bu 2 Me m Si t Bu 3 N n TMS t Chapter 5 Shortcuts and Hotkeys 44 of 315 ChemBioDraw 14 0 i Eee Perkin For the Better Atom Label Key C C Na N X X Cl Corl O 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 below Function Key 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 left Change to quadruple bond 4 Center a double bond C Change to bold bond b Chapter 5 Shortcuts and Hotkeys 45 of 315 ChemBioDraw 14 0 Function Position a double bond to the right Change to wedged bond Bring bond to front Change to hashed bond Open a bond properties text box Change to h
214. k the structure to select all labels in the structure 3 Navigate to Structure gt Expand Label You can also use the Expand Label tool in the Structure toolbar Your structure is redrawn in its expanded form Below is an example of expanding labels Contracted Ph CH sCHCH CH Expanded tin When you expand a label that contains a divalent nickname for example H Ala OH the attachment order depends on the order in which the bonds are created Multiple Atoms Labels can comprise a group of atoms When you expand the label it expands to create the structure Contracted Chapter 9 Advanced Drawing Techniques 120 of 315 W P CH CH NHCCH Expanded Adding a Label of Multiple Atoms 1 Using the text tool click an atom in the structure where you need to place the label 2 Type the formula such as CH2NHCH3 3 Using a selection tool select the formula 4 Right click the formula and select Expand Label or navigate to Structure gt Expand Label You can also use the Expand Label tool in the Structure toolbar Ph CH CH JH CH ee Ph CH CH3CHCH Figure 9 3 Adding bonds to a label You can determine the orientation of the resulting bond by dragging If you click to add a bond there are several pref erential orientations for the resulting bond as outlined below Adding from the end of an atom label creates bonds that are preferentially horizontal Adding from the m
215. 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 Note that the central ring in the example below is not selected Chapter 6 Basic Drawings 80 of 315 W P l Resizing Objects You can resize objects by dragging the resize handle of a selected object or by scaling To resize a selected object proportionately 1 Select the objects to resize The resize handle is located in the lower right corner of the selection rectangle 2 Point to the Resize handle The cursor becomes a double headed arrow f a 3 Drag the resize handle until the object is the size you want In most cases when you resize an object the aspect ratio of the object the ratio of the height to width does not change However it is possible to distort certain objects including chemical structures circles boxes and ovals To distort an object in the horizontal or vertical direction 1 Select the object 2 Doone of the following Drag the handle on the desired side Chapter 6 Basic Drawings 81 of 315 W P a lt Shift gt drag the Resize handle in the desired direction The lt shift gt key modifies the resize operation so that you can distort objects along the X axis or Y axis Rotating Objects 1 Select an object to rotate For objects that can be rotated the rotation handle appears at the top of the selection rect
216. l 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the lone pair from the palette Chapter 11 Chemistry Features 156 of 315 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 Electron and Radical Pushing ChemBioDraw provides the Electron Pushing and Radical Pushing tools for illustrating electron transfer Electron transfers can be drawn between atoms bonds and orbitals For more information see Electron and Radical Push ing on page 132 Radical Use the radical symbol to indicate a single non bonded electron To use the radical symbol 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 _ Note The lone pair symbol is interpreted as a diradical when it is placed next to an unlabeled carbon atom Radical Cation and Radical Anion Use the charge radical symbols to represent radicals that are charged To use the charge radical symbols 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the symbol from the palette 2 Click and drag the atom to where you want the symbol 3 Click an atom to add a radical cation or radical anion symbol in a horizontal orientation Charge Symbols To draw a charge and associate it with a structure 1 Hold down the mouse button over the Chemical Sym
217. l The bonds in the new structure appear at standard 120 angles Changing Fixed Values By default bond lengths are 4176 inches and bond angles in a chain are 120 To change fixed values 1 Navigate to File gt Document Settings and click the Drawing category Lira Dirr aia Fib Borchi s Capitan es wedle arin cadre E sao khl 82 ice Labe Prope Lites Biot yr Cipry r 2 Enter a value in the Fixed Length text field Use in cm pt or picas for units 3 Enter a value in the Chains Angle text field 4 Click OK For more information on drawing settings see Drawing Settings on page 24 Chapter 6 Basic Drawings 56 of 315 ChemBioDraw 14 0 i oe Perkin For the Better Atoms By default when you draw structures with the various bond ring or chain tools simple hydrocarbons are created You can add atom labels to the atoms using the Text tool You can also use the Text tool to add textual captions to a document For example you can add the atom label OH to a drawing of toluene to create phenol OH 1 Draw the toluene structure 2 Using the Text tool click the methyl carbon A text field appears 3 Type OH in the text field 4 Click outside the text field To edit the atom label click in the text field with the text tool and begin typing You can either enter the atom label in a text field or type the hotkey while hovering over an atom For more information about
218. l temperature to liquefy a gas Critical temperature Reported in Kelvin this is the temperature above which a gas cannot be liquefied regardless of the pressure applied Critical volume Reported in cm mol this is the volume occupied by one mole of a substance at the critical temperature and pres sure Exact mass This is the sum of the masses of the individual isotopes in the molecule For example the exact mass of water con taining two hydrogen 1 1H and one oxygen 16 160 is 1 0078 1 0078 15 9994 18 0106 The exact mass of heavy water containing two hydrogen 2 deuterium or 2H and one oxygen 16 160 is 2 014 2 014 15 9994 20 027 Formal charge This is the charge assigned to an atom in a molecule assuming that electrons in a chemical bond are shared equally between atoms regardless of relative electronegativity The formal charge of any atom in a molecule can be calculated using the formula FC V N B 2 Where V is the number of valence electrons of the atom in isolation atom in ground state N is the number of non bonding electrons on this atom in the molecule and B is the total number of electrons shared in covalent bonds with other atoms in the molecule Freezing point The freezing point for the structure at 1 atm Units Kelvin Gibbs free energy Reported in KJ mole Gibbs free energy is defined as G p T U pV TS which is same as G p T H TS Chapter 12 ChemDraw Ex
219. le is outside of the alternative group definition This isolated bond is probably not intended to have chemical sig nificance The atom is very close to another atom or bond The stereocenter has no ste reobonds specified There is a valence and charge error somewhere in this aromatic sys tem The stereocenter has conflicting or ambiguous stereobonds specified This label has an unrecognized iso topic Mass Chapter 16 Chemical Interpretation P gt Perkin For the Better Description Displayed for any Alternative Group Box whose border crosses part of a structure This is a status message only Displayed for unlabeled single bonds unattached to other bonds All bonds are interpreted chemically usually as C H R results if intended as a graphical line only This is a status message only and may cause unexpected 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 pro duces incorrect results This is a status message only Displayed for any asymmetric center without attached wedged hashed dashed or bold bonds This is a status message only and appears only when Show Stereochemistry is tuned on and there is at least one other wedged hashed dashed or bold bond in the structure Displayed for any odd membered ring drawn as a delocalized system with a circle in the middle where there is no correspon
220. le of an arrow you are restricted to multiples of 15 if Fixed Angles is enabled Hold down the lt Alt gt key to drag to any angle You can also create an arrow by drawing an arbitrary spline using the pen tools and adding an arrow head Arrow Heads There are three arrow head shapes solid hollow and angled To change the shape right click an arrow and choose the shape from the context menu ae y A B C Arrow heads shapes are A Solid arrow head B Hollow head and C Angled head Arrow Types ChemBioDraw offers a variety of arc types and arrow types such as crossed no go arrows equilibrium arrows of unequal lengths and elliptical arcs Arc Arrows There are two ways to create an arc arrow 1 Click and drag the arc adjustment handle of a straight arrow A f Figure 6 5 A Arc adjustment handle 2 Select an arc arrow from the Arrows palette You can customize arc arrows as easily as straight arrows Some examples are Chapter 6 Basic Drawings 71 of 315 P gt Perkin For the Better ChemBioDraw 14 0 a To undo all changes made to an arrow except for the change in length click the arrow with the same arrow tool b Click an unmodified arrow or one that has had only its length changed to reverse its direction Hollow Arrows You can rotate hollow arrows and change their length and width You can also modify the angle and create hollow arc arrows just as with regular arrows D gt You
221. lectron pair transfer such as Figure 9 9 Example of electron pushing To display the transfer of one electron Chapter 9 Advanced Drawing Techniques 132 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 1 Select the Radical Pushing Tool from the Chemical Symbols toolbar 2 Click and drag the mouse from the source object to the target object and release the mouse A half head arrow sig nifying only one electron transfer appears such as Figure 9 10 Example of radical pushing You can delete the electron transfer arrow by either selecting or hovering over the arrow and pressing the lt DELETE gt key You can modify the electron transfer arrow shape by using either the Arrow tool or the Electron Pushing Tool When you hover over the electron or radical pushing arrows the associated objects are highlighted in addition to the arrows Stoichiometry Grid Use the Stoichiometry Grid to calculate stoichiometric data for a reaction The grid fills in as you modify a reaction drawing and all calculations are done automatically To create a stoichiometry grid 1 Draw a reaction or open a file containing a reaction 2 Navigate to View gt Show Reaction Interpretation Turning on Show Reaction Interpretation ensures the reac tion is properly interpreted by ChemDraw When you hover over the reaction for example C6BH6 cHaci C6H5CH3 CIH Reactants in red m Products in magenta m Anything above a
222. lly by typing the appropriate characters listed below m centered amp c right amp r a left default amp l For example Document Settings for RAN1 cdx lf Footer Position lo s in From bottom of page Comment B e Figure 3 1 A Variables to display file name center aligned in the header B Variables to display page number aligned right in the header Chapter 3 Page Layout 11 of 315 hemBioD 14 f ChemBioDraw 14 0 PerkinElmer For the Better RAN I cds A a i a i 7 Hi alh Figure 3 2 A The filename is displayed center aligned in the header B The page number is displayed aligned right in the footer Page Setup To setup the page navigate to File gt Page Setup Page setup options are Paper Choose the size of the paper on which to print the document and the printer tray Orientation Select either Portrait or Landscape Margins By default margins are set to 0 5 inches Printer Click to select a printer and set preferences You can also choose the printer in the Print Options dialog Printing ChemBioDraw uses the standard system commands to print documents Available options depend on the printer you use Refer to your printer s documentation for more information In general to print a document 1 Navigate to File gt Page Setup 2 Make all appropriate selections for your printer and click OK 3 Navigate to File gt Print 4 Make your selections in the Print dialog
223. lly solvent excluded volume Critical pressure Critical temperature Critical volume Exact mass About molecular networks Formal charge Freezing point G Gibbs free energy H Heat of formation Henry s Law constant Ideal gas thermal capacity M Mass Melting point Molar refractivity MOLECULAR_NETWORKS_ LOGP MOLECULAR_NETWORKS_ LOGS MOLECULAR_NETWORKS_PKa Molecular formula Molecular weight N Num rotatable bonds O Ovality Pp Polar surface area Principal moment Of inertia R Radius Shape attribute Shape coefficient Sum Of degrees Sum of valence degrees T Topological diameter Total connectivity Total Valence Con nectivity V Vapor pressure W Water solubility Wiener index MOSES pKa MOSES logS and MOSES logP for predicting acid dissociation constants aqueoues solubility and octanol water distribution coefficients of chemical compounds are computational calculator modules based on Molecular Networks chemoinformatics platform MOSES MOSES is developed maintained and owned by Molecular Networks GmbH Erlangen Germany For further information please visit www molecular networks com moses All rights reserved Molecular Networks GmbH Erlangen Germany www molecular networks com Balaban index Chapter 12 ChemDraw Excel and CombiChem 203 of 315 W P l _ q ee oe i PEN 2 S S edgesij Where qis the number of edges in the molecular graph
224. lored 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 See example below a en Figure 9 2 A The structure colored pink as an integral group B The structure colored pink as a group Labels In addition to representing atoms labels can represent regions of a structure that you define For example you can assign a label to an unimportant region of a molecule and then contract that region to reduce the size of your drawing You can then expand the label to see the whole molecule Creating Labels To create a contracted label 1 Select the area of the structure to contract 2 Navigate to Structure gt Contract Label The Contract Label dialog appears 3 Type a label for the contracted structure Chapter 9 Advanced Drawing Techniques 119 of 315 4 Click OK The label replaces the selected portion of the structure i gt Hexylbenzene 7 Note If the area of the structure you contract contains errors an error dialog appears Click Ignore to view other errors Click Ignore All to ignore all errors or Stop to end the contract process Expanding Labels If your structures contain defined nicknames long atom labels or contracted labels ChemBioDraw can restore your structures to the fully expanded form To expand atom labels 1 Select a selection tool 2 Select the label to expand or double clic
225. lysis and Chemical Properties dialog boxes remain unaffected To change the names of the properties 1 Navigate to File gt Document Settings 2 Select the Property Labels category See figure below Chapter 4 Preferences and Settings 26 of 315 W P 3 Inthe Analysis window select the property to rename 4 Click Edit Label and type a new name in the Edit Label text box Click OK 5 Type the new name and click OK 6 Repeat step 4 for other properties 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 a Line spacing a Alignment Setting Font Parameters Changing text formats in the Document Settings dialog affects the current document only You can also change set tings for individual objects by using the Object Settings dialog 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 Inthe Document Settings dialog click Text Captions or Atom Labels 3 Change the settings as desired The options are described in the following sections 4 Click OK The formatting is applied to the current document Setting the Baseline Style You can specify these baseline styles Baseline Style Formula ka Normal Subscript Superscript Formula
226. mary bonds to thet ued Ca i 3 To continue checking the structure click Ignore 4 To ignore all subsequent errors click Ignore All 5 Tostop checking for errors click Stop Checking Copied Structures To automatically perform a check structure analysis each time you copy a structure from the clipboard 1 Navigate to File gt Preferences 2 From the General tab click Check Structure When Copying to Clipboard or Exporting This change affects all documents Chemical Warnings ChemBioDraw checks chemical syntax as you draw If it finds an error in your structure a wavy red box appears around the object The box displays on the screen only and does not print Disabling Chemical Warnings Warnings display by default To disable chemical warnings navigate to View gt Show Chemical Warnings Chapter 6 Basic Drawings 89 of 315 To disable error checking on a specific object right click the object and deselect Display Warnings on the context menu When Display Warnings is disabled for an object A red box does not appear around the object Problems are reported by the Check Structure command Navigate to Structure gt Check Structure To view a description of the problem perform one of the following Point at the warning with the mouse to display a tool tip that describes the error a Right click the warning and select Explain This Warning Select the structure and navigate to Structure gt Check Structure Warning
227. mber and Technical Support For more information on obtaining serial numbers and registration codes see the online Services Web site Technical support is available to registered users through the Internet and our Technical Support department When contacting Technical Support always provide the serial number of your ChemBioOffice application Our Technical Support Web pages contain answers to frequently asked questions FAQs and other information To access our Technical Support in ChemBioDraw navigate to Online gt Browse PerkinEImerTechnical Support If you are unable to find a solution on the Web site follow these steps before you contact Technical Support 1 Check the system requirements for the software 2 Read and follow suggestions outlined in Troubleshooting on page 3 3 If your attempts to resolve a problem fail contact Technical support Before you Call a Try to reproduce the problem before contacting us If you can reproduce the problem please record the exact steps Record the exact wording of any error messages that appear Record your attempts to correct the problem Additional sources of ChemOffice information are ChemBioDraw online Help The PerkinElmer Informatics Web site PerkinElmer Informatics Services Chapter 1 Introduction 2 of 315 Troubleshooting This section describes steps you can take that affect the overall performance of CS Desktop Applications as well as steps to follow if your c
228. mistry for a group 1 Select all atoms in the group using SHIFT click 2 Goto Structure gt Enhanced Stereochemistry and select a stereochemistry marker See Relative stereochemistry on page 153 for information on showing and hiding indicators You can save enhanced stereochemistry notation in any of these formats CDX CDXML MOL V3000 RXN V3000 SKC TGF When saving to SKC or TGF format the indicators are converted into corresponding Data SGroups Whenever you open SKC or TGF files containing such Data SGroups they are converted into true Enhanced Stereochemistry val ues Chemical Annotations ChemBioDraw provides the following tools and tool palettes that enable you to add chemical annotations to your doc uments 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 Chapter 11 Chemistry Features 154 of 315 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 navigate to Object gt Fixed Lengths or Fixed Angles 7 Note Orbitals are not normally a 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 structu
229. n data for proton prediction to supplement the existing data that the ChemNMR algorithm uses You provide your data in an SDfile and use the file to update the ChemBioDraw ChemNMR database Using a third party tool such as ACD Labs software or Mnova Lite you can enhance your prediction results thereby Supporting your analysis process With Mnova Lite you can assign your spectra in Mnova NMR and save those assignments to an SD file Add them to ChemNMR database With enough added data the prediction results improve Consult your application s User Guide for instructions NMR Data Format The correction data that you add to your SDF file must be in this format gt lt SHIFT gt sacon 20 gt lt Shite value lt ignored gt For example gt lt BHIFT1 gt Vee em op eee UU gt lt SHIFT2 gt Spp eI 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 ChemBioDraw 2 Locate the ChemBioDraw ChemNMR directory 3 Open a DOS prompt n Windows 8 navigate to Start gt Run and enter cmd in the Run window Click OK n Windows 7 go to Start and enter cmd in the search field Press the lt Enter gt key 4 At the DOS prompt navigate t
230. nalogs Hydroperoxides Peroxides 143 of 315 ChemBioDraw 14 0 Perkin For the Better Non Ringed Structures Isolating and naming the functional groups Identifying the base chain of the molecule Identifying and building substituents Nomenclature of groups cited only by prefixes Heteroacyclic compounds m Naming of substituent groups Locants Name generation alphabetization punctuation etc Ringed Structures Struct gt Name supports the these types of ringed structures Carbomonocyclic structures Heteromonocyclic structures Fused polycyclic structures Fused polycyclic trivially named structures Ring fusions of multiple rings Ring fusions of two multiple ring systems Ring fusions of more than two ring systems m Bridged monocyclic structures a Spiro ring systems Some of these ring structures are defined below Ring Assemblies A ring assembly has two or more identical cyclic systems joined together by single or double bonds All the cyclic sys tems are either a single ring fused system alicyclic von Baeyer system spiro system phane system or fullerene Chapter 10 Struct Name Ultra Feature 144 of 315 ChemBioDraw 14 0 i PerkinE mer For the Better Figure 10 1 An example of a ring assembly structure 1 1 2 1 terphenyl Fused Ring Systems Struct gt Name supports fused ring systems of two or more rings such as the structure below Figure 10 2 cyclopenta
231. nd below the reaction arrow in cyan and blue 3 Select the reaction and navigate to Structure gt Analyze Stoichiometry The grid with several data fields filled with default values appears under the reaction Chapter 9 Advanced Drawing Techniques 133 of 315 ChemBioDraw 14 0 Reactants Formula NIV Limiting Equivalents Sample Mass Co Weight Molarity Density Volume Reactant Moles Reactant Mass P gt PerkinElmer For the Better Products Formula MV Equivalents W Completion Expected Mass Expected Moles Measured Mass Purity Product Mass Product Moles Yo Yield Note If a catalyst or condition label is above the reaction arrow right click the label and deselect Interpret Chem ically in the context menu before creating the grid To enter data in the grid 1 Set the limiting compound If the default setting is incorrect right click the word No in the limiting row and select Set Limiting from the context menu Reactants Formula MW Limiting Equivalents Sample Mass vo Weight Molarity Density Volume Reactant Moles Reactant Mass Products Formula MV Equivalents SYoCompletion Expected Mass Expected Moles Measured Mass Purity Product Mass Product Moles w Yield 2 Select the Text tool and click where to enter the data 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 requir
232. nd tool Branched Peptides A branched peptide is formed where a residue has multiple possible leaving groups For example Arg has two amino groups and Asp has two carboxyl groups A polymerization reaction could potentially take place at either of these groups or at both Hence protecting groups are often employed during the polymerization reactions to selectively allow polymerization at only a single site Consider the following example in which the peptide is branched at the Asp residue H Ala Phe Gly Asp Met Val OH Phe Thr Gin OH In the following example the residue is branched at the Arg residue H Ala Phe Arg Met Val OH H Phe Gin Gly You can create a branched peptide using the solid bond tool to connect the branching residue in the first chain to the branching residue in the second chain If the residues have leaving groups that can be automatically found then it branches at those points Otherwise the Modify nickname dialog appears and you need to manually define the third attachment point Consider the following example for creating branched peptide 1 Draw two biopolymer chains as shown below H Ala Phe Arg Met Val OH H Phe Gin Gly OH Chapter 8 Drawing Biopolymers 114 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 2 Using the solid bond tool drag from the lower chain s Gly 3 to the upper chain s Arg 3 The terminal hydrogen on the lower chain is removed and the branched
233. nd turns into a pair of diradicals If more than one bond is 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 displays Chapter 9 Advanced Drawing Techniques 126 of 315 ChemBioDraw 14 0 i ee Perkin For the Better Chemical Formula CgH Exact Mass 64 09 You can reposition the formula and mass displays or delete them Synthesis and Retrosynthesis ChemBioDraw includes two tools to help you draw synthesis reactions The Synthesis tool draws a synthesis reac tion based on a product structure that you specify Alternatively the Retrosynthesis tool draws the reaction with the product on the left and an 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 use the Retrosynthesis tool to create this reaction NH R J Quinline synthesis Drawing Reactions To demonstrate how to draw reactions we will use this example Chapter 9 Advanced Drawing Techniques 127 of 315 Q 5 Q OH OH 2 propanone 4 hydroxy 4 methylpentan 2 one Drawing an Arrow Starting with 2 propanone see Tutorial 1 Drawing a Structure on page 298 draw
234. ndividual caption or label from the Text menu or toolbar 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 Navigate to File gt Document Settings 2 Click Text Captions or Atom Labels in the Document Settings dialog 3 Select the appropriate options 4 Click OK These settings affect all new captions or atom labels in the current document To use these settings in new doc uments save them in a style sheet For more information see Document and Object Settings on page 23 Formatting a Caption or Label You can set the text format for an individual caption or atom label before you type The format change is applied only to the current text To set the text format before you type 1 Select the Text tool and click in the document window A text box appears 2 Toset the text format do one of the following Chapter 4 Preferences and Settings 30 of 315 Navigate 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 Subsequent text you type uses the default document settings Changing Text Setting You can change the text settings for a selected caption or atom label You can choose to have the settings applied to the selected text and to all subsequent text you type
235. ng Objects on page 83 3 To create another column with this same spacing as the previous select the Text tool and press lt tab gt A third cap tion text box appears Creating New Rows To start a new row that is aligned with the first press lt tab gt twice at the end of a row A caption text box appears under the first caption positioned exactly 20 points below the first caption in the first row To change the spacing between rows as you create the table 1 Select all the captions in a row 2 Move the captions using the arrow keys For more information on moving objects see Moving Objects on page 83 Adjusting Row or Column Spacing 1 Select all the captions in the row or column with a selection tool Chapter 3 Page Layout 18 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 2 lt Shift gt and drag the captions The movement is constrained to the X axis or Y axis so that you can maintain the row or column alignment Inserting New Rows To insert a row Select a selection tool and select a row of captions lt Shift gt drag the selected row lt Shift gt constrains the movement to the Y axis to maintain the column alignment Select the first caption in the row above or below the space you created lt Control gt lt shift gt drag to create a copy of the caption and position it in the empty space you created oa F Wn gt The placement of this copied caption sets the position of the inserted ro
236. ngle letter to triple letter and vice versa For example A Ala HO H HO HI 1 Select the sequence 2 Right click and select Toggle from Amino Acid Style AA1 lt gt AA3 You can also change the amino acid representation of expanded substituted and protected amino acids For example A OUT rt hla aie ae ee wN H Arg OH OH The Toggle Amino Acid Stereo L lt gt D option lets you change the stereochemistry of the amino acid from L to D and vice versa To toggle amino acids 1 Select the sequence 2 Right click and select Toggle Amino Acid Stereo L lt gt D Protecting Groups You can add protecting groups such as Trt and Fmoc to amino acids containing additional NH or OH groups Arg 2 Aad Protected groups are specified within brackets To add a protecting group 1 In a sequence enter after a completed residue name as shown below H Ala Arg Gin WH 2 Enter the name of the protecting group and enter Y at the end of the name H Ala Arg Gin Trt OH The name of the protecting group determines if it will protect the NH or OH group If prefixed by O then it protects the 2 OH group You can expand and contract protected residues just like any other residue Chapter 8 Drawing Biopolymers 103 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 HN ii NH w YH WAN NAA on whe Trt Ala Arg Gin Trt If no leaving group is found
237. nickname to your drawing For more information on defining nicknames see Defining Nicknames on page 138 Using Nicknames Using nicknames you can add short names for functional groups to use as an atom label or part of a label When an atom is labeled with a nickname the chemical significance of the expanded structure is retained Chapter 6 Basic Drawings 62 of 315 ChemBioDraw 14 0 PerkinElmer For the Better Commonly used nicknames such as Me Et and Ph are stored in your ChemDraw Items folder You can edit or delete nicknames in this list You can assign hotkeys to nicknames For example the hotkey lt 4 gt labels an atom with Ph which represents a phenyl group Applying Nicknames You can either type the nickname or select it from the nicknames list For more information on defining nicknames see Defining Nicknames on page 138 To use a nickname to label an atom 1 In a structure double click an atom with a bond tool or click an atom with the Text tool An atom label text field appears Do one of the following a Type a nickname label such as Et m Navigate to File gt List nicknames The List Nicknames dialog appears Select the required nickname and click Paste m Click Done An example is shown below Et NHOH To select a nickname to apply to an atom using a hotkey 1 Point to an atom 2 Press the hotkey lt gt equal sign The Choose Nickname dialog appears Choose N
238. nt value Oo ON O Oo A W N gt 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 returns all molecules in the query database that include a template structure that you provide For example assume you want to find all molecules 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 Chapter 12 ChemDraw Excel and CombiChem 185 of 315 W P l To illustrate assume that you have a small database comprising of four molecules o m and p cresol and bro mobenzene Further assume you want to run an R group analysis on this database to find all molecules that contain toluene in its structure You will find that the results include three main parts a The list of molecules that contain the toluene template In this example the results include o m and p cresol Bro mobenzene 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 a The functional g
239. o the ChemNMR directory in step 2 5 Enter the command MakeChemNMRUserDB exe lt input file gt lt resource directory gt lt output directory gt where a lt jnput file gt is the full path and filename of the SDF file that contains the correction data lt resource directory gt and lt output directory gt are the full path to the ChemNMR directory 6 Restart ChemBioDraw Restoring Default NMR Data To stop using your own data and restore ChemBioDraw to its original settings Chapter 11 Chemistry Features 176 of 315 ChemBioDraw 14 0 i eae Perkin For the Better Exit ChemBioDraw Locate the ChemNMR directory Delete the files Ushiftdb5H1 txt andUsimilvecx hl Restart ChemBioDraw w opo wN a Example Supplementary Data The example below represents an SDF file that includes supplementary NMR data for two structures The sup plementary data follows the structure data and is shaded gray for clarity ACD Labs07190711112D 141400000000 15 V2000 5 7578 1 9992 0 0000 CO0O0000000000 5 7578 3 3267 0 0000 CO0O0000000000 4 6062 1 3275 0 0000 COO0000000000 4 6062 3 9825 0 0000 NOOO0O000000000 3 4547 1 9992 0 0000 CO0O0000000000 3 4547 3 3267 0 0000 CO0O0000000000 6 9094 1 3275 0 0000 NO30000000000 8 0609 1 9992 0 0000 0050000000000 6 9094 0 0000 0 0000 O0O00000000000 2 3031 1 3275 0 0000C 000000000000 2 3031 0 0000 0 0000C000000000000 1 1516 1 9992 0 0000C000000000000 1 1516 3 3267 0 00000000000000000 0 00
240. oDraw includes a library of document settings based on those found in many well known scientific pub lications For example some journals may require submitted articles be formatted with specific margins fonts page size and so on If you plan to submit your document to a specific journal open in ChemBioDraw the style sheet for that journal You can also create style sheets of your own _ Note The changes you make to the document settings is reflected only in the current document and is not avail able throughout the application To create your own style sheet Create anew document Enter the settings in the Page Setup Drawing Text Settings and Color palette dialog boxes Navigate to File gt Save As KR OD Inthe Save As dialog box a Select the ChemBioDraw style sheets file format b Type a name for the document c Save the template in the ChemDraw Items folder 5 Click OK Chapter 4 Preferences and Settings 38 of 315 ChemBioDraw 14 0 ACS Document 1996 Adv Synth Catal J Chin Chem Soc Chapter 4 Preferences and Settings P gt PerkinElmer For the Better 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 Atom Label Size 10 pt Caption Font Caption Size 10 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction
241. ode or zigzag mode Expanding and contracting labels Lets you expand the entire sequence or any part of it The sequence is auto matically cleaned following expansion When you contract a sequence the Clean Up Biopolymer command cleans and re arranges the sequence so that the residues are aligned and wrapped Numbering residues Lets you display residue numbers above any residue For more information see Numbering Residues on page 110 Hide Show termini and bonds Lets you hide bonds and termini without affecting the underlying chemistry Nickname Enhancements In ChemBioDraw 14 0 many new residues for example non standard amino acids non standard nucleotides linkers have been added to the nickname library Defining nicknames is much easier and more flexible now For more inform ation on nicknames see Defining Nicknames on page 138 Struct gt Name Enhancements Struct gt Name in ChemBioDraw 14 0 is enhanced to support many homopolymers copolymers and alternating poly mers and stoichiometry specified as bracket properties including fractional stoichiometry For more information see Struct gt Name on page 143 Electron Pushing ChemBioDraw 14 0 introduces the Electron Pushing tool for illustrating electron transfer For more information see Electron and Radical Pushing on page 132 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved vii hemBioD
242. oes 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 structures with support for the Cahn Ingold Prelog rules for ste reochemistry 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 PerkinElmer Informatics product packages and levels allow unlimited structure to name con versions while others impose a daily limit Chemical composition When this function is called with just a cell reference 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 fraction by weight of the given element in the structure Functions CHEM COMPOSTTEON ee LI rer CHEM COMPOSITION cell ref atomic symbol Examples In cell CHEM COMPOSITION A2 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 structure s in the cell Functions CHEM FORMULA cell ref CHEMPROPSTD MOL FORMULA cell ref Examples In cell CHEM FORMULA A2 Result C12H140 In cell CHEMPROPSTD MOL FORMULA A2 Chapter 12 ChemDraw Excel and CombiChem 189 of 315 Result C12H140 Molecular weight Displays the average molecular mass of the structure wher
243. oint is rather than between them Geometry and constraint objects update when you change the structure they cannot be moved independently They may be used with CDX MOL SKC and TGF files full read write compatibility they are not compatible with other formats They can however be saved in print only formats such as TIFF Export Compatibility Because query properties are useful only in a chemical database you must transfer your structures from ChemBioDraw into your search system Not all file formats support the same query properties and not all chemical databases support the same file formats Consult the documentation for your database for which file formats are sup ported The following table lists the query properties that ChemBioDraw writes to SKC TGF and Clipboard file formats The CDX format retains all query properties Exported Query Properties ISIS Mol Rxn Atom Properties Substituents Unspecified X X X Free Sites b b b m Upto a a a Exactly xe xe xe Implicit Hydrogens Not allowed X X X m Allowed X X X Ring Bond Count a Any X X X m No ring bonds X X X m As drawn X X X Simple ring X X X Fusion X X X Chapter 14 Query Structures 262 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Exported Query Properties ISIS Mol Rxn m Spiro or higher X X X Unsaturation Unspecified X X X Must be absent Must be present X X X Reaction Change a May be anything X X m Mus
244. ol and select the s Open orbital 2 Point to the left center carbon and click drag outward The size of the orbital is constrained just as bonds are The constraint is based on a percentage of the Fixed Length setting in the Drawing tab of the Document settings dialog box 7 Note Orbitals are not automatically grouped with the structure To group the orbital with the existing structure so you can move them together go to Object gt Group 1 Click the Marquee tool The orbital is selected Click an empty space to deselect it 2 Point above the structure and drag around the upper fragment to select the three bonds Do not select the bond con necting the two fragments pan HAE D a i I i n S a H He peewee H H B H Pa a bas H My H H se IH 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 With the rotated bonds still selected change the structure layering so that the selection is in front 3 Goto Object gt Bring to Front there is no visible change when you do this Move the front part of the structure to create a 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 Chapter 19 Tutorials 310 of 315 hemBioD 14 f ChemBioDraw 14 0 PerkinElmer For the Better Note If c
245. omputer crashes when using a CS software product Performance Below are some ways you can optimize the performance of ChemBioOffice Desktop Applications From the Performance tab in the System control panel allocate more processor time to the application Install more physical RAM The more you have the less ChemBioOffice desktop applications will have to access your hard disk to use Virtual Memory Increase the Virtual Memory VM Virtual memory extends RAM by allowing space on your hard disk to be used as RAM However the time for swapping between the application and the hard disk is slower than swapping with phys ical RAM Applications and Drivers As with most complex software applications there may be unusual circumstances in which ChemBioDraw may become unresponsive Below are some recommended steps for you to follow to try to resolve software and driver issues 1 Restart Windows and try to reproduce the problem If the problem recurs continue with the following steps 2 Themost common conflicts concern video drivers printer drivers screen savers and virus protection If you do need to contact us be sure to determine what type and version of drivers you are using Video Driver related issues If you experience problems displaying any ChemBioOffice Desktop Application first try switching to the VGA video driver in the display Control Panel or System Setup and then retest the issues If using a different driver hel
246. on 100 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 Atom Label Size 10 pt Caption Font Caption Size 10 pt Drawing Area Width x Height 19 79 cm x 27 15 cm Page Size A4 Reduction 100 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 Atom Label Size 10 pt Caption Font Caption Size 10 pt 42 of 315 ChemBioDraw 14 0 Verlag Helvetica Chimica Acta Wiley Document Chapter 4 Preferences and Settings P gt Perkin For the Better Drawing Area Width x Height 12 cm x 26 7 cm Page Size A4 Reduction 100 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 Atom Label Size 10 pt Caption Font Caption Size 12 pt Drawing Area Width x Height 368 x 720 pts Page Size US Letter Reduction 100 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 Atom Label Size 12 pt Caption Font Caption Size 12 pt Drawing Area Width x Height 19 79 x 27 15 cm Page S
247. on is being cor rectly perceived and lets you adjust the reaction to correct the interpretation CH CH2OH Chapter 9 Advanced Drawing Techniques 131 of 315 To interpret the reaction 1 Navigate to View gt Show Reaction Interpretation 2 Hover your cursor over the reaction arrow 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 should be linked by a sign Reaction conditions must reside completely within the left and right boundaries of the reaction arrow a The reaction cannot include a curved arrow The reaction is colored as follows Reactions are red Products are magenta Everything above the reaction arrow is cyan Everything below the reaction arrow is blue Electron and Radical Pushing A common practice when illustrating organic reaction mechanisms is to use electron pushing arrows to display the transfer of electrons ChemBioDraw provides the Electron Pushing and Radical Pushing tools for illustrating electron transfer Electron transfers can be drawn between atoms bonds and orbitals To display the transfer of an electron pair 1 Select the Electron Pushing Tool from the Chemical Symbols toolbar 2 Click and drag the mouse from the source object to the target object and release the mouse A full head arrow appears signifying the e
248. ondensed digital rep resentation of an InChl string All InChiKey strings are the same length whereas InChl strings are not This standard Chapter 15 Sharing Information 268 of 315 ChemBioDraw 14 0 i see Perkin For the Better 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 Navigate to Edit gt Copy As gt InChiKey For more information on InChI and InChIKey see www iupac org inchi Creating CDXML or MOL Text To create the CDXML text or MOL text for a structure 1 Select the structure you want to create the CDXML or MOL text for 2 Navigate to Edit gt Copy As gt CDXML Text or MOL Text The CDXML text or MOL text is transferred to the clipboard Pasting CDXML or MOL Text To paste and display the CDXML text or MOL text from the clipboard to the document window 3 Navigate to Edit gt Paste Special gt CDXML Text or MOL Text Edit View Object Structure Text Curve Undo not available Ctrl Z Redo not available Shift Ctrl 2 Cut Ctri X Copy Ctr c Paste Ctrl V Clear Del Select All Ctr A Repeat not available Ctrl Copy As Paste Special d SMILES Alt Ctrl P Name as Structure InChI CDXML Text MOL Text Alt Shitt Ctrl P Biopolymer FASTA Peptide FASTA DNA FASTA RNA Scrap and Clipping Files You can use scrap files to copy parts of a drawing to other applications after saving the file in ChemBioDraw
249. only one substituent 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 substituent options are Unspecified Default The target base determines the search Some databases find compounds with any sub stitution 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 substituents up to the number spe cified plus the number 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 In both the free site or inexact substitution you define the maximum number of substituents an atom can have The number you use in the inexact count must include the sub stitution s shown in the query structure whereas the free site count does not Up to Finds compounds in which the selected atoms may contain a range of substituents up to the number spe cified Exactly Finds compounds in which the selected atoms contain the exact number of substituents as specified up to 15 substituents _ Note You can specify a substituent count of up to 4 using the Substituents option from the context menu To specify a substituent count of up to 15 select Atom Properties option from the context menu Clicking with th
250. only when created using Structure gt Add Multi Center Attachment Multi center attachments create a pseudo atom that is disregarded during chemical calculations but still lets you create Chapter 16 Chemical Interpretation 283 of 315 ChemBioDraw 14 0 i aa Perkin For the Better diagrams that look meaningful to an experienced chemist A few examples are shown below n or m Allyl complex Cp TiCl another Aryl complex Cl Sly Ve Nil n C H Mn CO Cahn Ingold Prelog Absolute stereochemistry is calculated for tetrahedral atoms and double bonds according to the Cahn Ingold Prelog CIP priority 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 Chapter 16 Chemical Interpretation 284 of 315 W P l 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 inform ation see the references Rule 1 Higher atomic number precedes lower Rule 2 Higher atomic mass precedes lower Rule 3 cis prece
251. ons You can resize region arrows to indicate different 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 2 Click and drag a resize handle to adjust the size of the arrow Chapter 7 BioDraw Ultra feature only 99 of 315 ChemBioDraw 14 0 i gt PerkinElmer For the Better To extend an arrow click and drag its center handle as indicated by the cursor in the figure above Enhancing the Drawing A plasmid map is like any other drawing You can add color and add shade to it change line widths or modify its text Chapter 7 BioDraw Ultra feature only 100 of 315 W P l Drawing Biopolymers Biopolymers are complex molecular assemblies that adopt precise and defined shapes and structures Their defined shape and structure are in fact keys to their role Biopolymers are chain like molecules made up of repeating chemical blocks and can be very long in length Biopolymers are classified in three groups depending on the nature of the repeating unit they are made of Polysaccharides are made of sugars Proteins of amino acids Nucleic acids of nucleotides ChemBioDraw provides a friendly interface allowing users to draw biopolymers and create sequences easily Using the Biopolymer editor users can draw polypeptides and nucleotide sequences using pre defined labels
252. or EAR ie anny Tram qunged eaqerimerdal data li E RT Te a Mie kx Carel 3 Specify the new frequency in the Frequency text box 4 Click OK 5 Navigate to Structure gt Predict 1H NMR Shifts The predicted NMR spectrum appears Assigning Structures to Spectra ChemBioDraw Ultra lets you assign structures to spectra You can then display the structure associated with a spe cific peak by placing the pointer on that peak To assign structures to spectra Open a spectral file Draw the structure or structures to assign to the spectrum Select specific atoms and bonds in the structure a w Noa lt Shift gt click the peak or peaks to which you want the structure assigned The selection rectangle surrounds the selected objects 5 Navigate 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 To view spectral assignments 1 Click the Lasso or Marquee tool 2 Place the pointer over a peak The assigned atoms or bonds are highlighted Removing Spectral Assignments To remove spectrum to structure assignments Chapter 11 Chemistry Features 175 of 315 W P l 1 Click the Lasso or Marquee tool 2 Select the objects from which to remove the assignment 3 Navigate to Structure gt Clear Spectrum Structure Custom Shift Correction Data You can add your own shift correctio
253. or where you want the functional group 3 Press lt 3 gt the hotkey for tert butyl on the keyboard t Bu is added to the structure 4 Select t Bu in the structure and navigate to Structure gt Expand Label Chapter 6 Basic Drawings 61 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Using the hotkeys lt n gt nitrogen lt O gt oxygen and lt I gt iodine you can turn ethylbenzene into pyridin 2 yl hypoiod ite You can also label several atoms at a time For example you can change neopentane figure A below into meth anetetraamine figure B A B NH2 an NH NHs 1 Create the neopentane structure 2 Use lt SHIFT gt click to select all the terminal carbon atoms and press lt n gt on the keyboard 7 Note For a complete list of hotkeys see Shortcuts and Hotkeys on page 44 Nicknames The simplest way to add an atomic symbol to a structure is to type the symbol into a text field However you are not limited to entering atoms one at a time Using nicknames you can add functional groups chains or any other struc tural feature without drawing each atom A nickname is an alphanumeric abbreviation that represents a substructure Nicknames are useful for drawing large structures or structures that repeatedly use similar features Note that you can assign a nickname to the structural feature You can also assign hotKeys to nicknames that you can later use as a quick way for adding the
254. orial libraries of structurally related molecules You can then screen your libraries for various properties to determine which compounds you want to synthesize CombiChem is a plugin for Microsoft Excel and is included with ChemDraw Excel If you are familiar with Excel you will find CombiChem simple to use However if you need help see the Excel User s Guide Getting Started When you install ChemBioFinder or ChemBioOffice the CombiChem add in is also installed CombiChem requires Microsoft Excel 2003 or later Assistance with Combichem Combichem provides Help in the Excel worksheets Go to ChemOffice14 gt CombiChem gt Help By default each worksheet you create also includes brief instructions to help guide you If you do not see the instruc tions 1 Goto ChemOffice14 gt CombiChem gt Preferences 2 Select Add Instructions to Every Sheet 3 Click OK The instructions appear on new worksheets that you create Creating combinatorial libraries To create a combinatorial library you first need a generic reaction This reaction resembles the real reaction you will use in the lab to synthesize compounds The generic reaction contains one or more query structures that represent the reactants and products in the real reaction An example of a generic reaction is shown below Chapter 12 ChemDraw Excel and CombiChem 212 o0f 315 Ro mi y J H 0 HN D NH R NH3 You use the generic reaction to search your chemical datab
255. ortcuts and Hotkeys DMTr DNP Dnp DNS Phenyl Pht Piv PMB PMBM PNB Poc PPi Pr Pro Pv s Am s Bu Gly His I Am i Bu i C3H7 s Butyl s C4H9 s C5H11 SEM Ser SES t Am t BOC t Boc t Bu t Butyl t C4H9 t C5H11 P gt Perkin For the Better m Phenylene m Tolyl MDIPS MDPS Me TBDMS Thr TBDPS TIPDS TBMPS TIPS TBS TMS TDS Tos Tf trans Cin namyl Tfa Troc TFA Trp Thexyl Trt THF Ts Thf Tyr THP Val Thp Xyl 51 of 315 ChemBioDraw 14 0 i eae Perkin For the Better Basic Drawings ChemBioDraw provides a variety of tools for drawing everything from simple chemical structures to complex reac tions In this section we introduce basic techniques 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 Ultra feature only on page 92 and Advanced Drawing Techniques on page 118 Bonds The Main toolbar and Multiple Bonds toolbar offer numerous options for drawing bonds Some tools are for drawing specific types of bonds while others are for drawing structures for database queries For additional information on vari ous bond types see Bond Conventions on page 278 Drawing Bonds To draw the first bond of your structure select the solid bond tool in the Main toolbar and click in the document win dow The bond appears in the drawing window To draw another bond at
256. orted Name gt Struct is not intended to interpret trade or common names A chem ical database such as ChemBioFinder com is more appropriate for obtaining these structures Note Use the words alpha and beta when entering forms of amino acids For example alpha alanine and beta alanine are valid name gt struct chemical names 7 Note Name gt Struct can also interpret many German names Converting Names to Structures To enter the name and convert it to its structure 1 Navigate to Structure gt Convert Name to Structure The Insert Structure dialog box appears 2 Type the name example 2 bromobenzoic acid or paste the copied name from the clipboard Tip You can paste the name using keyboard commands lt CTRL gt lt V gt 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 structure Chapter 10 Struct Name Ultra Feature 147 of 315 1 Click in the document window 2 Navigate to Edit gt Paste Special gt Name as Structure The structure appears in your document Converting Captions You can convert a caption to a structure 1 Select the caption 2 Navigate to Structure gt Convert Name to Structure Supported Structures Struct gt Name can name compounds in classes of structures Principal Groups in Rings and Chains Acid Halides Amide derivatives of acids m Alcohols and chalco
257. otkeys 49 of 315 ChemBioDraw 14 0 Drawing Command Copy a selected object Copy a selected object constrained to X and Y axes Distort limit resize to X or Y axis Toggle the Lasso and the previous drawing tool Change direction of a chain Change orientation of double bonds Create resonance delo calized ring Remove a curve segment Nicknames AC Ad Ala Alloc Allyl Am Arg Asn Bz BOM Bs Bt Btm Bu Bzh Bzl Key Combination CTRL drag SHIFT CTRL drag SHIFT drag with resize handle CTRL ALT Tab CTRL Drag with alkane chain tool SHIFT Click with saturated double bond ring tools CTRL Click with ring tools except chairs ALT SHIFT Click with the pen tool c C7H13 c C8H15 c Hx C10H20 C10H21 Cbz CHx CoA Chapter 5 Shortcuts and Hotkeys cyclopropyl Cys Dan DEAE DEIPS DMIPS DMPM DMPS DPIPS DPTBS DTBMS DTBS Et Fmoc Gln Glu P gt Perkin For the Better i C4H9 i C5H11 i Pr lle Im Leu Lys m C6H4 50 of 315 ChemBioDraw 14 0 Asp Benzoyl Benzyl Bn Boc MEM Mes Met MMTr MOM MPM MTM n Am n Bu n C3H7 n C4H9 n C5H11 BZOM c C3H5 c C4H 7 c C5H9 c C6H11 n Pr N3 Cy cyclobutyl cyclohepty cyclooctyl cyclopentyl neo Am neo C5H11 Np o C6H4 o Phenylene o Toly p C6H4 p Phenylene p Tolyl Ph Phe Chapter 5 Sh
258. ou can also store templates as groups or even integral groups so that they are treated as an individual entity within the documents into which they are dropped To create a template palette Navigate to File gt Open Templates gt New Templates Click a template pane 1 2 3 Inthe document window draw a new structure 4 Click another template pane and draw another structure as desired 5 After you draw all the templates you want go to File gt Save _ Note Save your palette in the ChemDraw Items folder to ensure it appears in the Main toolbar 6 In any drawing select the Template tool on the Main toolbar to use you palette Modifying a Template 1 Navigate to File gt Open Templates and choose a palette 2 Inthe palette click a template pane The template appears in the document window 3 Inthe document window edit the template 4 Save the template To add or delete a palette row or column in a palette 1 Inthe palette click a cell in the row or column 2 Select the appropriate option in the Edit menu Adding a Template To add a template click in an empty template pane and draw the template in the document window Navigate to File gt Save Annotating a Template 1 Navigate to File gt Open Templates and choose a palette 2 Right click on an empty space in a template pane and select Annotate The Annotate dialog appears Chapter 9 Advanced Drawing Techniques 137 of 315 hemBioD 14 j ChemBioDraw 0 Perkin
259. ou have drawn Name gt Struct lets you convert chemical names into their corresponding chemical structures It is designed to interpret chemical names as they are 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 recommendations Struct gt Name Struct gt Name can interpret a variety of chemical structures This means that you can draw a structure and Struct gt Name will provide its name It also updates the name when you modify the structure Using Struct gt Name To generate the name of your structure 1 Select the structure 2 Navigate to Structure gt Convert Structure to Name The name appears under the structure Supported Structures However Struct gt Name will interpret Stereochemistry Principal Group in Rings and Chains Carboxylic Acids Peroxy acids Amide derivatives of acids Carbonic acids Nitric acids Acid Halides Carboxylic Esters Salts Anhydrides Hydrazides Imides Amides Hydrazines Nitriles Amines and Imines Chapter 10 Struct Name Ultra Feature 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 a
260. pKa_table html For more information ChemDraw Excel Functions on page 188 LogP on page 290 Property Calculations on page 290 and pKa CLogP and CMR on page 291 Topological Polar Surface Area The polar surface area of a molecule measured in square angstroms can be used to predict of pharmaceutical trans port properties in the body ChemBioDraw implements a more innovative algorithm Historically this property has been calculated using time consuming 3D techniques However a recent paper provided a remarkably accurate way of predicting it rapidly Other Properties Normal Boiling Point and Melting Point Estimated in K using two methods Method One Joback s fragmentation method Method Two Joback s fragmentation method as modified by Stein All boiling points are estimated for a pressure of 1 atm Miscellaneous Properties Heat of Formation Gibbs Free Energy Ideal Gas Thermal Capacity Freezing Point Critical Temperature Critical Pressure and Critical Volume are estimated using Joback s fragmentation method Chapter 17 Property Calculations 292 of 315 ChemBioDraw Web Resources The PerkinElmer Informatics Web site is a valuable source of helpful information 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 software downloads and more You can navigate to the site directly from
261. port Web page Here you can find desktop support resources including the PerkinElmer Informatics Knowledge Base product downloads FAQ and documentation 1 Navigate to Search gt Browse PerkinElmer Technical Support The Technical Support Web page opens 2 Click Desktop Support Suppliers on ChemACX com ChemACX Available Chemicals Exchange provides a database of commercially available chemicals The database contains catalogs from research and industrial chemical vendors To link to the ChemACX com record of suppliers for compounds that you draw Chapter 18 ChemBioDraw Web Resources 293 of 315 1 In ChemBioDraw select a structure you have drawn 2 Navigate to Search gt Find Suppliers on ChemACX com The ChemACX com page opens with information about the selected structure For more information on using the ChemACX Web site see the ChemOffice Enterprise Workgroup amp Databases Guide ACX Structures and Numbers ChemBioDraw searches ACX and returns information about related structures and numbers You can place the returned information 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 Navigate to Search gt Find Structure from ACX Number The Find Structure from ACX Number dialog appears 2 Type the ACX registry number in the dialog 3 Click OK The structure appears in your document To find a structure by name 1 Navigate to Sea
262. port gt Import ChemFinder List 2 If you are prompted to start ChemBioFinder click Yes 3 Inthe message box click Yes to import the hit list The records are imported into Excel Exporting tables ChemDraw Excel lets you export tables to MDL SDFiles format The first column of the area you select to export must have the word Structure in its top cell Structures outside the first column are discarded To export data 1 Select the cells to export including the cell that contains the word Structure Ei Note You can export selected rows and columns from a structure table Ensure that the cell selection is continuous See examples below Chapter 12 ChemDraw Excel and CombiChem 181 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 Ad os amp Structure Structure Formula MolWeight Mol ID Molname 1 60 074 3 Furan CaHg0 118 133 24 Benzofuran A3 M fe C6H5Br el a Lees 1 Structure MOLREGNO MOLNAME CORP _ID DATE ACTIVITY CeHs 2 Benzene MUSE00000002 1 1 91 E 3 Bromobenzene MUSE00000003 1 1 91 Ld 4 Chlorobenzene MUSE00000004 1 1 91 r 2 Goto ChemOffice14 gt Import Export gt Export Table 3 Inthe Save Table To dialog box type the file name and click Save The status bar displays the progress Synchronizing Tables You can synchronize a table in your worksheet with a ChemBioFinder database for example a CFX file On syn chronizing a ChemDraw table with a ChemBioFin
263. pping to show the symbols only when you select the Reaction Atom Atom Map tool The symbols do not print Automatic Mapping To create a reaction map 1 Select the reaction Tip Double click the arrow with a selection tool to select the reaction 2 Navigate to Structure gt Map Reaction Atoms The symbol Rxn appears next to the bonds in the reactant and product that are modified by the reaction For more information about the Reaction Center bond property see Bond Properties on page 239 Figure 14 18 Automatic reaction mapping Manual Mapping When manual atom to atom mapping is required you can use the Reaction Atom Atom Map tool This might be neces sary when the automatic mapping is applied to complicated reactions but gives incorrect results In these cases you Chapter 14 Query Structures 258 of 315 ChemBioDraw 14 0 i aa Perkin For the Better can manually readjust the reaction mapping The figure below shows the initial mapping being amended by using the Reaction Atom Atom Map tool a Rxn Ran Figure 14 19 Automatic mapping to be amended When you manually map reactions with the Reaction Atom Atom Map tool you can suppress automatic re mapping of atoms other than your target atom To suppress automatic remapping 1 Navigate to File gt Preferences 2 On the General tab de select Automatic Reaction Mapping 3 Click OK To use the Reaction Atom Atom Map tool to supplement the automatic mappin
264. ps your original driver may need to be updated contact the maker of the driver and obtain the most up to date driver If you still encounter problems contact us with the relevant details about the original driver and the resulting problem Printer Driver related issues Try using a different printer driver If using a different driver helps your original driver may need to be updated contact the maker of the driver and obtain the most up to date driver If you still encounter problems contact us with the relevant details about the original driver and the resulting problem 3 Reinstall the software Before you reinstall uninstall the software and disable all background applications including screen savers and virus protection Read complete uninstall instructions on the Technical Support web page 4 Ifthe problem still persists use our online contact form to provide details to Technical Support Chapter 1 Introduction 3 of 315 W P l Getting Started This topics covered in this chapter will help you become familiar with the user interface About ChemBioDraw Tutorials There are seven tutorials available in the Tutorials chapter e Tutorial 1 Drawing a Structure e Tutorial 2 Using Rings e Tutorial 3 Fischer Projections e Tutorial 4 Perspective Drawings e Tutorial 5 Newman Projections e Tutorial 6 Stereochemistry e Tutorial 7 Templates These tutorials provide step by step instructions to help you work with the
265. pter 6 Basic Drawings 59 of 315 ChemBioDraw 14 0 Coloring Text You can color captions and atom labels before or after you type them and as a whole or in part To color a caption or atom label 1 Select the Text tool 2 Click inside the document where you want to place the text 3 Choose acolor from the Color menu 4 Type the caption or atom label OH Phenol To color individual characters 1 Select part of an existing caption or atom label using the Text tool 2 From the Color menu choose a color Phenol To color several captions or atom labels at once 1 Select the captions or labels using a selection tool 2 Choose a color from the Color menu Caption Width To edit the width of a caption 1 Select the caption using the Text tool A resize handle appears on the right side of the caption 2 Drag the resize handle to change the width of the caption About Fonts P gt Perkin For the Better ChemBioDraw uses the fonts installed on your computer If a ChemBioDraw document contains fonts that are not available on a particular computer they are substituted with the available fonts Character Map The floating character map window displays the 256 ASCII characters in any font The default font is Symbol Chapter 6 Basic Drawings 60 of 315 W P l Use the character map to add symbols to your document in various font styles To show or hide the map navigate to View gt Show Ch
266. r ChemBioDraw 14 0 To create a link node 1 Open an atom label text box 2 Type the link node in this format CH2 3 7 Flip Type For ladder polymers 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 only for brackets with exactly two crossing bonds Because of its prevalence the No Flip type does not receive special annotation The example below illustrates a flip type in ladder polymers Alternative Groups You can create a search query that contains variable functional groups or substructures Instead of submitting mul tiple queries on structures that share a common substructure you can submit a single query with the parent structure The parent structure can have attachment points to a list of alternative groups that you define Chapter 14 Query Structures 248 of 315 P gt Perkin For the Better ChemBioDraw 14 0 Defining Alternative Groups You can create alternative group definitions R G and so on that represent a set of substituents each of which is used in the query To define alternative groups 1 Navigate 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 atitle suchas R J in the Alternative Group Title box and draw the substructur
267. r it to be returned as a result 4 For If R i select R3 This indicates that the R location must consist of either Br or 5 Click Add 6 Click OK Rest H Select Rest H in the R Logic Query dialog to indicate that if you have two possible R group locations and only one is filled the other must be a hydrogen to return a positive result Atom to Atom Mapping You can create correspondences between atoms in different structures for searching a reaction database The reac tions mapped can be single or multi step A drawing that includes atom to atom mapping can be added to a database or be used to search You can assign atom mapping in two ways Automatic mapping navigate to Structure gt Map Reaction Atoms m Manual mapping using the Reaction Atom Atom Map tool on the main tools palette Using either method ChemBioDraw assigns a reaction center for the reactants and products Chapter 14 Query Structures 257 of 315 ChemBioDraw 14 0 i eae Perkin For the Better When a reaction map is established you can point to an atom in one structure with the Reaction Atom Atom Map tool to highlight the mapped atom in the other structure Displaying and Printing To display reaction mapping symbols on screen and in print 1 Navigate to File gt Preferences 2 Inthe Preferences dialog click the Building Display tab 3 Select Always Display and Print Reaction Mapping 4 Click OK Deselect Always Display and Print Atom Ma
268. r on the selected structures 3 Click drag the resize handles to resize a structure Any changes you make to a picture is proportionately reflected in the other structures 4 To end resizing click a cell and the structures are deselected By default the structure s resize property is set to Move and Resize with cells to avoid bunched up structures To change the resize property or to allow structure ovelapping Excel 2007 Select the cells whose structures you want to resize Go to ChemOffice14 gt Structure gt Resize Resize handles appear on the selected structures Right click and select Size and Properties from the context menu Click on the Properties tab Select Don t move or size with cells Click Close o w e SN a ChemDraw Excel Functions ChemDraw Excel supplies a library of functions that return chemical properties of structures in a ChemDraw Excel worksheet To insert a ChemDraw Excel function into your worksheet 1 Select the target cell 2 Go to ChemOffice14 gt ChemBioDraw Functions Options gt ChemBioDraw Functions in Excel 2010 The ChemDraw for Excel dialog box appears 3 Double click the function you want to insert from the list available in the Functions tab A Functions Argument dia log box appears 4 Select the structure Chapter 12 ChemDraw Excel and CombiChem 188 of 315 5 Click OK Each property is calculated using the best available method If the cell reference argument d
269. r plate with an origin line solvent front and one or more lanes The lanes can be populated with spots of dif ferent R size shape or color To create a TLC plate 1 Select the TLC tool from the Chromatography toolbar 2 Drag in any direction from the point of origin The width of the plate determines the number of lanes 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 Show or hide the origin solvent front borders or Right click in the plate and select the appropriate side ticks action Use the Transparent option to overlay the TLC plate on a scanned plate Change the order of lanes Drag the origin tick to the new location Add delete or duplicate a lane 1 Position the cursor on the lane to delete or duplicate Chapter 11 Chemistry Features 168 of 315 ChemBioDraw 14 0 If you want to Move a spot Duplicate a spot Delete a spot Display or set the R for a spot add a custom spot Change the style or color of a spot Enlarge or smear a spot Rf Display P gt Perkin For the Better Then or between lanes to add 2 Right click in the plate 3 Select the appropriate action 4 Optional To delete a lane click on it with the Eraser tool Drag the spot The R displays as you drag lt CTRL gt dragthe spot to a
270. rag the indicator to another location See the example below Figure 6 9 B center of rotation moved 3 To rotate the object click and drag the rotation handle To reset the center of rotation to its default position deselect the object Note If you drag close to an atom the center of rotation will snap to the atom position 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 lt shift gt drag the selected objects Small incremental movements are often useful for aligning objects To move an object a incrementally 1 Select the object 2 Press an arrow key The selected object moves 1 point in the direction of the arrow Note To move ina larger increment hold down the lt alt gt key while pressing an arrow key The selected objects moves 10 points in the direction of the arrow Copying Objects 1 Select one or more objects 2 lt Control gt drag the object s to create a copy and position it Chapter 6 Basic Drawings 83 of 315 W P To constrain the copy to move only vertically or horizontally while positioning it hold down the lt shift gt lt control gt keys The Info Window This window displays the size and position of the pointer and of anything you have selected To show or hide the win dow navigate to View gt Show Info Window Info x Pointer a U 0521 in Y
271. rce based representation The bracket type Mixture unordered mix may be used to represent a collection of substances that may all be present but not necessarily in known amounts Bracket type Component c indicates each mixture element as shown below Chapter 14 Query Structures 245 of 315 ChemBioDraw 14 0 i as PerkinE 3 For the Better COOH Figure 14 6 Brackets used to indicate mixtures Bracket type Mixture ordered fy is primarily used to describe manufacturing processes where component order is critical As with unordered mixtures individual elements of an ordered mixture should be surrounded by brackets with a bracket usage of Component c However components of ordered mixtures must be numbered to show their order You can do this by editing the c label with the text tool to include a number c1 c2 and so on Multiple Groups You use the bracket type Multiple Group to indicate that the enclosed items are repeated a known number of times Multiple group brackets may enclose entire structures or part of the structures Some examples are OH UA Figure 14 7 Brackets to indicate multiple groups Because multiple group brackets represent a specific repeat count you can display the molecular weights and related data for the enclosed structures in the Analysis window Chapter 14 Query Structures 246 of 315 Repeat Pattern For simple linear polymer
272. rch gt Find Structure from Name at ChemACX com The Find Structure from Name dialog appears 2 Type either a chemical name or trade name in the dialog 3 Click OK The structure appears in your document ACX Numbers To Find an ACX number for a structure 1 Select the structure 2 Navigate to Search gt Find ACX Numbers from Structure The ACX number appears in the Find ACX Numbers from Structure dialog ChemBio3D ActiveX Control The ChemBio3D ActiveX Control page provides Chem3D Plugin Activex documentation for end users as well as administrators web developers who want to incorporate the controls within the Web pages SciStore com SciStore offers life science desktop software enterprise solutions chemical databases and consulting services to biotechnology pharmaceutical and chemical industries To visit SciStore navigate to Search gt Browse SciStore com or visit SciStore at www scistore com Chapter 18 ChemBioDraw Web Resources 294 of 315 PerkinElmer Informatics To open the PerkinElmer Informatics Home page navigate to Search gt Browse PerkinEImer com Check the PerkinElmer Informatics Web site for new product information You can also visit ChemNews Com and other pages through PerkinElmer Informatics Home page Using the ChemOffice SDK The ChemOffice Software Developer s Kit SDK lets you customize your applications To browse the ChemOffice SDK navigate to Search gt Browse ChemOffice SDK The ChemO
273. re navigate to Object gt Group See Grouping Objects on page 85 S orbitals The s orbital is shown below O Q 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 The sigma orbital is shown below Co a To draw ao orbital 1 Hold down the mouse button over the Orbital tool and drag to select the o orbital tool from the palette 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 will be attached P orbitals The p orbital is shown below R 8 To draw ap 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 will be attached Hybrid Orbitals The hybrid orbital is shown below Y ra To draw a hybrid orbital sp3 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 will be attached Chapter 11 Chemistry Features 155 of 315 ChemBioDraw 14 0 i ean Perkin For the Better D orbitals Th
274. rements Adding Chains to Structures To add an Acyclic chain to an existing structure 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 in a document window The Add Chain dialog appears 3 Type the number of carbon atoms in the chain 4 Click Add To add another chain of the same length anywhere in a document window lt ALT gt click where you want the chain to begin Chapter 6 Basic Drawings 70 of 315 Objects Use the tools on the main toolbar to add shapes to your documents You can tear off the palettes and place them where you want within your drawing window You can rotate an object using its rotation handle and scale or distort an object by using the resize or distortion handles Arrows You can use arrows to show the conversion of reactants to products and to indicate electron flow 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 create an arc the angle of the arrow is modified When you mouse over an arrow with the Lasso Marquee or an Arrow tool selected the adjustment handles appear for example Drag the adjustment handles to change the arrow length angle or shape When changing the ang
275. ressure 1 atm molar heat capacity at 298 15 K for an ideal gas compound Units J mole K Function CHEMPROPPRO IDEAL GAS THERMAL CAPACITY Cell ref Example In cell CHEMPROPPRO IDEAL GAS THERMAL CAPACITY A2 Result 201 036 LogP The logarithm of the partition coefficient for n octanol water Chapter 12 ChemDraw Excel and CombiChem P gt Perkin For the Better 194 of 315 ChemBioDraw 14 0 i Perkin For the Better 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 COEFFICIENT A2 Result 2 243 Molar refractivity The molar refraction index Units cm3 mole Functions CHEMPROPPRO MOL REFRACTIVITY Cell ref CLOGP DRIVER MOL REFRACTIVITY cell ref 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 structure 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 Chapter 12 ChemDraw Excel and CombiChem 195 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Function
276. rmation on these properties and how to calculate them see the ChemBioFinder online help B H Balaban Index Heat of Formation Boiling Point Henry s Law Constant C I Chemical Name Ideal Gas Thermal Capacity Cluster Count L Critical Pressure LogP Critical Temperature LogS Chapter 11 Chemistry Features Pp Partition Coefficient pKa Polar Surface Area Principal Moment R Radius S 164 of 315 ChemBioDraw 14 0 Critical Volume Connolly Accessible Area Connolly Molecular Area Connolly Solvent Excluded Volume E Elemental Analysis Exact Mass F Formal Charge G Gibbs Free Energy Viewing Chemical Properties To view chemical properties M Mass Melting Point Mol Formula Mol Formula HTML Mol Refractivity Mol Weight Molecular Topological Index m z N Num Rotatable Bonds O Ovality 1 Select the structure whose properties you want to view P gt Perkin For the Better Shape Attribute Shape Coefficient Sum of Degrees Sum of Valence Degrees 7 Topological Diameter Total Connectivity Total Valence Connectivity V Vapor Pressure W Water Solubility Wiener Index 2 Navigate to View gt Show Chemical Properties Window The Chemical Properties window appears 3 To paste the basic properties into your document click Paste 4 To create a report and view results for other fragmentation methods click Report 3D Viewing As you create your drawing you can view it in t
277. rom ChemScriptl4 import The first command imports the python system The second and third commands import the operating system mod ules The last command imports all the ChemScript functions After you include these command lines how you develop the rest of your script is entirely up to you Introducing the ChemScript API ChemScript includes a ChemScript API reference guide You can find the guide at Start gt All Programs gt ChemBioOffice 2014 gt ChemScript 14 0 gt API Reference It provides links and information for the ChemScript classes The ChemScript object model comprises two fundamental levels of functionality described below ChemScript Classes At the top level the API consists of four classes Atom Chemical element charge bonds to neighboring atoms drawing coordinates 3D coordinates if available ste reochemistry etc Bond Bonded atoms bond order etc Molecule Mol A chemical connection table which can represent one or more molecular fragments This class also includes file I O capabilities and other advanced chemistry functionality such as stereochemistry Reaction Rxn A chemical reaction with one or more steps Functions and Algorithms The secondary level consists of the core set of high level features that you can modify to meet your specific business needs Some examples are described below Template Based Normalization Enforce standard representations of functional group structures in chemic
278. rompted to delete each existing worksheet click Yes New reactant work sheets will be created and the previous workbook will be available as a saved file Creating an experiment An experiment is a library of product structures that is created when the reactant search results are applied to the gen eric reaction You can create or enumerate multiple experiments per workbook Chapter 12 ChemDraw Excel and CombiChem 215 of 315 For example you can take all the reactants you imported and enumerate an experiment containing all possible com binations of reactants After calculating properties on these products you might decide that 10 of these products are worth synthesizing in the lab You could then create an experiment with just those products that the calculations show to be promising The Use Y N column in a reactant list determines whether the associated reactant in the list will be used Y in the experiment or not N By default Y appears _ Note Only the Structure and Use Y N columns are necessary Other columns may also be included but Com biChem ignores them You can delete them if you want To create a new experiment 1 In each reactant list select the reactants to use by typing Y in their Use Y N column Type N for those reactants you do not wish to use E Note Cells without n or N default to Y 2 Go to ChemOffice14 gt CombiChem gt Experiments gt New or use the floating
279. rotein DNA Membrane line Membrane arc Membrane ellipse Micelle Plasmid map Ribosomes tRNA Customization Options width shape height width of the strands width of the cyl inders spacing 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 pro portion to the size length arc size of subunit size of subunit size of subunit add adjust markers and regions resize color resize color These tools in the BioDraw toolbar cannot be customized lon channel G protein alpha subunit lon channel G protein beta subunit Immunoglobulin Golgi body Endoplasmic Mitochondrion reticulum Cloud resize color Chapter 7 BioDraw Ultra feature only 95 of 315 W P Membrane Line 1 Select the membrane line tool from the BioDraw toolbar 2 Click and drag to draw a membrane line of the size you want or click for the default size When orienting the membrane note that you are constrained to 15 degree increments when fixed angles are applied navigate to Object gt Fixed Angles To override the constraint press lt shift gt key as you drag To resize the membrane units click and drag the adjustment handle at the membrane center Tip To change the length select the membrane and drag the left or nght handle of the selection box You can deselect it and readjust the subunit si
280. roup found at each Rn position for each search result For a given returned molecule look across its row to view the functional group at each R group position In this example the search results consist of a hydro gen and hydroxyl group for R1 R2 and R3 Working with Structures ChemDraw Excel lets you rename structures and use the clipboard to cut copy and paste structures Renaming Structures Excel recognizes certain characters as formulas To prevent the system from interpreting a chemical structure name as an Excel formula you can rename the structure To rename a structure 1 Select the structure 2 Goto ChemOffice14 gt Molecule gt Name If multiple cells are selected go to ChemOffice14 gt Molecule gt Name All Selected The Name Molecule dialog box appears Chapter 12 ChemDraw Excel and CombiChem 186 of 315 Name Molecule Structure Name 6H56rQ Use Default a dear Cancel _ Note You can remove a structure name by clicking Clear If you select Use Default the name of the structure will be replaced by the default name i e Chemical Formula 3 Type the name and click OK Using the Clipboard You can cut copy and paste structures using the clipboard The Copy As command in ChemDraw Excel lets you copy a structure as InChl InChlkey or SMILES string To cut a structure from a cell 1 Select the structure 2 Goto ChemOffice14 gt Molecule gt Cut The structure is placed on the clipboard When yo
281. rted by ChemDraw for Excel SDF Files can either be V2000 or V3000 The default value is V2000 which limits the number of atoms and bonds in a molecule V2000 files allow up to 1000 of each V3000 is a superset of V2000 and offers an enhanced ste reochemistry specification Unlike V2000 the V3000 format does not limit the number of atoms and bonds ina molecule Chapter 12 ChemDraw Excel and CombiChem 211 0f 315 Misc e Ask Before Clearing Cells Prompts a message when you attempt to delete the cell content ina ChemOffice worksheet by either pressing lt Delete gt or lt Backspace gt keys e Copy Structure to MS Word As Lets you select the format that you want to use to copy your structure to an MS Word document for example Bitmap or OLE Object e Search Results By default the search result appears in the same worksheet on which the search is per formed The Display in a new worksheet option creates a new worksheet with the name SearchResults X where X is 1 2 3 and displays the search results in this new worksheet without changing anything in the ori ginal worksheet e Default Style Sheet Specifies the style sheet always applied to the structures when structures are added using Import Table Load Molecule or by Add Molecule commands To apply a style to particular molecules navigate to ChemOffice gt Molecule gt Style The default style sheet is New Document cds CombiChem Using CombiChem you can build virtual combinat
282. s Distributing Objects Use the distribute command to distribute objects horizontally or vertically and at an equal distance apart To distribute three or more objects 1 Select the objects to distribute 2 Navigate to Object gt Distribute and choose Vertically or Horizontally Figure 6 10 Distributing objects The space between the objects is equalized The upper lower right and left positions of objects in your selection remain unchanged Chapter 6 Basic Drawings 87 of 315 ChemBioDraw 14 0 i Perkin For the Better Clean Up Structure The Clean Up Structure command is used to neaten the appearance of molecules by regularizing bond lengths and angles Graphic objects such as arrows and aromatic circles are not affected You can use this command to redraw structures that you may have drawn freehand or to neaten structures that you may have imported from another applic ation For certain 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 objects on page 86 and Page Setup on page 12 The Clean Up Structure feature follows these rules Bonds are set to the target Fixed Length specified in the document settings For more information see Document Settings on page 38 A ring is redrawn only if all of its bonds are selected m Multi attached atom labels
283. s select Filled Faded or Shaded under the Curve menu or in the Curve toolbar Curves can also have arrowheads which lets you create arbitrarily shaped arrows To add color select a color in the Color menu 22 g 64 a g Figure 6 7 A freehand curve with different properties A A simple curve B enclosed C filled D faded and E shaded Selecting Objects Use the Lasso for freehand selections and the Marquee to select rectangular regions eq When you select a structure or object the selection displays with a colored frame around it The frame includes handles for rotating distorting and resizing your selection The Lasso Tool Use the Lasso tool to make a 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 Chapter 6 Basic Drawings 79 of 315 W P The Marquee Tool Use the Marquee tool to select objects and structures within a rectangular area 1 Select the Marquee tool 2 Click and drag diagonally over the structures or other object As you drag a rectangle appears that defines the selection area Objects are selected only if their center or a major portion of the object
284. s 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 The head to tail type is the default repeat pattern as shown below A i Ag Oe ae B PAP Roo AY C AN Bi Figure 14 8 Head to tail repeat pattern A and B represent the polymers shown C represents a mixture of A and B Removing Bracket Usage Labels To remove the bracket usage labels do one of the following m Hover on the label and press lt delete gt Use the Eraser tool to delete the label Note Setting the bracket usage type to Unspecified removes any specific bracket usage assignment Link Nodes You can specify a variable length chain or ring by indicating that one of the atoms can repeat a number of times using link nodes Link nodes must have exactly two connecting bonds The atom label must meet these conditions t must consist of a generic name or no more than one element symbol The last part of the label must be in the form number hyphen number with the numbers and hyphen subscripted Parentheses or braces can be used instead of brackets Ei Note ChemBioFinder supports only brackets for link nodes Parentheses or braces cannot be used for link nodes in ChemBioFinder Brackets can be omitted if not required for clarity for example with O Chapter 14 Query Structures 247 of 315 P gt Perkin For the Bette
285. s at the click of the mouse Using other features you can m Add bonds to characters in atom labels Create bonds whose attachment is not explicitly defined m Add atom numbers Contract and expand sections of structures a View structure perspective Create mass fragmentation retrosynthesis and synthesis drawings Draw with templates Create and edit templates Label functional groups with nicknames Coloring Objects You can select and color objects part or all of a chemical structure boxes curves arrows orbitals and reaction mechanism symbols To color an object 1 Select the object 2 Doone of the following Click the Color button on the Style toolbar and select the color from the menu that appears Choose a color from the Color menu m Right click and select the color from the context menu Navigate to Object gt Object Settings and select the color in the Drawing tab Click OK when finished Coloring Groups ChemBioDraw colors groups differently from integral groups When you color an integral group its objects acquire the new color but retain the original shading When you color a normal group the new color is applied and the original shad ing is ignored Chapter 9 Advanced Drawing Techniques 118 of 315 hemBioD 14 i ChemBioDraw 0 Perkin For the Better Figure 9 1 A The mitochondrion structure in its default color B The structure colored blue as a group C The struc ture co
286. s based on topology Function CHEM NUM HBDONORS cell ref Example In cell CHEM NUM HBDONORS A2 Result 0 SMILES string Displays the SMILES string for the structure Function CHEM SMILES cell ref Example In cell CHEM SMILES A2 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 Chapter 12 ChemDraw Excel and CombiChem 191 of 315 Does cell have a structure drawing Returns TRUE if the cell has a ChemOffice Excel structure drawing or reaction drawings returns FALSE otherwise Function ISSTRUCTURE cell ref Example In cell ISSTRUCTURE A2 Result False Does cell have reaction drawing Returns TRUE if the cell contains a drawing of a reaction Function ISREACTION cell ref Example In cell ISREACTION A2 Result True Boiling point The boiling point for the molecule at 1 atm Units Kelvin Function CHEMPROPPRO BOILING POINT cell ref Example In cell CHEMPROPPRO BOILING POINT A2 Result 540 059 Melting freezing point The melting freezing point for the structure at 1 atm Units Kelvin Function CHEMPROPPRO MELTING POINT cell ref Example In cell CHEMPROPPRO MELTING POINT A2 Result 331 31 Chapter 12 ChemDraw Excel and CombiChem 192 of 315 Vapor pressure The vapor pressure for the structure at 25 C Units
287. sages that may affect the final analysis Message Description There are too many bonds to this Displayed for every unlabeled atom with more than four filled valences unlabeled Carbon Filled valences include sum of bond orders charge radicals and free sites Chapter 16 Chemical Interpretation 287 of 315 ChemBioDraw 14 0 Message An atom in this label has an invalid valence ChemDraw can t interpret this label Parentheses don t match This label has conflicting or unas signable charges Formula cannot be computed for queries Text not in Formula style won t be interpreted This named alternative group con tains no attachment point This named alternative group con tains fragments with inconsistent valences This named alternative group con tains no fragment Chapter 16 Chemical Interpretation P gt Perkin For the Better Description 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 Substituents 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 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 lis ted in the Isotopes Table fil
288. search the reaction database whether selected structure s is a reactant or a product All reac tion searches are substructure searches If you have selected an entire reaction sequence the following window will open to confirm your reaction search Search SciFinder SciFinder Perform Substructure Reaction Search Proxy Settings Cancel Press OK and SciFinder will be launched to retrieve the results of your search and display them in a browser win dow If you submit a second or later search to SciFinder you will see an intermediate screen warning that you already have a SciFinder answer set To proceed with the latest search click OK Note Fora search to proceed you must Beconnected to the Internet Chapter 18 ChemBioDraw Web Resources 296 of 315 P gt Perkin For the Better ChemBioDraw 14 0 Have a valid SciFinder individual subscription to access the database 7 Note If your subscription is through a university and utilizes a proxy server to connect you to SciFinder you must click the Proxy Settings button Windows or the arrow next to the Proxy server indicator line Mac and enter the proxy server URL for the account you are using This will only be necessary for the first search you run a f you are not logged in or do not have a valid SciFinder subscription you will be redirected to the main SciFinder page There you can either log in or find information about
289. sidue 3 Using the Text tool rename the residue label to reflect a new structure In the example below the Ser label has been renamed as hSer for homoserine 0 H i a Ner a cy D Gly piiss Figure 8 1 Two expanded serine residues The residue on the left has been modified to create homoserine To contract a label 1 Using a selection tool right click the residue label and select Select Linked Objects or double click on the label for the expanded residue and the associated structure is selected 2 Navigate to Structure gt Contract Label OH H Gly h Ser Gly Ser Gly OH Figure 8 2 The contracted label You must define a new nickname to ensure that the contracted label includes your changes For example you can define a new nickname hSer which includes the hydroxyl group in the residue definition itself Merging Sidechains with Residue The Merge Sidechains With Residue feature lets you edit an expanded residue and then integrate those changes into the residue definition To merge a side chain 1 Double click the residue label to select the residue Chapter 8 Drawing Biopolymers 107 of 315 P gt PerkinElmer For the Better ChemBioDraw 14 0 2 Right click and select Biopolymer gt Merge Sidechains With Residue from the context menu The entire side chain is merged with the residue Clear Del v Display Warnings Align Distribute i Add Fran p A Sen
290. strate how you can develop your own custom code to meet your business needs Many of the scripts we use are in the ChemScript samples directory By default this directory is where ChemBioOffice 2014 auxillary files are installed On Windows 7 and 8 C ProgramData CambridgeSoft Chemoffice2014 ChemScript Examples 1Premium functionality that may be licensed from PerkinElmer Chapter 13 ChemScript 224 of 315 For the sake of brevity we won t repeat the scripts in this manual or try to teach Python However we briefly describe what you can do with the code examples so that you can modify and expand upon them for your own use As you read the tutorials you are encouraged to view the code in IDLE and edit it as desired to see how each example works For more on IDLE see Getting Started on page 221 Example 1 Automated Structure Clean up This sample script cleans up the structures in multiple ChemBioDraw files all at the same time It uses the same cleanup function that is in ChemBioDraw The script is in the directory Example 001 script py The script reads the CDX structure files from a source directory applies the cleanup feature to each structure and write the modified files to an output directory The original files remain unchanged Ha N T Figure 13 1 The structure cleanup script reads a structure file left and creates a new cleaned up structure file right This example uses the CDXML format Other formats suc
291. sult 17 07 Radius Function MOLECULAR TOPOLOGY RADIUS Cell ref Example In cell MOLECULAR_ TOPOLOGY RADIUS A2 Result 4 Shape attribute Function MOLECULAR TOPOLOGY SHAPE ATTRIBUTE Cell ref Example In cell MOLECULAR TOPOLOGY SHAPE ATTRIBUTE A2 Result 11 076923 Shape coefficient Function MOLECULAR TOPOLOGY SHAPE COEFFICIENT cell ref Example In cell MOLECULAR TOPOLOGY SHAPE COEFFICIENT A2 Result 0 Chapter 12 ChemDraw Excel and CombiChem P gt Perkin For the Better 198 of 315 ChemBioDraw 14 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 DIAMETER Cell ref Example In cell MOLECULAR TOPOLOGY TOPOLOGICAL DIAMETER A2 Result 7 Total connectivity Function MOLECULAR TOPOLOGY TOTAL CONNECTIVITY cell ref Example In cell MOLECULAR TOPOLOGY TOTAL CONNECTIVITY A2 Result 0 009821 Total valence connectivity Function MOLECULAR TOPOLOGY TOTAL VALENCE CONNECTIVITY cell ref Example In cell MOLECULAR TOPOLOGY TOTAL VALENCE CONNECTIVITY A2 Result 0 001157 Chapter 12 ChemDraw Excel and CombiChem P gt Perkin For the Better 199 of 315
292. t Page Setup Set options such as the page size used and text displayed in footers You can apply document settings in the following ways Customize settings for the entire document using the Document Settings dialog Apply settings to the entire current document from an existing document Apply settings to selected objects in the current document from an existing document 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 For the entire document navigate to File gt Document Settings and select the Drawing category Foran object use the Object Settings dialog box Changes you make to the drawing settings affect the active document window only You can save drawing settings in style sheets To apply settings from other documents to your document navigate to File gt Apply Document Settings The various options available under Drawing category includes Document Settings for RAMI cdx Spacing F oflength 12 C absoute oon Line width 0013n Bold width 0 0556in Piangin Width 0 0278 in Hash Spacing osn Chiri Anga fizo a degrees Irnckc ators Atoms Bont fh Show Query Indicators M Show Query Indicators Show Stereochemishry Show Stereochemistry hF Show Enhanced stereochemistry Show Reaction Indicators Show Atom Numbers Fixed Length Constrain the bonds
293. t be as specified X X Reaction Stereo a Any X X Inversion X X m Retention X X Translation m Equal m Broad a Any m Narrow Abnormal Valence Not Allowed X X X m Allowed X X X Bond Properties Bond Type m Single X X X Dashed X d X Hashed d d d Chapter 14 Query Structures 263 of 315 ChemBioDraw 14 0 Exported Query Properties Wedged Hashed Bold Wedged Wavy Hollow Wedged Dative Double Double Either Double Bold Aromatic Tautomeric Triple Quadruple Any S D D A S A Topology Unspecified Ring Chain Reaction Center Unspecified Center Make Break Chapter 14 Query Structures ISIS X X X X e f xg X X X K 7 x lt Mol xXx XxX x X X X gt X lt Rxn lt x DF Zm x Ea ke gt X lt P gt Perkin For the Better 264 of 315 Exported Query Properties ISIS Mol Rxn Change X X a Make amp Change X X Not Center X X Other Query Attributes Generic Nicknames x x xi Element Lists xko xko xko Element Not Lists xk xk xk a Alternative Groups X xm m Anonymous Alternative n n Groups Link Nodes Bracket properties X X X m Atom Atom mapping X X m Variable Attachment Pos itions 3D query properties a Converted to the appropriate number of exact substituents b Free sites counts of zero translated to Substitution as drawn all other free sites values written as substitution counts equal to t
294. tached to the first click either end of the first bond The second bond appears in the drawing window as shown below Ne Figure 6 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 mu j Tai AA Ta T Ta Ta h i kn Figure 6 2 Adding a bond by dragging 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 See Shortcuts and Hotkeys on page 44 Right click any bond and select Double gt Plain in the context menu Chapter 6 Basic Drawings 52 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Double Either Bonds Double either bonds or crossed double bonds indicate unspecified double bond configuration or a mixture of con figurations To draw a double either bond use the double either bond tool from the Multiple Bonds toolbar or 1 Draw a bond using the Wavy Bond tool 2 Click the center of the bond to create a double 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
295. tandard 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 ChemBioDraw You can also use the Copy As tool to translate a selected structure toa SMILES SLN or InChi string If the Clipboard contains structures and you paste into another ChemBioDraw document the pasted information is scaled to the settings in the new document For more information see Autoscaling on page 270 Text Line Notation Use text line notation to expand a line of text into the structure that it represents Several software packages use SMILES strings to enter and store chemical structure information 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 is pasted into your document Creating SMILES Strings To create the SMILES string for a structure 1 Select the structure 2 Navigate to Edit gt Copy As gt SMILES The SMILES string is transferred to the Clipboard To display the SMILES 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 ChemBioDraw to the Clipboard the SMILES string are separated by a perio
296. te properties Execute Struct Name or generate physical property features found in ChemBioDraw Common scaffold orientation Enforce standard orientations of structures based on the established orientation of a common substructure 2D Structure Diagram Generation SDG and Cleanup Generate new 2D structures from connection tables without coordinates and clean up existing 2D structure using the ChemBioDraw algorithms 1ChemScript lets you convert up to 10 000 data records per day For greater capacity you will need ChemScript Ultra For inform ation contact PerkinElmer Chapter 13 ChemScript 220 of 315 ChemBioDraw 14 0 i aaa Perkin For the Better How ChemScript works The most fundamental use for ChemS cript is to read data from one source modify the data using a script and write the modified data to another location You can retrieve data from or write to almost any database file s or applic ation Figure 13 1 A ChemScript script can retrieve data from one source modify the data and write it to another location How the data is modified is determined entirely by the script The script can delete data calculate or add new data or edit existing data The data can be either text structures or both Since ChemScript scripts are like any other Python scripts or NET program you can execute the scripts using either the Windows command line or any development environment Getting Started By default ChemScript and P
297. ted atom at the location specified by R B The results include either a single or double bond at the location specified by S D To perform a query you first draw the query structure in ChemBioDraw You then enter the structure in a database application such as ChemBioFinder The application searches one or more databases that you specify 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 structure requires that no carbon atoms in an aromatic structure can be part of any ring you are likely to return no results or an error depending on the query system used The search application you use can also affect your query If the application does not accurately interpret your query structure or the structures in the database you could receive inaccurate results Generic Labels A generic label represents a nonspecific attachment It can be either an unspecified atom functional group or struc tural feature When you perform a query the query looks for structures based on the type of generic label you use and where it is in the query structure Records that match the query structure are returned in the search results For example the query structure below uses the letter Q to indicate that a nonhydrogen nonc
298. th 0 4167 in Cancel T Scale selected objects so that median bond is C Scale by 100 Hy Scale Atom Labels and Settings 3 Doone of the following To scale bonds so that the Fixed Length becomes the new median bond length select Scale selected objects so that median bond is Fixed Length 0 4167 in Chapter 6 Basic Drawings 86 of 315 ChemBioDraw 14 0 i aa Perkin For the Better To scale the bonds to a new fixed length that you specify select Scale selected objects so that median bond is and type the new median bond length in the text field To scale the object to a percentage of the current size select Scale by and specify the percentage in the text field 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 objects on the page 1 Select the object 2 Navigate to Object gt Center on Page The selected object moves so that the center of the selection rectangle is at the center of the page Aligning Objects You can align objects vertically and horizontally along their centers or edges 7 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 Navigate to Object gt Align _ Note If you select only part of a structure or group with a selection tool only that part is used for the alignment but the entire structure or group move
299. the label for the atoms text SPROUT Addition of bonds to an atom CHARGE Changes the charge of an atom FREE_SITE Increment decrement free sites of an atom UPTO SITE Increment decrement the UpTo number of sub stituents of an atom EXACT SITE Increment decrement the number of sub stituents of an atom ATOMNUMBER Show hide the atom numbers ATTACHMENTPOINT Sets the value of the attachment point Bond BONDORDER Sets the bond order BONDDISPLAY Sets the bond display BONDPOSITION Sets the position of bonds BONDDOUBLEPOSITION Sets the alignment for double bonds FUSERING Fuses a ring to a bond Generic DIALOG Display a dialog TOOLMODE Changes the current tool AA1 AA1 Sets the label for the single letter amino acids DNA DNA Sets the label for the DNA sequence RNA RNA Sets the label for the RNA sequence E Note You cannot add to the command list Value This is the parameter value associated with the command For example if the command is LABELTEXT the value is the label that appears If the command is BONDDISPLAY the value corresponds to the bond display type To create a hotkey that switches to a particular tool choose TOOLMODE for a command and use any of these com mand names for a value LASSO TLCPLATE MARQUEE BENZENE 3DTRACKBALL CYCLOPENTADIENE MASSFRAG CYCLOHEXANECHAIR2 ERASER CYCLOHEXANECHAIR1 TEXT CYCLOOCTANE Chapter 4 Preferences and Settings 34 of 315 ChemBioDraw 14 0 i aa Perkin For the Better SOLIDBOND CYCLOHEPTANE MULTI
300. the reaction arrow 1 On the Arrows toolbar click the third arrow from the left in the top row as shown below x gt Arrows 2 Inthe document window click and drag the mouse horizontally to the right of the 2 propanone structure The arrow appears 3 Select the Text tool 4 Click above the arrow A text box appears 5 Type OH and press lt ESC gt Re align 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 you change tools or open another text box indicating an error Ignore this for now Add a charge symbol using the Chemical Symbols tool palette 1 Inthe Main Tool toolbar click the Chemical 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 Objects that you add from the Chemical Symbols palette are associated chemically with the structure they are near Note that the red valence error warning disappears when you add the minus charge Drawing the Product We now create 4 hydroxy 4 methyl 2 pentanone using a copy of the 2 propanone structure You can create the product from scratch or you can copy an existing structure Chapter 9 Advanced Drawing Techniques 128 of 3
301. timates over 95 of the shifts with a mean deviation of 0 29 ppm and standard deviation of 2 8 ppm NMR References Sources for ChemBioDraw NMR data include the following publications Furst A Pretsch E Anal Chim Acta 1990 229 17 Pretsch E Furst A Badertscher M Burgin R Munk M E J Chem Inf Comp Sci 1992 32 291 295 Burgin Schaller R Pretsch E Anal Chim Acta 1994 290 295 Burgin Schaller R Arnold C Pretsch E Anal Chim Acta 1995 312 95 105 Burgin Schaller R Munk M E Pretsch E J Chem Inf Comput Sci 1996 36 239 243 Chapter 11 Chemistry Features 179 of 315 ChemDraw Excel and CombiChem ChemDraw Excel is an add in for MicrosoftExcel for Windows You can add chemical structures and other data from ChemBioDraw or a ChemBioFinder database to an Excel worksheet Afterward you can calculate any of a vast array of structural properties or examine search results from an SDfile It has the same search features as ChemFinder 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 ChemBioDraw ChemDraw Excel is also installed The ChemDraw Excel add in adds a new tab to Excel 2007 Excel 2010 Excel 2013 ribbon interface If the ChemDraw Excel add in is disabled to enable it 1 Go to File gt Options gt Add ins 2 Select ChemDraw for Excel and click Go 3 From Add Ins window make sure C
302. ting in ChemBioDraw Adding a structure from a file 1 In Excel select the cell into which you want to add the structure 2 Goto ChemOffice14 gt Molecule gt Load The Choose Molecule To Load dialog box appears 3 Type or select the file name of the structure and click Open The following formats are supported ChemBioDraw cdx MDL Rxn rxn ChemBioDraw XML cdxml MDL Graphic tgf ChemDraw 3 5 chm Connection Table ct ChemBio3D XML c3xml MSI Molfile msm MDL Molfile mol SMD 4 2 smd MDL Sketch skc SMILES strings You can insert SMILES strings into cells and convert them to structures 1 Type or paste the SMILES strings into one or more cells 2 Select the cells to convert 3 Goto ChemOffice14 gt Convert gt SMILES to Molecule Alternatively you can use the context menu command to convert SMILES to molecule If the cell does not contain a valid SMILES string a warning indicating that the num ber of SMILES strings that cannot be converted appears Inchi strings You can insert Inchi strings into cells and convert them to structures 1 Type or paste the Inchi strings into one or more cells 2 Select the cells to convert Chapter 12 ChemDraw Excel and CombiChem 183 of 315 ChemBioDraw 14 0 i aa Perkin For the Better 3 Go to ChemOffice14 gt Convert gt Inchi to Molecule If the cell does not contain a valid Inchi string an error mes sage appears Adding structures by name
303. tion 4 In ChemBioDraw go to File gt Exit You will be returned to Excel and the reaction will appear in the worksheet Tip To display or hide the reaction click the Show Picture or Hide Picture icon _ Note Do not add more than one reaction to a reaction template Creating reactant worksheets The generic reaction contains at least one generic reactant a reactant that has one or more R group attachments After you enter the generic reaction in Excel you create a worksheet for each generic reactant CombiChem uses the reactant worksheet s to search your database for structures that may be used in synthesis In multi step reactions CombiChem searches for reactants in the first step but ignores intermediate reactants To create reactant worksheets 1 Select the Reactions worksheet tab 2 Goto ChemOffice14 gt CombiChem gt Reactants gt Make Reactant Worksheets A new worksheet is added for each generic reactant CombiChem creates a worksheet for each generic reactant typically either one or two reactant worksheets for the reaction you entered Searching for reactants Reactant worksheets are empty when CombiChem creates them To populate each worksheet with structures from your database you must either import the database as an SD file or use ChemBioFinder to search for records To search for reactants in an SD file 1 Select a Reactant worksheet tab 2 Goto ChemOffice14 gt CombiChem gt Reactants gt Search for Reactants
304. tion 6 When you are finished click Apply Assigning plates The next step is to assign plates to each reactant and product To assign the reactants or products to plates 1 Select an Experiment Reactant worksheet 2 Goto ChemOffice14 gt CombiChem gt Plates gt Assign to Wells 3 Select a product worksheet Chapter 12 ChemDraw Excel and CombiChem 217 of 315 ChemBioDraw 14 0 PerkinElmer For the Better 4 Goto ChemOffice14 gt CombiChem gt Plates gt Assign to Wells Three columns are added to the reactant or product worksheet Well Plate Well Row and Well Column Well Plate Well Row Well Column it E w KJ To change specific plate assignments edit the values on the worksheet To remove all plate well assignments 1 Select the worksheet where you want to remove assignments 2 Go to ChemOffice14 gt CombiChem gt Plates gt Remove well assignments Browsing plates After assigning reactants or products to wells you can view which one has been assigned to each well Select either a reactant or product worksheet Go to ChemOffice14 gt CombiChem gt Plates gt Browse Plates The Plate Browser dialog box appears In the Plate scroll list select or enter the plate number to view e o YS In the dialog box select the well to view The worksheet scrolls to the reactant or product assigned to the well you select 4 Structure Reactant Well Plate Well Row Well Column 0 F Plate Y of total 45 plates
305. tion and type a value To Position Type a value for From the atom or bond centerto Angle degrees or clock o clock indicator center From the atom or bond center to Offset horizontal and vertical bottom left of indicator baseline At specified coordinates Absolute horizontal and vertical 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 properties from an atom 1 Select the atom 2 Navigate 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 properties to remove m Navigate to Structure gt Atom Properties and click the atom properties to remove m With query indicators shown click the query indicators using the Eraser tool Atom Property Options The properties you can assign to atoms are described below Substituents A substituent is defined as a non hydrogen atom connected by a bond of any order The substituents properties spe cify the number of substituents that may be bonded to the selected atoms Chapter 14 Query Structures 233 of 315 W P l 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 aldehyde oxygen has
306. tion Size 12 pt Drawing Area Width x Height 7 5 in x 10 in 40 of 315 ChemBioDraw 14 0 New Slide Phytomedicine RSC Chapter 4 Preferences and Settings P gt Perkin For the Better Page Size US Letter or A4 as selected Reduction 100 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 Atom Label Size 12 pt Caption Font Caption Size 16 pt Drawing Area Width x Height 7 5 in x 10 in Page Size US Letter Reduction 100 Fixed Length 20 pt Bold Width 1 33 pt Line Width pt Margin Width 1 25 pt Hash Spacing 3 pt Chain Angle degrees 120 Bond Spacing of length 8 Atom Label Font Atom Label Size 12 pt Caption Font Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 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 41 0f 315 ChemBioDraw 14 0 Science of Synthesis Synthesis Synlett Chapter 4 Preferences and Settings P gt Perkin For the Better Chain Angle degrees 120 Bond Spacing of length 20 Atom Label Font Atom Label Size 9 pt Caption Font 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 Reducti
307. tion and choose a format from the list Chapter 2 Getting Started 9 of 315 W P l Page Layout Object alignment page size orientation and other factors affect the presentation quality of your document The Drawing Area The document window may not be the same size as the drawing area of the page A document window may cover only a part of the drawing area These options let you set the drawing area on your screen Document Settings and Page Setup let you modify the page margins headers footers document type and size a View menu options Actual Size Show Document Magnify and Reduce Magnification Controls enlarge and reduce Dragging to enlarge the drawing area The Document Type You can set up a document as either a page or a poster Pages A single document containing one or more sheets each of which is printed on a single piece of paper Posters A single large document comprising as many sheets of paper as necessary Paged Document Setup To create a document with one or more pages 1 Navigate to File gt Document Settings The Document Settings dialog appears 2 On the Layout tab select Pages 3 Specify the number of pages in the Document Size section The Page Setup settings determines the size of the pages For more information see Page Setup on page 12 4 Type the Margin settings You set the units of the margins in the Preferences dialog The paper size minus the mar gins determines the
308. to the other end m Using any bond or selection tool point to an existing bond and type 3 on your keyboard Quadruple Bonds There are three 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 on your keyboard 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 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 or using Hotkeys See Bond Properties on page 239 _ Note To reduce the bond order select the Eraser tool and click the bond Dative Bonds Dative bonds are a specific type of covalent bond in which the pair of electrons shared by the atoms in the formation of a bond is contributed by one of the atoms only The atom contributing the pair of electrons is Known as donor while the atom which does not contribute but shares the pair of electrons is referred to as acceptor 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 Dative bonds are drawn with a fixed orientation in a document window To change the orientation of a dative bond Click the bon
309. tom Labels If you use a nickname that is the same as an element name a message indicates that the element is replaced with the nickname For example 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 these Nickname Element conflicts Symbol Nickname Element Ac Acetyl Actinium Am Amyl Americium Np para Nitrophenyl Neptunium Pr Propyl Praeseodymium 7 Note If you use the Periodic Table dialog to insert atoms into structures the elements will preferentially be depos ited Selecting Ac from the Periodic Table and clicking on an atom will place Actinium rather than Acetyl To remove the overriding nicknames navigate to File gt List Nicknames and delete the overriding nickname definition Deleting Nicknames To delete a nickname from the nickname library 1 Navigate 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 m A connection point that is not present m More than two connection points that are defined m A connection point that is not a single bond In Figure a below the entire functional group was selected Because 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
310. tool 2 Select the label to expand or double click the structure to select all labels in the structure 3 Navigate to Structure gt Expand Label Your structure is redrawn in its expanded form To contract expanded nicknames 1 Inthe biopolymer structure select the expanded part 2 Navigate to Structure gt C ontract Label Your structure is redrawn in its contracted form E Note This is applicable only to biopolymers Annotations Annotation is a brief description of an object or a comment about properties of an object Annotations are useful in identifying features and categories of objects in searching and browsing Annotations are categorized using keywords There are several default keywords Name Description GUID Globally Unique Identifier Type and Other Info You can also add your own keywords Many of the objects in the template files have associated annota tions to help you identify them in files To annotate an object 1 Select the object 2 Navigate to Object gt Annotate The Annotate dialog appears 3 In the Keyword list do one of the following Select a keyword Select Add New Keyword 4 Inthe Content text field enter the notes annotation to apply to the object or drawing 5 Click OK Deleting a Keyword When you delete a keyword all notes annotation for that keyword are also deleted 1 Inthe Annotate dialog select the keyword from the Keyword list 2 Click Delete Keyword 3 Click OK
311. tool and use the Text menu or Text format ting toolbar to change the style Positioning Atom Numbers You can position each atom number anywhere around its corresponding atom and its distance from the atom To reposition an atom number 1 Right click the indicator to move and click the Position command on the context menu The Position Indicators dialog appears 2 Click the appropriate position option and enter a value Position Indicators Position automatically Position by angle 3EY degrees cr chock j 4 gt oO chock Position by offset 0 0848 in horizontal 0 0486 in vertical Postion absolute 3 5597 in horizontal l gt 743 in vertical To position Type a Value for Position From the atom or bond center to the indicator cen By angle or by ter clock From the atom or bond center to bottom left of By offset hori indicator baseline zontal and vertical At specified coordinates Absolute hori zontal and vertical Structure Perspective You can tilt molecules or portions of molecules through three dimensions with the Structure Perspective tool To tilt a structure Chapter 9 Advanced Drawing Techniques 125 of 315 W P l 1 Select the structure with either a selection tool or the Structure Perspective tool 2 With the Structure Perspective tool click and drag the selected structure Place the cursor inside the marked rect angle and drag in any direction Tip Use lt SHIFT gt arag to
312. top For distance the highest value 1 is at the bottom A label appears for every lane You can rename and rotate it to any desired angle When one of the labels is rotated all the other labels are also rotated by the same angle fang 7 ane gt ane ang y A dialog box prompting for the new range appears The expected values entered in this dialog are always kDa The default value for range is 10 to 10 00 000 Mass 1 to 6 Log and 0 to 1 Distance When you change the range the bands that fall out of range are hidden A dialog box prompting for the mass of the new bands to be cre ated in the selected lane appears Space is used as a Separator Only numbers are allowed You can also add bands by hovering over the plate lane with the ALT key pressed The cursor changes to and clicking on the plate will deposit a new band Adds a new lane Adds a duplicate lane CTRL dragging a selected lane also duplicates a lane Deletes a lane P gt Perkin For the Better All of the items in a particular lane can be modified simultaneously by hovering over the lane and selecting the required context menu option For example you can display all the items in a lane in a specific color or have them dis play specific styles Chapter 11 Chemistry Features 171 of315 ChemBioDraw 14 0 I 7 PerkinElmer For the Better Lana fan e gt fan e3 Lan eg You can perform the following action on a band
313. torials 222 2 2 22 o icc ccc ccc cc cece cece cece cece eee e ee ce cece ceececeeeececeeeeeeeees 298 Tutorial 1 Drawing a Structure 2 2 2 2 ccc cece cece cece cece ec eeceecccccceceeceeccceeeecceseeceeeeees 298 Tutorial 2 Drawing rindS 2 2 e cece ccc ee cee cece cee cece cc eec cee ceeceeceeceecceeceeceececcceeseeeeeceuceees 299 Tutorial 3 Fischer projections 0 2 ccc ccc eee eee eee cece cece ec cee cee ceeccecceccceceeccecceceeeceeceeeeees 301 Tutorial 4 Perspective Drawings 2 cc cece cece cece ec ee cece cece eceeceeceeccecceeceeceeceeceeeceeseecees 304 Tutorial 5 Newman projections 0 22 c cece cee cece cee cece ec cee cee ceeceececcceeceeccececceeeceeceeceeee 308 Tutorial 6 Stereochemistry 2 222 c cece cece cece ccc ee cece cece cceceeeceeeccecccecececececeeeeeceececeeers 311 Tutorial 7 Templates 2 2 c occ cece cece cece cece cee cece ec eeceececcecceceeceecesceseececcereeseeeees 314 Copyright 1998 2014 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved V hemBioD 14 i ChemBioDraw 0 Perkin For the Better Recent Additions Windows 8 1 Microsoft Office 2013 and Mac OS X 10 9 x ChemDraw strives to be a vital and preferred tool for illustrating chemical and biological concepts Compatibility with the latest operating systems and tools is an essential part of that Having the ChemDraw Active X control functional w
314. tors such as solubility melting and boiling points and partition coefficients such as CLogP properties related to the three dimensional shape and volume of a chemical such as the Connolly sur face area and volume In total you can calculate more than 100 chemical properties for a given structure For alist of properties available in any specific applications click the respective link below For more information on the properties available in any specific applications see the respective online help available or visit the PerkinElmer Informatics Web site a Property predictions in ChemDraw Excel on page 203 a Property Predictions in ChemBioDraw on page 158 a Property Predictions in Chem3D on page 163 Chapter 12 ChemDraw Excel and CombiChem 202 of 315 ChemBioDraw 14 0 Property predictions in ChemDraw Excel P gt Perkin For the Better ChemDraw Excel includes a variety of functions for reporting properties for a given structure Each property is cal culated using the best available method To view the properties for a given structure 1 Select the structure cell 2 Right click the cell and select Structure gt Properties from the context menu The Properties dialog box displaying various properties and its values appears The properties include Balaban index Boiling point C Cluster count Connolly accessible area Connolly molecular surface area Connolly solvent accessible sur face area Conno
315. ts Specifying the margin width You can adjust the white space surrounding the atom label so that some of the attached bond is hidden Chapter 4 Preferences and Settings 31 of 315 Zo aa 0278 in 0978 in To adjust the white space 1 Goto File gt Document Settings The Document 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 Settings from other documents To apply document settings to the active window that are contained in a different document go to File gt Apply Docu ment 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 that you choose 7 Note Applied settings are for the current document only To make them the default settings for all documents you open go to File gt Open Style Sheets To apply the document settings from a document or style sheet not listed in the menu 1 Goto 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 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 or to all new objects drawn in the current document To
316. ts are commonly used to illustrate polymers For more information on polymers see Polymers on page 243 Single brackets You can draw a single bracket in any orientation Select a single bracket tool from the Brackets palette m lt 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 be placed only in a vertical orientation A rectangle or box defines their position To draw paired brackets 1 Select a paired bracket tool from the Brackets palette 2 Point where you want a corner of the bracket 3 Drag diagonally from one corner of the box to the opposite corner Daggers To draw a dagger 1 Select a dagger tool from the Brackets palette 2 Click in the drawing window 7 Note To resize a dagger select the dagger and click and drag one of its resize handles Framing Objects You can enclose your drawings or group structures with a rectangle brackets parentheses or braces To enclose your object 1 Select the drawing to enclose 2 Navigate to Object gt Add Frame and select a frame type Pen Tools The pen tools are useful for drawing freehand curves and shapes To draw a curve do one of the following Select the Draw Curve tool from the Pen Tools palette on the Main toolbar and click and drag your cursor across the drawing window Navigate to View gt Other Toolbars gt Pen Tools Select the Draw Curve tool and click an
317. tter Finally arrows can be rotated using the Structure Perspective tool as well as the Lasso or Marquee For more inform ation on using the Structure Perspective tool see Structure Perspective on page 125 Combining these methods lets you draw an unlimited number of arrows Equilibrium Arrows With equilibrium arrows changing the length changes both arrows proportionately changing the shape of the arrow head changes both arrowheads identically To change the length of one arrow hold down the lt Alt gt key Two new adjustment handles appear When adjusting one arrow of an equilibrium arrow the arrow cannot be extended beyond its original length e Curved Arrows You can curve most arrows found on the Arrows toolbar After you paste an arrow in your drawing click and drag the selection point in the middle of the arrow As you drag the selection point the angle of the arc appears measured in degrees Colored Arrows To color an arrow 1 Inthe drawing window select the arrow to color 2 Select acolor from the Color menu Coloring Block Arrows For block arrows those that are not made of simple lines you can apply colored effects using the filled faded and shaded options To apply color effects on block arrows 1 Select a block arrow from the Arrows palette and right click the block arrow Chapter 6 Basic Drawings 74 of 315 hemBioD 14 f ChemBioDraw 14 0 PerkinElmer For the Better
318. u can resize spots by holding down the lt Shift gt 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 Drag from any of the other four corners to scale all three values Customizing 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 Gel electrophoresis tool Gel Electrophoresis tool is available in the Chromatography toolbar and functions much like the TLC tool It consists of a plate containing several lanes with one or more bands The bands can be resized and moved along the lane For example consider the figure below 4 b aryl i aS aa Mass kDa You can perform the following action on a plate Option Action Show scale A scale bar appears on the right of the plate By default the unit is displayed in kDa However you can change it to Log Mass Chapter 11 Chemistry Features 170 of 315 ChemBioDraw 14 0 Option Show Lane Labels Set Range Add Bands Add Lane Duplicate Lane Delete Lane Action Mass or distance from the Units submenu For Log Mass and Mass the highest value is on the
319. u select Paste the struc ture will be removed from the cell and pasted in the specified cell To copy a structure from a cell 1 Select the structure 2 Goto ChemOffice14 gt Molecule gt Copy The structure remains in the cell and a copy is placed on the clipboard To copy a structure as InChl InChlkey or SMILES 1 Select the structure 2 Goto ChemOffice14 gt Molecule gt Copy As and select from these options m InChi a InChiKey a SMILES The structure remains in the cell and a copy in the desired string format is placed on the clipboard To paste a structure in a cell 1 Select the cell where you want to paste the structure 2 Goto ChemOffice14 gt Molecule gt Paste The structure is pasted from the clipboard Chapter 12 ChemDraw Excel and CombiChem 187 of 315 W P Displaying Structures You can display or hide structures in your spreadsheet You can also adjust the size of cells to display their entire con tents To show or hide structures 1 Select the structures 2 Select ChemOffice14 gt Structure gt Show or Hide Aligning Structures A structure may be too big for its cell or be improperly positioned To align structures select the cell that contains the structure and go to ChemOffice14 gt Structure gt Align The cells adjust to display their contents Resizing Structures 1 Select the cell s whose structure s you want to resize 2 Goto ChemOffice14 gt Structure gt Resize Resize handles appea
320. ue is 2 points 0 278 in 0 071 cm File Formats The file formats available in ChemBioDraw are Format Windows ChemDraw CDX YES Chapter 15 Sharing Information 273 of 315 ChemBioDraw 14 0 Format ChemDraw XML CDXML ChemDraw CHM ChemDraw Style Sheets CDS Connection Table CT Chemical Markup Language CML Bitmap BMP TIFF file TIF Graphic Image Format GIF ISIS SKC TGF RXN JCAMP JDX DX JPEG JPG JPEG MDL SDfile SDF MDL MolFile MOL MSI ChemNote MSM PNG Image PNG Standard Molecular Data 4 2 SMD Galactic Spectra SPC Windows Metafile WMF EnhancedMetafile EMF ChemDraw Templates CTP ChemDraw Templates Style sheets CTS PDF MDL Molfile V3000 Reaction Molfile V3000 RXN Chapter 15 Sharing Information Windows YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES NO YES YES P gt Perkin For the Better 274 of 315 ChemBioDraw 14 0 i eae Perkin For the Better Format Windows PICT PICT Scaled 4x NO Encapsulated PostScript YES Scalable Vector Graphics YES ChemBioDraw 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 ChemBioDraw products Refer to Importing on page 272 Format Import Export ChemDraw CDX YES YES ChemDraw XML
321. ue returned by the function CHEMPROPPRO LOGP for that structure is within the range 0 4 to 5 6 it satisfies Ghose modification s fourth criteria 3 Calculate the number of criteria satisfied If the number of violations is less than two then the Ghose modifications requirement is satisfied Congreve rule of three The Congreve Rule of Three uses these criterias a Three or fewer H bond donors Three or fewer H bond acceptors A molecular weight under 300 daltons LogP lower than 3 Fewer than two violations of the above four rules To determine if the substance meets the Congreve Rule of Three requirement 1 Calculate the value of each of these functions CHEM NUM HBDONORS CHEM NUM HBACCEPTORS CHEM MOLWEIGHT CHEMPROPPRO LOGP 2 Verify that the value returned by the functions meets the Congreve Rule of Three criteria For example if the if the function CHEMPROPPRO LOGP returns a value for the structure that is lt 3 it satisfies Congreve Rule of Three s fourth criteria 3 Calculate the number of criteria satisfied If the number of violations is less than two then the Congreve Rule of Three is satisfied Chemical Properties Chemical property prediction is an important feature that ChemBioOffice applications support It enables you to cal culate values for a wide range of methodologies for example topological descriptors such as the Weiner index and Balaban index thermodynamic descrip
322. uid at standard atmospheric pressure At the melting point the solid and liquid phase exist in equilibrium The formula to calculate melting point is T AH AS Where T is the temperature at the melting point AS is the change in entropy of melting and AH is the change in enthalpy of melting MR The Molar Refractivity is estimated by Crippen s fragmentation and Viswanadhan s fragmentation method Additional empirical LogP data appears for selected substances in the report file pKa pKa is the negative log of the acid dissociation constant K It describes the tendency of compounds or ions to dis sociate in solution It is calculated using the formula pKa logio Ka Empirical pKa data appears for selected substances in the report file Note pKa calculations are available only in Microsoft Windows version of ChemBioDraw tPSA Calculation of polar surface area based on fragment contributions Property Predictions in ChemDraw Excel The Properties feature in ChemDraw Excel lets you view the values of different properties for a given structure Each property is calculated using the best available method A list of properties available in ChemDraw Excel is listed in the table below For more information on these properties see ChemDraw Excel online help or visit the PerkinElmer Informatics website The properties available include B F Melting Point Shape Attribute Balaban Index Formal Charge Molar Refract
323. ulate melting point is Where T is the temperature at the melting point AS is the change in entropy of melting and AH is the change in enthalpy of melting Chapter 12 ChemDraw Excel and CombiChem 207 of 315 Molar refractivity Is a measure of the total polarizability of one mole of a substance It is dependent on the temperature index of refrac tion and pressure The molar refractivity A is expressed as A Ny o 3 Where N k is the Avogadro constant and a is the mean polarizability Molecular formula This is the molecular formula of the compound Molecular weight This is the sum of the atomic weights of all atoms in a molecule Num rotatable bonds Is the number of rotatable bonds in a molecule A rotatable bond is defined as an acyclic bond drawn as a single bond amide C N bonds O C N are rotatable where the atom on each end has at least one other non hydrogen sub stituent This topological parameter is a measure of molecular flexibility Unsaturated bonds and single bonds con nected to hydrogens or terminal atoms single bonds of amides sulphonamides and those connecting two hindered aromatic rings having at least three ortho substituents are considered non rotatable Ovality This refers to a measure of how the shape of a molecule approaches a sphere at one extreme or a cigar shape at the other Ovality is described by a ratio of volume to area O Al 4xrx 3xV 4 x wy 3 Wh
324. ument a structure or a part of a structure using the Analysis window Values for selected objects in the document window are shown If no structure is selected in your document values for the entire document are shown You can have this window open as you draw in the document It shows the current values as you draw see example below Analysis x Iw Formula CG Hed0 Iw Exact Mass 128 00 Ww Mol Whe 126 56 I mz 126 00 100 0 130 00 32 0 129 01 6 5 iw Elem Anal 56 06 H 3 92 Cl 27 56 O 12 45 Paste The Decimals setting applies to Exact Mass Molecular Weight and m z only The values displayed in the Analysis Decimals E window includes 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 The weights of the most common isotopes and a graphical representation of the isotopic abund ance is shown The molecular weight accounts for the isotopes for each atom and their natural abundance Where there is more than one abundant isotope this feature computes multiple molecular weights Low abundance combinations whether b
325. up Settings You can save page setup settings in a style sheet The settings are saved with the text settings drawing settings and the color palette 35mm Slide Boundary Guides If you create 35mm slides from a hard copy of a document or from a screen shot you can display 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 are not printed The drawing area of the page must be at least 7 x 10 5 inches for these boundary lines to be vis ible To display the 35mm slide boundary lines 1 Navigate to File gt Preferences 2 Select the Building Display tab 3 Select the Show 35mm Slide Boundary Guides check box 4 Click OK Chapter 3 Page Layout 13 of 315 ChemBioDraw 14 0 i aa Perkin For the Better Two 35mm Slide Boundary Guides appear in the orientation chosen in the Page Setup dialog These guides appear in every document Viewing Drawings Magnification Magnification changes how large or small your drawing appears without changing its dimensions You can either select a value in the magnification drop down list or enter your own value between 1 and 999 Magnify 1 Select an object to keep in view as you magnify the drawing 7 Note If you do not select an object the last object drawn is the center point of the magnification 2 Select an option below Toincrease the magnification navigate to View gt Magnify To reduce t
326. uted from the Connolly Molecular Surface Area and Solvent Excluded Volume properties Chapter 12 ChemDraw Excel and CombiChem 196 of 315 ChemBioDraw 14 0 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 cell ref Example In cell MOLECULAR TOPOLOGY BALABAN INDEX A2 Result 29909 Cluster count Function MOLECULAR TOPOLOGY CLUSTER COUNT cell ref Example In cell MOLECULAR TOPOLOGY CLUSTER COUNT A2 Result 13 Topological index Function MOLECULAR TOPOLOGY MOLECULAR TOPOLOGICAL INDEX cell ref Example In cell MOLECULAR TOPOLOGY MOLECULAR TOPOLOGICAL INDEX A2 Result 1998 Chapter 12 ChemDraw Excel and CombiChem P gt Perkin For the Better 197 of 315 ChemBioDraw 14 0 Number of rotatable bonds Function MOLECULAR TOPOLOGY NUM ROTATABLE BONDS cell ref Example In cell MOLECULAR TOPOLOGY NUM ROTATABLE BONDS A2 Result 2 Polar surface area Function MOLECULAR TOPOLOGY POLAR SURFACE AREA cell ref Example In cell MOLECULAR TOPOLOGY POLAR SURFACE AREA A2 Re
327. variable attachment points and multi center bonds cannot be cleaned Structures are rotated so that as many bonds as possible are directed at a multiple of 15 degrees Clean Up Structure preserves stereochemical meaning rather than the precise identity of wedged or hashed bonds as shown below OH OH OH Ho l pe a OE OH OH OH OH a4 OH ii ie ited OH OH To use Clean Up Structure 1 Select the structure or part of the structure to clean up 2 Navigate to Structure gt Clean Up Structure or type lt shift gt lt ctrl gt lt K gt 7 Note The Clean Up Structure command redraws your structure in iterations Therefore you may need to select the command more than once Chapter 6 Basic Drawings 88 of 315 ChemBioDraw 14 0 PerkinElmer For the Better You can also clean up a reaction or a biopolymer For more information see Clean Up Reactions on page 130 and Clean Up Biopolymers on page 106 Checking Structures You can check the chemistry of a selected structure part of a structure or caption in Formula style with the Check Structure command The structure is checked using normal valences and elements and defined nicknames To check the valences of all selected atoms in a structure 1 Select a structure part of a structure or caption 2 Navigate to Structure gt Check Structure If a structure is incorrect a message window appears for example Possible Error in Drawing There se fod
328. w To fill in the inserted row with caption text 1 Click the Text tool and select the first caption in the inserted row 2 Type new text 3 Press lt tab gt to move to the second caption in the inserted row and so on Chapter 3 Page Layout 19 of 315 ChemBioDraw 14 0 f i PerkinElmer For the Better Preferences and Settings You can customize ChemBioDraw by configuring Preferences and Document Settings to match the way you work Preferences allow you to change the default behavior of certain options that apply to every open document The changes you specify in the document settings are applicable only within the document and is not applicable through out the application The changes you specify in the object settings are specific to the selected object For more information see the topics found in this chapter e Setting Preferences e Customizing Toolbars e Document Objects and Settings e Customizing Hotkeys e Working with Color Setting Preferences Preferences affect how ChemBioDraw works regardless of the document with which you are working 1 To open the Preferences dialog box navigate to File gt Preferences Prele remei fing Tels rien A Ee a lrg l Inara g Diii Chenier Tam pepe ce Graphics Deport Border 0 0770 n a lhs ikon M h nnak A an Gir a AA e He ea ke Prini Beagrie k D iek Dii Fi O hak Dhe Whe a bo ligand or te R Abona Aio Hippi E lirik air Dokan Doimi Gb Aie ari g Liri
329. xole can never form double bonds as its two neighbors oxygen atoms have no free valences While preferred IUPAC PIN name for that structure is 2H 1 3 dioxole Struct gt Name generates the name 1 3 dioxole The name produced by Struct gt Name conforms to CAS nomenclature recommendations in this regard Unsupported Structures This feature has a few limitations for interpreting some structures such as Sulfones and chalcogen analogs Chapter 10 Struct Name Ultra Feature 146 of 315 W P sotopically modified compounds Radicals ions and radical ions Auto Update You can include chemical properties including the chemical name and analysis in a caption and the caption content will update automatically when you modify the structure For more information on adding chemical properties to cap tions see Analysis Data on page 66 To toggle the auto update feature 1 Point to the caption 2 Right click and select Auto update A check mark appears next to the command when it is selected Successive clicks toggle the command on and off When auto update is on default the label updates each time you modify the structure _ Note For large structures the new label may not appear for a few seconds You do not have to wait for the new label to appear before continuing to modify your structure Name gt Struct You can type a chemical name and Name gt Struct will draw the structure Although some trade names are supp
330. y Fit to window Toggle ruler Toggle crosshair Object Command Toggle fixed length Toggle fixed angles Select multiple objects Group selected objects Ungroup objects Join selected objects Bring to front Send to back Flip horizontal Flip vertical Rotate 180 horizontal Rotate 180 vertical Key Combination Delete Key Combination F5 F8 F7 F6 F11 CTRL H Key Combination CTRL L CTRL E SHIFT Click with Lasso Marquee or Structure Perspective tools CTRL G SHIFT CTRL G CTRL J F2 F3 SHIFT CTRL H SHIFT CTRL V ALT SHIFT CTRL H ALT SHIFT CTRL V Chapter 5 Shortcuts and Hotkeys P gt Perkin For the Better 48 of 315 ChemBioDraw 14 0 i Perkin For the Better Command Key Combination Rotate opens Rotate Objects CTRL R dialog Scale opens Scale Objects dia CTRL K log Structure Command Key Combination Clean up structure SHIFT CTRL K Convert name to structure SHIFT CTRL N Convert structure to name ALT CTRL N Text Command Key Combination Flush left SHIFT CTRL L Center SHIFT CTRL C Flush right SHIFT CTRL R Justified SHIFT CTRL J Automatic justification SHIFT CTRL M Plain CTRL T Bold CTRL B Italic CTRL I Underline CTRL U Formula CTRL F Subscript selected character or F9 in a label next character typed Superscript selected character or F10 ina label next character typed Adds a degree sign ALT 248 in a label Chapter 5 Shortcuts and H
331. ython 3 2 are installed on your local computer when you install ChemBioOffice After the installation we suggest that you follow the simple exercises in this section to familiarize yourself with ChemScript For editing ChemScript files we recommend that you use one of the many programming tools that are available One of these tools IDLE is included with the Python installation To learn more about IDLE see the online Help in the IDLE main menu Starting IDLE From the Start menu go to All Programs gt Python 3 2 gt IDLE Python GUI After Python starts a Python shell opens in IDLE and the header indicates a version of Python Ex 3 2 and a version of IDLE Ex 1 2 A prompt will also appear gt gt gt Loading the ChemScript Library At the command prompt type the line below and press lt Enter gt import ChemScriptl4 Chapter 13 ChemScript 221 of 315 E Note The command is case sensitive A Welcome to CS ChemScript message appears followed by a command prompt ChemScript Help You can read a description of any ChemScript class within IDLE For example enter the line below to return Help for the ChemScript Atom class help Atom The help will begin with a message such as Help on class Atom in module ChemScript14 Enter SMILES Data You can also test to verify that ChemScript is working correctly One common use for ChemScript is to apply func tions to SMILES strings For example you can assign a SMILES
332. ze Membrane Arc To create a membrane arc click and drag in a curve using the Membrane Arc tool in the BioDraw toolbar The tool has three adjustment handles a The handle at the starting point controls the length a The center handle controls the subunit size a The handle at the leading edge controls the arc Helix Proteins To create a helix protein 1 Select the Helix Protein tool from the BioDraw toolbar 2 Drag in the document window or click to draw the default size When orienting the protein note that you are constrained to 15 degree increments when fixed angles are applied nav igate to Object gt Fixed Angles To override the constraint press lt shift gt key as you drag Chapter 7 BioDraw Ultra feature only 96 of 315 The helix protein has four adjustment handles height width of the strands width of the cylinders and spacing Figure 7 1 Adjustment handles on a helix protein A height adjustment B width of strands C width of cylinder and D spacing between cylinders DNA Molecules To create a DNA molecule 1 Select the DNA tool from the BioDraw toolbar 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 pressing lt alt gt key as you drag DNA has four adjustment handles height width of the strands offset of t

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