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ConQuest 1.12 User Guide and Tutorials 2010 CSDS Release

1. Ali Parameters Current Selection TR2 Define selected Atoms 1 selected Tabulate Atom label _ Atomic number J Atomic radius Vd radius _ Number of connected atoms e Click on the Atom label radio button then click OK to finish the selection e Tabulating the element symbol is useful because the search will find structures containing a ConQuest User Guide range of different transition metals By tabulating the precise element type in each hit structure it is possible to separate e g Fe from Co from Ni hits in Vista or Excel thus allowing analysis of differences and similarities between the metals There are no more parameters to define so close the Geometric Parameters pop up by hitting Done 6 Run the search and view the geometric parameters for specific hits Hit the Search button Set the filters to exclude polymers disordered structures and structures with R factors greater than 0 1 Also switch on the No errors filter This will exclude structures which contain errors that the editorial staff at CCDC have been unable to resolve Start the search with the Start Search button Underneath the diagram display for the first entry there will be a check box labelled Show Parameters Click on it to display the values in this particular structure of the various parameters you have defined Browse through some of the other hits Occasionally you may come across a
2. ConQuest User Guide 181 e Similarly define the centroid of the other ring named by default CENT2 6 Define the ring planes in a similar way e Click on the six atoms of one of the rings and hit the Define button next to the word Plane By default the plane is called PLN e Repeat for the second ring named by default PLN2 7 Define the distance between the centroids and the angle between the planes e Click on the names of the two centroids CENTI and CENT2 in the box headed Defined Objects To construct Parameter Object Select atoms main window or object list below Hit Define to construct Parameter Object Current Selection CENT1 CENT2 Valid Parameters All Parameters Distance Define Defined Objects PLN1 Valid Objects PLN2 Vector Define Dummy Point Define Centroid Define Reset Done e Then hit the Define button next to the word Distance This specifies a parameter DISTI which is the distance between the two ring centroids e Similarly click on PLN and PLN2 and Define the angle between these planes 8 Constrain the search so that it will only find structures in which the phenyl groups are cis e Click on the four atoms defining the conformation around the central C C bond 182 ConQuest User Guide To construct Parameter Object pele Options 3 Current Selection c6 C13 C14 C7 Select atoms main window or
3. Geometric Parameters To construct Parameter Object Select atoms main window or object list below Hit Define to construct Parameter Object Current Selection CENT1 05 Valid Parameters All Parameters Atom Properties Define Distance Define Defined Objects Valid Objects Vector Define Dummy Point Define t Centroid Define iene Delete Reset Done e Then hit the relevant Define button next to the word Distance in the above example e Once a parameter has been defined its value can be constrained see Applying Geometric Constraints page 88 4 5 5 Renaming Geometric Parameters By default labels are named LABI LAB2 etc distances DIST DIST2 etc angles ANGI ANG2 etc torsions TOR TOR2 etc To rename a parameter e Select it in the 3D Parameters list top right hand corner of Draw window e Hit the Options button underneath this list Alternatively you can rename a parameter immediately after creating it by hitting the Options button in the Geometric Parameters dialogue box opened by hitting ADD 3D e Type the new name maximum 6 alphanumeric characters into the RENAME input box e g ConQuest User Guide 87 PARAMETER ANG1 Angle Limits are applied after application of any selected function APPLY FUNCTION None LIMIT From to Range w Value tolerance RENAME ANGI e Hit OK Cl
4. Delocalised Pi any Size 3 Bonds Single e Only carbon rings can be specified but it is easy to change individual element types later see Changing the Current Element Type page 56 e Some complex ring systems e g crown ethers are available by clicking on Templates in the bottom left hand corner 3 5 2 Adding a Ring to an Atom in an Existing Substructure e Select the ring see Adding a Ring to a Blank Drawing Area page 52 then click on the desired atom in the existing substructure with the left hand mouse button e For example selecting a 6 membered aromatic ring and clicking on the N atom in cae a will create ConQuest User Guide 53 3 5 3 Fusing a New Ring to an Existing Ring e Select the new ring see Adding a Ring to a Blank Drawing Area page 52 then click on the desired fusion bond in the existing ring e For example selecting a 6 membered saturated ring and clicking on the N N bond in i S c N ne Ye will create a ae Se er 3 5 4 Creating a Spiro Fusion e Select the required ring see Adding a Ring to a Blank Drawing Area page 52 then click on the desired spiro atom in an existing ring e For example selecting a 3 membered saturated ring and clicking on the N atom in T ae an EN a T 54 ConQuest User Guide will create T Saa 3 5 5 Fusing Rings by Moving One Ring onto Another It is possible but sometimes tedious and not re
5. lt a All Text 1 New in Text Search Required Fields lt All Text 1 Query gt iO Text Search Required Fields Not all CSD entries have data present in the fields listed below Not all CSD entries have data present in the fields listed below To retrieve only those entries where data is present for a particular field select it and Add it to the Required Fields list To retrieve only those entries where data is present for a particular field select it and Add it to the Required Fields list Optional Fields Required Fields Bioactivity Habit Colour Melting point Natural source Polymorph lt Remove Pressure Radiation source Recrystallisation solven Sensitivity Optional Fields Required Fields Xx i Add gt Radiation source Recrystallisation solven i Sensitivity Cancel Z L Search Store Cancel saan e To find all entries that contain Habit and crystal Colour information select Colour then Add This will result in Habit and Colour entries in the Required Fields list e To find entries that contain either Habit or crystal Colour information create and store two separate queries and combine them see Complex Query Combinations page 21 e To remove a field from the Required Fields list select the appropriate word then click on Remove ConQuest User Guide 137 15 2 3 Combining All Text and Required Fields Searches All Text and Required
6. always evident from a publication that an entry belongs to one of the specified categories Find entries classified as Steroids and not defined ITT Search Store Cancel Reset e To find structures classed as Steroids or containing the keywords acetyl or hydroxy create and store three separate queries one for Class Steroids one for Name acetyl one for Name hydroxy and then combine them see Complex Query Combinations page 21 8 3 Hints for Compound Name and Chemical Class Searching e Chemical nomenclature is complex Always consider a substructure search instead e You should familiarise yourself with the CSD Compound Name Conventions see page 219 e Compound name searching can be useful as a quick way of finding examples of a particular type of structure since it is often quicker to type a name than draw a substructure However substructure searching is usually better if you want to be sure of finding all examples of a particular type of compound since compounds may be named in unexpected ways e Use several short syllables rather than one long text string e g buta and diene is better than butadiene since the CSD will contain 4 butadiene and buta 1 4 diene For the same reason 118 ConQuest User Guide we recommend ticking the Ignore non alphabetic character box e In general and particularly in locating natural products search for only the key root part of the name e g picolin penicil
7. 273 K Query 2 Search Reset ConQuest User Guide 2 9 Managing Hitlists 2 9 1 Hitlist Combinations e A hitlist is a subset of CSD entries which can include search results refcode lists or the results of combining these The Manage Hitlists screen can be used to find CSD entries that satisfy a logical combination of hitlists this can be a combination of search results refcode lists or a combination of the results from either a search or a refcode list e Hitlist combinations are best illustrated with an example e Set up the following search for all porphyrin structures having z 2 see Simple Query Combinations page 20 File Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results Drag Query Icons into Boxes Find entries that must have boolear AND must not have must have at least one of 2A e Set up the search as described in Simple Query Combinations see page 20 for all those structures that contain magnesium and a benzene ring and were determined at a temperature below 273K You now have 2 sets of search results i e hitlists available which can be combined ConQuest User Guide 23 24 e Hit the tab labelled Manage Hitlists On the left hand side of the Manage Hitlists screen the pull down menus under List A and List B have search listed as the default select search2 from the pull down menu under List B Both
8. Delocalised Double Bonds see page 223 Element Group Symbols see page 225 Hydrogen Atoms in 2D 3D Substructure Searching see page 227 Metal Carboxylates see page 232 Pi Bonds see page 236 ConQuest User Guide 217 e Polymeric Bonds see page 236 e Variable Bond Type see page 246 e Variable Element Type see page 246 Chemical Formula Since a crystal structure may contain more than one type of molecule there are basically two sorts of formulae in the CSD e The formula of an individual molecule e g Cjo Hig N2 Ni Os The sum formula i e the formula of all the different molecules in a structure added together For example the dihydrate Cjo Hig N gt Ni O5 2 HO would have a sum formula of Both types of formula can be searched for in ConQuest The letter n which may sometimes be seen in formulae displayed in View Results indicates that the compound is polymeric e g C3 H3 O6 Sc1 n The formula enclosed in the brackets is that of the monomer repeat unit To Search e Select the Formula button in the Build Queries pane see Using the Formula Dialogue Box page 123 Exact searches involving charges and multipliers can be done using the All Text option see Using the All Text Dialogue Box page 135 but they run slowly Related Topics e Element Group Symbols see page 225 CIF Format The Crystallographic Information File CIF format was developed as the standard crystallographic data exchange format
9. Find crystals with specific morphology e g rhombs acicular etc 15 2 Using the All Text Dialogue Box The All Text dialogue box has two tabs e All Text see All Text Searching page 135 e Required Fields see Specifying Required Fields page 137 It is also possible to combine A Text and Required Field searches see Combining All Text and Required Fields Searches page 138 15 2 1 All Text Searching Open the dialogue box by hitting All Text in Build Queries Either select the desired keyword from the scrolling list please note that this is not an exhaustive list or type directly into the input box The example below will find all entries containing the keyword drug ConQuest User Guide 135 Alf Text 1 New Text Search Required Fields New Box Either select from list or enter in box es below ard You can type partial or complete word s If two or more words are typed into the same box the search will be for the exact phrase specified Search Store Cancel a sansa e Iftwo or more words are typed into the same input box the search will find only those entries containing the exact phrase specified The example below will find entries containing the exact sequence of characters methanol solvate i e these two words separated by a single space New Box or enter in box es below methanol solvate e To find entries containing two or more words that need not be adjacent use t
10. Hall Allen and Brown Acta Cryst A47 655 1991 http www iucr org iucr top cif home html Related Topics e CIFMIF Format see page 219 218 ConQuest User Guide CIFMIF Format cifmif is an output format option for structure data from the CSD This format combines CIF crystallographic data names with chemical data names from the Molecular Information File MIF Allen Barnard Cook and Hall J Chem Inf Comput Sci 35 412 1995 Related Topics e CIF Format see page 218 Comments A great variety of comments are included in the CSD e g e There appears to be an error associated with the coordinates of C17 e Solvate coordinates have not been reported e Dx is reported as 1 39 we calculate 1 50 e Formula weight is reported in the paper as 552 we calculate 718 e IUCr br1217 e IUC9900093 The last two are examples of Deposition Numbers see page 224 To Search e Select the All Text button in the Build Queries pane see All Text Searching page 135 Compound Name Conventions Compound names usually follow the rules of standard chemical nomenclature Occasionally a trivial drug or trade name might be used A few conventions are used in constructing compound names e Lower case Greek characters are spelt out e g alpha Upper case Greek characters are spelt out and prefixed by c e g cdelta e The names of elements Al Cs and S are spelt aluminium cesium sulfur Bridging ligands in polymeri
11. Select Subset Cear Subset J No powder structures Only Single query being used Search will find structures where this query is true Start Search Cancel e Note a search for entries modified before after a particular date will return entries added before after the particular date 18 3 2 Searching on entires in a pre defined hitlist e Build the query as usual and hit Search Then hit the Select Subset button in the Search Setup dialogue box e Select Entries in a pre defined hitlist e Click on the button underneath the words Restrict on pre defined hitlists and select the required 148 hitlist The following pre defined hitlists are available e The best representative of a structure The CSD can contain multiple determinations of the same crystal structure reporting improved structural models or new experiments performed at different temperatures pressures or using different radiations These multiple inclusions could introduce bias in statistical surveys Searches can be restricted to just the best representative of each unique polymorph thus eliminating hits from duplicate crystal structures 4 best representative subsets are available These are based on R factor the presence of hydrogens room temperature and lowest temperature determinations Further information can be found here Searching the Cambridge Structural Database for the Best Representative of Each Unique Polymorph J van de Stree
12. Select this option to find non bonded interactions between these fragments Any If you select this option then the distance calculated may be arbritarily calculated for some entries unless you define a Contact or Intramolecular distance between these fragments e Also define the O H N and C O H angles as geometrical parameters a any More Groups G Bond Single ConQuest User Guide 3D Parameters DISTI DIST2 ANGI To construct Parameter Object Select atoms from main window Hit Options to set constraints or change options Current Selection Valid Parameters Options Defined Objects Valid Objects Also define the Labels of O and H See Tutorial 3 Defining and Saving Geometric Parameters see page 174 6 Run the search and save the parameters and the coordinates of the hit fragments Hit Done if you have not already done so to close down the Geometric Parameters window then hit Search Hit the Advanced Options tab and switch on the Normalise terminal H positions check box This will apply a correction to remove systematic errors in N H bond lengths determined by X ray diffraction Hit the Filters tab select the R factor lt 0 1 filter and hit Start Search The interacting atoms are highlighted in the chemical diagram and the hydrogen bond distances can be displayed by switching on the Show Parameters check box The intermolecular
13. Since the choice of unit cell axes is often arbitrary it is clearly desirable to conduct unit cell searches against cells which have been converted to a standard reduced form This is reduced cell searching The cell reduction process involves determining the primitive cell which has the shortest possible cell lengths the Buerger cell Mighell and Rodgers Acta Cryst A36 321 1980 Example Unit cell 12 132 14 662 13 153 90 127 84 90 Reduced cell 11 154 12 132 14 662 90 90 111 36 In a number of cases further restrictive rules have to be applied for a unique choice the Niggli cell P Niggli Handbuch der Experimentalphysik Vol 7 Part 1 Leipzig Akademische Verlagsgesellschaft 1928 Unfortunately although the Niggli cell is unique it can under special circumstances be unstable A small variation in an input cell dimension may lead to a discontinuous change in the Niggli cell and this will give rise to problems for searches which allow for reasonable error bounds on cell dimensions Fortunately only the cell angles are subject to abrupt change This has lead to the suggestion Andrews Bernstein and Pelletier Acta Cryst A36 248 1980 that cell lengths alone be used for comparison purposes This is what is done in ConQuest Hence two reduced cells will be held to match if their cell lengths are identical within the specified tolerance even if their cell angles are very different
14. UND Not an alpha amino acid Next bond is Any UND Normal peptide bond User Defined Non peptide bond QAA w Either Construct N terminus Right click on outer residues to Terminate an acyclic sequence C terminus m lt GLU AIB SER AA ee ALA ee Cyclicity Cyclic sequence Acyclic sequence w Either Search Store Cancel Reset ConQuest User Guide 111 6 3 Hints for Peptide Searching e If you include a chemically modified residue in a sequence you cannot specify the type of chemical modification For example selecting Chemically Modified and TYR will match with any modified form of tyrosine but not with tyrosine itself e A peptide search will find any peptide containing the sequence you have specified For example ALA SER would match with GLY ALA SER ALA SER ASN ARG ALA SER PHE etc as well as with ALA SER itself 112 ConQuest User Guide 7 AUTHOR AND JOURNAL SEARCHES 7 1 7 2 Typical Uses of Author and Journal Searching Finding publications by specific author s Finding structures mentioned in particular papers Reviewing publications in specific journal s and year s Using the Author Journal Dialogue Box Open the dialogue box by hitting Author Journal in Build Queries You can search for Authors names see Authors Names page 113 Journal name see Journal Name page 114 Journal volume see Journal Volume page 114 Journal page num
15. click on the bond s to be changed with the left hand mouse button and hit Done In EDIT mode select the bond s pick Bonds from the top level menu Type from the resulting pull down menu then pick the required bond type this may be Variable see Variable Bond Type page 246 3 7 4 Defining Cyclic or Acyclic Bonds It is possible to specify that a particular bond must be cyclic i e part of a ring or acyclic i e not part of a ring This can be done in several ways including In DRAW or EDIT mode click on the centre of the bond with the right hand mouse button pick Cyclicity from the resulting pull down menu then select the required option from the second 62 ConQuest User Guide pull down menu Unspecified in this menu means the bond may be either cyclic or acyclic If the bond is already part of a ring the Acyclic option will be greyed out e In DRAW or EDIT mode click on Bonds in the top level menu select Cyclicity from the resulting pull down menu then select Cyclic Acyclic or Unspecified The Select Bonds pop up appears click on the bond s to be changed with the left hand mouse button and hit Done In EDIT mode select the required bond s see Selecting Atoms and Bonds page 50 Pick Bonds from the top level menu Cyclicity from the resulting pull down menu then select Cyclic Acyclic or Unspecified as required 3 8 Avoiding Unwanted Bonds and Rings When drawing substructures it is possible to e
16. coordinates and bond lengths If errors are detected which cannot be fixed the problem is sent to the author In the meantime the entry is archived to the CSD with a comment summarising the suspected problem Inevitably some authors do not respond so the CSD contains entries with unresolved errors To Search to exclude entries with unresolved errors e Select the Experimental button in the Build Queries pane see Using the Experimental Dialogue Box page 133 Van der Waals Radii Standard van der Waals radii are assigned to the common elements They are taken from Bondi J Phys Chem 68 441 1964 Other elements are assigned van der Waals radii of 2 0A Standard van der Waals Radii A Element Radius Ag 1 72 Ar 1 88 AS 1 85 Au 1 66 Br 1 85 ConQuest User Guide 243 244 Element Radius C 1 70 Cd 1 58 Cl 1 75 Cu 1 40 F 1 47 Ga 1 87 H 1 20 He 1 40 Hg 1 55 I 1 98 In 1 93 K 2 75 Kr 2 02 Li 1 82 Mg 1 73 N 1 55 Na 2 27 Ne 1 54 Ni 1 63 1 52 P 1 80 Pb 2 02 Pd 1 63 Pt 1 72 S 1 80 Se 1 90 Si 2 10 Sn 2 17 ConQuest User Guide ConQuest User Guide Element Radius Te 2 06 Tl 1 96 U 1 86 Xe 2 16 Zn 1 39 245 Variable Bond Type ConQuest allows the user to specify that a bond in a substructure may be of variable type e g single double or aro
17. or partial compound name into the input box If the tick box Ignore non alphabetic character is ticked the search will find structures even if the specified name is interrupted by numbers commas hyphens etc e g thiazolyl would find a structure with the name Azobenzene N 4 5 bis methoxycarbony thiazol 2 yl imide If the tick box Find exact word only is ticked the search will only find structures in which the compound name matches an exact word e g hydrazine will not match acetylhydrazine This type of search cannot be used in conjunction with the ignore non alphabetic character option When finished click Add beneath the Find exact word only tick box The query text will be added to the Contains box To remove an entry from the Contains box select the relevant word and click on the Delete button To edit an entry in the Contains box select the relevant word make the amendment then click on the Replace button The query text will be updated To search for more than one name or partial name type the new query text into the Compound Name box and click Add The example below would find all structures whose compound names contain both thiazol and fluoro e g 4 4 5 5 tetrafluoro 1 3 2 dithiazolidine ConQuest User Guide lt Name Class 1 New ai Compound Name Contains a thioazol fluoro Ignore non alphabetic characters a e g butadiene will match buta 1 3 diene A ESNA z SS s cee e To f
18. select File from the top level menu bar and Save Queries from the resulting pull down menu It is then possible to save either one particular query or all queries in a single file Reading queries Go to Build Queries or Combine Queries select File from the top level menu bar and Read Queries from the resulting pull down menu MDL MOL files can be used as queries If the MOL file contains geometric objects such as planes and centroids these will normally be transferred to ConQuest If the MOL file contains defined distances angles and dihedral angles then these too will normally be transferred so long as a corresponding geometric parameter can be defined in ConQuest The following table indicates the equivalencies between MDL and ConQuest geometric features Those MDL features for which no ConQuest feature exist are ignored by ConQuest Names for features will be retained unless they are not present or are more than six characters long In these cases names will be automatically assigned If duplicate names are loaded the second incidence is renamed Loading of Multi MOL files will result in one query for each substructure loaded MDLID MDL Feature CQ Feature lco Prefix 1 Point defined by two points and a distance in Angstroms Dummy point DUM 2 Point defined by two points and a percentage 3 Point defined by a point a normal line and a distance 4 Line defined by two or more points 5 Plane defined by three or more points P
19. the CSD The Class field is added to an entry only if it is obvious from a publication that the structure belongs in a particular category If searching for a specific entry that is not returned in a Class search an alternative search method e g a substructure search may be more successful ConQuest User Guide 119 9 CHEMICAL ELEMENT SEARCHES 9 1 9 2 Typical Uses of Chemical Element Searching Finding structures containing particular elements Finding structures containing one of a group of elements e g any transition metal Limiting the element types that may be present Using the Elements Dialogue Box Open the dialogue box by hitting Elements in Build Queries You can Search for structures containing specific elements see Searching for Specific Elements page 120 Search for structures containing one of a group of elements e g any halogen see Searching for Any of a Group of Elements page 121 Specify the heaviest element that may be present in hit structures see Specifying the Heaviest Allowed Element page 121 9 2 1 Searching for Specific Elements 120 Open the Elements dialogue box Type the chemical symbols of the required element s into the input box Symbols must be separated by at least one space Alternatively hit Select from Table and pick the required elements from the Periodic Table If two or more elements are specified they must all be present The example below would find molecules or str
20. values between 60 and 60 degrees PARAMETER TORI Torsion Limits are applied after application of any selected function APPLY FUNCTION None i LIMIT From 60 to 60 Range w Value tolerance 180 See Query Options in the 3D menu for Enantiomer Inversion RENAME TORI e Alternatively the parameter may be set to a value plus or minus a tolerance In the example below the torsion has been constrained to lie within 70 degrees the tolerance of 780 the value PARAMETER TORI Torsion Limits are applied after application of any selected function APPLY FUNCTION None LIMIT Yalue j 80 l jio Range value tolerance 180 See Query Options in the 3D menu for Enantiomer Inversion RENAME TORI e A distance constraint may be applied to any pair of atoms whether bonded or not Hit OK Apply or Close ConQuest User Guide 8 amp 9 4 6 1 3D Search Options e Enantiomer Inversion see page 90 e Symmetry Check see Counting the Number of Contacts to an Atom page 106 e Number of Matches see page 90 Enantiomer Inversion 3D substructure search options are available which allow control of enantiomer inversion when analysing torsion angles In the Draw window once you have defined your geometric parameter of interest select 3D in the top level menu and Query Options from the resulting pull down menu The 3D Se
21. 224 Details of corrected or residual errors Details of non standard experimental conditions Special text strings drug activity polymorphism absolute configuration etc General remark 1 5 5 Filters Secondary Search Criteria The CSD contains a number of flags indicating the presence or absence of certain characteristics in each entry These flags may be used as secondary filters to restrict the output of searches to e g error free non disordered structures 1 6 Atoms with 3D Coordinates see page 234 R factor within preset range see page 239 Not disordered see Disordered Structures page 224 No errors see Unresolved Errors page 243 Not polymeric see Polymeric Bonds page 236 No ions No powder structures see Powder Data page 237 Only Organics see page 235 Only Organometallics see page 235 A Typical CSD Entry Bibliographic and chemical text information Refcode ACACCS Author s F 4 Cotton C E Rice G W Rice Joumal norg Chim Acta Volume 24 Page 231 Year 1977 ConQuest User Guide Chemical Diagram 3D Molecular Structure 10 Formula C10 H14 Cri 04 Name his 2 4 Pentanedionato chromium Spacegroup Hame P21 n Humber 14 Cell Parameters a 11 445 b 4 748 e 10 325 alpha 90 00 beta 91 60 gamma 90 00 Volume 560 851 Reduced Cell Parameters a 4 748 b 10 325 c 11 445 alpha 91 60 beta 90 00 gamma 90 00 Volume 560 848 ConQuest User Guide 3D exte
22. Acad Sci Ser c Chim 1948 1967 1983 1983 1983 1993 2001 1849 1877 1926 1965 1966 1971 1966 1971 1966 1971 1972 2002 2003 1972 2002 1972 2002 2003 1957 1964 1965 1968 1969 1971 1972 1995 1996 1947 1973 1974 1988 1974 1988 1989 1999 1896 1996 1997 1997 1998 2001 ConQuest User Guide C R Chim 2002 Anal Sci 1987 Anal Sci X ray Struct Anal Online 2003 J Mol Struct 1968 J Mol Struct THEOCHEM 1981 Z Kristallogr Kristallgeom Kristallphys Kristallchem 1921 1930 1954 1977 publication suspended 1945 1954 Z Kristallogr Mineral Petrogr Abt A 1930 1945 Z Kristallogr 1978 ConQuest User Guide 249 24 APPENDIX C ACKNOWLEDGMENTS The CCDC gratefully acknowledges the following copyright works which are used under licence in ConQuest and Vista for Windows bsddb 1990 2004 Sleepycat Software http www sleepycat com Software from the Independent JPEG Group 1991 1998 Thomas G Lane http www jpeg org Mesa 1999 2001 Brian Paul http www mesa3d org MetaKit 1996 1999 Jean Claude Wippler http www equi4 com metakit Numerical Python 1999 2000 2001 The Regents of the University of California http www numeric scipy org PDF and Adobe Acrobat Reader 1987 1999 Adobe Systems Inc http www adobe com Pmw 1997 2001 Telstra Corporation Limited Australia 2000 2002 Really Good Software Pty Ltd Australia http pmw sourceforge net pybs
23. Avoid unwanted bonds between two or more atoms in the substructure see Avoiding Unwanted Bonds between Atoms in a Substructure page 64 e g to specify that a pair of atoms must not be bonded to each other The usual reason for doing this is to avoid links across a ring e g to avoid finding decalin when searching for cyclodecane En ee i z c c c c we e rat AEn ae C T Cc c c e Me cyclodecane decalin e Avoid unwanted cyclic bonds to atoms outside the substructure see Avoiding Unwanted Cyclic Bonds to Atoms outside the Substructure page 65 e g to ensure that there are no rings fused or spiro linked to the substructure you have drawn e Ensure that ring systems in the substructure are isolated see Ensuring that a Ring System has no Additional Bridging or Fusion page 66 i e have no fusion or bridging other than what you have specified ConQuest User Guide 63 3 8 1 Avoiding Unwanted Bonds between Atoms in a Substructure e Select Bonds from the top level menu and Exclude from the pull down menu e Select Direct Links e Click on the atoms which must not be directly linked i e the atoms you want to prevent being bonded to one another e Hit OK e In the example below atoms 3 and 6 have been specified to form no direct links Ring Closure Direct Links nal Nn Disallow direct links between selected atoms x Note at least two atoms must be selected Does not effect explicitly drawn bonds Cu
24. Delete Selected will give a choice Click with the right hand mouse button on a blank point in the white area and pick Delete Selected or Cut from the resulting pull down menu e To delete all atoms and bonds in DRAW EDIT or ERASE modes move the cursor onto a blank point in the white area click on the right hand mouse button and pick Clear All from the pull down menu e Use Edit Undo see Undoing Mistakes when Drawing Substructures page 50 to delete an atom or bond just drawn 3 5 Drawing and Fusing Rings 3 5 1 Adding a Ring to a Blank Drawing Area e Rings may be drawn manually but the easiest way is to use the pre drawn rings in the bottom left hand corner of the Draw window O 9 Aja RingMaker Templates Ifthe desired ring is one of the four on display see above select it by clicking on its icon move the cursor into the white area then click with the left hand mouse button e Ifyou click again you will create a second copy of the ring Use Edit Undo if this is not what was wanted Click on DRAW to resume normal drawing e Ifa different ring size is required hit RingMaker type the desired ring size into the box select the required bond type hit OK then click in the white area In the example below a saturated cyclopropane ring has been defined 52 ConQuest User Guide RingMaker Ring Size 3 W Single Double Triple _j Quadruple Aromatic uf Polymeric Can
25. Draw window In the example below the current element type is chlorine c H ojnN s P F a Any More Groups Cl The current element type may be changed by hitting any of the element symbols at the bottom of the Draw window e Alternatively it may be typed into the white box at the bottom of the Draw window e Any means any atom i e an atom of any element type and is denoted by the symbol X in the drawn substructure e More displays a pull down menu Selecting Other Elements from this menu allows selection of any element in the Periodic Table Use Single Pick mode unless a variable element type is needed see Setting Variable Element Types page 56 3 6 2 Setting Variable Element Types e Atoms in a substructure may be variable e g F or Cl or Br or I e Any means any atom i e an atom of any element type and is denoted by the symbol X in the drawn substructure e There are a number of pre defined element groups e g 4B means any of Ti Zr Hf The current element type can be changed to one of the groups by typing the element group symbol into the white box at the bottom of the Draw window e The current element type see Changing the Current Element Type page 56 may be made variable by hitting the More button at the bottom of the Draw window This displays a menu from which common variable element types e g Not Hydrogen Any Metal etc can be selected Alternatively selecting Other Elements f
26. Porphyrin Combined_hitlist_1 Search Search ConQuest User Guide e To remove a search Refcode list or hitlist combination from the current ConQuest session Select it from the list of hitlists bottom right hand side of the screen Hit the Delete button underneath this list the change will appear immediately in the Manage Hitlists screen If you wish to restore this information because for example it was deleted in error Select Edit from the top level menu followed by Restore Hitlists and then select either Searches Combinations or Refcode Lists from the resulting pull down menu Deleting hitlists in this way will not delete any saved files 2 10 Starting Searches A search may be started by hitting a Search button These can be found in several different places e Hitting Search in the Draw window see Layout of the Draw Window page 47 starts a search for the substructure query currently displayed in that window not for any other query including substructure queries that may previously have been built and stored e Hitting Search in any of the dialogue boxes used to build queries e g Author Journal starts a search for the current contents of that dialogue box not for any other query that may previously have been built and stored e Hitting Search on the Build Queries screen starts a search for structures that satisfy all of the queries currently turned on i e whose icons are coloured green see Simple Que
27. Run the search e Save the 3D coordinates of the hit entries The Example e The tutorial explains how to search for the following fragment Jo C C 0 I 7A D ar ae Z where 7A F Cl Br or I QA C N or O Z any atom except H QA cannot be part of a ring Bond C O can either be single or double 168 ConQuest User Guide Menu Commands Required 1 Start ConQuest and hit the Draw button to open the Draw window 2 Draw the acetoxy structure as shown in Tutorial 1 Basic Substructure Search see page 164 Cc fA i o 3 Adda cyclopentane ring to the drawing area e Click on the saturated 5 membered ring icon at the left hand side of the Draw window i e the top left of the four rings Then click in an empty space in the white drawing area 4 Move the cyclopentane ring if necessary In a moment you will make a bond between the O atom of the acetyl group and one of the cyclopentane atoms Before doing this you may want to move the ring into roughly the right position to produce a tidy diagram To do this click on the EDIT button on the left hand side of the Draw window not the Edit button in the top level menu bar This puts you into edit mode previously you were in draw mode e Select the cyclopentane ring by pressing the left hand mouse button and dragging the cursor until the ring is enclosed in a rectangle e Move the ring to its desired position by moving the cursor into the rectang
28. To Search e Select the Unit Cell button in the Build Queries pane see Using the Unit Cell Dialogue Box page 129 Related Topics e Unit Cell Parameters see page 242 Refcode entry ID Each CSD entry has a unique identifier known as a refcode The refcode contains six letters e g ABACOF If more than one study of a compound is present in the CSD the second and subsequent entries will have two numbers after the six letters e g ABACOF01 ABACOF10 ABACOFO03 Deuterated forms of a compound have the same six letter code as the non deuterated form 238 ConQuest User Guide Stereoisomers have different 6 letter codes To Search e Select the Refcode entry ID button in the Build Queries pane see REFCODE SEARCHES page 140 e Select View Databases from the top level menu see REFCODE SEARCHES page 140 R factor The crystallographic R factor is the traditional figure of merit for crystal structures and provides a measure of how well the refined structure agrees with the experimental model Authors often also report a weighted R factor wR The value stored in the CSD is the lower of R and wR A rough guide to the quality of structure determinations 1s R factor Quality 0 01 0 03 Exceptional 0 03 0 04 Very high 0 04 0 05 High 0 05 0 07 Good 0 07 0 09 Average 0 09 0 10 Fair 0 10 0 15 Poor gt 0 15 Bad To Search e Select the Experimental button in the Build Q
29. User Guide 2 9 2 Saving and Reading Hitlist Combinations To save a combination of two hitlists ensure that the hitlist combination is selected in the Manage Hitlists screen if it is not display it by using the Results top level menu option then select Combinations from the resulting pull down menu to display the hitlist combination of your choice Pick File from the top level menu and Save Hitlist Combination or Save Hitlist Combination As in the resulting pull down menu The first of these options will only be available if the hitlist has already been saved and since modified Saved hitlist combinations will be given the extension ch which can be read back into ConQuest and displayed in View Results as if the combination had just been created and modified To read a previously saved hitlist combination pick File from the top level menu followed by Open and then select Hitlist Combination from the resulting pull down menu Loading a hitlist either when reading from a file or when viewing hitlist combinations for the first time may result in a progress window If you have previously saved hitlist combinations resulting from searches in the same ConQuest session these can be viewed by selecting Results from the top level menu followed by Combinations in the resulting pull down menu to display the search of your choice Alternatively you can read in a hitlist combination Refcode list or search saved from an earlier ConQuest
30. antiviral hypoglycaemic trypanocidal antibiotic antihyperglycemic anxiolytic hypolipidermic vaso co constrict i on ive anticancer antihypertens ion beta adrenergic hypotension vasodialt ive or ive anticholinergic antiinfective beta blocking immunosuppres s ant ive Please note that both English and American spellings are used It is advisable to search for both if you are unsure which should be used Related topics e Drug Activity see page 225 ConQuest User Guide 215 Bond Type Conventions It is necessary to understand the CSD bond type conventions in order to do accurate substructure searching For example a benzene ring in the CSD is coded using an aromatic bond type rather than alternate single and double bonds Thus a substructure search for benzene will fail unless the substructure is drawn with aromatic bonds The CSD bond types are single double triple quadruple aromatic polymeric delocalised double and pi The following conventions are used for common functional groups terminal carbonyl C 0 cyano C N cyanato O C N thiocyanato C N isocyanato N C 0 isothiocyanato N C S nitro O N 0 Problems with substructure searching are very often due to bond type issues either a misunderstanding of CSD conventions or an inconsistency in the CSD itself These inconsistencies principally apply to the structure types given below in related topics Related Topics 216 A
31. atom select Number of Bonded Atoms then select 3 T a 4 Specify nonbonded search criteria Hit the CONTACT button at the left hand side of the Draw window e Click on the O and H atoms and hit the Define button 186 ConQuest User Guide 3 to define ConQuest User Guide CONTACT lt new gt Hit Define to create contact or deselect atoms ATOM 04 ATOM H10 wv Centroid wv Centroid wv Closest Atom y Closest Atom Define Groups CONTACT CONI Modify options and hit OK when done W Inter molecular _j Intra molecular enarsied by E to fess k See Query Options in the 3D menu for Symmetry Checking Distance range From J to J A Range w Value tolerance Shorter than sum of VdW radii 0 0 Set Radii User Defined Radii None Normalisation of terminal H positions To normalise terminal H atom positions see Advanced Options after pressing the Search button This is recommended where a terminal hydrogen atom contributes to the specification or analysis of a contact Current status OFF 187 e By default the search is for intermolecular contacts which is what we want in this example e By default the search will find all contacts shorter than the sum of the van der Waals radii of the interacting atoms However in this example we want to find contacts shorter than 2 1A Click on the Distance Range radio button and typ
32. atoms are poorly defined by X ray diffraction the direction of D H bonds is usually satisfactory but the D H valence bond distances are shortened You can correct for this by normalising H atom positions e Other geometric constraints can be used to further define the non covalent interaction especially if the interaction is directional The angle D H A in a hydrogen bond prefers to be linear so some constraints on this angle may be appropriate particularly for stronger hydrogen bonds It is wise to examine typical values in the CSD before setting such geometrical constraints e Scattergrams from IsoStar distributed as part of the CSD System are valuable for assessing search constraints e Sometimes it is better to combine searches For example all H bonds involving N or O acceptors and N H or O H donors can be found with a generic search for X H X where X is assigned the variable element type N or O see Setting Variable Element Types page 56 The labels of the X atoms actually found in any interaction can be output by ConQuest so that the different types of H bonds can be separated out after searching e g in Vista see page 246 Searches for common interactions e g O H 0 sp hydrogen bonds can generate very large numbers of hits The number of hits can be reduced by either a defining the chemical environment of the groups more exactly keto O carboxylate O etc or b lowering the R factor see page 239 accepta
33. be corrected by normalising the hydrogen atom positions This involves moving the hydrogen atom along the covalent bond vector X H so as to make the X H distance equal to the average neutron diffraction value hydrogen atoms are accurately located by neutron diffraction Normalisation of hydrogen atom positions 1s available for C H O H and N H bonds the H atom will be moved along the bond vector to make the bond length equal to the average neutron diffraction value see Hydrogen Atom Location in Crystal Structure Analyses page 228 To switch it on set up the nonbonded contact search as usual and hit a Search button This opens the Search Setup dialogue box Hit the tab labelled Advanced Options and switch on the Normalise terminal H positions check box Then start the search Once you have switched on the Normalise terminal H positions option it will remain on for the rest of the ConQuest session i e for any subsequent searches you may perform unless you turn it off again Customisation of the values for C H N H and O H H normalisation is available from the Search Setup dialogue box Hit the tab labelled Advanced Options and switch on the check box labelled User Defined then hit Edit this generates a H Normalisation Setup dialogue box into which you can type the relevant values It is also possible to specify values to normalise the position of H atoms bonded to other elements ConQuest User Guide 105 Select from Current Setti
34. be numerically unstable ConQuest User Guide 13 CRYSTAL DENSITY AND UNIT CELL CONTENT SEARCHES 13 1 Typical Uses of Density and Unit Cell Content Searching Finding crystals with densities in a particular range Finding crystals with unusually high or low densities Finding crystals with specific unusual Z values Finding crystals with specific unusual Z values Finding crystals with two or more crystallographically independent molecules i e Z gt 1 Finding molecules that lie on crystallographic symmetry elements i e Z lt 1 Finding crystals containing a specific number of chemical units molecules ions etc Limiting the number of atoms in a structure e g to exclude very small structures or very large structures 13 2 Using the Z Density Dialogue Box Open the dialogue box by hitting Z Density in Build Queries Z Number of Molecules per Unit Cell see page 246 Select the required mathematical operator see Mathematical Operators page 18 and type a number into the input box In this context Molecule means the whole formula unit which may actually consist of more than one chemically discrete entity e g an ion pair or a solvated structure Z Number of Molecules per Asymmetric Unit see page 247 Select the required mathematical operator see Mathematical Operators page 18 and type a number into the input box In this context Molecule means the whole formula unit which may actually consist of mo
35. between them e g 3 7 bonds or both see Searching for Molecules Containing Chemical Groups Separated by a Specified Distance Pharmacophore Searching page 91 Select Contact if you wish to search for short nonbonded contacts e g hydrogen bonds between the substructures You will then be able to choose whether the contacts are intramolecular intermolecular or both see NONBONDED CONTACT SEARCHES page 96 Select Any if you just want the distance you have selected to be tabulated and intend to define or have already defined an intramolecular distance constraint or a nonbonded contact between other atoms in the disconnected substructures Never select Any if you do not intend to a define another distance between the two disconnected substructures and b subject that distance to either an intramolecular distance constraint or a nonbonded contact constraint If this rule is not followed the resulting search will be meaningless because only distances in the Crystal Chemical Unit see page 221 will be searched and the choice of this unit is arbitrary in some space groups Hints for Tabulating Geometries and 3D Substructure Searching Geometric parameters are most often defined to generate tables for later analysis using histograms scattergrams and statistical tests see Transferring Data to Other Programs for Analysis page 44 All required geometric parameters must be defined in the Draw window when the substructure is Co
36. coincident with a crystallographic symmetry element For example the molecule might possess a mirror plane so that half of the atoms are related to the other half by symmetry In this case the crystallographer must determine the coordinates of only 18 atoms Related Topics e Atomic Labels see page 213 e Crystal Chemical Unit see page 221 e Molecule see page 233 e Z Number of Molecules per Unit Cell see page 246 e Z Number of Molecules per Asymmetric Unit see page 247 Atomic Charge Where appropriate atoms are assigned formal charges In the CSD there is no concept of delocalised charge charges must be associated with specific atoms and must be integral Formal charges are often rather arbitrary particularly when assigned to metal atoms so their use in substructure searching is not recommended except for simple organic structures Related Topics e Chemical Diagram see page 217 Atomic Coordinates Atomic coordinates are not available for about 10 of entries in the CSD This situation usually arises for structures published as short communications in certain journals or if data has not been received from an author Atomic coordinates may be written out as fractions of the unit cell edges i e x a y b z c so called fractional coordinates or as orthogonalised Cartesian coordinates To Search to exclude entries which have no atomic coordinate data in the CSD e Select the appropriate filter in the Search
37. ensure that you will only find CSD entries for which 3D atomic positions are available Hit Start Search 7 Look at the results As soon as you start the search the ConQuest interface moves to the View Results pane After a few moments the refcodes of hit structures start to appear in the list on the right hand side Click on any structure to see its chemical diagram Click on the Detach Diagram button this allows the 2D diagram to be shown in its own window enabling the 2D diagram and any other results panes to be viewed simultaneously Now use the tabs Author Journal Chemical etc to see other types of information Rather than allowing the search to go to completion you can stop it by hitting the Stop Search button in the bottom right hand corner The blue progress bar indicates how much of the CSD has been searched so far A pop up menu asks if you really wish to stop the search as it cannot be resumed once stopped 8 View structures in 3D Click on the 3D Visualiser tab to see the currently selected structure in 3D Rotate the structure by moving the cursor in the 3D display area while pressing on the left hand mouse button Change the display style by clicking anywhere in the 3D display area with the right hand mouse button Select Display Style from the pull down menu then select a display style 9 Suppress unwanted hits 166 Suppose you don t want to keep the first hit Suppress it by clicking on the green tick
38. entry only or e all unsuppressed structures in the hit list turn on All selected entries see Suppressing Unwanted Entries page 40 Available formats are e CIF see CIF Format page 218 International Union of Crystallography format for crystal structures The check button Additional CIF data items will be switched on by default Switch on the check button for Structure data only if you do not wish to export additional text and numeric ConQuest User Guide 4 42 fields When saving all the structures in the hit list use the buttons to control whether each structure is written to a separate file or all structures are written one after another in a single file It is also possible to export information on connectivity and defined geometric parameters To export bond connectivity information switch on the check button Include Bonds This will allow _geom_bond data items to be included in the CIF To export data calculated via the use of defined geometric parameters switch on the check button Include defined parameters This will allow the inclusion of _ccdc_geom data items in the CIF Distance angle and torsion data items can all be saved It is not possible to link parameters derived from centroids planes or those resulting from combinations back to atom site labels CIFMIF see CIFMIF Format page 219 This format combines CIF crystallographic data names with chemical data names from the Molecular Information File CIFMIF has add
39. formula colour melting point etc plus additional chemical property information where provided by the publishing author e Crystal unit cell and space group information Further information such as the solvent s of crystallisation crystal habit polymorph information is also provided where supplied by the publishing author e Experimental information about experimental conditions accuracy and precision Extra details are provided where supplied by the publishing author CSD editorial notes or comments arising from the data processing are also included e g discrepancies between calculated and reported formula weights discrepancies with density etc e Diagram chemical structural diagram If the search has been for a substructure then the substructure will be highlighted in the diagram see Viewing the 2D Chemical Diagram page 31 e 3D Visualiser a 3D view of the molecule providing some basic display options see Using the 3D Visualiser page 33 e CSD Internals additional information relating to the entry e Search Overview a summary of the query or queries filter s etc 2 12 4 Viewing the 2D Chemical Diagram Each entry in the CSD has a 2D chemical structure diagram associated with it see Chemical Diagram page 217 which can be seen in the Diagram tab of View Results screen If the search has been run for a substructure then the substructure will be highlighted ConQuest User Guide 31 CCDC ConQuest 1 searchi Sea
40. hand mouse button In EDIT mode a series of atoms or bonds can be selected by clicking on each in turn while keeping the Shift key pressed down e In EDIT mode a group of atoms and bonds can be selected by clicking with the left hand mouse button on a blank point in the white area and moving the cursor while keeping the mouse button pressed down Everything enclosed in the resulting rectangular box gets selected when the mouse button is released e In any mode everything can be selected by hitting Edit in the top level menu and Select All in the resulting pull down menu In any mode the current selection can be reversed by hitting Edit in the top level menu and Invert Selection in the resulting pull down menu Everything that was selected becomes unselected and vice versa 3 4 8 Deleting Atoms and Bonds There are several methods including e In DRAW mode click with the right hand mouse button on the atom or bond to be deleted and pick Delete Atom or Delete Bond from the resulting pull down menu e Change to ERASE mode click on the ERASE button and click with the left hand mouse button on the atom or bond to be deleted e Change to EDIT mode click on the EDIT button Select the atoms or bonds to be deleted see Selecting Atoms and Bonds page 50 Then either ConQuest User Guide 51 Pick Edit from the top level menu and then Cut or Delete Selected from the resulting pull down menu Cut will delete both atoms and bonds
41. in the main ConQuest interface Drawing area see Fundamentals of Drawing page 49 Mode buttons see Modes in the Draw Window page 49 responses to mouse clicks in the drawing area will depend on which mode is active Pa er ConQuest User Guide 47 48 Area for selecting basic ring templates basic carbon rings to aid drawing see Adding a Ring to a Blank Drawing Area page 52 Area for selecting other templates molecular building blocks to aid drawing see Using Chem ical Groups and Substructure Templates page 68 Area for changing the current element type see Changing the Current Element Type page 56 and bond type see Changing the Current Bond Type page 61 Buttons for starting a search storing a substructure query or cancelling everything that has been done Area for listing displaying and editing 3D see Geometric Parameters page 82 and nonbonded contact parameters see Nonbonded Contacts between Atoms page 96 ConQuest User Guide 3 3 Modes in the Draw Window The five buttons down the left hand side of the Draw window are mode buttons which affect what happens when the mouse is used in the drawing area 3 4 DRAW Click on this button when you want to draw a substructure The DRAW mode button is active if coloured white activate if necessary by clicking on it EDIT Click on this button when you want to perform editing tasks such as moving rotating or resizing substructures or selecting a
42. l c c iaa P a 7 3 Specify the central C atoms to be acyclic e Select Atoms from the top level menu Cyclicity from the pull down menu and Acyclic from the next menu e Click on the two central carbon atoms Select atoms to which this property is to be applied then hit 1 7 2 nn A Atom Property 2 T 6o Acyclic 9 Sy we 14 wr Sy an Ga G Cc Current Selection C c8 ieg 10d 3 Cancel Done Hit Done in the Select Atoms pop up 180 ConQuest User Guide 4 Specify the number of attached hydrogens e Select Atoms from the top level menu Hydrogens from the next menu and Other from the third menu e Type 2 into the Hydrogen Count box and hit OK e Click on the two central carbon atoms 2 ox A Atom Property a Se iq Hydrogens 1 2 Select atoms to which this 3 c 5 c poparty is to be applied then hit SN co Done 54 wee 14 a C c Current Selection c cs j ec IN Sis e Hit Done 5 Define the centroids of the phenyl rings e Click on the ADD 3D button e Click on all six atoms of one of the phenyl rings and hit the Define button next to the word Centroid This defines the centroid of the ring named by default CENTI Options To construct Parameter Object Select atoms main window or object list below Current Selection valid Parameters Defined Objects CENTI Valid Objects Centroid
43. object list below Hit Define to construct Parameter Object Valid Parameters All Selected Define Torsion Define Valid Objects Define Define Delete a any More Groups C Bond Reset Done e Define the C C C C torsion angle by hitting the Define button next to the word Torsion e Hit the Options button e Type the required limits From 90 to 90 into the 3D Limits and Options window The specified torsion angle range is displayed graphically PARAMETER TOR1 Torsion Limits are applied after application of any selected function APPLY FUNCTION None LIMIT From 30 to 30 Range w Value tolerance 180 See Query Options in the 3D menu for Enantiomer Inversion RENAME TORI e Hit OK in this window and then Done in the Geometric Parameters window ConQuest User Guide 183 9 Run the search e Hit Search set the filters R factor lt 0 1 Not disordered No errors and Not polymeric and then hit Start Search e View some of the hits in the 3D visualiser to confirm that the search is only finding structures in which the phenyl rings are cis e Use the arrows on either side of the boxes labelled Param and Objects to control whether or not distances angles centroid and planes are displayed E Show substructure matches a Param ajar Objects pal e A file of the parameters yo
44. of atoms by least squares fitting Pluto A CCDC program for visualising crystal and molecular structures hydrogen bonding networks etc Only available for Unix Linux Pluto is available as a free download from http www ccdc cam ac uk free_services rpluto Polymeric Bonds Two kinds of polymers are found in the CSD e Coordination polymers in which bridging between metals causes an indefinite extension of the structure e Organic polymers i e molecules identified by the multiple repetition of one of more types of groups or atoms linked to each other e g poly vinyl chloride Both may be regarded as characterised by a repeating unit Bonds between repeating units are assigned the polymeric bond type To Search to exclude structures containing polymeric bonds e Select the appropriate filter in the Search Setup dialogue box see Applying Filters page 143 Related Topics e Chemical Diagram see page 217 e Bond Type Conventions see page 216 e Delocalised Double Bonds see page 223 236 ConQuest User Guide e Metal Carboxylates see page 232 Polymorphism Polymorphism is the occurrence of two or more crystalline forms of the same substance CSD entries known to be polymorphic contain comments which include the word polymorph e g non triboluminescent polymorph To Search e Select the All Text button in the Build Queries pane then click on the Required Fields tab and select the keyword Polymorph from the
45. on its Refcode entry ID see page 238 in the list on the right hand side of View Results Alternatively type the code into the box above the list e Only one structure can be viewed at a time e The structure currently on display is highlighted in orange BASLIQ Analyse Hitlist y AECLPADI AECLPAIO VY ANAPHS y AQFYMG V AQMEDA y BACSON y BACSONI0 y BADTEX y BADTEX01 y BADTEXIO y BALMGT y BASLIQOI y BASLIQIO y BAWGOV y BAWZII y BAXFUB y BAYJIU y BAYJOA y BEKCID y BEWFOY lt lt gt gt The buttons labelled lt lt and gt gt can be used to step through the structures backwards or forwards one by one e Caution clicking on the green tick next to an entry in the hit list will suppress that entry see Suppressing Unwanted Entries page 40 This means it will not be written out when results are saved in some file formats 2 12 3 Viewing Information for Individual Structures Information for the currently selected entry i e the one highlighted in orange in the View Results hit list is divided into sections Each section can be displayed by clicking on the appropriate tab at the left hand side of the View Results screen To detach the selected results pane into its own window click on the Detach button This enables the selected pane and any other panes in View Results to be viewed simultaneously The following results panes are available All Text All CSD information fields that are di
46. opts experimental Details of the structure determination such as R factor density are written to the tsv or txt file export opts crystallographi C Crystallographic information e g cell parameters space group is written to the tsv or txt file export opts internal Data of internal relevance to CCDC e g accession date additional notes are written to the tsv or txt file include disordered atoms export opts Exports all atoms including those identified by the CSD editors as being disordered export opts largest molecule only Exports the largest chemcial unit i e molecule in the structure only export params tsv Exports geometric parameter data as tab seperated values to the file lt jobname gt tsv 160 ConQuest User Guide CSV Exports geometric parameter data as comma seperated values to the file lt jobname gt csv vista Exports geometric parameter data as VISTA files to lt jobname gt tab lt jobname gt fgd lt jobname gt fgn sum Exports geometric parameter data as a QUEST summary file to lt jobname gt sum 20 7 The above options correspond to the export formats available in GUI ConQuest see Saving Individual Structures and Lists of Structures page 41 For tab and txt the default is to output bibliographic chemical experimental
47. page 216 e Chemical Diagram see page 217 e Metal Carboxylates see page 232 e Metal Metal Bonds see page 232 e Pi Bonds see page 236 e Polymeric Bonds see page 236 e Variable Bond Type see page 246 Density This is the density of the crystal calculated from the reported chemical formula and unit cell data using the relationship Density 1 66 x formula weight x Z unit cell volume where Z is the number of molecules in the unit cell To Search e Select the Z Density button in the Build Queries pane see Using the Z Density Dialogue Box page 131 ConQuest User Guide 223 Deposition Numbers Many journals have an arrangement with the CCDC whereby the author deposits the crystallographic data at the CCDC in advance of publication and receives a 6 digit CCDC deposition number e g CCDC 103296 which is printed in the paper The number is stored in the corresponding CSD entry and is a useful search term for finding the entry In certain cases journals print their own deposition codes e g e IUCR bk1432 used for Acta Cryst sections B and C e TUC9900104 used for CIF Access papers in Acta Cryst Section C e CCDC 186 456 used by the Royal Society of Chemistry 186 is the CCDC journal identifier for J Chem Soc Dalton Transactions e CSD 400922 used in the data depository maintained by FIZ Karlsruhe To Search e Select the Author Journal button in the Build Queries pane see CCDC number deposit
48. page 224 When coordinates for two alternative sites are reported those corresponding to the site of minor occupancy are suppressed in the CSD If a set of atoms is disordered equally over two sites one set is arbitrarily retained and the other is suppressed Disordered parts of structures tend to be very imprecise and should not be used for geometrical analysis In many cases however only the solvent molecules in a structure are disordered and the molecule of major relevance is well characterized Unresolved Errors see page 243 If a search yields very few hits it may be worth relaxing the conditions to allow entries with unresolved errors The errors may relate to irrelevant parts of the structures such as solvent molecules Average e s d of C C Bonds see page 214 Structures with average e s d lt 0 005A are of high experimental quality Structures determined by neutron diffraction are useful because the hydrogen atom positions are much more accurate than those in X ray structures ConQuest User Guide 15 GENERAL TEXT SEARCHES 15 1 Typical Uses of Text Searching Find crystals of a specific colour Find structures whose absolute configuration was determined by X ray methods Look for the words drug activity agent etc to find biologically pharmaceutically or agrochemically active molecules Search for particular experimental conditions such as neutron synchrotron powder Find polymorphs by searching for the word polymorph
49. scrolling list see Specifying Required Fields page 137 Note that this will retrieve hits only where polymorph information is available Powder Data A comment is included if a structure has been determined by powder diffraction e g powder data This information will be included in the Extra Information field under the Experimental tab in the View Results window of ConQuest To Search e Select the All Text button in the Build Queries pane see All Text Searching page 135 PreQuest A CCDC program which allows users to convert their own crystal structures to CSD format and hence create a database of in house structures This database can then be viewed and searched with ConQuest Private Communications The CSD contains many private communications In such entries the journal name is Private Communication There will be an indication of the source of the structure e g Contribution from Department of Chemistry University of Delaware Newark DE 19716 USA To Search e Select the Author Journal button in the Build Queries pane see Journal Name page 114 Protein Data Bank The Protein Data Bank is maintained by the Research Collaboratory for Structural Bioinformatics http www rcsb org and is the single international repository for the processing and distribution of 3D macromolecular structure data primarily determined experimentally by X ray crystallography and NMR ConQuest User Guide 237 Reduced Cell Parameters
50. shown to the right of the Define all menu e g 12 selected in the screenshot above To define all geometric parameters described by manually selected atoms in a substructure e Draw the substructure as normal then click on the ADD 3D button e Select the atoms that make up the parameters of interest then click on the Define button next to the All Selected option e This will allow all bond distances angles and torsions defined by the selected atoms to be tabulated e Whichever option is used above geometric parameters are selected by choosing the relevant geometric parameter from the Define all pull down menu and clicking on the Values radio button Further data may also be output depending on the item chosen in the Define all menu e For atoms the Atom label Atomic number Atomic radius VdW radius or Number of connected atoms can be defined for output by clicking on the radio button next to the relevant text Note that the output value for Number of connected atoms 3D reflects the number of bonded atoms in the 3D structure not the 2D diagram Thus if H atom positions have not been determined for the structure e g the Os atom in WATWIX or a particular atom e g the Re atom in VUDSOC10 the bonds to the H atoms will not be included in the Number of 84 ConQuest User Guide connected atoms tabulated value e For bonds and angles values for the following derived parameters can be defined by selecting the radio button next
51. styles is offered wireframe capped stick ball and stick and space 34 ConQuest User Guide filling Also the display of hydrogen atoms can be switched on or off e To change the display style of the whole molecule or unit cell right click anywhere in the visualiser box Select Display Style from the resulting pull down menu and then pick the required style e To change the style of just a few atoms select them by clicking on them with the left hand mouse button while keeping the Shift key pressed down Then right click anywhere to get the pull down menu hit Display Style and pick the required style e To increase the thickness of the lines used for the bonds in wireframe style right click anywhere in the visualiser area to get the pull down menu select Settings and pick Thicken Wireframe e Right click anywhere in the visualiser area to get the pull down menu select Settings and pick Show Circles for Aromatics to distinguish aromatic rings e Drag the right hand mouse button while keeping the Shift key depressed to change the field of view i e to go from orthographic projection the default to perspective projection with increasingly large viewing angles e Right click anywhere in the visualiser area and select Display Hydrogens to switch the display of hydrogen atoms on and off e Right click anywhere in the visualiser area and select Display Disordered Atoms from the pull down menu to control the display of atoms that have been id
52. substructure Co will create the following 58 a Pe mf H 1 OH To add hydrogens to all atoms go to DRAW or EDIT mode click on Atoms in the top level menu hit Hydrogens in the resulting pull down menu then hit Generate followed by All Atoms To add hydrogens to one or more specified atoms go to EDIT mode select the required atoms see Selecting Atoms and Bonds page 50 click on Atoms in the top level menu hit Hydrogens in the resulting pull down menu then hit Generate followed by Selected Atoms Alternatively go to DRAW or EDIT mode click on Atoms in the top level menu hit Hydrogens in the resulting pull down menu then hit Generate followed by Selected Atoms Click on the atoms to which you want to add hydrogens and hit Done Alternatively go to DRAW or EDIT mode right click on an atom select Hydrogens from the resulting pull down menu and Generate from the next menu To remove hydrogens go to DRAW or EDIT mode click on Atoms in the top level menu hit Hydrogens in the resulting pull down menu then hit Clear followed by All Atoms or Selected Atoms You can remove hydrogens from a particular atom by right clicking on the atom and selecting Hydrogens and Clear from the resulting pull down menus ConQuest User Guide e Occasionally the program may assign the wrong number of hydrogens to an atom This is especially likely for hydrogen bridged metals the oxygen atoms of metal coordinated alco
53. the CSD For these reasons the default and safest mode of operation for the 3D search routines is exhaustive fragment searching the default setting However in some special cases you may wish to alter this default setting 90 ConQuest User Guide e In the Draw window once you have defined your geometric parameter of interest select 3D in the top level menu and Query Options from the resulting pull down menu The 3D Search Options dialogue box can only be opened when there is a substructure in the white drawing area and you have defined a geometric parameter The 3D Search Options dialogue box enables you to select Find only one matching fragment from Number of Matches Enantiomer Inversion Symmetry Check Number of Matches amp search involving 3D parameters will attempt to find all unique fragments matching your query For some searches it may be necessary to restrict the search to finding just one matching fragment in each entry so that it will complete in a reasonable time Turn on the option below if you want to find only the first matching fragment in each entry It is likely that other valid matches will not be located E Find only one matching fragment Defaults Cancel OK J 4 7 Searching for Molecules Containing Chemical Groups Separated by a Specified Distance Pharmacophore Searching e Draw two or more disconnected fragments e g i Y a e If necessary create any required ob
54. the CSD more current between each major release of the CSD System The following URL will take you to the download page which describes what you need to do http www ccdc cam ac uk products csd_system conquest csd_updates e You will be required to enter your Site Code and Confirmation Code in order to download an update e The updates will need to be placed in the same directory as your CSD database files for more details see CSDS Release amp Installation Notes Each update will be shown separately in the View Databases menu e The update packages can be searched either with the main database or separately as desired this is controlled via options in the Search Setup dialogue box Search Setup Search Name search1 Available Databases CSD version 5 27 November 2005 CSD version 5 27 updates Feb 2006 You can search complete database s or a subset e g hits found in a previous search Select Subset where this query is true Single query being used Search will find structures Filters Advanced Options 3D coordinates determined Rfactor lt 0 05 Vv Vv Not disordered No errors Not polymeric _ No ions No powder structures 4 Only Organics gt Start Search 150 Cancel ConQuest User Guide 19 USING CONQUEST FOR TEACHING CLASSROOM CONQUEST 19 1 Main Features of Classroom ConQuest Classroom ConQuest is a version of ConQ
55. the check boxes next to List A and List B should be deselected these can enable a combination of hitlists to include suppressed entries see Suppressing Unwanted Entries page 40 The three check boxes listed on the left hand side of the Manage Hitlists screen labelled common to List A and List B in either List A or List B in List A but not in List B represent the logical operations available for combining search results Select common to List A and List B and hit OK The results of combining these two hitlists search and search2 are given in the Hitlist Overview pane and indicate that 5 entries are common to both searches The default name for the hitlist combination combination 1 appears under Name on the bottom right hand side of the screen along with the searches used to create this hitlist combination File Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results Combine Hitlists Hitlist Overview Combination Name combination2 combination 5 Entries _ Full overview W Single line List A List B searchl and search search search Include deselected entries in _j Lst d List B Generate a List of Entries common to List A and List B in either List A or List B in List A but not in List B OK combination1 search Search search Search Delete Rename Notes View ConQuest
56. the cursor onto the desired atom the atom will go red while keeping the mouse button depressed then release the button 3 4 5 Drawing a Bond between Two Existing Atoms e Ensure you are in DRAW mode e Move the cursor onto the first atom the atom will go red e Press down the left hand mouse button e Move the cursor onto the second atom the atom will go red while keeping the button depressed then release the button 3 4 6 Undoing Mistakes when Drawing Substructures e Pick Edit in the top level menu and Undo in the resulting pull down menu to undo the last action performed e Alternatively move the cursor to a blank point in the white area click the right hand mouse button and select Undo from the pull down menu e If necessary Edit Undo may be used several times in a row to undo a sequence of actions one by one 3 4 7 Selecting Atoms and Bonds e Selection of atoms or bonds is useful for assigning properties such as charge element type bond type for moving substructures around the drawing area for cutting and pasting 50 ConQuest User Guide e A selected atom is coloured orange and enclosed in a box If the two atoms at either end of a bond are selected then the bond itself is selected too In the example below the N O and Cl atoms and the N O bond are selected JA Atoms and bonds may be selected in several ways In EDIT mode an individual atom or bond can be selected by clicking on it with the left
57. to the appropriate text Sum Average Minimum or Maximum e For torsions values for the following derived parameters can be defined by selecting the radio button next to the appropriate text Sum Minimum Maximum or Use absolute value e Constraints can be set for individual bond angle and torsion measurements but not for Sum Average Minimum Maximum or Absolute values e If you delete a geometric parameter or bond included in a Sum tabulation ConQuest will issue the following warning T a a A nnn al Q The following parameters involve calculation of the items just deleted SUM2 angle SUMI distance SUM3 torsion Do you want these parameters to be updated to exclude the deleted items Yes No e Clicking Yes will delete the parameter from the 3D Parameters list and the Sum calculation and the Sum calculation will be updated Clicking No will delete the parameter from the 3D Parameters list but retain the bond angle or torsion in the Sum calculation e It is quite easy to generate a lot of parameters using the All Parameters or All Selected options The following features of the 3D Parameters list in the main Draw window may help when manipulating parameters in these situations e Ifthe Shift key is pressed whilst clicking on 3D parameters a continuous range of items will be selected deselected e If the Control key is pressed whilst clicking on 3D parameters individual items will be selected des
58. used to find structures which simultaneously satisfy two or more conditions e g structures that contain magnesium and a benzene ring and were determined at a temperature below 273K Build each query separately and store Go to the Build Queries screen Click on the check boxes labelled use this query or on the query icons themselves to turn each query on or off as desired Hit the Search button bottom left hand corner The resulting search will find structures that satisfy all of the queries that are turned on The example below will find structures that contain magnesium and a benzene ring and were determined at temperatures below 273K Query 3 space group P21 c is turned off so it is ignored ConQuest User Guide Fle Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results Draw Elements Mg Search on Sum of molecules Peptide Allow other elements Yes Author Journal Compound Name Elements Formula Space Group Space Group P21 c and equivalent space groups Unit Cell ZDensity Temperature lt 273 K Experimental All Text Refcode entry ID Search Reset 2 8 3 Complex Query Combinations The Combine Queries screen can be used to find structures that satisfy a logical combination of queries e g structures which contain magnesium or a benzene ring do not crystallise in space group P21 c and were determined at a temperatu
59. wf 0 n 5 ef Fc vl a e Hit Define This defines a group called GRP which contains the atoms you have selected the N and H atoms in the above case e Pick all the required atoms in the second group ConQuest User Guide 101 CONTACT lt new gt Hit Define to create a group or deselect atoms ATOM ATOM a Defined Groups ce es ERPI Define Delete Close r Current Selection 05 N1 H o Nf 3 Pf Fl al ay e Hit Define This defines a second group GRP2 containing in the above example the N and O atoms of the ring e Select GRP and GRP2 from the Nonbonded Contact Definition pop up e Specify whether the search is to be based on the distance between the centroids of the two groups see Searching for Chemical Groups whose Centroids are Separated by a Specified Distance page 102 or the distance between their closest atoms see Searching for Chemical Groups whose Closest Atoms are Separated by a Specified Distance page 104 5 3 2 Searching for Chemical Groups whose Centroids are Separated by a Specified Distance Define the two groups see Defining Groups for Use in Nonbonded Searching page 101 e Select both of the groups in the Defined Groups list box and ensure that the Centroid check buttons are switched on 102 ConQuest User Guide H 0 isd E a E0 ConQuest User Guide CONTACT lt new gt Hit Define to create contact or deselect atoms grou
60. 6 particularly for groups that can be drawn in several valence bond forms e g Azides see page 214 Drawing substructures with incorrect bond types is the usual reason for getting fewer hits than expected If you are unfamiliar with chemical substructure searching try a few simple searches e g for 6 membered carbocyclic rings 4 coordinate transition metals Finding exact structures requires complete definition of the target molecule including H atoms If the CSD does not contain the target then relax the H atom specification to see if simple derivatives are present In an initial search do not over specify the substructure e g in terms of allowed substitution It is better to get too many hits and then impose tighter chemical constraints Let the database tell you what it contains If you wish to specify an unsaturated bond but are uncertain as to how it is coded then use a variable bond type incorporating double or aromatic or delocalised double bonds see Variable Bond Type page 246 If you are unsure of the bond type which might have been used in the CSD for a particular substructure use the bond type Any and examine the bond types in the hits generated to formulate a more precise query In many cases the pattern of bonded atoms is sufficiently specific that close attention to bond types adds little to the search specification This is particularly true if elements other than C N or O are specified ConQuest User Guide
61. 77 78 In tautomeric situations the crystal structure will contain a specific tautomer The safe procedure is to formulate the principal tautomers and search for them all Atomic Charge see page 212 must be associated with specific atoms in a structure The concept of delocalised charge is not used in the CSD We do not recommend users to specify charges on transition metal atoms since the assignment can be rather arbitrary The CSD Element Group Symbols see page 225 can be used to retrieve families of substructures e g halogeno derivatives complexes of a specific ligand with any transition metal etc You may also define your own element group s see Setting Variable Element Types page 56 The following situations may cause searches to run slowly e Substructures that contain only the most common elements C N O connected by single or any bond types e Substructures that contain one or more locally symmetric units e g t butyl e Searches for large gt 12 membered rings especially if they are carbocyclic Searches may produce zero hits or far fewer hits than expected due to e Chemical errors in the search specification so check your query carefully e Drawing a resonance hybrid that differs from the CSD convention e Over specification of the search substructure ConQuest User Guide 4 TABULATING GEOMETRIES 3D SUBSTRUCTURE SEARCHES 4 1 4 2 Typical Uses for 3D Substructures Generating geometry tables for l
62. CT SEARCHES see page 96 PEPTIDE SEARCHES see page 108 AUTHOR AND JOURNAL SEARCHES see page 113 COMPOUND NAME and Chemical class SEARCHES see page 116 CHEMICAL ELEMENT SEARCHES see page 120 CHEMICAL FORMULA SEARCHES see page 123 SPACE GROUP AND CRYSTAL SYSTEM SEARCHES see page 126 UNIT CELL SEARCHES see page 129 CRYSTAL DENSITY AND UNIT CELL CONTENT SEARCHES see page 131 SEARCHES FOR EXPERIMENTAL DETAILS see page 133 GENERAL TEXT SEARCHES see page 135 REFCODE SEARCHES see page 140 FILTERS SECONDARY SEARCH CRITERIA see page 143 VIEWING and SEARCHING IN HOUSE DATABASES DATABASE SUBSETS and Previous CSD Versions see page 145 19 20 21 22 23 24 USING CONQUEST FOR TEACHING CLASSROOM CONQUEST see page 151 RUNNING ConQuest IN BATCH MODE see page 153 TUTORIALS see page 164 APPENDIX A GLOSSARY AND TECHNICAL DETAILS see page 208 APPENDIX B CHANGES IN JOURNAL NAMES see page 248 APPENDIX C ACKNOWLEDGMENTS see page 250 ConQuest User Guide 1 THE CAMBRIDGE STRUCTURAL DATABASE CSD 1 1 Chemical Coverage of the CSD The CSD contains X ray and neutron diffraction analyses of carbon containing molecules having up to 1000 atoms including hydrogens e Organics e Compounds of the main group elements e Organometallics e Metal complexes The CSD covers peptides of up to 24 residues higher oligomers are covered by the Protein Data Bank see page 237 The CSD covers mono di and tri nu
63. Chem Ber 123 485 1990 Menu Commands Required 1 Start ConQuest and hit the Author Journal button 2 Specify the journal reference e It is not necessary to type in all of the authors journal name volume number page number and year just the journal volume and page would be enough but we will do them all for illustrative purposes 3 Specify the authors names e Type H Braunschweig into the Authors Names box there must be no blank space between the initial and the surname Authors Names New Box H Braunschweiq _4 Required format F H Allen O Hara Murray Rust etc Brown will hit Browning unless Exact surname is selected e Only one name can be typed into each box so hit the New Box button and type in the second author P Paetzold 198 ConQuest User Guide Authors Names New Box H Braunschweig zf P Paetzold a Required format F H Allen O Hara Murray Rust etc Brown will hit Browning unless Exact sumame is selected e Hit New Box again and type R Boese into the third box e Author names are input to the CSD as they appeared in the paper or in the deposited data if received as a Private Communication 4 Specify the journal name volume page and year e The journal name that you specify must match exactly i e character for character the name that is stored in the CSD The safest way of specifying journals is therefore to pick them from the li
64. ConQuest 1 12 User Guide and Tutorials 2010 CSDS Release Copyright 2009 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System CSD System comprising all or some of the following ConQuest Quest PreQuest Mercury Mercury CSD and Materials module of Mercury VISTA Mogul IsoStar SuperStar web accessible CSD tools and services WebCSD CSD Java sketcher CSD data file CSD UNITY CSD MDL CSD SDfile CSD data updates sub files derived from the foregoing data files documentation and command procedures each individually a Component is a database and copyright work belonging to the Cambridge Crystallographic Data Centre CCDC and its licensors and all rights are protected Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence In particular e The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location e The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re distribut
65. Current Selection N1 CENT2 Valid Parameters 3 ies Define Define Defined Objects All Parameters Valid Objects Vector Define Dummy Point Define ri Centroid Define mee Delete Groups N Bond Single Reset Bone e Hit OK in the resulting pop up window to specify that the defined distance is intramolecular i e both the trimethylammonium group and the carbonyl group must be in the same molecule CHOOSE DISTANCE TYPE Intramolecular Distance Select this option to calculate distances between these fragments but only if they are in the same molecule Contact Select this option to find non bonded interactions between these fragments Any If you select this option then the distance calculated may be arbritarily calculated for some entries unless you define a Contact or Intramolecular distance between these fragments 5 Specify the required distance range ConQuest User Guide 193 e Hit Options e Type 5 0 in the From box and 5 8 in the to box e Hit OK PARAMETER DIST1 Distance Modify options and hit OK when done Hit Create to search CONTACT Create crystal structure for e g short non bonded interactions LIMIT From 5 0 to A Range w Value tolerance WE Fragments must be in the same molecule Separated by f to 999 bonds RENAME prsti
66. Excel to transfer data to Vista or Excel 2 20 2 Saving Data for Later Analysis in Vista Excel etc Data fields and 3D parameters for unsuppressed hit structures see Suppressing Unwanted Entries page 40 can be saved to a file for later analysis e Select File from the top level menu and then Export Parameters and Data from the resulting pull down menu this generates the Export Files dialogue box Export Files Sisal x Selectthe items you wish to include from the choices below Filetype Vista tab i Field Separator V Include Defined Parameters Crystal data l Rfactor J Space Gp Symbol J Space Gp Number M No of Coordinates J Z2 Value M ZPrime J Study Temp J Cale Density Cell data B Tb ES M Alpha l Beta l Gamma M Cell Volume M Reduced Cella J Reduced Cell b J Reduced Cell c M Reduced Cell Volume J Reduced Cell Alpha J Reduced Cell Beta Reduced Cell Gamma Other M Publication Year J No of Chemical Units J Compound Name 0 Reset Cancel Save 44 ConQuest User Guide e Select the File type you wish to save e Vista tab for viewing data in Vista Spreadsheet spr to save a file where data items for each entry are on a single line separated by a character selected from the Field Separator menu This allows data to be saved for input to spreadsheet packages such as Excel If 3D parameters were defined in a substructure search the option of saving a lega
67. Fields searches can be combined in an AND search within the All Text dialogue box The following search will return all entries containing the keyword fluorescent and information present in the Natural Source field Text Search Required Fields Text Search Required Fields New Box Not all CSD entries have data present in the fields listed below Either select from list or enter in box es below To retrieve only those entries where data is present for a particular absolute configuration iN uorescent Sd field select it and Add it to the Required Fields list acicular activity agent air sensitive i ivi Natural source eee lt Remove Optional Fields Required Fields Radiation source colorless f Recrystallisation solven 5 Sensitivity You can type partial or complete word s If two or more words are typed into the same box the search will be for the exact phrase specified To find entries containing either a keyword e g fluorescent or keywords or the presence of information content in a CSD field e g Natural Source information create and store separate queries for each keyword field and combine them see Complex Query Combinations page 21 15 3 Hints for All Text Required Field Searching 138 Use of the All Text tab will cause all of the textual information to be searched This includes some information which can be searched more quickly and effectively through
68. Hf 5B V Nb Ta 6B Cr Mo W 7B Mn Tc Re 8B Fe Co Ni Ru Rh Pd Os Ir Pt 8X Fe Ru Os 8Y Co Rh Ir 8Z Ni Pd Pt 1M 1A 2A 2M Al Ga In TI Ge Sn Pb Sb Bi Po 3M IM 2M 4M IM 2M TR LN AN ce all metallic elements NM non metallic elements Any all elements R any alkyl group 1 e C or H 226 ConQuest User Guide TR all transition metals but not the lanthanides or actinides IR the first row transition metals i e Sc to Zn 2R the second row transition metals i e Y to Cd 3R the third row transition metals 1 e La to Hg not the lanthanides L the lanthanides 1 e Ce to Lu but not including La AN the actinides i e Th to Lr but not including Ac FDAT Format FDAT is a file format used for storing the crystallographic data contained in an entry Its use is no longer recommended but as many people have written programs that read the format it is still available as an output option Flack Parameter This is a parameter Flack Acta Cryst A39 879 1983 that can be used in the determination of Absolute Configuration see page 210 Related Topics e Absolute Configuration see page 210 Habit Crystal habit 1 e the shape of the crystal such as needle or plate is stored for some entries The most common words or phrases used to describe habit are included in the scrolling list in the All Text dialogue box see All Text Searching page 135 To Search e Select the All Text button in the Build Queries pane click o
69. Quest User Guide Ring Closure Direct Links Disallow direct links between selected atoms Note at least two atoms must be selected Does not effect explicitly drawn bonds Current Atom Selection 21 C2 C3 C4 C5 C6 Select All Deselect All e This query would not find any of the following C G ZN DN C T E c e ery er On ae ie a Cc bona we S C G ms ie E EN AN oe ee el a en al c i c C ec C C borta i 3 9 Specifying Variable Points of Attachment If you wish to search for both o bromo chlorobenzenes and m bromo chlorobenzenes for example then you can do this in a single search by specifying the o and m positions as a variable point of attachment for the bromine atom e Having drawn for example a chlorobenzene fragment and a Br in the Draw window select Bonds from the top level menu and Variable Attachment from the resulting pull down menu This generates a Variable Points of Attachment dialogue box ConQuest User Guide 67 Fle Edit Atoms Bonds 3D Options Help Select the fixed atom and atoms Next Atom Br 3D Parameters to which it may be attached Next Bond Single Options Delete Contacts Select Atom to Variably Attach Bd Select Points of Attachment Options c5 C6 J Delete Bond type Single Reset Cancel OK Templates e Select the atom having a variable point of attachment i e B
70. Results from the top level menu followed by Refcode Lists in the resulting pull down menu to display the Refcode list of your choice Alternatively you can read in a Refcode list search or hitlist combination saved from an earlier ConQuest session by picking File from the top level menu followed by Open and then select Recent Files from the resulting pull down menu ConQuest User Guide 17 FILTERS SECONDARY SEARCH CRITERIA 17 1 Typical Uses of Filters Filters are secondary search criteria used to restrict more general searches on the basis of for example precision whether disorder is present whether there are unresolved errors in the structure or whether the structure is organic or organometallic 17 2 Applying Filters e All displayed filters see Default Filter Settings page 144 are listed in the Search Setup dialogue box which is displayed every time a search is requested e Click on the check button next to a filter to change its setting In the example below the filters R factor lt 0 05 and Not disordered are turned on i e will be used in the search about to be started the others are turned off Current Filter Settings J 3D coordinates determined E Rfactor lt 0 05 v lt 0 075 v 01 W Not disordered No errors Not polymeric J No ions _ No powder structures l E Only OK Cancel Reset When the Search Setup dialogue box is opened for the second and subsequent searches in
71. STMET see page 232 Missing Atoms see page 233 Mol2 Format see page 233 Molecule see page 233 Neutron Diffraction see page 233 No Errors see page 233 No Ions see page 234 Nucleic Acids Database see page 234 Number of Atoms with 3D Coordinates see page 234 Number of Chemical Units molecules ions etc see page 234 Occupancy Factor see page 234 Only Organics see page 235 Only Organometallics see page 235 pdb Format see page 235 Physical and Chemical Properties see page 235 Pi Bonds see page 236 Planes see page 236 Pluto see page 236 Polymeric Bonds see page 236 Polymorphism see page 237 Powder Data see page 237 PreQuest see page 237 Private Communications see page 237 Protein Data Bank see page 237 Reduced Cell Parameters see page 238 Refcode entry ID see page 238 R factor see page 239 Rogers Parameter see page 239 ConQuest User Guide 209 SD Format see page 240 Sohncke Groups Chiral Space Groups see page 240 Source of Crystal see page 240 Space Group see page 240 Temperature Factor see page 241 Temperature of Structure Determination see page 241 Torsion Angles see page 242 Unit Cell Parameters see page 242 Unresolved Errors see page 243 Van der Waals Radii see page 243 Variable Bond Type see page 246 Variable Element Type see page 246 Vectors see page 246 Vista see page 246 Z Number of Molecules per Uni
72. Saving Visualiser Images page 38 e Save your current visualiser settings for use in subsequent ConQuest sessions see Saving Visualiser Settings page 38 2 13 1 Visualiser Basics e Hit 3D Visualiser in View Results to see the currently selected structure in 3D e Use the mouse buttons to move the molecule e Right click anywhere in the visualiser area to produce the menu for measuring geometry changing display styles and generating packing diagrams 2 13 2 Rotating Translating and Scaling e Movement Rotate by moving the cursor around in the 3D window while keeping the left hand mouse button pressed down Rotate around the z axis the axis perpendicular to the screen by keeping the left hand mouse button and the Shift key pressed down Translate by moving the cursor in the 3D window with the centre button depressed requires 3 button mouse e Scale Zoom in or out by moving the cursor up and down in the 3D window while keeping the right hand mouse button pressed down e Reset Right click anywhere in the visualiser area and select Reset View to set the scale and orientation back to the default e If you are using a display style other than wireframe you can increase the speed of rotation translation or scaling by selecting Wireframe During Move from Settings the display style will automatically switch to wireframe when you move the molecule 2 13 3 Changing Display Styles and Display of Hydrogen Atoms e A choice of four display
73. Setup dialogue box see Applying Filters page 143 Related Topics e CIF Format see page 218 e CIFMIF Format see page 219 e COORD Format see page 221 e FDAT Format see page 227 e Mol2 Format see page 233 212 ConQuest User Guide e pdb Format see page 235 e SD Format see page 240 Atomic Displacement Parameters ADPs Atomic displacement parameters are not currently available in the CSD Atomic Labels Each atom in a structure has a label which consists of the element symbol followed by a number and sometimes a prime CSD atom labels are normally identical to or closely related to those used by the author Atoms generated by symmetry i e not belonging to the asymmetric unit will have an extra letter at the end of their label which indicates which symmetry operation was used Related Topics e Crystal Chemical Unit see page 221 Authors Names Typical author names are e A B Smith e A T McPhail e J J MacDougall e C J O Connor e P Murray Rust e F de Bergevin e J P Dubois e W Van Riel e D van der Helm e Yu T Struchkov Authors names are stored exactly as given in the paper with forenames abbreviated and stored as initials e g FAllen and FH Allen may both occur The use of initials in queries can therefore result in a loss of relevant hits Some author names may include dynastic tags e g S S Simons Junior A J Arduengo III Authors names are stored in the CSD without umlaut
74. The program will not prevent you from changing a non terminal atom to a chemical group but it will never make chemical sense to do so as a group only has one point of attachment 3 11 3 Expanding a Chemical Group By default chemical groups are shown as simple special symbols e g Et for ethyl A chemical group may be expanded so that each atom and bond is shown explicitly For example e To expand a chemical group right click on the group and select Expand Group e Alternatively select Atoms from the top level menu Expand Chemical Groups from the resulting pull down menu then either Selected or All if you pick the former you will be asked to pick the groups to be expanded 3 11 4 Accessing Standard Substructure Templates Several pre drawn fragments are available to aid substructure drawing To view them hit the Templates button in the bottom left hand corner of the Draw window then select View in the resulting pull down menu Alternatively hit File in the top level menu of the Draw window followed by Import Template and then View The resulting dialogue box not only shows the available templates but allows you to select a template and Load it into the drawing area Alternatively you can add a template to the drawing area by hitting the Templates button in the bottom left hand corner of the Draw window selecting List in the resulting pull down menu and then choosing the required structural type from the resulti
75. User Guide By default the 2D diagram is the first results pane displayed when viewing an entry To change this select Options from the top level menu Default Results Pane from the resulting menu and choose the pane you want displayed by default when first viewing an entry 2 12 6 Hyperlinking Between Entries If an entry contains a cross reference to another CSD entry identified by a Refcode entry ID see page 238 in e g the Chemical and Experimental tabs see Viewing Information for Individual Structures page 30 then it is possible to hyperlink to that entry by clicking on the refcode For example entry AACFAZ includes the following information in the Chemical pane of the View Results screen CCDC ConQuest 1 Eile Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists gt View Results Alll Text i aacFaz Refcode AACFAZ CSD version 5 30 November 2008 Author Journal Ha _ Analyse Hitlist Chemical Formula C35 H33 Cl No Og AABHTZ a AACANI10 Crystal Name anti anti bis 2 0 Chlorophenyl 4 methoxy 5 oxo dihydrofura AACANI11 Experimental n 3 ethylidenejazine AACFAZ10 AACMAL AACMHX10 Diagram Synonym 3D Visualiser CCDC Class CSD Internals Source AACRHA Search Overview Melting Point 190 2deg C seen Colour red AACRUBO1 AADAMC AADMPY AADMPY10 AADRIB AAGAGG10 AAGGAG10 AALCFE AALPRO AAMAND AAMTCO es Extra for sterecisomer see SACFAZ Inf
76. Valid Parameters Distance aiam Defined Objects Options Valid Objects e This defines a variable DISTI which will store the value of the TR Cl bond length To change the name of the parameter hit Options and type the name you want into the ConQuest User Guide 175 RENAME input box ConQuest puts some restrictions on the name you can use for a parameter If you type an unacceptable name the input box will turn pink and you will not be able to hit OK to close the pop up Similarly define the other CI TR distance the two TR N distances and the C C distance Define the Cl TR Cl and N TR N angles Note that depending on how many atoms you have picked the Geometric Parameters dialogue box only allows you to define meaningful parameters e g if you have picked three atoms you can define an angle but not a distance or torsion Define the N C C N torsion angle At this point all the parameters you have defined will be listed in the 3D Parameters box in the top right hand corner of the Draw window 3D Parameters DIST1 DIST2 DIST3 DIST4 DISTS ANGI ANG2 TOR Options Delete 5 Request tabulation of the specific element symbol of TR in each hit 176 e The last parameter to define is the element symbol of TR Click on TR and then hit the Define button next to the words Atom Properties This launches the All Parameters window where a number of atom properties can be selected for output
77. a session filter settings are remembered from the previous search e It is possible to control which filters are by default displayed when the Search Setup dialogue box is opened for the first time in a ConQuest session see Default Filter Settings page 144 ConQuest User Guide 143 17 3 Available Filters 3D coordinates determined Switch on to exclude structures for which no 3D information is available R factor see page 239 Switch on the check button and then click on one of the three radio buttons to restrict the search to structures with R factors less than or equal to 0 05 0 075 or 0 1 If an R factor limit other than one of these is required set up as a query using the Experimental dialogue box see Using the Experimental Dialogue Box page 133 Ifan R factor query and this filter are set at different levels the more stringent 1 e lower of the two criteria will be used Not disordered Switch on to exclude structures which contain crystallographic disorder see Disordered Structures page 224 This can also be done in the Experimental dialogue box see Using the Experimental Dialogue Box page 133 No errors Switch on to obtain only those structures which are error free at the 0 05A level Not polymeric Switch on to exclude polymers and metal catena structures see Polymeric Bonds page 236 No ions Switch on to exclude structures containing ions Zwitterions will not be excluded No powder structures Sw
78. a ConQuest output option Molecule The word molecule in this document is used generically to refer to a molecule or ion For example sodium acetate monohydrate has 3 molecules C H307 Na H30 Neutron Diffraction A relatively small proportion of structures in the CSD have been determined by neutron rather than X ray diffraction The advantage of neutron diffraction is that it locates hydrogen atoms with good precision To Search e Select the Experimental button in the Build Queries pane see Using the Experimental Dialogue Box page 133 No Errors Selecting this filter restricts the search to entries which have atomic coordinates and do not contain unresolved errors ConQuest User Guide 233 To Search e Select the appropriate filter in the Search Setup dialogue box see Applying Filters page 143 No Ions Selecting this filter excludes structures that contain ions Zwitterions will not be excluded To Search e Select the appropriate filter in the Search Setup dialogue box see Applying Filters page 143 Nucleic Acids Database The Nucleic Acids Database Berman et al Biophys J 63 751 1992 http ndb mirror 2 rutgers edu contains structures of oligonucleotides and nucleic acids Number of Atoms with 3D Coordinates The number of atoms with 3D coordinates is more precisely the number of atoms in the Crystal Chemical Unit see page 221 with 3D coordinates In other words it is the number of experimen
79. abelling no atoms No Labels all atoms All Atoms all atoms except C H N and O No C H N or O all atoms except C and H No C or H all atoms except H No H or selected atoms Selected If you choose Selected click on the particular atoms you want labelled 2 13 6 Displaying Crystallographic Unit Cell Contents Right click anywhere in the visualiser area select Packing from the resulting pull down menu and then 1 Unit Cell from the menu that follows To switch off the display of the unit cell axes right click anywhere in the visualiser area select Packing from the resulting pull down menu and disable the Show Cell Axes option in the menu that follows This option to display the unit cell axes is only available when packing is shown To go back to displaying the molecule right click in the visualiser area and select Packing followed by Molecule 2 13 7 Highlighting Hit Fragments and Showing Results of Nonbonded Contact Searches 36 If the check box labelled Show substructure matches is switched on the visualiser will highlight the hit fragment i e the atoms in the 3D structure that match those of the query substructure This check box may be found directly underneath the main visualiser display area If the search was for nonbonded contacts the contacts will be displayed in the visualiser if and only if the Show substructure matches check box is switched on The highlighting of the hit fragment can be made more or less obv
80. aded indicated by the progress bar reaching 100 The hit OK Hit Start Search to begin the search The resulting search will find all the entries from the previous search that satisfy your new query Hit Clear Subset when the Search Setup dialogue box is next opened to revert to searching on the complete database 18 3 4 Searching the Hits from a Search Previously Saved to Disk Build the query as usual and hit Search Then hit the Select Subset button in the Search Setup dialogue box Select either Entries in saved search file or Entries in saved refcode list depending on whether the subset you wish to search was saved in native ConQuest cqs format see Saving and Reading Searches page 41 or as a list of refcodes gcd respectively see Saving Individual Structures and Lists of Structures page 41 Click on the Browse button and select the required file Wait while the subset is loaded indicated by the progress bar reaching 100 This may take some time Hit OK when the subset is loaded Hit Start Search to begin the search The resulting search will find all the entries in the saved search file or refcode list that satisfy your new query Hit Clear Subset when the Search Setup dialogue box is next opened to revert to searching on the complete database ConQuest User Guide 149 18 4 Searching CSD Data Updates From April 2002 it has been possible to download CSD data updates at regular intervals This will keep your copy of
81. age 213 Average e s d of C C Bonds see page 214 Azides see page 214 Bioactivity see page 215 Bond Type Conventions see page 216 Centroids see page 217 Chemical Diagram see page 217 Chemical Formula see page 218 CIF Format see page 218 CIFMIF Format see page 219 Comments see page 219 Compound Name Conventions see page 219 Compound Name Keywords Indicating Structure Type see page 220 COORD Format see page 221 Coordination Geometry see page 221 Crystal Chemical Unit see page 221 Crystal Systems see page 222 Cyclicity see page 222 Delocalised Double Bonds see page 223 Density see page 223 Deposition Numbers see page 224 Disordered Structures see page 224 Distances see page 225 Drug Activity see page 225 Dummy Points see page 225 Element Group Symbols see page 225 FDAT Format see page 227 Flack Parameter see page 227 ConQuest User Guide Habit see page 227 Hydrogen Atoms in 2D 3D Substructure Searching see page 227 Hydrogen Atom Location in Crystal Structure Analyses see page 228 Inorganic Crystal Structure Database ICSD see page 229 Internal Comparison see page 229 Journal Name see page 229 Journal Page see page 230 Journal Volume see page 230 Lattice Type see page 231 Logical Operators see page 231 Mercury see page 232 Metal Carboxylates see page 232 Metal Metal Bonds see page 232 Metals and Alloys Crystallographic Database CRY
82. ailable Filters page 144 powder Structures determined from powder X ray diffraction are filtered during the search see Available Filters page 144 organometallic Organometallic structures are filtered during the search see Available Filters page 144 organic Organic structures are filtered during the search see Available Filters page 144 disorder Disordered structures are filtered during the search see Available Filters page 144 polymeric Polymeric structures are filtered during the search see Available Filters page 144 e For example disordered CSD entries can be excluded from a search using a command of the 156 ConQuest User Guide 20 6 type e cqbatch j lt jobname gt rerun lt query filename gt exclude disorder More than one filter can be applied for example to exclude ionic CSD entries without 3D coordinates a command of the following type could be used Cqbatch j lt jobname gt rerun lt query titename gt exclude ionic no3d The rfactor and exclude commands can be used simultaneously If the source of a query is a cqs file then CQBatch will override filters used for the original search if these are specified via the command line If the source of a query is a QUEST instruction file then CQBatch will attempt to identify any SCREEN instructions and over ride these as appropriate if filters are specified via the command line Output By defaul
83. al metal bond of type 1 or 2 or 3 or 4 using a variable bond type Related Topics e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Variable Bond Type see page 246 Metals and Alloys Crystallographic Database CRYSTMET CRYSTMET contains crystallographic information relating to metal and alloy structures Originally developed at the National Research Council in Ottawa Canada it is now maintained by Toth Information Systems 2045 Quincy Avenue Gloucester Ontario K1J 6B2 Canada 232 ConQuest User Guide Missing Atoms Atoms may be missing from CSD structures for several reasons e The crystallographer did not report them in the paper i e only space group and cell parameters were given e Hydrogen coordinates are occasionally not reported in the paper or deposited at the CCDC with the rest of the atomic coordinates e Solvate atoms are occasionally not reported a comment is given in this case e The crystallographer did not locate them e g in the case of a bridging hydrogen atom e CCDC staff may suppress one or more atoms A common example is when the author reports two sets of atomic coordinates for major and minor sites in a disordered structure In most cases the atoms of the minor site will be suppressed Related Topics e Disordered Structures see page 224 Mol2 Format mol2 is a molecular file format produced by Tripos Inc 1699 South Hanley Road St Louis MO 63144 2913 USA and is
84. ally Modified Hse we wa ieu Lys MET NLE nva ORN PHE PRO sar Either SER THR Ter TYR val l ANY Any residue UND Not an alpha amino acid Next bond is N we Normal peptide bond d Non peptide bond J User Defined Construct amp N terminus Right click on outer residues to Terminate an acyclic sequence C terminus Either i oa _ AlB en ae Cyclicity Cyclic sequence wy Acyclic sequence Either Search Store Cancel Reset e Some of the amino acids are non standard leave the cursor over a button to get a display of the full chemical name e By default both cyclic and acyclic peptide sequences will be found This can be altered by using the buttons in the Cyclicity section of the dialogue box For example only acyclic peptides will be found with the following setting N terminus Right click on outer residues to Terminate an acyclic sequence C terminus GLU AIE SER e GAA gt Cyclicity Cyclic sequence Acyclic sequence w Either Search Store Cancel Reset The buttons underneath Next bond is can be used to specify whether the next residue to be added is to be linked by a Normal peptide bond a Non peptide bond or Either A peptide bond is defined as a link between the C O group bound to the alpha carbon of one of the residues and the NH group bound to the alpha carbon of the n
85. ample the setting below will result in the diagrams and literature references being written out for all unsuppressed structures in the hit list 4 per page in US Letter format and with no summary page The file will be called example pdf ConQuest User Guide 45 46 Select what to export v Current entry only All selected entries No Summary Page w Summary Page No parameter information y Include parameter information Select components to write W Reference Chemical d Crystal Experimental E Diagram Either Edit Filename and Write Jexample paf Write Per Page vivd2 tts 4 8 Options _j Colour Scale Diagram to Fit _ Compress W US Letter Or Write via File Popup Cancer ConQuest User Guide 3 SUBSTRUCTURE SEARCHES 3 1 Typical Uses of Substructure Searching Substructure searching e g find all 8 membered carbocycles e Finding particular molecules e g find caffeine e As the essential preliminary to geometrical studies and 3D searching 3 2 Layout of the Draw Window Open the substructure drawing window by hitting Draw in Build Queries Fle Edit Atoms Bonds 3D Options Help Click and drag to create a bond Next Atom Cl 3D Parameters Drag to an existing atom to make a connection Next Bond Single Templates c H ol N S P Fila Any More Groups co ee Cancel e Help messages Top level menu different from the menu
86. and crystallographic data unless one or more of bibliographic chemical experimental or crystallographic are specified via export opts when only those categories listed will be exported Specifying internal will add CCDC internal data items to those being exported Not all options apply to all formats if an option is not relevant to a particular format it will be ignored If SAVE BCCAB is included in a QUEST instruction file then CQBatch will export a file of hit entries in BCCAB format at the end of the search This option is provided for those maintaining in house databases created using PreQuest Progress output will be written to the console window being used to run CQBatch as a search progresses unless redirected to another file via the log option Available Commands Some commonly used commands and their usage are given below Further options can be found by typing cqbatch help Other commands are outlined in other sections e Logic options see Logic page 153 e Database options see Databases page 154 e Filter options see Filters page 155 e Export options see Output page 157 ConQuest User Guide 161 cqbatch help Provides guidance about how to use CQBatch and exits version Shows the ConQuest and CSD version numbers and exits 1log lt log_filname gt This command writes diagnostic output to a log file in the directory the search is being run from j lt
87. and phane There are a number of variants of the word calixarene e g calix 4 crown calix 4 resorcinarene etc The safe procedure is to search for the root calix There are a number of variants of the word fullerene e g fulleride fullerenyl etc The safe procedure is to search for the root fuller Related Topics e Compound Name Conventions see page 219 220 ConQuest User Guide COORD Format The COORD format file extension cor is a simple ASCII listing of 3D coordinates and where appropriate cell data You may choose to write out orthogonal or fractional coordinates see Atomic Coordinates page 212 either for all the atoms in the Crystal Chemical Unit see page 221 or just the atoms that matched the search substructure Coordination Geometry Metal coordination geometries are not explicitly stored in the CSD To search for a particular coordination geometry e g square planar rather than tetrahedral you must do a 3D substructure search see Basic Guide to 3D Substructure Searching page 79 Crystal Chemical Unit In some cases molecular symmetry coincides with the symmetry elements of a crystallographic space group For example a molecule might have a mirror plane which coincides with a crystallographic mirror plane in the space group In the crystal structure the molecule has exact m symmetry the Asymmetric Unit see page 211 is half a molecule and the crystallographer only determines the coordinates of half of
88. apply the change to your current ISIS DRAW session Now draw your substructure in ISIS Draw and copy all or part of the substructure select Edit from the ISIS Draw top level menu and Copy from the resulting pull down menu To paste a copy of a substructure drawn in ISIS Draw into the Build Queries area e Hit Edit in the top level menu of Build Queries and Paste in the resulting pull down menu The pasted substructure will appear listed as a query in the Build Queries pane To paste a copy of a substructure drawn in ISIS Draw into the ConQuest Draw window either e Click on a blank point in the ConQuest white drawing area with the right hand mouse button and select Paste the option will be greyed out if there is nothing available to paste or e hit Edit in the top level menu of the ConQuest Draw window and Paste in the resulting pull down menu Not all query features specified in ISIS Draw can be translated to ConQuest query features ConQuest attempts to convert the following ISIS query features e The majority of atom types including Atom Lists and some Beilstein Atom Generics If conversion is not possible the ConQuest Any Atom X type will be used e Bond Type excluding stereochemical features ConQuest will convert alternating double single bonds in a six membered ring to the CSD aromatic bond type These are the only ring systems where such a conversion is made e Zero H count no implicit hydrogens e Substitution count n
89. appropriate through the IUCr A subscription to the publication in question will normally be required to view the article 1 5 2 Chemical Information in the CSD e Compound name see Compound Name Conventions page 219 e Chemical formula used for element and formula searches see Chemical Formula page 218 e Chemical diagram used for 2D and 3D substructure searches non bonded interaction searches see Chemical Diagram page 217 Further chemical property information is also available e g absolute configuration bioactivity conformer isomer racemate where provided in the published literature 1 5 3 Crystallographic Information in the CSD e Atomic Coordinates see page 212 e Unit Cell Parameters see page 242 e Reduced Cell Parameters see page 238 e Crystal Systems see page 222 e Space Group see page 240 e Crystal density colour habit and source of crystal e Number of formula units per unit cell Z see Z Number of Molecules per Unit Cell page 246 e Number of formula units per asymmetric unit Z see Z Number of Molecules per Asymmetric Unit page 247 e R factor see page 239 8 ConQuest User Guide Average e s d of C C Bonds see page 214 Temperature of Structure Determination see page 241 Disordered structure flag see Disordered Structures page 224 Unresolved errors flag see Unresolved Errors page 243 1 5 4 Text Information in the CSD Details of disorder see Disordered Structures page
90. arch Options dialogue box can only be opened when there is a substructure in the white drawing area and you have defined a geometric parameter The 3D Search Options dialogue box enables you to toggle Enantiomer Inversion on and off Enantiomer Inversion Symmetry Check Number of Matches When testing for a torsion angle constraint the mirror image of a molecule will always be tested provided that it can be generated by space group symmetry operators Turn on the option below if you want to test the mirror image of a molecule regardless of space group symmetry and for example invert pure enantiomers E Allow inversion in any space group Defaults Cancel OK _l Number of Matches A substructure search involving 3D parameters will attempt to find all unique fragments matching your query The need for exhaustive fragment location is due to the fact that although the 2D chemical structure is identical in every case the 3D structure is almost certainly different Some crystal fragments may pass the 3D search criteria and be classified as hits others will not In crystal structures there are more problems to consider when carrying out the exhaustive fragment location We must consider molecules having internal symmetry and where the molecular symmetry coincides with an appropriate symmetry element in the crystal Also the asymmetric unit of a crystal structure can contain more than one example of the chemical molecule stored in
91. ater analysis Locating substructures with specific conformations torsion angles Locating specific metal coordination geometries e g tetrahedral rather than square planar Pharmacophore searching Basic Guide to Tabulating Geometries In order to tabulate geometric parameters they must be defined in the Draw window before the search is run as follows Draw the required substructures see Fundamentals of Drawing page 49 If necessary define geometric objects such as planes or centroids see Defining Geometric Objects page 80 Define the required geometric parameters e g the distance between two atoms see Defining Specific Geometric Parameters Involving Only Atoms page 82 or the angle between two planes see Defining Geometric Parameters Involving Objects page 86 Run the search Transfer the results into Vista or Excel to view the parameters in a spreadsheet see Transferring Data to Other Programs for Analysis page 44 Basic Guide to 3D Substructure Searching Draw the required substructure see Fundamentals of Drawing page 49 If necessary define geometric objects such as planes or centroids see Defining Geometric Objects page 80 Define the required geometric parameters i e the parameters you want to constrain These may involve just atoms see Defining Specific Geometric Parameters Involving Only Atoms page 82 or atoms and objects see Defining Geometric Parameters Involving Objects page 86 ConQues
92. ates for some or all H atoms may be absent in reported structures In modern experiments it is usual to either e model H atoms into the structure at positions calculated using chemical knowledge e g carbon hybridisation states or e to locate them in difference electron density maps in the final stages of structure determination A variety of H atom refinement strategies are then employed 228 ConQuest User Guide Because X rays see electron density and the density around an H atom is aspherically displaced towards the atom to which it is bonded X H distances reported from X ray analyses are usually significantly shorter than the true X H internuclear distance see e g Acta Cryst B42 515 1986 However hydrogen atoms are precisely located using neutron diffraction and in generating geometrical descriptions of substructures involving H atoms particularly the geometry of hydrogen bonds it is common to neutron normalise the H atom positions It is assumed that the experimentally determined X H vector direction is correct and the H atom is then moved along this vector so that the X H internuclear distance corresponds to the value determined by neutron diffraction ConQuest will carry out this normalisation using either e C H 1 083A N H 1 009A and O H 0 983A these distances are averages J Chem Soc Perkin Trans 2 S1 S19 1987 taken over good neutron data available at that time or e X H distances specified by the
93. ayed when each Classroom ConQuest session is started see Basics of Using Classroom ConQuest page 151 Although Classroom ConQuest will start if your refcode list is too big it will issue an error message when you attempt to start a search 152 ConQuest User Guide 20 RUNNING CONQUEST IN BATCH MODE e ConQuest can be run from the command line using the following commands e On Windows platforms lt CQDIR gt exe cqbatch exe e On UNIX platforms lt CQDIR gt bin cqbatch e Any queries or problems should be directed to support ccdc cam ac uk e Command line ConQuest is referred to as COBatch throughout this section 20 1 Input Query Files e The following queries can be run using CQBatch e query gry or search cqgs files These are generated and saved via ConQuest Manual editing of either file type is discouraged as it may cause CQBatch to behave in an unexpected way a QUEST instruction file con or que created externally to ConQuest Information about QUEST instruction files can be found in the QUEST documentation ttp www ccdc cam ac uk support documentation quest volume 1 z1c02009 html 2_5 Note not all QUEST instruction file commands may be recognised MDL MOL files mol created externally to ConQuest These may contain geometric parameters see Bibliographic Information in the CSD page 8 Input files can be provided to CQBatch via the following combinations of command line options e rerun lt file
94. ber see Journal Page page 115 Year of publication see Journal Year page 115 CCDC number or refcode see CCDC number deposition number page 115 7 2 1 Authors Names Type the required surname into the input box Optionally authors initials may be specified e g F H Allen Each initial must be followed by a full stop with no spaces between initials or between initials and surname All initials must match exactly e g F H Allen would not find F Allen If the Exact surname check button is turned off a search for Allen would also find Allenby Allenford etc If the box is turned on only the exact name Allen would be found The Exact surname option cannot be used if initials are specified Only one name is allowed per box use the New Box button if you wish to search for structures published by two or more authors The example below would find structures in papers on which both Raithby and Allen are authors Authors Names New Box 5 Exact Exact Ralthby E sumame M sumame To find structures published by either Raithby or Allen create and store two separate queries one for Author Raithby one for Author Allen and combine them see Complex Query Combinations page 21 ConQuest User Guide 113 7 2 2 Journal Name e The journal name must be abbreviated exactly as it is stored in the CSD It is therefore safer to select it from the list box rather than type it in e To find the journal in the list either scroll
95. ble to specify a range e Page numbers occasionally contain letters 7 2 5 Journal Year e Select the required option during after between etc e Type a four digit year e g 1998 into the input box If between is selected two years must be specified and the second must be later than the first e g 1978 1980 is valid 1978 1977 is not 7 2 6 CCDC number deposition number e Type the entire deposition number e g 243822 1267 1231 e It is not possible to search for IUCr deposition codes e g A20110 using this method e Recent CCDC numbers 200000 or greater are shown as hyperlinks if the hyperlink is selected ConQuest will attempt to open the CCDC CIF Repository Request Form in a Web browser This form is also available from the CCDC website www ccdc cam ac uk products csd request 7 3 Hints for Author and Journal Searching e It is easy to miss hits unless you understand the CSD conventions for Authors Names see page 213 e Select journal names from the list box rather than typing them in since you need to use the same abbreviations as are used in the CSD e Some journals have changed their names over time often by dividing into two or more sections see APPENDIX B CHANGES IN JOURNAL NAMES page 248 e Some volume numbers contain letters e g C471 However in other cases the alphabetic part of a volume number is absorbed into the journal name e g Acta Cryst Section B You can usually work out which convent
96. both queries so if you have de selected one or both of them make sure they are selected again i e both coloured green Fle Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results Draw use this query Name dimolybdenum alphabetic Peptide AOpen eee fuse this 1 query aS iti Name Class i a Text Search air sensitive Elements 5 Run the search e Hit the Search button at the bottom left hand corner of the window e The pop up confirms that the search will be for entries that satisfy both queries 202 ConQuest User Guide Summary of queries to be used Search will find structures where these queries are true e Hit Start Search e Click on the Chemical tab to show that the hit entries contain dimolybdenum or di molybdenum in their compound name and also contain the words air sensitive This ends the tutorial ConQuest User Guide 203 21 10Tutorial 10 More Complex Combinations of Queries Objectives To create a formula query To create a space group query To create two queries concerning experimental conditions To combine the four queries in order to find entries that satisfy the formula constraint do not belong to the specified space group and satisfy either of the experimental constraints Steps Required Construct and store a formula query Construct and store a space group query Construct and store two experimental queries Combine the qu
97. c metal coordination complexes are identified by the bridging indicator mu with the polymer identified by the prefix catena e g catena mu 2 5 dihydroxy p benzoquinonato zinc e Names of hydrates will contain the words hemihydrate monohydrate dihydrate etc otherwise just hydrate if the multiplier is a non integer value e If other solvents are present the name will contain the word solvate clathrate is used for ConQuest User Guide 219 solvates which are clathrated as in host guest compounds e Deuterated species will always contain the name characters deuter To Search e Select the Name Class button in the Build Queries pane see Compound Name Searching page 116 Related Topics e Compound Name Keywords Indicating Structure Type see page 220 Compound Name Keywords Indicating Structure Type To assist searching some types of compounds always contain certain words in their compound name e calixarene see below e catenane e clathrate e cyclophane see below e electride e fullerene see below e hydrate monohydrate dihydrate etc e pseudopeptide or pseudo peptide e radical e retropeptide or retro peptide e rotaxane e trefoil knot There are a number of variants of the word cyclophane e g cyclophanyl cyclophanone etc The safe procedure is to search for the root cyclophan To find compounds such as cyclo octaphane or cyclo octacosaphane it is best to search for the roots cyclo octa
98. ce in a particular entry this will be indicated by the presence of the words Multiple Hits Show beneath the diagram Clicking on the arrows next to this text shows each substructure match in turn along with the values of the associated 3D parameters 38 ConQuest User Guide ConQuest User Guide Refcode ACFCUA Parameters Pe 2 016 tT OY o cr lI l i a H I 3 IL SL a arn WIN Fc wee 57 Multiple Hits Show i of2 W Show Parameters 39 2 15 Switching between Searches e Any number of searches may be run in a single ConQuest session New searches can be started while an existing search is still running e By default View Results will display the latest search to be started e To switch between searches click on Results in the top level menu and select the required search from Searches in the resulting pull down menu The currently selected search i e the one currently displayed in View Results will be greyed out in this menu e A star next to a search means that it has not been saved or has been modified i e entries suppressed or unsuppressed see Suppressing Unwanted Entries page 40 since it was last saved 2 16 Cancelling and Stopping Searches e A search may be cancelled by hitting Cancel in the Search Setup dialogue box see Naming Searches and Setting Filters page 28 or stopped by hitting the button labelled Stop Search on the View Results screen e Once stopped a search cannot be re
99. ch can be done for structures e containing selenium AND with a density gt 1 5 but e NOT containing iron and e solved by neutron diffraction OR at a temperature below 200K This type of search is done in the Combine Queries part of the interface see Complex Query Combinations page 21 ConQuest User Guide 231 Mercury Mercury is a CCDC program for crystal structure visualisation which allows users to view either their own structures or those retrieved via a ConQuest search Mercury is also available as a free download from Attp www ccdc cam ac uk products csd_system mercury Metal Carboxylates When both oxygen atoms of a carboxylate group are bonded to one or two metal atoms then by convention both C 0 bonds are of type delocalised double However for simple acid salts e g sodium acetate our convention is to use localised single and double bonds The same principles apply to the analogous thiocarboxylates dithiocarbamates xanthate thioxanthates etc Related Topics e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Delocalised Double Bonds see page 223 e Variable Bond Type see page 246 Metal Metal Bonds There are two problems associated with metal metal bonds e In some cases it is difficult to judge whether or not a bond exists e The bond order is often debatable Probably the safest approach is to search for structures with no metal metal bond and also structures with a met
100. cleotides higher oligomers are covered by the Nucleic Acids Database see page 234 There is a small overlap between the CSD and the Inorganic Crystal Structure Database ICSD see page 229 in the area of molecular inorganics Information on other metal containing structures can also be found in the Metals and Alloys Crystallographic Database CRYSTMET see page 232 1 2 Literature Coverage of the CSD The CSD reflects the published literature It is fully retrospective and is updated on a current basis All information is abstracted from primary journals and associated supplementary information in both hard copy and electronic forms The CSD is the official depository for crystal structure data for more than 80 journals The CSD also accepts direct deposition of crystal structure data preferably electronically in CIF Format see page 218 These are included in the database as Private Communications see page 237 6 ConQuest User Guide 1 3 Database Entries Each entry in the CSD relates to an individual publication of a specific crystal structure A paper that reports two or more crystal structure determinations will generate two or more entries in the CSD Multiple determinations of the same structure by the same or different authors are included in the database These may report improved structural models or new experiments performed at different temperatures or pressures or using different radiations Each CSD entry contains the
101. commended to fuse two separate rings in the white area by selecting all the atoms in one ring see Selecting Atoms and Bonds page 50 and moving it towards the other see Moving Atoms page 73 e Spiro fusion is achieved by overlapping one atom in the moveable ring with one atom in the stationary ring indicated by the overlapped atoms going red Fusion will occur when the mouse button is released e Bond fusion is achieved by overlapping two bonded atoms in the moveable ring with two bonded atoms in the stationary ring It may be necessary to overlap one of the pairs and then rotate the moveable ring by holding down the Control key until the second pair overlap see Rotating Substructures page 74 3 6 Atom Properties Atoms may have the following properties e Element type this may be a variable type e g N or O see Changing the Current Element Type page 56 e Attached hydrogens these may be generated automatically see Automatic Addition of Hydrogen Atoms page 58 or added manually see Adding Hydrogen Atoms Manually page 59 e Formal charge see Setting Atomic Charges page 60 e Coordination number see Setting Atom Coordination Numbers page 60 e Cyclicity status see Defining Cyclic or Acyclic Atoms page 61 ConQuest User Guide 55 3 6 1 Changing the Current Element Type e The current element type determines the type of any new atom created when drawing It is displayed in the white box at the bottom of the
102. contact can be viewed in the 3D visualiser Stop the search when you have a few hits Select File from the top level menu and then Export Entries as from the pull down menu Select the file type as COORD This format enables you to write out either 1 orthogonal or ii crystallographic fractional atomic coordinates of either a all the atoms in each structure or b just those atoms involved in the contact Select Orthogonal and Hit Fragment Only to save the Cartesian coordinates of the atoms involved in the hydrogen bonding interaction This ends the tutorial 190 ConQuest User Guide 21 6 Tutorial 6 Pharmacophore Search Objectives e To draw two chemical fragments substructures e To specify the distance required between the two fragments i e to specify a pharmacophore e To find molecules in the CSD containing the specified pharmacophore Steps Required e Draw the fragments e Define one of the fragments as a group for use in nonbonded searching e Specify the required distance between the fragments e Ensure that the search is for intramolecular nonbonded distances only i e both fragments must be in the same molecule e Run the search e Save the file of hits The Example e The tutorial explains how to search for the following pharmacophore where the distance between the cationic nitrogen and the centre of the carbonyl bond is in the range 5 0 5 8A This is the distance range required b
103. creen Viewing a hitlist combination for the first time may result in a progress window Alternatively If you have previously created or loaded hitlists in the same ConQuest session ConQuest User Guide 25 26 these can be viewed by selecting Results from the top level menu followed by Searches Combinations or Refcode Lists in the resulting pull down menu to display the hitlist of your choice The full overview for the hitlist combination is shown below you can toggle between the full overview and the brief overview shown by default by selecting the appropriate check boxes In this example the hitlist combination has been annotated and renamed and both searches have been renamed to something more meaningful Edit Options View Databases Results Help Combine Hitlists eS Manage Hitlists View Results Hitlist Overview Combination Name combination Combined_hitlist_1 5 Entries m Full overview List A List B Section 2 6 2 Porphyrin Include deselected entries in J List A _j List B Combined hitlist of porphyrin search AND query from section 2 8 2 Search Section_2 8 2 Elements Mg Search on Sum of molecules Generate a List of Entries common to List A and List B in either List A or List B wv in List A but not in List B Allow other elements Yes Temperature lt 273 K Search Porphyrin Name porphyrin alphabetic Z 2 Section_2 6 2
104. ct Settings and Make Hit Transparent from the resulting pull down menu This can aid the visualisation of objects which would otherwise be obscured ConQuest User Guide 37 2 13 9 Saving Visualiser Images e An image displayed in the 3D visualiser can be saved by right clicking anywhere in the visualiser area and selecting Save as JPEG from the resulting pull down menu e Alternatively the 3D image can be copied and pasted into other Windows applications Please note that this is a Windows only feature Ensure the complete diagram is visible on the screen and select Edit from the top level menu then click on Copy The keyboard shortcut Ctr C may also be used 2 13 10 Saving Visualiser Settings e Your current visualiser settings e g of display styles hit fragment highlighting etc can be saved by right clicking anywhere in the visualiser area and selecting Save current setting from the resulting pull down menu e The effect of this will be that the settings you have saved will be used by default in future ConQuest sessions You will be able to change them again if you wish 2 14 Displaying the Values of Defined Geometrical Parameters e If3D geometric parameters were defined in a substructure search see Geometric Parameters page 82 their values in a hit structure can be seen by moving to the Diagram display in View Results and turning on the check button labelled Show Parameters Ifthe query substructure occurs more than on
105. ctures not a collection of atoms which form part of a substructure In EDIT mode select see Selecting Atoms and Bonds page 50 the substructure to be rotated move the cursor to a corner of the box surrounding the selected atoms press the Control key and then the left hand mouse button The cursor should change shape to two curved arrows e Rotate by moving the cursor keeping both the mouse button and the Control key depressed 3 13 3 Resizing Substructures It is only possible to resize complete substructures not a collection of atoms which form part of a substructure In EDIT mode select see Selecting Atoms and Bonds page 50 the substructure to be resized e g e To resize in the horizontal direction only move the cursor to one of the solid pink squares at the middle of a vertical edge of the fragment s bounding box press the left hand mouse button and move the cursor left or right keeping the mouse button depressed e To resize in the vertical direction only move the cursor to one of the solid pink squares at the middle of a horizontal edge of the fragment s bounding box press the left hand mouse button and move the cursor up or down keeping the mouse button depressed e To resize equally in both directions move the cursor to one of the solid pink squares at a corner of the fragment s bounding box press the left hand mouse button and move the cursor keeping the mouse button depressed e To resize unequally in bo
106. cular atom W Find all symmetry related contacts Defaults Cancel OK 5 6 Hints for Nonbonded Contact Searching Searches for intermolecular interactions take longer than those for purely covalent substructures 106 ConQuest User Guide Searches for patterns involving two or more non covalent interactions can be very time consuming e A typical search consists of two occasionally more covalent substructures and the non covalent interactions required between them The non covalent interactions must be defined geometrically For example if you are searching for O H 0 hydrogen bonds you must specify the maximum permissible O O or H O distance The most common geometrical constraints are maximum and minimum distances e g D A or H A distances for hydrogen bonds D H A D donor A acceptor e In choosing non covalent distance constraints it can help to carry out a preliminary search using quite generous limits e g sum of van der Waals radii plus 0 5A This establishes the range of values in the CSD e It is only sensible to specify distance constraints with respect to van der Waals radii if you are searching for contacts between the common non metallic elements unless you choose to set your own van der Waals radii e H atoms are not always present in CSD entries particularly in older entries You may need to use D A distance constraints instead of H A constraints in H bonding studies e H
107. cy Quest3D Summary file is also available QUEST Summary sum e Select data fields and parameters of interest and hit Save 2 21 Viewing Results in Mercury Mercury see page 232 is an advanced crystal structure visualiser distributed as part of the CSD system for viewing either your own crystal structures or those retrieved from a ConQuest search To view the hits from a ConQuest search in Mercury hit Analyse Hitlist and select View in Mercury from the pull down menu Alternatively select File from the top level menu and View in Mercury from the resulting pull down menu 2 22 Printing Search Results Search results diagrams literature references etc can be written out as pdf files which may then be viewed and printed with Adobe Acrobat Reader included on your ConQuest CD ROM and also freely available from http www adobe com Acroread on UNIX has a toPostscript option which converts PDF to Postscript and could be used to save postscript e In View Results select File from the top level menu and Write PDF file to view print from the resulting pull down menu e Use the buttons in the Write PDF File dialogue box to control the contents of the PDF file e g number of entries per page which items diagram journal reference etc are to be included whether information is to be written for the structure currently on display or for all unsuppressed structures in the hit list see Suppressing Unwanted Entries page 40 e For ex
108. ddb 1999 2001 Digital Creations Fredericksburg VA USA and Andrew Kuchling http pybsddb sourceforge net PyOpenGL 1997 1998 2000 2001 by James Hugunin Cambridge MA USA Thomas Schwaller Munich Germany and David Ascher San Francisco CA USA http pyopengl sourceforge net Python 2 2 1 2001 2002 Python Software Foundation http www python org The Python Imaging Library PIL 1997 2002 by Secret Labs AB 1995 2002 by Fredrik Lundh http www pythonware com 250 ConQuest User Guide ReportLab 2000 2001 ReportLab Inc http www reportlab com Tcl Tk Regents of the University of California Sun Microsystems Inc Scriptics Corporation and other parties http www scriptics com software tcltk zlib 1995 2002 Jean loup Gailly and Mark Adler http www gzip org zlib Allegro 1998 2004 Shawn Hargreaves plus contributors http alleg sourceforge net AllegroFont 2001 2002 Delerium Software http nekros freeshell org delirium alfont php FreeType2 The FreeType Project http www freetype org MinGW 2004 http www mingw org Bitstream Vera Mono Font 2004 Bitstream Inc http www bitstream com py2exe 2000 2001 2002 2003 2004 Thomas Heller http www py2exe org ConQuest User Guide 251
109. display something like this Multiple Hits Show aj 1 gt of 3 W Show Parameters This means that the search fragment occurs more than once in the database structure As you click on the left and right arrows alongside the Multiple Hits Show box you will see highlighted in red the way in which the search fragment is contained within the chemical diagram of the database entry If there is no change in the atoms which are highlighted it means there are two or more crystallographically independent molecules in the structure the 3D visualiser display will confirm this Save the geometric data for analysis in Vista or a spreadsheet such as Excel Depending on whether ConQuest is being run under Unix or Windows the parameter values may be exported to Vista or a spreadsheet such as Excel for statistical analysis Select File from the top level menu and then Export Parameters and Data from the resulting pull down menu In the resulting pop up window switch on R factor This will ensure that the R factor of each entry is written out as well as the geometrical parameters you have defined Select either Vista tab or Spreadsheet spr as File type Hit Save and specify the required file name in the Save Parameters dialogue box then hit Save in this dialogue box The resulting file may then be read into Vista or a spreadsheet package such as Excel ConQuest User Guide 177 depending on which type you have saved This ends the tut
110. down using the scroll bar or type the first letter or two of the journal name into the input box As the name is typed the list in the box is narrowed down Journal Name J Am Type part of Joumal name above to narrow list displayed Select required journal in list below J Am Chem Soc 1928 2000 J Am Oil Chem Soc 1966 J Am Soc Mass Spectrom 2000 L e Pick the required journal with a single mouse click e Ifyou type in part of a journal name and the input box turns pink and or the list box becomes empty this means that there is no journal in the CSD beginning with the letters you have typed Backspace to empty the input box completely and browse down the list of journals to see if you can spot the one you want e Some journals were only published between certain years see APPENDIX B CHANGES IN JOURNAL NAMES page 248 The years in parentheses next to a particular journal name in the list box refer to the years for which entries are included in the CSD for that particular journal title e Searching for the partial name Acta Cryst would find all the different sections of Acta Crystallographica 7 2 3 Journal Volume e Type the required volume number into the input box e It is not possible to specify a range e Volume numbers sometimes contain letters e Some journals do not use volume numbers 114 ConQuest User Guide 7 2 4 Journal Page e Type the starting page number into the input box e It is not possi
111. e 0 and 2 into the From and to boxes respectively CONTACT CONI f Modify options and hit OK when done Inter molecular Intra molecular fa EEE See Query Options in the 3D menu for Symmetry Checking Distance range From 0 to 21 Ay Range w Value tolerance Shorter than sum of Vaw radii Nonnalisation of terminal H positions To normalise terminal H atom positions see Advanced Options after pressing the Search button This is recommended where a terminal hydrogen atom contributes to the specification or analysis of a contact 7 Current status OFF e Hit OK and then Done to finish definition of the contact 5 Define the required geometrical parameters and atom labels e Hit the ADD 3D button and define the O N distance as a parameter to be tabulated This is done by clicking on the O and N atoms and hitting the Define button next to the word Distance in the Geometric Parameters pop up Hit OK in the Distance Type pop up that then appears to specify that the defined distance is a contact 188 ConQuest User Guide 1 ef uf ofn S e E a any more crus e Hit the Define button OK and then Done in the Geometric Parameters dialogue box to finish the definition CHOOSE DISTANCE TYPE Current Intramolecular Distance Select this option to calculate distances between these fragments but only if they are in the same molecule Contact
112. e CCDC program PreQuest see page 237 to build a database of your own crystal structures in CSD format the database can be viewed in ConQuest e You must first configure ConQuest so that it can find the database see CSDS Release amp Installation Notes e All entries in the database can then be viewed by clicking on View Databases in the top level menu This will display a list of all the databases that ConQuest has been configured to use including the CSD itself and any in house database s Select the one you want e If you have a configured in house database in a directory separate to the main CSD files the in house database can be viewed by selecting the Available Databases option from the View Databases menu a Directory tmpfcsd CSD_V5S27 Add Directory W Default CSD location W CSD version 5 27 November 2005 OK Cancel e Click on Add Directory browse to the folder where the in house database files are stored and select the inf file Available Databases ai Directory home robertson inhouse_database Add Directory z W Inhouse test version 0 9 Februar 2005 The radio button next to the database name will need to be activated to complete the selection The Directory pull down menu can then be used to toggle between the configured databases e Databases can be removed from the View Databases pull down menu by deselecting the radio button adjacent to their name in the Avai
113. e Hit Done in the Geometric Parameters dialogue box to finish definition of the pharmacophore 6 Run the search Hit Search set the filters R factor lt 0 1 Not disordered and No errors and then hit Start Search e View some of the hits e g ACYPAC10 which is a close acetylcholine analogue e You can save the hits once the search is finished by selecting File from the top level menu then Export Entries as from the pull down menu A variety of formats are available This ends the tutorial 194 ConQuest User Guide 21 7 Tutorial 7 Cell Parameter Search Objectives e To find out if the unit cell dimensions of a particular crystal match those of any entries in the CSD The usual reason for this type of search is to find out whether a crystal of known cell dimensions has already had its structure determined Steps Required e Perform a reduced cell parameter search The Example e Find structures whose cell dimensions match those of a primitive monoclinic cell with a 6 638 b 7 550 c 23 180 beta 95 98 Menu Commands Required 1 Start ConQuest and hit the Unit Cell button 2 Turn on the option Yes do a reduced cell search e The unit cell of a crystal can be chosen in many different ways strictly speaking an infinite number of ways though not many of the choices will be convenient In order to assess whether two structures might have the same unit cell dimensions it is therefore necessar
114. e button to ensure that all specified elements are in the same bonded moiety Switching off the button Other elements allowed in molecule structure restricts hits to contain only the specified elements The Heaviest permitted element in Formula Unit option can be used to eliminate structures containing heavy atoms This is useful because the presence of heavy atoms can reduce the precision with which light atoms are located in an X ray structure ConQuest User Guide 10 CHEMICAL FORMULA SEARCHES 10 1 Typical Uses of Chemical Formula Searching e Finding structures with particular molecular formulae e g C6 H12 O6 e Limiting the number of atoms of specific type s that may be present e g at least two osmium atoms 10 2 Using the Formula Dialogue Box Open the dialogue box by hitting Formula in Build Queries You can e Specify the chemical formula to be searched for see Specifying a Chemical Formula page 123 e Specify whether the formula is that of a molecule or a complete crystal structure see Specifying Whether the Formula Applies to a Molecule or a Crystal Structure page 124 e Specify whether any other elements are allowed apart from those contained in the formula you have specified see Specifying Whether Other Elements are Allowed page 125 e Special considerations apply if it is desired to retrieve polymeric structures see Hints for Chemical Formula Searching page 125 10 2 1 Specifying a Chemical Formula Open the F
115. e cell parameters of hit entries Two sets of unit cell dimensions are shown for each hit the cell parameters chosen by the author and the reduced cell parameters to which they correspond These may or may not be identical depending on whether the author s choice of cell happened to correspond to the standard reduced cell Similarly the reduced cell dimensions of a hit may or may not look like the parameters you typed in depending on whether your choice of cell dimensions happened to be standard In this example it was In comparing the reduced cell dimensions of a database structure with the reduced cell parameters of the input structure only the cell lengths are compared This is because the cell angles can be mathematically unstable i e a very small change in input cell dimensions may produce large changes in reduced cell angles the same problem does not occur for the cell lengths ConQuest User Guide e In this example there are several database entries which match the input cell dimensions once cell reduction has been performed Any one of these might therefore be the same structure as that whose cell dimensions were typed in This ends the tutorial ConQuest User Guide 197 21 8 Tutorial 8 Journal Reference Search Objectives To find a structure from its journal reference Steps Required e Perform a journal search The Example Find the structure published by H Braunschweig P Paetzold and R Boese in
116. e element types or brings up the Periodic Table which amongst other things allows creation of customised variable element types see Setting Variable Element Types page 56 In DRAW mode change the current element type see Changing the Current Element Type page 56 and then click on the atom with the left hand mouse button e In DRAW or EDIT mode click on Atoms in the top level menu select Element from the resulting pull down menu and select the required element More allows selection of some common variable element types or brings up the Periodic Table see Setting Variable Element Types page 56 The Select Atoms pop up appears click on the atom or atoms to be changed with the left hand mouse button and hit Done In EDIT mode select the atom s to be changed see Selecting Atoms and Bonds page 50 Pick Atoms from the top level menu Element from the resulting pull down menu and select the required element More allows selection of some common variable element types or brings up the Periodic Table which amongst other things allows creation of customised variable element types see Setting Variable Element Types page 56 ConQuest User Guide 37 3 6 4 Automatic Addition of Hydrogen Atoms Hydrogen atoms may be added automatically to substructures The number of hydrogens added to each atom is sufficient to satisfy the atom s unfilled valencies For example auto addition of hydrogens to the following
117. e the queries using logical operations e g to specify a search for structures containing arsenic but not antimony Hit the Search button to start the search see Starting Searches page 27 This opens up the Search Setup dialogue box see Naming Searches and Setting Filters page 28 which can be used to set filters e g for excluding structures with poor R factors see FILTERS SECONDARY SEARCH CRITERIA page 143 Use View Results see Viewing Search Results page 29 to look at the structures found by the search Save the search results see Saving and Reading Searches page 41 or the queries see Saving and Reading Queries page 19 or run another search or exit the program New queries may be built and new searches started while an existing search is running Use the tabs Build Queries Combine Queries and View Results to move between different parts of the program ConQuest User Guide 13 2 2 Building Queries Overview 14 e Queries are built in the Build Queries area This is displayed by default when ConQuest is opened and is accessible at any time by hitting the tab labelled Build Queries The buttons on the left of the Build Queries screen allow different types of queries to be built Button Type of Query Example Draw see SUBSTRUCTURE SEARCHES page 47 Substructure 2D or 3D Find structures containing a cyclopropane ring JOURNAL SEARCHES page 113 Peptide Peptide sequence Find
118. earch Note that the results of a search on Class may not be comprehensive since it is not always evident from a publication that an entry belongs to one of the specified categories Find entries classified as Carbohydrates and Organic polymers Search Store Cancel Reset e To find structures classed as either Carbohydrates or Organic Polymers create and store two ConQuest User Guide 117 separate queries one for Class Carbohydrate one for Class Organic Polymers and then combine them see Complex Query Combinations page 21 e Chemical class searches can be combined with a compound name search see Combining Compound Name and Chemical Class Queries page 118 8 2 3 Combining Compound Name and Chemical Class Queries e Compound name queries can be combined with chemical class searches The Name Class dialogue box would resemble the following if searching for all CSD entries classed as Steroids containing the keywords acetyl and hydroxy NameiClass Quey4 om e Compound Name Contains ceni acetyl hydroxy mt Ignore non alphabetic characters e g butadiene will match buta 1 3 diene a i Delete Chemical Class CCDC Chemical Class is assigned to some categories of entries in the CSD particularly when it would be difficult to locate these categories using a substructure or compound name search Note that the results of a search on Class may not be comprehensive since it is not
119. ed Errors page 243 Turn on the check button to exclude structures containing unfixed errors This can also be done in the Filters section see FILTERS SECONDARY SEARCH CRITERIA page 143 of the Search Setup box Average e s d of C C Bonds see page 214 Select Any allows all structures or lt 0 005A allows only precisely determined structures Exclude powder structures see Powder Data page 237 Turn on the check button to exclude structures determined from powder diffraction studies This can also be done in the Filters section see FILTERS SECONDARY SEARCH CRITERIA page 143 of the Search Setup box Temperature of Structure Determination see page 241 Choose units degrees K or C Select the required mathematical operator see Mathematical Operators page 18 Type a value into the input box ConQuest User Guide 133 eara aira 274 Kyerc Alternatively select room to find structures determined at room temperature 283 303K 14 3 134 Radiation source Select Any to allow all structures X Rays to restrict to structures determined by X ray diffraction Neutron to restrict to structures determined by Neutron Diffraction see page 233 Hints when Searching for Experimental Details R factor In general the lower the R factor the better the structure Look at the Glossary entry on R factor see page 239 for a rough guide to the relationship between R factor and experimental quality Disordered Structures see
120. ed in any form in whole or in part to any third party e Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC Such prior approval is also needed for joint projects between academic and for profit organisations involving use of the CSD System e The CSD System and its Components may be used for scientific research including the design of novel compounds Results may be published in the scientific literature but each such publication must include an appropriate citation as indicated in the Schedule to the Licence of Access Agreement and on the CCDC website e No representations warranties or liabilities are expressed or implied in the supply of the CSD System or its Components by CCDC its servants or agents except where such exclusion or limitation is prohibited void or unenforceable under governing law Licences may be obtained from Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ United Kingdom Web http www ccdc cam ac uk Telephone 44 1223 336408 Email admin ccdc cam ac uk UNITY is a product of Tripos L P and MDL is a registered trademark of Elsevier MDL miomeryata nh Ww Nv 11 12 13 14 15 16 17 18 THE CAMBRIDGE STRUCTURAL DATABASE CSD see page 6 GENERAL FEATURES OF CONQUEST see page 13 SUBSTRUCTURE SEARCHES see page 47 TABULATING GEOMETRIES 3D SUBSTRUCTURE SEARCHES see page 79 NONBONDED CONTA
121. eft hand button again and draw a second bond and then a third to produce ye en E C If you make a mistake here or elsewhere in the drawing area click on Edit in the top level menu and then Undo 3 Add the carbonyl group e Select O from the list of common elements at the bottom of the Draw window e Click on the button next to the word Bond at the bottom of the Draw window and change the bond type from Single to Double e Move the cursor back into the white area and draw a bond to the second carbon in the chain Since the current atom type is O and the current bond type is double this creates an O C bond 0 Ga A 4 Create an acetoxy group e O is the current element so click on the first carbon in the chain to change it to an oxygen D oO A A 5 Create a halogen substituent e Click with the right hand mouse button on the carbon at the other end of the chain Select Element from the pull down menu followed by More from the next menu then Any Halogen ConQuest User Guide 165 The terminal carbon should now have changed to 7A the symbol used in ConQuest to denote the halogen group of elements 6 The fragment is now drawn Do the search Hit the Search button in the bottom right hand corner of the drawing window This produces a pop up window telling you which version of the CSD you are going to search This window allows you to specify some filters Click on 3D coordinates determined to
122. either query or query2 The above commands can be combined e g cqbatch j lt jobneme gt require query Eile name gt not lt query2 file name gt either lt query3 tile name gt lt query3 Tile name gt will retrieve all CSD entries matching guery and either guery3 or query4 which do not match query2 If a qry file has more than one query in it then these will be treated as follows e require rerun the search will find entries that match all queries e not search will find all entries that match none of the queries e either search will find entries that match at least one of the queries If rerun is used with cqs files then the logic from the cqs file will be used If rerun is used with a QUEST instruction file then e ifa QUEST instruction line is present in the file this will be used to dictate the logic e if no QUEST instruction line is found AND boolean logic will be applied to the queries or tests in the file 1 e the search will retrieve entries that match all queries 20 3 Databases e CQBatch will search all databases found in the main CSD directory by default e If this cannot be located the location must be provided via the GUI or through a number of CQBatch command line options none All database files in the default CSD directory will be searched db One or more database _file Full path to one or more database files Only these will be searched if this is the only op
123. elect the All Text button in the Build Queries pane then click on the Required Fields tab and select the keyword Natural Source from the scrolling list see Specifying Required Fields page 137 Space Group There are 230 possible arrangements of symmetry elements in the solid state They are called space groups see International Tables for Crystallography Volume A Kluwer Academic Publishers 1983 Any crystal must belong to one and only one space group The space groups are numbered from 1 to 230 and each is represented by a space group symbol e g space group number 19 has the symbol P212121 For certain space groups it is possible to choose the unit cell axes and or origin in more than one way alternative settings This means that a given space group number can correspond to several space group symbols For example space group number 25 corresponds to Pmm2 P2mm and Pm2m 240 ConQuest User Guide The following trigonal space groups can be described with respect to hexagonal or rhombohedral axes 146 R3 148 R 3 155 R32 160 R3m 161 R3c 166 R 3m 167 R 3 In the CSD the rhombohedral setting is identified by appending the letter r to the space group symbol e g R 3cr In certain situations there is an unresolved ambiguity in the space group determination For example if the crystallographer cannot decide between Pmaa and P2aa then the space group is represented by the so called aspect
124. elected If more than one item is selected from the 3D parameter list the following is possible Ifthe Delete button is hit all selected items will be deleted e Ifthe Options button is hit only those selected will be available via the resulting dialogue When using the All Parameters or All Selected it is possible to define large numbers of geometric parameters A maximum of 150 geometric parameters can be calculated in any one ConQuest User Guide 85 search ConQuest will issue a warning if this number is exceeded BM Too many parameters A The number of defined parameters exceeds search engine limits Number defined 158 Maximum permitted 150 4 5 4 Defining Geometric Parameters Involving Objects The procedure is exactly the same as for parameters involving only atoms see Defining Specific Geometric Parameters Involving Only Atoms page 82 except that objects are picked from the Defined Objects list e For example to specify the distance between an atom and a centroid first create the centroid see Defining Geometric Objects page 80 To construct Parameter Object Select atoms main window or object list below Current Selection Valid Parameters All Parameters Defined Objects CENTI Valid Objects Centroid CENT e Select the atom by clicking on it and the centroid by clicking on its object name CENTI in the above example 86 ConQuest User Guide
125. en gives clues about molecular flexibility Any search in which the number of chemical units or residues is specified is best used in conjunction with other tests to exclude for example multi residue entries containing solvates or ionic compounds ConQuest User Guide 14 SEARCHES FOR EXPERIMENTAL DETAILS 14 1 Typical Uses of Searching for Experimental Details To find structure determinations carried out at high or low temperatures To find structures with accurate hydrogen atom positions i e determined by neutron diffraction To ensure that only precise structures are found or to exclude disordered structures or those with unresolved errors 14 2 Using the Experimental Dialogue Box Open the dialogue box by hitting Experimental in Build Queries R factor see page 239 Choose whether to input as a decimal number valid range 0 1 or a percentage valid range 0 100 Select the required mathematical operator see Mathematical Operators page 18 the usual choice will be lt or lt since structures with low R factors are the most precise Type a value into the input box R factor lt wv fractional Exclude disordered structures see Disordered Structures page 224 Turn on the check button to exclude structures with crystallographic disorder This can also be done in the Filters section see FILTERS SECONDARY SEARCH CRITERIA page 143 of the Search Setup box Exclude structures with unresolved errors see Unresolv
126. end on how the hydrogens are defined when drawing the substructure Hydrogen atoms can be drawn in two ways e Implicitly e g by right clicking on a non hydrogen atom and selecting the menu item Hydrogens from the pull down menu this will be shown as e g SH Hydrogens added in this way are terminal atoms 1 e they cannot be used to retrieve hits with bridging H atoms e Explicitly by actually drawing them this will be shown as e g S H Hydrogens added in this way can be used to define hydrogen bridging positions If a 3D parameter has also been defined then these two alternative ways of defining hydrogen atoms will give different results even if that 3D parameter does not involve the hydrogen atom Thus e Ifthe hydrogen has been defined implicitly it does not matter whether its coordinates are present or absent e Ifthe hydrogen atom has been drawn explicitly its coordinates must be present in the CSD otherwise a structure will not be counted as a hit even if it contains the substructure you have drawn In addition H atoms are considered to form part of a substructure if they might be present by virtue of an Any atom or a multipick selection even if you have not defined H atoms explicitly you may obtain unexpected results Hydrogen Atom Location in Crystal Structure Analyses Hydrogen atoms can be difficult to locate using X ray crystallography especially if atoms of high atomic weights occur in the structure and coordin
127. entally determined bond vector to make the bond length equal to the average neutron diffraction value see Hydrogen Atom Location in Crystal Structure Analyses page 228 Switch on the check box labelled Export largest molecule only if you wish to only write out the largest distinct chemical unit i e molecule in the structure see Molecule page 233 e SHELX simulated SHEL X res file e TAB Tab separated list of text items Click on the check buttons next to individual text items Bibliography Chemical etc to indicate which are to be included e TXT Plain text format Click on the check buttons next to individual text items Bibliography Chemical etc to indicate which are to be included ConQuest User Guide 43 2 20 Transferring Data to Other Programs for Analysis 2 20 1 Transferring Results Directly to Vista or Excel e Depending on whether ConQuest is being run under Unix or Windows data fields and 3D parameters for unsuppressed hit structures see Suppressing Unwanted Entries page 40 can be transferred to Vista and or Excel for statistical analysis Select File from the top level menu and then View in Vista or View in Excel from the resulting pull down menu Alternatively right click in the box containing the hitlist and pick View in Vista or View in Excel from the resulting pull down menu e This generates a dialogue box from which data fields and parameters can be selected e Hit View in Vista or View in
128. entified as being disordered atoms Specifically the display of any atoms that have been suppressed by the CSD editors can be controlled using this feature 2 13 4 Measuring Distances Angles and Torsions There are two ways of measuring distances angles and torsions Method 1 e Right click anywhere in the visualiser area select either Measure or Picking Mode from the resulting pull down menu then select either Pick Distances Pick Angles or Pick Torsions Depending on which mode has been chosen you can then click on two three or four atoms respectively to measure a distance angle or torsion e You will remain in the chosen measurement mode so after measuring the first distance or angle or torsion you can continue measuring others e To get out of the measurement mode right click and select Measure followed by Default Picking Mode Method 2 e If you are in Default Picking Mode select two three or four atoms by clicking on them with the left hand mouse button while keeping the Shift key pressed down Then right click and select Measure from the pull down menu Depending on how many atoms were selected 2 3 or 4 you will be able to click on Distance Angle or Torsion to measure the appropriate parameter e To clear measurements from the display right click and select Clear Measurements ConQuest User Guide 35 2 13 5 Labelling Atoms Right click anywhere in the visualiser area and select Label You will be given the choice of l
129. eries apply Boolean logic Run the search The Example Find structures that e contain 1 or 2 osmium atoms and gt 6 oxygen atoms e do not belong to space group P2 c e were determined either by neutron diffraction or with an R factor lt 0 06 Menu Commands Required l Start ConQuest and hit the Formula button 2 Specify that 1 2 Os atoms and gt 6 O atoms are required 204 e Click in the white box and type Os1 2 O gt 6 ConQuest User Guide Formula New ID Formula Type in formula e g C6 H12 O6 You may specify an inexact formula e g Cal 3 O gt 4 finds entries with 1 2 or 3 Calciums and more than 4 Oxygens or Select from Table Formula applies to an individual molecule all molecules in structure added together W Other atoms allowed in molecule structure Search Store Cancel Reset Hit Store to transfer the query to the Build Queries page 3 Setup a space group query for P21 c e Hit the Space Group button e Type P2 c into the space group box or select this symbol from the list Space Group 1 New Space Group Enter full or partial space group symbol or number P21ic oF pick from list Click on symbol to select Panen Current Space Group with alternative settings gg Include alternative settings P21 c of selected space group B21fa B2lic Only include space groups in which a chiral molecule can crystall
130. ery labelled Query 1 press down on the left hand mouse button and drag the icon into the box labelled must have 206 ConQuest User Guide Find entries that must have booieat AND Query 1 e Drag the space group query icon Query 2 into the box labelled must not have e Drag both of the remaining queries into the box labelled must have at least one of Find entries that must have booieat AND Query 1 must not have NOT Query 2 must have at least one of 2A Query 3 Query 4 7 Run the search e Hit the Search button at the bottom left hand corner of the window e The pop up confirms that the search will be for structures that satisfy Query 1 i e have Os1 2 O gt 6 do not satisfy Query 2 i e do not belong to the space group P21 c and satisfy Query 3 or Query 4 i e determined by neutron diffraction or with an R factor lt 0 06 or both e Hit Start Search to begin the search This ends the tutorial ConQuest User Guide 207 22 APPENDIX A GLOSSARY AND TECHNICAL DETAILS This section is a glossary of information fields and terminology you may come across when using ConQuest 208 Absolute Configuration see page 210 Angles see page 210 Aromatic Bonds see page 211 Asymmetric Unit see page 211 Atomic Charge see page 212 Atomic Coordinates see page 212 Atomic Displacement Parameters ADPs see page 213 Atomic Labels see page 213 Authors Names see p
131. etween these two functional groups when acetylcholine and its analogues bind to the enzyme acetylcholinesterase Menu Commands Required 1 Start ConQuest and hit the Draw button to open the drawing window ConQuest User Guide 191 2 Draw the two fragments e Remember to put a charge of 1 on the nitrogen e g by right clicking on the N atom and selecting Charge Positive and then 1 from the resulting pull down menu e If you have problems drawing the substructures go back and do tutorials 1 and 2 cH CH3 cH 3 Define the centroid of the carbonyl group e Hit the ADD3D button at the left hand side of the Draw window e Click on both atoms of the carbonyl group e Click on the button labelled Define next to the word Centroid To construct Parameter Object Hit Define to construct Parameter Object Current Selection C506 Valid Parameters i All Parameters All Selected Define SRE RURAL Distance Define Defined Objects Valid Objects Dummy Point Define Centroia Define Done 192 ConQuest User Guide 4 Define the distance between the N atom and the centroid of the C O group e Select the N atom by clicking on it e Select the centroid of the carbonyl group by clicking on CENTI in the box headed Defined Objects e Hit the Define button next to the word Distance To construct Parameter Object Hit Define to construct Parameter Object
132. example below the centroid of the three ring carbon atoms has been defined 80 ConQuest User Guide To construct Parameter Object Select atoms main window or object list below Current Selection Valid Parameters All Parameters Defined Objects CENTI valid Objects comua ETN e An extra step is required for the definition of a dummy point definition of the distance from the second selected atom at which to create the dummy point this distance can be negative see Dummy Points page 225 Method 2 e Go to EDIT mode and select see Selecting Atoms and Bonds page 50 the atoms required for the object Hit 3D in the top level menu and then pick the relevant object in the resulting pull down menu e The object will be defined immediately except for Dummy Points see page 225 where an extra step 1s required see above Once defined objects can be used to create geometric parameters e g distances between centroids or angles between planes see Defining Geometric Parameters Involving Objects page 86 4 4 3 Displaying Geometric Objects in the Draw Window A defined object may be displayed by clicking on its name in the Defined Objects list This may be found in the Geometric Parameters dialogue box opened by hitting the mode button ADD 3D 4 4 4 Deleting Geometric Objects An object may be deleted by opening the Geometric Parameters dialogue box click on the ADD 3D button clicking on t
133. ext residue e A residue can be deleted from a sequence by right clicking on it and selecting Delete from the resulting pull down menu ConQuest User Guide 109 A residue in a sequence can be changed by right clicking on it selecting Replace by in the resulting pull down menu and then Residues in the next menu This produces a series of menus from which the desired amino acid can be selected Alternatively hitting Replace by followed by Other or User defined allows selection of a variable amino acid type An end residue in a sequence can be specified as terminal by right clicking on it A bond in a sequence can be changed to a different type i e peptide non peptide or either by right clicking on it selecting Modify in the resulting pull down menu and then picking the required type Variable residues can be defined and included in the sequence if desired 6 2 2 Specifying a Variable Amino Acid Residue Searches may be performed for generified sequences where one or more of the residues is variable e Use the ANY button to add a residue which will match any amino acid For example GLU ANY SER will find all of GLU AIB SER GLU ALA SER GLU ARG SER etc e To define a variable residue hit the Construct button select the required amino acids from the resulting Build user defined residues dialogue box and hit Apply This will add a new button labelled QAA to the Peptide builder dialogue box Clicking on this button after cl
134. find molecules or structures containing C and any of the Group 4B elements Ti Zr or Hf Elements Required to be Present 4B Cl e The element groups are pre defined in the CSD and cannot be changed but there is a way to define and search for any required combination of elements in the Draw window see Setting Variable Element Types page 56 9 2 3 Specifying the Heaviest Allowed Element e Specifying the heaviest allowed element is a way of avoiding imprecise structures This is because there may be large experimental errors in light atom positions when a structure containing a very heavy element is determined by X ray diffraction e To specify the heaviest allowed element type the required element symbol into the appropriate input box in the Elements dialogue box Alternatively you can avoid typing by hitting Select from Table and picking from the Periodic Table e The search will reject any structure containing an element heavier than the one specified The example below would reject any structures containing an element heavier than Br This does not ConQuest User Guide 121 9 3 122 mean that Br must be present only that nothing heavier than Br can be present Heaviest Pennitted Element in Formula Unit Br Br Bromine Select from Table Hints for Chemical Element Searching Normal Periodic Table element symbols and CSD preset element group symbols may be used see Element Group Symbols page 225 Use the same molecul
135. following information fully described elsewhere e Bibliographic textual and numerical information e Chemical diagram e Crystal structure data e Filters secondary search criteria 1 4 Refcodes CSD Entry Identifiers and Deposition Numbers Each CSD entry is identified by a unique Refcode entry ID see page 238 comprising e Six letters e g ABACOF e Two digits identifying additional structure determinations e g ABACOF03 The CSD also records a variety of Deposition Numbers see page 224 published by many primary journals to identify crystallographic data deposited with the CCDC 1 5 Information Content of the CSD The searchable information fields for a CSD entry may include those listed above ConQuest User Guide 7 1 5 1 Bibliographic Information in the CSD e Authors Names see page 213 e Journal Name see page 229 e Journal Volume see page 230 e Journal Page see page 230 e Journal Year e Publication DOI Further information is also stored with the above information e g cross references to related structures details of re interpretations or re determinations or if the entry is a has come from a source other than a the published literature see Private Communications page 237 Approximately three quarters of the structures in the database also have a hyperlink to the article that discloses the structure This is normally accessed via CrossRef http www crossref org though links are also available where
136. fy whether the formula is that of a single 124 molecule or of all the molecules in the structure added together For example the crystal structure acetylcholine perchlorate contains two individual ions with formulae C7 H16 N1 O2 acetylcholine and C11 O4 perchlorate the formula of the individual ions added together is C7 H16 N1 O6 Cll Choose one of the buttons an individual molecule or all molecules in structure added together to select whether the specified formula applies to an individual molecule or ion or all the molecules or ions in the structure added together ConQuest User Guide 10 2 3 Specifying Whether Other Elements are Allowed In searching for a chemical formula you can specify whether any other elements are allowed apart from those contained in the formula you have specified Ifthe check button Other atoms allowed in molecule structure is turned off then no element other than those in the specified formula may be present The example below would find benzene C6 H6 but not phenol C6 H6 O because the Other atoms allowed in molecule structure option is switched off Formula CeH Type in formula e g C6 H12 06 You may specify an inexact formula e g Cal 3 0 gt 4 finds entries with 1 2 or 3 Calciums and more than 4 Oxygens or Select from T able Formula applies to an individual molecule C all molecules in structure added together T Other atoms allowed in molecule structure 10 3 Hints for Che
137. g 12 Specify that the ring atoms cannot be directly linked to one another e Return to DRAW mode e Select Bonds from the top level menu and Exclude from the pull down menu e Select Direct Links and click on all of the atoms in the 5 membered ring e Hit OK 13 Start the search and reject structures with R gt 10 e Hit the Search button e Switch on the R factor filter in the pop up window and select lt 0 1 This will exclude structures with R factors greater than 10 which tend to be inaccurate Hit Start Search 14 Save the hits in mol2 format e Stop the search after you have found a few hits Note that in each chemical diagram the search substructure is highlighted in red e Save the 3D coordinates of the hits by selecting File from the top level menu and Export Entries as from the pull down menu Set the file type to MOL2 make sure All selected entries is switched on to save all the structures not just the one currently on display and hit Save This ends the tutorial ConQuest User Guide 173 21 3 Tutorial 3 Defining and Saving Geometric Parameters Objectives e To draw a chemical fragment and define geometric parameters of interest e To search the CSD for entries which contain the fragment e To view the geometric parameters for each hit entry e To write out a file of the geometric parameters for analysis in Vista or Excel Steps Required e Draw the fragment e Define the 3D para
138. g a density is unlikely to be exactly 2 000 Specify a range instead Calculated Deneity ig cat3 range fi 35 2 4 5 Closing and Resetting Dialogue Boxes Most dialogue boxes have the following four buttons e Search Starts a search with the query that has been defined in the dialogue box Also closes the dialogue box and stores the query in the Build Queries and Combine Queries areas e Store Stores the query in the Build Queries and Combine Queries areas and closes the dialogue box but does not start a search e Cancel Cancels all input and closes the dialogue box e Reset Deletes all input but leaves the dialogue box open 2 5 Keyboard Shortcuts A set of keyboard shortcuts are available for some menu items These are indicated next to the menu item for example in the top level File menu Fle Edit Options View Databases PEU aiat Open Read Queries Ctri R 18 ConQuest User Guide 2 6 2 7 Editing and Deleting Queries Editing queries Go to Build Queries or Combine Queries and click on the Edit button next to the query to be edited or double click on the contents of the query box Deleting queries Go to Build Queries or Combine Queries and click on the Delete button next to the query to be deleted To undo this action select Edit from the top level menu bar and Undelete Queries from the resulting pull down menu Saving and Reading Queries Saving queries Go to Build Queries or Combine Queries
139. gt where lt file gt is either a cqs gry mol or QUEST instruction file e one or more of require not either with each followed by one or more qry or mol files A jobname must be provided using the j lt jobname gt command Note rerun cannot be used with require not either To run a straightforward query using CQBatch assuming the correct environment variables and aliases are set the following command would be used where structure qry is the query cgbatch j lt jobname gt rerun structure qry 20 2 Logic e Boolean logic can be applied to searches run using CQBatch The following commands correspond to the AND NOT and OR options available in ConQuest s Combine Queries pane see Combining Queries page 20 e require will perform a boolean AND search using the specified queries e g the command ConQuest User Guide 153 cqbatch j lt jobname gt require lt queryl file name gt lt query2 file name gt will retrieve all CSD entries that match query1 and query2 e not will perform a boolean NOT search using the specified queries e g the command cqbatch j lt jobname gt not lt queryl file name gt lt query2 file name gt will retrieve all CSD entries that do not match guery and query2 e either will perform a boolean OR search using the specified queries e g the command eqbatch j lt jobname gt either lt queryl file name gt lt query2 file name gt will retrieve all CSD entries that match
140. h for refcodes which contain less than six characters e g CYCBO This search will return all refcodes with the query text however please note that these refcodes are not necessarily related to one another 16 3 Saving and Reading Refcode Lists 142 To save a list of Refcodes ensure that it is currently on display in View Results if it is not display it by using the Results top level menu option then select Searches from the resulting pull down menu to display the search of your choice see Switching between Searches page 40 Pick File from the top level menu followed by Export Entries as in the resulting pull down menu then click on the file type bar and select Refcode csd entry identifier list from the pull down menu to save e the individual structure currently being displayed turn on Current entry only or e all unsuppressed structures in the hit list turn on All selected entries see Suppressing Unwanted Entries page 40 Saved Refcode lists will be given the extension gcd which can be read back into ConQuest and displayed as if the search had just been run To read a previously saved Refcode list pick File from the top level menu followed by Open and then select Refcode List from the resulting pull down menu Loading a refcode list for the first time may result in a progress window If you have previously loaded Refcode lists resulting from searches in the same ConQuest session these can be viewed by selecting
141. he Draw window In the example below the N O distance has been defined and named DISTI by default To construct Parameter Object Select atoms from main window Hit Define to construct Parameter Object Current Selection N1 05 Valid Parameters All Selected Define Distance GET Defined Objects Options Valid Objects Define Define Delete Reset Done e Once a parameter has been defined its value can be constrained see Applying Geometric Constraints page 88 4 5 3 Defining All Geometric Parameters Involving Atoms All geometric parameters in a substructure or all parameters described by manually selected atoms within a substructure can be defined ConQuest User Guide 83 To define all geometric parameters in a substructure Draw the substructure as normal then click the ADD 3D button e Click on the All Parameters button in the Geometric Parameters window Current Selection All atoms Define all Bonds 12 selected Tabulate J Values _ Sum Average J Minimum J Maximum AEA pa 6 a ny eee erowps e The whole substructure will become highlighted and the All Parameters window will appear e From this window it is possible to define all parameters for atoms bonds angles and or torsions The number of selected atoms bonds angles or torsions in the substructure will be
142. he New Box button and type the required words into separate input boxes The example below will find entries containing the words methanol and solvate but these words do not need to be next to each other in the text comment New Box or enter in box es below methanol To find entries containing either of two keywords e g needle or plate create and store two separate queries and combine them see Complex Query Combinations page 21 136 ConQuest User Guide e All Text and Required Field searches can be combined in an AND search within the All Text dialogue box see Combining All Text and Required Fields Searches page 138 15 2 2 Specifying Required Fields This sort of search will retrieve hits based on information being present in particular fields e g crystal colour habit etc Field information is stored with the CSD entry if it has been provided in the publication thus some entries may not have details present in particular fields It is possible to combine a Required Fields search with an All Text search to refine the hitlist obtained see Combining All Text and Required Fields Searches page 138 e Open the dialogue box by hitting All Text in Build Queries then click on the Required Fields tab e Select the desired keyword from the Optional Fields scrolling list and click Add to create an entry in the Required Fields box The example below will find all entries containing information in the Habit field
143. he object name in the Defined Objects list and then hitting the Delete button underneath this list ConQuest User Guide 8l 4 5 Geometric Parameters Geometric parameters may be defined when drawing a substructure in the Draw window These parameters can then be listed or tabulated after the search has been run see Basic Guide to Tabulating Geometries page 79 They can also be used to set up 3D substructure searches e g a search for a substructure in which a distance has been constrained to a particular range see Applying Geometric Constraints page 88 4 5 1 Valid Geometric Parameters Valid geometric parameters are Atomic Labels see page 213 although not strictly geometrical parameters it is useful to be able to tabulate the labels of variable atoms i e atoms in the substructure whose element type can vary see Setting Variable Element Types page 56 It is then possible in programs such as Vista see page 246 to discern differences and trends between different elements at that particular position Distances see page 225 between atoms and or objects the atoms do not need to be bonded to each other Angles see page 210 between atoms and or objects the atoms do not need to be bonded to one another Torsion Angles see page 242 involving atoms and or objects the atoms do not need to be bonded to one another 4 5 2 Defining Specific Geometric Parameters Involving Only Atoms 82 e Geometric parameters must be e
144. hich hydrogens are to be added and hit Done In EDIT mode select see Selecting Atoms and Bonds page 50 the atom s to which hydrogens are to be added Then hit Atoms in the top level menu Hydrogens in the resulting pull down menu and pick the required number of hydrogens as above e Hydrogen atoms may also be added automatically see Automatic Addition of Hydrogen Atoms page 58 ConQuest User Guide 59 3 6 6 Setting Atomic Charges The formal integer Atomic Charge see page 212 of an atom may be specified in several ways including In DRAW or EDIT mode click on the atom with the right hand mouse button pick Charge from the resulting pull down menu then select the charge required from the second pull down menu Unspecified in this menu means that any charge is allowed Any means any non zero charge Clicking on Other opens up a dialogue box which allows the specification of variable charges The example below specifies that the atom must have a charge of or 2 Charge Enter charge Values can be between and including 6 and 6 Multiple values can be entered separated by a space or comma In DRAW or EDIT mode click on Atoms in the top level menu select Charge from the resulting pull down menu then pick the required charge as above The Select Atoms pop up appears click on the atom s to which the charge is to be assigned and hit Done In EDIT mode select see Selecting Atoms and B
145. hols and boron atoms in boron cages It is advisable to check the number of H atoms added to these types of structures You can alter or explicitly define the number of hydrogens on an atom by adding them manually see Adding Hydrogen Atoms Manually page 59 3 6 5 Adding Hydrogen Atoms Manually Hydrogen atoms may be drawn in the same way as any other type of atom or they may be defined implicitly These two different ways may occasionally give different search results see Hydrogen Atoms in 2D 3D Substructure Searching page 227 Hydrogens may be added implicitly in several ways including In DRAW or EDIT mode click on an atom with the right hand mouse button pick Hydrogens from the resulting pull down menu then select the number of hydrogens required from the second pull down menu Unspecified in this menu means that any number of hydrogens is allowed Clicking on Other opens up a dialogue box which allows the specification of numbers greater than 4 or variable numbers of hydrogens The example below specifies that the atom must be bonded to 1 2 or 3 hydrogens Hydrogen Count Enter number of hydrogens 0 9 Multiple values can be entered OK separated by a space or comma P Ae Cancel In DRAW or EDIT mode click on Atoms in the top level menu hit Hydrogens in the resulting pull down menu then select the required number of hydrogens as above The Select Atoms pop up appears click on the atom s to w
146. ill resemble the following Select Previous CSD Version W Restrict based on CSD version added before CSD version 5 27 Nov 2005 y 1_ Sep 2004 The Entries pull down menus are used to indicate if the search should include Entries added before or after a particular CSD release or if the Entries have been modified before or after a particular CSD release e Select the CSD version of interest from the central pull down menu e g CSD version 5 25 Nov 2003 e The date underneath the database menu will update automatically to reflect the choices made in the Entries and database pull down menus e To restrict the search to a particular date select Other located at the bottom of the databases pull down menu and pick the date of interest e Once the selection has been made click OK to save the changes then click OK again to return to the Search Setup window e The Search Setup window will reflect the changes made in the Select Previous CSD Version window ConQuest User Guide 147 Search Setup a IO Search Name search Filters Advanced Options i Available Databases _ 3D coordinates determined I R factor lt CSD version 5 27 November 2005 J Not disordered Enines modifed since CSD version 5 25 Nov 2823 oniy J No errors Not polymeric You can search complete database s or a subset e g hits found in a previous search 1 No ions
147. ind structures whose names contain either thiazol or fluoro create and store two separate queries one for Name thiazol one for Name fluoro and then combine them see Complex Query Combinations page 21 If two separate words are typed into the same box e g benzoic acid a hit will only occur if the whole text string including the space is matched e Compound name searches can be combined with a chemical class search see Combining Compound Name and Chemical Class Queries page 118 8 2 2 Using the Chemical Class Dialogue Box CCDC Chemical Class is assigned to some categories of entries in the CSD to further facilitate searching Please note that the results of a chemical class search are not comprehensive since it is not always obvious from a publication if an entry belongs to a particular category e Open the dialogue box by hitting Name Class in Build Queries e Select the appropriate class from the Find entries classified as pull down menu e g Carbohydrates e Clicking Search at this point will return all CSD entries classed as Carbohydrates Alternatively a second category can be specified using the second pull down menu e g Organic Polymers This will return hits classed as Carbohydrates AND Organic Polymers Chemical Class CCDC Chemical Class is assigned to some categories of entries in the CSD particularly when it would be difficult to locate these categories using a substructure or compound name s
148. indow draw two separate i e unconnected substructures a substructure may consist of a single atom e g 96 ConQuest User Guide e Either select Define Nonbonded Contact from the top level 3D menu or hit the CONTACT button located at the left hand side of the drawing area e Pick the two atoms which are to be in contact c CONTACT lt new gt Hit Define to create contact or deselect atoms ATOM O5 ATOM H4 Vv Vv v Vv Define Groups Hf ofn s e Fl al nyt e Hit Define e By default the search will find all intermolecular contacts shorter than the sum of the Van der Waals Radii see page 243 of the atoms involved To accept this default hit Done and then Search in the Draw window The use of van der Waals radii to specify contact distances is only meaningful for interactions between non metals e If you are searching for contacts to C H N H or O H hydrogen atoms you may wish to normalise the H atom positions which corrects for systematic errors in the location of hydrogen atoms by X ray diffraction This cannot be done in the Draw window Instead it must be done in the Search Setup dialogue box which is displayed whenever you hit a Search button e To allow intramolecular contacts see Searching for Intramolecular Contacts page 97 or to alter the distance constraint see Specifying Distance Limits for Nonbonded Contacts page 99 hit Edit 5 2 2 Searching for Intramolecular Contact
149. ing Searches page 41 e Elect to run the search on a subset of the CSD or on an in house database of crystal structures should you have one available see VIEWING and SEARCHING IN HOUSE DATABASES DATABASE SUBSETS and Previous CSD Versions page 145 e Select filters i e additional search requirements e g reject disordered structures reject polymers see FILTERS SECONDARY SEARCH CRITERIA page 143 e Set advanced options currently the only one available is to standardise hydrogen atom positions e Cancel if Search was hit by accident e Select Reset to return to the status of the Search Setup dialogue box when first displayed e Hit Start Search to run the search 28 ConQuest User Guide 2 12 Viewing Search Results Structures found by a search can be viewed on the View Results screen 2 12 1 Monitoring Progress During a Search e As structures are found their refcodes are transferred into a list on the right hand side of View Results see Selecting Individual Structures for Viewing page 30 e Structures can be viewed as soon as they are found The progress of the search is indicated by a bar showing the percentage of the database that has been searched The number of hits found so far is also shown 716 hits ConQuest User Guide 29 2 12 2 Selecting Individual Structures for Viewing e Any structure found by a search can be selected for viewing whether or not the search is still running by clicking
150. ion number page 115 e For IUCr deposition numbers select the All Text button in the Build Queries pane see Using the All Text Dialogue Box page 135 Disordered Structures Disordered structures display a lack of regularity For example each of the F atoms in the trifluoromethyl group CF3 might be randomly distributed between 2 sites This means that the crystallographer will report two sets of coordinates for each F atom In some cases two alternative sites are occupied equally in other cases there is a major site and a minor site Disorder can involve more than two sites and it can also involve a whole molecule Disordered atoms can be hidden when viewing the structure in 3D see Changing Display Styles and Display of Hydrogen Atoms page 34 The nature of the disorder is briefly described in a text comment e g The anion is disordered over two positions with equal occupancy To Search to reject disordered structures e Select the Experimental button in the Build Queries pane see Using the Experimental Dialogue Box page 133 e Use the Filters menu in the Search Setup dialogue box see Applying Filters page 143 Related Topics e Occupancy Factor see page 234 224 ConQuest User Guide Distances Distances in A can be calculated between atoms dummy points centroids and planes Related Topics e Angles see page 210 e Torsion Angles see page 242 Drug Activity Comments about drug activity or biological ac
151. ion has been used by looking at the way in which the journal name is written in the list box e Some journals do not have volume numbers most notably the journals of the UK Royal Society of Chemistry e Journal pages are normally numeric but can occasionally contain letters e g C 43 e The year must contain four digits e g 1987 ConQuest User Guide 115 8 COMPOUND NAME AND CHEMICAL CLASS SEARCHES 8 1 8 2 Typical Uses of Compound Name or Class Searching Using names or partial names as a quick way of finding examples of a certain type of structure e g thiazole derivatives but search for thiazol not thiazole Using common names to locate drugs and natural products e g morphine Finding certain types of compounds which are difficult to find by substructure searching e g rotaxanes catenanes Retrieving all entries that belong to a specific class or classes of compounds e g Nucleotides and nucleosides Steroids Using the Compound Name and Chemical Class Dialogue Box The Name Class dialogue box is split into two parts Compound Name see Compound Name Searching page 116 Chemical Class see Using the Chemical Class Dialogue Box page 117 It is also possible to combine Compound Name and Chemical Class searches see Combining Compound Name and Chemical Class Queries page 118 8 2 1 Compound Name Searching 116 Open the dialogue box by hitting Name Class in Build Queries Type the required compound name
152. ious by right clicking anywhere in the visualiser area selecting Highlight Hit from the resulting pull down menu and then selecting Normal Contrast More Contrast or Less Contrast as desired Alternatively it can be switched off altogether by selecting No Contrast this is useful if you want to display nonbonded contacts without highlighting Rather than highlighting the hit fragment it can be shown in other ways by right clicking anywhere in the visualiser area selecting Highlight Hit from the resulting pull down menu and then selecting Hit as Capped Stick which displays the hit fragment in capped stick style only available if the current display style is wireframe or Single Colour which displays the hit fragment coloured by element type and the rest of the structure in one colour If an entry contains more than one hit fragment i e the query substructure can be matched onto the entry in two or more different ways this will be indicated by the presence of the words Which match beneath the visualiser display area Clicking on the arrows next to this text shows each substructure match in turn or all of them at the same time This option is only available if a 3D or nonbonded contact search has been done otherwise only one arbitrarily chosen hit fragment is shown even if the entry contains more than one ConQuest User Guide e Hit fragment highlighting is transferred to Mercury when View in Mercury is selected see see page 45 Fo
153. ise Dr not defined z e There are a number of alternative settings for this space group e g P21 c and P21 a are the same space group but with a different choice of cell axes We can choose to find all the alternative settings or just the P21 c setting The former is almost always the sensible choice So ensure that the Include alternative settings of selected space group check box is switched on ConQuest User Guide 205 Hit Store 4 Set up a query for neutron diffraction structures e Hit the Experimental button e Change the Radiation Source from Any to Neutron e Hit Store 5 Set up a query for structures with R factors lt 0 06 e Hit the Experimental button e Change the button next to R factor from to lt e Type 0 06 into the input box thus specifying structures with R factors below 6 R factor ool fractional v _j Exclude disordered structures Exclude structures with unresolved errors Average e s d of C C Bonds Any Exclude powder structures Temperature of a a Structure Determination aie M S a l 0 610K Room Temperature AR vaties in the range 283 303 K are stored as Room Temperature Radiation Source Any Search Store Cancel Reset ey e Hit Store 6 Combine the queries e Click on Combine Queries e Position the cursor over the top query icon i e the white square next to the formula qu
154. itch on to exclude structures in which the data was obtained from a powder diffraction study see Powder Data page 237 This can also be done in the Experimental dialogue box see Using the Experimental Dialogue Box page 133 Only Organics see page 235 or Only Organometallics see page 235 Switch on the check button and then click on the appropriate radio button to restrict the search to 1 organic structures only or 11 organometallic structures only 17 4 Default Filter Settings 144 To control which filters see Available Filters page 144 are displayed in the Search Setup dialogue box which is displayed every time a search is requested select the top level menu button Options followed by Filters then Filters to Display in the resulting pull down menus To make a filter available enable the check button next to the filter Settings are retained between ConQuest sessions To control which of the visible filters are by default turned on when the Search Setup dialogue box is opened for the first time in a ConQuest session select the top level menu button Options followed by Filters then Default Filter Settings in the resulting pull down menus To apply a filter enable the check button next to the filter Settings are retained between ConQuest sessions ConQuest User Guide 18 VIEWING AND SEARCHING IN HOUSE DATABASES DATABASE SUBSETS AND PREVIOUS CSD VERSIONS 18 1 Viewing In House Databases e If you have used th
155. itional non standard fields containing CSD specific information e g information about whether the structure has unresolved errors It is possible to export data calculated through the use of defined geometric parameters by switching on the Output defined parameters check button For more details refer to CIF export above COORD see COORD Format page 221 Use the buttons to control whether fractional or orthogonal atomic coordinates are written out and whether the complete structure is required or just those atoms in the structure that match the search substructure TSV Tab separated values This format can be used to import references into the EndNote software tool for publishing and managing bibliographic data see Attp www endnote com FDAT see FDAT Format page 227 CCDC format for crystal structures necessary for transferring structures into Pluto see page 236 MOL2 see Mol2 Format page 233 Tripos Inc format for 3D molecules and crystal structures Switch on the check box labelled Normalise H coordinates if you want C H N H and O H hydrogen atom positions standardised the H atom will be moved along the experimentally determined bond vector to make the bond length equal to the average neutron diffraction value see Hydrogen Atom Location in Crystal Structure Analyses page 228 The Use CCDC bond types check box can be used to specify whether or not CCDC bond type assigmants are written to output files see Bond Type Conve
156. jects see Defining Geometric Objects page 80 e g the centroid of a ring ConQuest User Guide 91 File Edit Atoms Bonds 3D Options Help Select atoms to define 3D Parameters or Objects Defined Centroid CENT1 C2 C3 C4 C5 C6 C1 3D Parameters Tef SA a DRAW EDIT ERASE To construct Parameter Object ADD 3D Select atoms main window or object list below CONTACT Current Selection e Valid Parameters All Parameters Defined Objects CENTI valid Objects RingMaker Delete Templates E HY Of R S Pf FY a orea Groupa J Reset Done In ADD 3D mode select the two atoms or objects involved in a distance that you wish to constrain Atoms are selected by clicking on them objects are selected by clicking on the object name in the list of Defined Objects e g ConQuest User Guide File Edit Atoms Bonds 3D Options Help Select atoms to define 3D Parameters or Objects DRAW EDIT ERASE To construct Parameter Object ADD ID Select atoms main window or object list below CONTACT Hit Define to construct Parameter Object Current Selection cenm or Valid Parameters l All Parameters i Atom Properties Define i Define Defined Objects i Valid Objects vector Define Dummy Point Define i Centroid Define ey eff of nf sf 6 af Any more crops m e Selec
157. jobname gt The CQBatch run requires a name lt j obname gt i e the cqs output file plus any other output files generated from the run are assigned the name lt j obname gt rerun lt query filename s gt Use this command to re run a search or query This option cannot be used with require not or either require lt query filename s gt Boolean AND logic is applied to the query files in the case of cqs files the command line logic is applied if no logic is stored within the file not lt query filename s gt Boolean NOT logic is applied to the query files in the case of cqs files the command line logic is applied if no logic is stored within the file either lt query filename s gt Boolean OR logic is applied to the query files in the case of cqs files the command line logic is applied if no logic is stored within the file restrict This option allows searches to be restricted to entries in a particular file e g a previ ously saved refcode list see Searching Hits from a Previous Search in the Current ConQuest Session page 149 query directory Rerun all valid files in directory 162 ConQuest User Guide file filter filter query directory valid only with query directory use as query Use entries or search results as queries query options Options controlling quer
158. k Acta Cryst B62 567 579 2006 DOI 10 1107 S0108768106019677 Classroom subset Classroom ConQuest is a version of ConQuest which has been designed for group teaching activities It has all the functionality of normal ConQuest with the limitation that searches can only be done on a subset of entries The subset of entries can either be the default selection supplied with Classroom ConQuest or one derived by the user ConQuest User Guide from the main CSD see USING CONQUEST FOR TEACHING CLASSROOM CONQUEST page 151 Once a pre defined hitlist has been selected wait a moment while the subset is loaded indicated by the progress bar reaching 100 Then hit OK Hit Start Search to begin the search The resulting search will be restricted to only those entries that are part of the pre defined hitlist Hit Clear Subset when the Search Setup dialogue box is next opened to revert to searching on the complete database 18 3 3 Searching Hits from a Previous Search in the Current ConQuest Session Build the query as usual and hit Search Then hit the Select Subset button in the Search Setup dialogue box Select Entries in a hitlist loaded this session Click on the button underneath the words Restrict based on search this session and select the required search If you are unsure which is which you will need to go back to View Results and look at the search results see Switching between Searches page 40 Wait a moment while the subset is lo
159. l This is because names may have derivative endings e In searching for the presence of specific elements use only the root name of the element e g platin Also remember variants such as iron ferr i ferr o etc It is normally better to use an element search see Searching for Specific Elements page 120 e Searches for trivial names drug names etc can be useful The trivial name is usually the only name stored for natural products such as alkaloids and terpenes e Names of certain compounds will always contain a keyword see Compound Name Keywords Indicating Structure Type page 220 included as a search aid e g catenane fullerene e Names of hydrates will contain the words monohydrate dihydrate etc If other solvents are present the name will contain the word solvate e Deuterated species will always contain the name root deuter e It is not yet possible to search for an exact compound name a search for an exact compound name will also retrieve all hits in which the exact compound name you specified is included so for example a search for ferrocene will also retrieve acetyl ferrocene The Find exact word only check box within the Name Class dialogue does provide the option to search on an exact word e g a search on hydrazine will not match acetylhydrazine however this does not represent an exact compound name search e A chemical class search for e g Steroids is not a comprehensive search for all steroids stored in
160. l atom in an existing substructure by a chemical group e Expand a chemical group so that all its atoms and bonds are shown in full e g e Access and add to the drawing area a standard templates i e one of a set of templates supplied ConQuest User Guide 69 with ConQuest see Accessing Standard Substructure Templates page 71 e Access and add to the drawing area a customised template which you have drawn previously and saved for future use see Saving and Using Customised Templates page 71 3 11 1 Adding a Chemical Group to an Existing Atom This can be done in several ways including In DRAW or EDIT mode right click on the atom to which the group is to be added select Add Group from the resulting pull down menu then pick the group you want from the subsequent menus In DRAW or EDIT mode select Atoms from the top level menu then hit Add Group and pick the group you want from the subsequent menus You will then be asked to pick the atom s to which the group is to be added Select the atoms to which you want to add a group Then hit Atoms in the top level menu Add Group from the resulting pull down menu and pick the group you require In DRAW mode change the current element type to a chemical group by hitting the Groups button at the bottom of the window and selecting the required group from the subsequent menus You can then draw groups in exactly the same way as you would normally draw an atom A comple
161. lable Databases window 18 2 Searching In House Databases e If you have used the CCDC program PreQuest see page 237 to build a database of your own ConQuest User Guide 145 crystal structures in CSD format the database can be searched in ConQuest e You must first configure ConQuest so that it can find the database see CSDS Release amp Installation Notes e You can then perform searches on the in house database either on its own or together with the CSD e Construct your query as usual and hit Search A list of available databases will be displayed in the resulting Search Setup dialogue box e g Search Setup Search Name search Filters Advanced Options Available Databases 3D coordinates determined RSE Rfactor W CSD version 5 27 November 2005 Inhouse Database 1 version 1 5 January 2005 _ Not disordered J No errors d Not polymeric You can search complete database s or a subset e g hits found in a previous search No ions Select Subset J No powder structures J Only Single query being used Search will find structures where this query is true Start Search Cancel e Switch on the database s that you want to include in the search e Once you have made your database selection hit Start Search to begin searching e ConQuest can handle more than one in house database if necessary 18 3 Searching Database Subsets Rather than searching the whole of the CSD it i
162. lane PLN 6 Plane defined by a point and a line pE 7 Centroid defined by points Centroid CENT 8 Normal line defined by a point and a plane 9 Distance defined by two points and a range Distance DIS 10 Distance defined by a point line and a range 11 Distance defined by a point plane and a range Distance DPP 12 Angle defined by three points and a range Angle ANG 13 Angle defined by two lines and a range 14 Angle defined by two planes and a range Angle APP 15 Dihedral angle defined by four points and a range Torsion TOR 16 Exclusion sphere defined by a point and a distance 17 Fixed atoms ConQuest User Guide 19 Queries saved from ConQuest are stored in files with the extension gry Queries which can be read into ConQuest have either a gry or mol extension 2 8 Combining Queries 2 8 1 Reasons for Combining Queries Finding entries that stmultaneously satisfy two or more search conditions e g contain arsenic and determined at low temperature Finding entries that do not satisfy a search condition e g do not contain arsenic Finding entries that satisfy some search conditions but do not satisfy others e g contain arsenic but were not determined at low temperature Finding entries that satisfy at least one of a number of search conditions e g contain arsenic or were determined at low temperature 2 8 2 Simple Query Combinations 20 Simple query combinations can be
163. ld Queries pane see Using the Space Group Dialogue Box page 126 Related Topics e Space Group see page 240 e Unit Cell Parameters see page 242 Cyclicity Cyclicity refers to whether or not an atom or bond is part of a ring i e cyclic or acyclic 222 Related Topics e Chemical Diagram see page 217 ConQuest User Guide Delocalised Double Bonds Delocalised double bonds are used in the CSD to describe the bonding in some delocalised structures An example is metal coordinated carboxylate Rather than drawing one of the C O bonds as single and one double i e O C O both bonds are assigned the delocalised double bond type O C O This is an attempt to reflect the fact that the C O bonds are equivalent to each other The correct bond types must be specified in substructure searching otherwise structures will not be found Unfortunately the CSD is often inconsistent in its use of delocalised double bonds For example about 50 of metal bound acetylacetonato ligands are coded with the 6 membered ring having 4 single bonds and 2 double bonds The other 50 have 2 single bonds and 4 delocalised double bonds Thus the safest way to conduct a search for acetylacetonato complexes is to use a variable bond type when drawing the substructure allowing the acetylacetonato bonds to be single double or delocalised double Related Topics e Aromatic Bonds see page 211 e Azides see page 214 e Bond Type Conventions see
164. le pressing down the left hand mouse button and dragging the ring ConQuest User Guide 169 5 Connecting the cyclopentane and acetoxy groups e Go back to draw mode by hitting the DRAW button at the left hand side of the Draw window e Position the cursor on the oxygen of the acetoxy group press down the left hand mouse button and move the cursor to one of the ring atoms This connects the two fragments ca pa 7A Me has 6 Change the linking oxygen to QA C N O e Right click on the O atom select Element from the pull down menu followed by More from the next menu then Other Elements e In the Periodic Table window click on Multi Pick so that you can define a multiple variable atom type e Click on the C N and O element symbols in the Periodic Table and then hit OK This should change the acetoxy oxygen into a variable atom type QA we 7A Soe eye e Move the cursor onto the QA symbol and look at the bottom left hand corner of the drawing area There should be a message explaining that QA C N or O 170 ConQuest User Guide 7 Define the C O bond to be single or double e Right click on the middle of the C O bond select Type from the pull down menu then Variable e In the pop up window switch on Single and Double and hit OK e Put the cursor on the middle of the C O bond and look at the message in the lower left hand corner which confirms that the bond type can be single
165. le if you wanted to run a search of hitlist combination file comb chl you would use a command of the type e cqbatch j lt jobname gt rerun lt query filename gt restrict comb chl 20 5 Filters Filters of the type found in the graphical interface version of ConQuest see Available Filters page 144 can be activated when using CQBatch To filter on R factor the rfactor command must be used e The rfactor command must be followed one of the following ConQuest User Guide 155 0 05 Hits with rfactors greater than 5 are filtered during the search see Available Filters page 144 0 075 Hits with rfactors greater than 7 5 are filtered during the search see Available Filters page 144 Oil Hits with rfactors greater than 10 are filtered during the search see Available Filters page 144 e For example to exclude CSD entries with R factors of greater than 7 5 from a search a command of the following type could be used e cqbatch j lt jobname gt rerun lt query filename gt rfactor 0 075 e Any filters other than R factor require the exclude command e The exclude command must be followed by one or more of ironic Ionic structures are filtered during the search see Available Filters page 144 errors Structures with errors are filtered during the search see Available Filters page 144 no3d Structures without 3D coordinates are filtered during the search see Av
166. ll parameters of the cell to be searched for Select the Lattice Type from the pull down menu obtained by hitting the button labelled not defined Type the cell parameters a b c alpha beta gamma into the input boxes see Unit Cell Parameters page 242 A tolerance value is required This is expressed as a percentage of the longest cell dimension and determines how much bigger or smaller a cell parameter in the CSD may be compared with the input value and still be considered a match The tolerance should reflect the accuracy of the input unit cell data a larger value being necessary if the cell parameters are imprecise The default tolerance value 1 5 has been selected to allow for typical experimental errors and for the average difference in cell dimensions observed between determinations at room and reduced temperatures ConQuest User Guide 129 12 2 2 Searching for Non Reduced Cell Parameters Choose by clicking on No do not do a reduced cell search 12 3 130 The lattice type may be set or left undefined Any or all of the cell parameters a b c alpha beta gamma may be typed into the input boxes see Unit Cell Parameters page 242 with appropriate mathematical operators see Mathematical Operators page 18 chosen from the pull down menus The example below would find structures with a cell lengths less than 4 0 A Yes do a reduced cell search No do not do a reduced cell search Tole
167. lume 47 For most journals the volume takes a single value for each journal year However some journals 230 ConQuest User Guide have more than one volume per year and others have volume numbers that span a year change Some journals have no volume number e g journals of the UK Royal Society of Chemistry such as J Chem Soc Dalton Transactions Volume numbers are absent from PhD theses and private communications To Search e Select the Author Journal button in the Build Queries pane see Journal Volume page 114 Related Topics e Journal Name see page 229 e Journal Page see page 230 Lattice Type The lattice type refers to the choice of unit cell that has been made If the smallest possible unit cell of a crystal has been chosen the lattice type is called primitive P In some space groups it is conventional to use a unit cell which is twice or four times the volume of the primitive cell These non primitive or centred lattice types may be A B or C centred A B C body centred 1 or face centred F The first character of a space group symbol always defines the lattice type e g P2 c Fdd2 It is essential to specify the lattice type correctly when doing a reduced cell parameter search Related Topics e Reduced Cell Parameters see page 238 e Space Group see page 240 Logical Operators Three types of logical operators can be used to combine CSD queries Boolean AND OR and NOT For example a sear
168. matic This is particularly useful if you are unsure about the bond type conventions that are used in the CSD e g the difference between double and delocalised double bonds or if a substructure contains a group that has several possible valence bond representations Related Topics e Aromatic Bonds see page 211 e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Delocalised Double Bonds see page 223 e Metal Carboxylates see page 232 e Metal Metal Bonds see page 232 e Pi Bonds see page 236 Variable Element Type ConQuest allows the user to specify that an atom can be a member of a preset element group for example the element group symbol 6A O S Se Te Po see Element Group Symbols page 225 Alternatively the user can define a variable element type in the Draw window e g element symbol QA O or S see Setting Variable Element Types page 56 Thus if a particular search yields a low number of hits it might be appropriate to consider running the search again using variable element types This can be very useful for the groups of transition elements Vectors Vectors can be calculated between pairs of atoms Vista A CCDC program for performing statistical analyses on ConQuest search results e g calculation of averages plotting of histograms and scattergrams Z Number of Molecules per Unit Cell Although Z is normally referred to as the number of molecules in the crystallographic u
169. meters of interest e Run the search e Save the parameters in Vista or Excel format The Example e The tutorial explains how to define and save important geometric parameters for the fragment Ta where TR any transition metal and the coordination number of TR is exactly 4 The parameters that will be saved are e TR Cl TR N C C bond lengths e CI TR CI and N TR N bond angles e N C C N torsion angle e Element symbol of TR e R factor Menu Commands Required 1 Start ConQuest and hit the Draw button to open the Draw window 174 ConQuest User Guide 2 Draw the above substructure in the usual way see Tutorial 1 Basic Substructure Search see page 164 1 if you are unsure how to draw substructures e TR meaning any transition metal can be selected from the Periodic Table which is accessible e g by hitting the More button at the bottom of the Draw window then Any Transition Metal 3 Specify TR as 4 coordinate e Right click on TR select Number of Bonded Atoms then select 4 cl Nee NO TR Noo cl 4 Define the geometric parameters e Click on the ADD 3D button to the left of the drawing area e Click on one of the Cl atoms and the TR atom then hit the Define button next to the word Distance in the Geometric Parameters dialogue box To construct Parameter Object Select atoms from main window Hit Options to set constraints or change options Current Selection
170. mical Formula Searching e A crystal structure may consist of more than one molecule In such circumstances each molecule is formulated separately e g C6 H5 N2 O3 H2 O1 see Chemical Formula page 218 To do an exact search for this structure construct separate queries for each of the two molecular formulae and combine them i e search for entries that have both see Simple Query Combinations page 20 e If polymeric structures are to be retrieved then it is important to apply the formula to all structures in the molecule together and not to an individual molecule The reason is that the latter search uses the information in the 2D diagram There are cases where atoms from adjacent monomeric units are included in the 2D diagram to illustrate connectivity see for instance the extra Mo atoms in AXABEG and BALFAV The former search will only look at the constitution of single monomeric units ConQuest User Guide 125 11 SPACE GROUP AND CRYSTAL SYSTEM SEARCHES 11 1 Typical Uses of Space Group and Crystal System Searching e Finding all entries in a particular crystal system e g tetragonal e Finding all entries in a particular space group e g P21 c e Restricting other searches to specific crystal systems or space groups 11 2 Using the Space Group Dialogue Box Open the dialogue box by hitting Space Group in Build Queries You can e Search for a particular space group see Searching for a Space Group page 126 e Specify whether al
171. n most cases e g hypoglycaemic tumour however American spelling is kept if it was used in the original publication e Parts of words or the root of the word can be used for searching e g if searching for the keyword immunosuppressant or immunosuppressive compounds use immunosuppress e Performing a Required Fields search will only return entries where there is information present in the chosen field Not all CSD entries contain information in the listed fields This information is generally gleaned from the publication citing the structure we do not actively seek further information ourselves ConQuest User Guide 139 16 REFCODE SEARCHES 16 1Exact Refcode Searching There are two ways of finding an entry whose Refcode i e CSD entry identifier is known see Refcode entry ID page 238 e Hit the Refcode entry ID button in Build Queries and type the required Refcode into the input box e g View Refcode g Ol Enter Refcode CSD entry code below Search for Refcode in the following Databases BAJFiB Go to entry in Database Find all Refcodes that begin with query text W CSD version 5 27 November 2005 Alternatively view full database s using the View Databases options on the top menu e Ensure the Go to entry in Database radio button is activated and hit Find The Refcode will consist of six letters and possibly two numbers e Select View Databases from the top level menu This enable
172. n the Required Fields tab and select Habit from the scrolling list see Specifying Required Fields page 137 Note this will return hits only for entries where habit information is available Hydrogen Atoms in 2D 3D Substructure Searching Hydrogen atoms can be difficult to locate by X ray crystallography and hence their coordinates are sometimes missing or incomplete in CSD entries However they are always completely defined in the Chemical Diagram see page 217 that forms the basis for 2D chemical substructure searching and these searches will proceed accurately under all circumstances so long as no 3D geometrical parameters are defined However if a moiety in a 2D diagram displays an agostic or bridging M H CH R interaction the agostic H atom must be defined explicitly to retrieve relevant entries from the CSD see Automatic Addition of Hydrogen Atoms page 58 and see Adding Hydrogen Atoms ConQuest User Guide 227 Manually page 59 If H atoms form part of a substructure and any sort of 3D parameter atom labels distances angles etc is defined then 3D coordinates must be accessed and the missing or incomplete set of H coordinates can cause you to miss hits For example if you are looking for structures with S H bonds in the range 1 0 1 3 A you will not locate any structures in which the H atom position is undefined because it is impossible to compute the S H distance in these cases Whether structures are missed may dep
173. n which a chiral molecule can crystallise tick box see Sohncke Groups Chiral Space Groups page 240 The space group window will update depending on whether the tick box is on or off Space Group 1 New Space Group Enter full or partial space group symbol or number OF pick from list Click on symbol to select Current Space Group with alternative settings Only include space groups in which a chiral molecule can crystallise SEE not defined 11 2 5 Searching for Crystal Systems e Open the Space Group dialogue box Space Group 1 New Space Group Enter full or partial space group symbol or number Al OF pick from list Click A112 on symbol to select l 4 Current Space Group with alternative settings Include alternative settings Al of selected space group Only include space groups in which a chiral molecule can crystallise pete not defined All structures belonging to a particular crystal system can be found by clicking on the button labelled not defined and selecting the required crystal system from the resulting pull down menu It is unnecessary to define a crystal system if a space group has already been specified 11 3 Hints for Space Group Searching e It is almost never sensible to switch off the check box labelled Include alternative settings of selected space group In many space groups it is possible to cho
174. nQuest User Guide drawn They cannot be defined after a search has been run Think carefully about the problem being studied to ensure that you have specified geometric parameters that adequately describe that problem The obvious choice is sometimes not the best Once defined any geometric parameter can be used as a search constraint by specifying suitable limiting values see Applying Geometric Constraints page 88 In setting geometric constraints it is often useful to survey typical values found in the CSD before deciding the limiting values to be used in a subsequent search Chemical environments are usually achiral so the signs of individual torsion angles may be ignored and limits on absolute torsion angle values are often satisfactory Use the APPLY FUNCTION option in the 3D Limits and Options box to take absolute values of torsion angles see Applying Geometric Constraints page 88 ConQuest User Guide 95 5 NONBONDED CONTACT SEARCHES 5 1 Typical Uses of Nonbonded Contact Searching e Finding intermolecular interactions e g hydrogen bonds halogen halogen contacts e Finding intramolecular non covalent interactions e Generating tables of geometries for nonbonded interactions 5 2 Nonbonded Contacts between Atoms Contacts are defined in terms of distance limits These can be set by the user see Specifying Distance Limits for Nonbonded Contacts page 99 5 2 1 Searching for Intermolecular Contacts e In the Draw w
175. nce limit e g R lt 0 05 ConQuest User Guide 107 6 PEPTIDE SEARCHES 6 1 Typical Uses of Peptide Searching e Finding peptide structures containing particular amino acid sequences e g ALA PRO PHE e Searching for sequences in which one or more of the residues is variable e g ALA XXX PHE where XXX GLY PHE or VAL e Finding peptide structures whose sequences contain unusual or chemically modified amino acids e g norvaline ornithine sarcosine or residues linked by non peptidic bonds 6 2 Using the Peptide Dialogue Box Open the dialogue box by hitting Peptide in Build Queries You can e Search for peptides containing a specific sequence of amino acids e Search for a generified sequence i e a sequence in which one or more of the residues can be variable e Search for a sequence containing a non amino acid unit or an amino acid that is chemically modified in some way 6 2 1 Searching for a Specific Peptide Sequence e Open the Peptide builder dialogue box by hitting Peptide in Build Queries e Specify the required peptide sequence by clicking on amino acid buttons 108 ConQuest User Guide Select residues to add them to your peptide sequence Build variable residues using the Construct button Click the right hand mouse button over an item in the sequence to modify properties Residues Next amino acid is aB aLa arc asn asP cys GLN GLP GLu aty HCY HIS Unmodified l w Chemic
176. nded crystal structure crystal packing e Not all of the possible CSD information fields are present in all entries e Atoms of the 2D chemical diagram are mapped onto those of the 3D molecular structure to provide a complete representation of the chemical and geometrical structure This representation is used for all 2D and 3D substructure searches and in conjunction with the symmetry operators of the crystallographic space group is also necessary when searching for intermolecular interactions e In cases where molecular symmetry coincides with crystallographic symmetry the CSD stores atomic coordinates for complete chemical molecules Thus although the crystallographer reported only the atomic coordinates for the Asymmetric Unit see page 211 one half molecule in the example above the CSD stores full coordinates for the symmetry related atoms that complete the molecule These atoms are identified by alphabetic suffixes in their atom labels The 3D atomic coordinates in the CSD describe what is termed as the Crystal Chemical Unit see page 221 ConQuest User Guide 11 12 ConQuest User Guide 2 GENERAL FEATURES OF CONQUEST 2 1 The Basics of Using ConQuest Use the Build Queries screen see Building Queries Overview page 14 to build one or more queries Each query defines something to be searched for e g a set of unit cell dimensions If necessary use Combine Queries see Complex Query Combinations page 21 to combin
177. next to ConQuest User Guide the refcode The tick turns into a red cross This structure will not be written out in any files you export 10 Writing out a file containing journal references e Click on File in the top level menu and select Export Entries as from the pull down menu e Click on the file type bar and select TXT Text representation from the pull down menu Turn the output off for everything except Bibliographic information i e click in the check boxes so that only the one next to Bibliographic is coloured red e Hit Save to save the file of journal references 11 Transferring the hits to Mercury e Mercury is an advanced crystal structure visualiser To view the hits from this search in Mercury hit Analyse Hitlist and select View in Mercury from the pull down menu This ends the tutorial ConQuest User Guide 167 21 2 Tutorial 2 Substructure Search with 2D Constraints Objectives e To search for a chemical fragment while controlling e The degree of substitution of atoms e The total coordination number hybridisation state of atoms e The cyclicity of atoms and bonds i e whether or not they are part of a ring e The chemical environment of the substructure Steps Required Draw the fragment in the substructure drawing window e Specify the 2D constraints e Reject inaccurate structures by selecting only entries with R factors lt 10 R factor is a measure of experimental precision e
178. ng pull down menu e g Boron cages The exact template required can then be selected from the next pull down menu e g Hexaborane The same list of templates can also be accessed by hitting File in the top level menu of the Draw window followed by Import Template and then List 3 11 5 Saving and Using Customised Templates To save the current contents of the white drawing area for future use as a template pick File from the top level menu followed by Save Template in the resulting pull down menu The default file extension is cqt To read in a previously saved substructural template pick File from the top level menu followed by Import Template and File from the resulting pull down menus To build up a library of customised templates save them in the templates sub directory of your search data directory typically the search data directory will be a sub directory in your user area called csds_data ConQuest User Guide 71 72 e Templates saved in this way can be read in by picking File from the top level menu Import Template from the resulting pull down menu and Custom in the next pull down menu ConQuest User Guide 3 12 Substructure Display Conventions Most of the conventions and symbols used in displaying substructures are obvious Those that are not include An atom whose symbol begins with the letter O OA QB etc has a variable element type Put the cursor over the atom to get a help message giving further de
179. ng the Experimental Dialogue Box page 133 Azides Azide bond types are inconsistent in the CSD sometimes one canonical form is used sometimes Related Topics e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Variable Bond Type see page 246 214 ConQuest User Guide Bioactivity A number of keywords are stored in the Bioactivity field of the CSD Examples of these can be found in the All Text scrolling list and some more common examples can be found in the table below adrenoreceptor anticoagulant antiinflammatory cancer inotropic agonist anticonvulsant antileukaemi a c carcinogenic insecticidal antileukemic analeptic antidepress ant io antimalarial cardiovascular lymphocytic n ive analgesic antidiabetic antimetastatic cholinergic metalloproteinases antagonist ic antidopaminergic antineoplastic cytostatic neurotoxicity anthelmintic antiestrogen antiparasit e oge cytotoxic ity osteoporosis nic antiAIDS antifertility antiparkinson drug psychostimulant antiadrenergic antifungal antipsychotic fungicidal psychotropic antiallergic antigenic antipyretic herbicidal receptor s antiandrogen ic antiglaucoma antispasmodic hypercholestero retroviral lemia antiarrhythmic antigonadotropic antitumour hyperglycaemia teratogenic antiasthmatic antihaemorrhagic antiulcer hypocholinergi therapeutic c antibacterial antihistamine
180. ngs or type an element symbol and the element tenninal H bond length Element Reset bond length to I e Normalised hydrogen atom positions may be written out when entries are exported in mol2 and sd formats see Saving Individual Structures and Lists of Structures page 41 5 5 Counting the Number of Contacts to an Atom In locating nonbonded contacts the normal ConQuest search mechanism will locate unique symmetry independent contacts e g O H N1 if a symmetry related contact O H N1 exists it will by default be ignored However if you need to know the precise number of contacts to an atom the Symmetry Check should be turned off In the Draw window once you have defined your geometric parameter of interest select 3D in the top level menu and Query Options from the resulting pull down menu The 3D Search Options dialogue box can only be opened when there is a substructure in the white drawing area and you have defined a geometric parameter The 3D Search Options dialogue box enables you to switch Symmetry Check on and off Enantiomer Inversion Symmetry Check Number of Matches During a non bonded contact search duplicate contacts involving symmetry related atoms will be ignored unless required to satisfy multiple contact criteria Turn on the option below if you want to find all symmetry related contacts This is necessary if for example you want to count the number of contacts to a parti
181. nit cell the word molecule should more strictly be formula unit e g would include both the metal containing moiety and the water molecule in a compound of formula Cjo Hjo Fe N O2 H30 To Search 246 ConQuest User Guide e Select the Z Density button in the Build Queries pane see Using the Z Density Dialogue Box page 131 Related Topics e Z Number of Molecules per Asymmetric Unit see page 247 Z Number of Molecules per Asymmetric Unit This is best explained with an example Consider a simple molecule C Hig Nz O72 e If Z 1 the asymmetric unit contains 1 molecule and the crystallographer must determine the coordinates of 36 atoms e If Z 2 the asymmetric unit contains 2 molecules and the crystallographer must determine the coordinates of 72 atoms The two molecules are crystallographically independent 1 e they are not related by symmetry so do not have to have exactly the same geometry e If Z 0 5 the asymmetric unit is half a molecule and this implies that the molecule possesses symmetry coincident with a crystallographic symmetry element The molecule might possess a mirror plane so that one half of the atoms are related to the other half across the crystallographic mirror plane In this case the crystallographer must determine the coordinates of only 18 atoms In crystal structures of solvates ion pairs clathrates and host guest complexes the word molecule should be taken to include the entire formula
182. ntions page 216 Switch on the check box labelled Export largest molecule only if you wish to only write out the largest distinct chemical unit i e molecule in the structure see Molecule page 233 When saving all the structures in the hit list use the buttons to control whether each structure is written to a separate file or all structures are written one after another in a single file PDB see pdb Format page 235 Protein Data Bank format for 3D molecules When saving all the structures in the hit list use the buttons to control whether each structure is written to a separate file or all structures are written one after another in a single file Refcode see Refcode entry ID page 238 simple ASCII refcode list default extension gcd SD see SD Format page 240 MDL Information Systems Inc format for 3D molecules The Use Any bond type check box should be switched on if you want CSD bond types that are ConQuest User Guide unrecognised in the MDL conventions to be set to the MDL Any bond type otherwise they will be written out as single bonds NB Some third party programs cannot read sd files containing molecules with bonds of type Any The Exclude any disordered atoms check box can be used to specify whether or not disordered atoms should be written out Switch on the check box labelled Normalise H coordinates if you want C H N H and O H hydrogen atom positions standardised the H atom will be moved along the experim
183. onQuest User Guide 15 2 3 Storage of Queries During a ConQuest Session e As queries are built they are listed in the Build Queries area In the example below the user has built two queries Query 1 a substructure search for decalin derivatives Query 2 to find structures determined by neutron diffraction File Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results Draw as Elements E Radiation Neutron Space Group Unit Cell ZiDensity Experimental All Text Refcode entry ID Search Reset Edit Delete Queries may be saved as files for later retrieval and re use see Saving and Reading Queries page 19 2 4 Use of Dialogue Boxes Most ConQuest dialogue boxes have the same basic behaviour 16 ConQuest User Guide 2 4 1 Typing into Input Boxes e Boxes that can be typed into are coloured white or grey e Most input boxes turn pink if they contain invalid input In the example below the program has recognised that the character is invalid in an author name Authore Namee New Box m Exact Dunitz if sumame Required format F H Allen O Hara Murray Rust etc Brown will hit Browning unless Exact sumame is selected e Some dialogue boxes automatically correct or reject invalid input 2 4 2 Case Sensitivity Searches for text are always case insensitive i e it does not matter whether upper or lower case i
184. onds page 50 the atom s to which a charge is to be assigned Then hit Atoms in the top level menu Charge in the resulting pull down menu and pick the required charge as above 3 6 7 Setting Atom Coordination Numbers It is possible to specify the coordination number of an atom i e the total number of atoms to which it is bonded This is necessary e g if the atom is bonded to only four atoms in the substructure that has been drawn but is required to be 6 coordinate overall Total coordination numbers can be specified in several ways including 60 e In DRAW or EDIT mode click on an atom with the right hand mouse button pick Number of Bonded Atoms from the resulting pull down menu then select the coordination number required from the second pull down menu Unspecified in this menu means that any coordination number is allowed Clicking on Other opens up a dialogue box which allows the specification of values higher than 8 ConQuest User Guide In DRAW or EDIT mode click on Atoms in the top level menu select Number of Bonded Atoms from the resulting pull down menu then select the required coordination number Click on the atom s to which the coordination number is to be assigned and hit Done e In EDIT mode select see Selecting Atoms and Bonds page 50 the atom s whose coordination number is to be defined Then hit Atoms in the top level menu Number of Bonded Atoms in the resulting pull down menu and select the req
185. or double woe Cc Cc a a Oa eee O 8 Specify CH at the ring substitution atom e Right click on the ring carbon atom that is bonded to the QA atom select Hydrogens from the pull down menu then click on 1 in the next pull down p C J fof C EH E 7A Sa Se 9 Specify that the next ring carbon must be substituted e Click on the button at the bottom labelled More then Not Hydrogen e This sets up a variable atom type Z which will match any element except hydrogen Draw a bond to one of the ring carbons ortho to the substitution atom ConQuest User Guide 171 a TA P Oh A O gt x O 10 Specify sp hybridisation at ring atoms e Go into edit mode by clicking on the EDIT button at the left hand side of the Draw window not Edit in the top level menu bar e Click and drag to select i e enclose in a rectangle all the ring carbons O X O f O A Z e Select Atoms from the top level menu bar then Number of Bonded Atoms then 4 from the next pull down All the ring carbons are now marked T4 which means that their total coordination number must be 4 i e each of the carbons must be bonded to four atoms and hence must be sp hybridised 172 ConQuest User Guide 11 Specify that QA cannot be part of a ring e Right click on the QA atom select Cyclicity then Acyclic The atom is now marked with a superscript meaning that it must be acyclic cannot be part of a rin
186. orial 178 ConQuest User Guide 21 4 Tutorial 4 3D Substructure Search Objectives e To draw a chemical fragment substructure e To select only those entries which adopt a particular conformation e To tabulate some parameters involving derived objects centroids planes Steps Required e Draw the fragment e Define centroids and planes e Define distances between the centroids and angles between the planes e Define a torsion angle and specify that it must lie in a certain range e Run the search e Save the file of geometrical parameters The Example e The tutorial explains how to search for the following fragment where the two central carbons are acyclic not part of a ring and are bonded to 1 or 2 hydrogen atoms The two phenyl groups will be required to be cis i e Cring C C Cring torsion angle between 90 and 90 degrees The following parameters will be saved e Distance between the centroids of the phenyl rings e Angle between the planes of the phenyl rings Menu Commands Required ConQuest User Guide 179 1 Start ConQuest and hit the Draw button to open the drawing window 2 Draw the basic fragment e Use the aromatic bond type for the ring bonds not alternate double single you will get the correct bond types automatically if you select the rings from the ring template area at the bottom left hand corner of the Draw window Ma sea oo a Ske a co e l l l
187. ormalised using the default H Normalise settings include disordered atoms export opts Exports all atoms including those identified by the CSD editors as being disordered export opts largest molecule only Exports the largest chemcial unit i e molecule in the structure only export fdat Exports the search results in CCDC s fdat format necessary for transferring structures into RPluto http www ccdc cam ac uk free_services rpluto export gcd Exports the search results in a simple ASCII refcode list see Refcode entry ID page 238 export pdb Exports the search results in pdb format the Protein Data Bank format for 3D molecules see Protein Data Bank page 237 export txt ConQuest User Guide 159 Exports the search results in plain text format Use the export opts below to control which data are written to the text file tab Exports the search results in tab separated value tsv format use the export opts below to control which data are written to the text file export opts bibliographic Publication details for each CSD entry in the results hitlist are written to the tsv or txt file export opts chemical Chemical data e g compound name formula for each CSD entry in the results hitlist are written to the tsv or txt file export
188. ormat for 3D molecules and crystal structures see Mol2 Format page 233 export opts ccdc bondtypes CCDC specific representations of bond types not recognised by the mol2 format are output export opts normalise h Distances of C N and O H bonds are normalised using the default H Normalise settings export opts largest molecule only Exports the largest chemcial unit i e molecule in the structure only export cor Exports the search results in a simple ASCII listing of 3D coordinates see COORD Format page 221 export opts hit fragment Exports only the coordinates for atoms in the hit fragment i e the chemical substructure used the define the search export opts orthogonal Exports orthogonal coordinates export emf Exports the search results in CIFMIF format see CIFMIF Format page 219 158 ConQuest User Guide include parameters export opts Data associated with geometric parameters defined in the search query are output export sd Exports the search results in sd format MDL Information Systems Inc format for 3D molecules see SD Format page 240 export opts single not any Outputs single bond types for CCDC bond types not recognised by the MOL SDfile format export opts normalise h Distances of C N and O H bonds are n
189. ormation lt lt gt gt 456637 hits Detach The refcode entry ID is shown in blue and underlined By clicking on this ConQuest will jump or hyperlink to the entry SACFAZ If the refcode entry ID is included within the current hitlist then it will move to this entry if the refcode is not included in the current hitlist then a new ConQuest browser window will be opened showing the cross referenced entry together with any other studies of the same chemical compound see Refcode entry ID page 238 2 13 Using the 3D Visualiser The 3D visualiser will allow you to ConQuest User Guide 33 e Rotate translate and scale molecules see Rotating Translating and Scaling page 34 e Select from a variety of display styles and specify whether hydrogen atoms are to be displayed see Changing Display Styles and Display of Hydrogen Atoms page 34 e Measure molecular geometry distances angles and torsions see Measuring Distances Angles and Torsions page 35 e Label atoms see Labelling Atoms page 36 e Display crystallographic unit cell contents see Displaying Crystallographic Unit Cell Contents page 36 e Highlight the hit fragment and show the results of nonbonded contact searches see Highlighting Hit Fragments and Showing Results of Nonbonded Contact Searches page 36 e Display 3D parameters and objects see Displaying 3D Parameters and Objects page 37 e Write out images as jpeg files see
190. ormula dialogue box There are two ways of entering the required formula Method 1 e Type directly into the input box e The formula may be exact e g C12 O4 H18 or inexact e g C6 8 O gt 2 which means 6 7 or 8 carbon atoms and more than 2 oxygen atoms e Element Group Symbols see page 225 may be used but must be enclosed in square brackets e g C6 7A 2 7A means any halogen atom so this would find molecules or structures containing 6 carbons and any two halogen atoms Method 2 e Hit Select from Table and set the formula up from the Periodic Table e Click on an element or any of the Element Group Symbols see page 225 The chosen element element group symbol appears in the list headed Select atom counts ConQuest User Guide 123 Select atom counts ja rage f Rae M range rage E M rage Then select the required mathematical operator see Mathematical Operators page 18 and type in the number s of atoms that must be present Continue until all elements and atom counts are defined The example below specifies a formula containing 2 chlorine atoms and less than 3 oxygens Select atom counts aJe 23 A rage j Range M _ Rae Hit Done when the required formula is specified 10 2 2 Specifying Whether the Formula Applies to a Molecule or a Crystal Structure e In searching for a chemical formula you can speci
191. ose or Apply 4 5 6 Displaying Geometric Parameters in the Draw Window A defined parameter may be displayed by clicking on its name in the 3D Parameters list top right hand corner of Draw window 4 5 7 Deleting Geometric Parameters A parameter may be deleted by clicking on its name in the 3D Parameters list top right hand corner of Draw window and then clicking on the Delete button underneath this list 4 6 Applying Geometric Constraints 3D substructure searches are performed by defining relevant geometric parameters see Defining Specific Geometric Parameters Involving Only Atoms page 82 and constraining their values To constrain the value of a defined parameter e Ifyou have just defined the parameter so that the Geometric Parameters dialogue box is already open hit the Options button Ifthe Geometric Parameters dialogue box is not already open select the parameter in the 3D Parameters list top right hand corner of the Draw window and hit the Options button underneath this list e In the resulting dialogue box apply if desired a function to the parameter e g take the sine of an angle This can be done by picking from the pull down menu obtained by pressing the button next to APPLY FUNCTION e Type the required limits in the From and to input boxes In the case of angles the chosen limits 88 ConQuest User Guide will be shown graphically in red In the example below a torsion angle has been constrained to
192. ose the unit cell axes or origin in more than one way e g Pmm2 P2mm and Pm2m are different settings of the same space group and the choice between them is essentially arbitrary see Space Group page 240 e Rhombohedral space groups can be expressed relative to hexagonal or rhombohedral axes If rhombohedral axes have been used the letter r is appended to the space group symbol e g R37 128 ConQuest User Guide 12 UNIT CELL SEARCHES 12 1 Typical Uses of Unit Cell Searching Finding structures with specific Reduced Cell Parameters see page 238 to find if a new crystal has already been studied Locating all structures with short axial lengths perhaps in a crystal engineering context 12 2 Using the Unit Cell Dialogue Box Open the dialogue box by hitting Unit Cell in Build Queries On entering the dialogue box it is first necessary to specify whether a reduced cell search is required see Reduced Cell Parameters page 238 The answer will be yes if the purpose of the search is to find out whether a crystal structure with known cell dimensions is present in the CSD e g when checking whether a particular structure has already been determined The answer will be no in a few unusual situations e g to find structures with a particular repeat distance along an axis 12 2 1 Reduced Cell Searching Choose by clicking on Yes do a reduced cell search It is essential to specify the Lattice Type see page 231 and all the ce
193. osing Build user defined residues dialogue box will then add a QAA residue to the sequence e g 110 Select residues to add them to your peptide sequence Build variable residues using the Construct button Click the right hand mouse button over an item in the sequence to modify properties Residues ne sa nc asn as cvs ain ee ctu aty nev voe ue a eu tvs er mee nva on pae Ps0 san sen a me ma va ANY Any residue UND Not an alpha amino acid ANY UND Next amino acid is Unmodified w Chemically Modified Either User Defined GAA Construct Next bond is Normal peptide bond Non peptide bond Either GLU AIB SER AA Cyclicity Cyclic sequence Acyclic sequence w Either amp N terminus Right click on outer residues to Terminate an acyclic sequence C terminus Search Store Cancel Reset ConQuest User Guide e QAA in this sequence will match any of the amino acids that you selected in the Build user defined residues dialogue box e Repeated use of the Construct button will create further buttons labelled QAB QAC etc each representing a variable residue type according to your specification e Use the Match any except selection button in the Build user defined residues dialogue box to specify a residue that can be anything except the amino acids you have clicked on 6 2 3 S
194. other parts of the interface e g author names journal information compound names and formulae Use the All Text option combined with the Required Field words to find out about absolute configuration colour crystal form i e polymorphism drug activity crystal habit miscellaneous physical and chemical properties how crystals were grown etc Browse through the scrolling lists in both dialogue boxes to get ideas for useful search terms or available CSD fields Note that the scrolling list is not exhaustive if a chosen keyword isn t present it can still be searched for by typing it in the accompanying dialogue box The All Text option can be used for finding entries by specifying the Deposition Numbers see page 224 that are printed in some journals For example CCDC 182 9 is a deposition number indicating a structure published in Chem Comm this number is cited in the paper ConQuest User Guide Comprehensive deposition number searching is provided through the Author Journal dialogue box accessed through the Build Queries window see CCDC number deposition number page 115 e A text search for form will produce some unexpected hits e g electron deformation density multiple deformation charge deformation conformation conformer e Searches for activity or agent will also produce some unwanted hits if the Required Field keyword Bioactivity is not defined e g photochemical activity dye agent e English spelling is used i
195. oup will be displayed in the lower pick list e g if P2221 has been typed in the input box the lower list will contain the alternative settings P2 22 and P2212 Space Group Enter full or partial space group P2221 symbol or number P222 or pick from list Click 1 on symbol to select f Current Space Group with alternative settings Include alternative settings P2221 of selected space group P2122 P2212 e Since the choice of space group setting is arbitrary it will be usual to leave this check box switched on 11 2 3 Searching for a Range of Space Groups e If only part of a space group symbol is typed in the search will find all space groups beginning with the specified string of characters e g P21 would find all of P21 m P2I a P21 c etc e However P21 being a valid symbol in its own right would find only this particular space group e To find structures in either of e g P27 and P2 m create and store two separate queries one for Space Group P21 and one for Space Group P2 m and combine them see Complex Query Combinations page 21 e Searches can be made on aspect symbols symbols for incompletely determined space groups where the character is used as a wild card character e g P aa see Space Group page 240 ConQuest User Guide 127 11 2 4 Restricting the Search to Sohncke or Chiral Space Groups e This option can be switched on by activating the Only include space groups i
196. pecifying a Chemically Modified Amino Acid or a Non Amino Acid Use the UND button to add a peptide residue to the sequence that will match anything except an alpha amino acid For example ALA UND ARG will find compounds containing an alanine and an arginine residue separated by something that is not an alpha amino acid e To allow an amino acid to be chemically modified in some unspecified way e g acetylated switch on the button labelled Either in the section of the dialogue box labelled Next amino acid is to force an amino acid to be chemically modified switch on Chemically Modified Then hit one of the residue buttons For example to add a chemically modified CYS to the sequence switch on Chemically Modified then hit CYS e Alternatively right click on a residue in the sequence you have built select Modifications from the resulting pull down menu then Unmodified Chemically Modified or Either as desired e Modified amino acids are indicated by an m on top of the peptide residue e g Select residues to add them to your peptide sequence Build variable residues using the Construct button dick the right hand mouse button over an item in the sequence to modify properties Residues Next amino acid is AIB ALA ARG ASN ASP cys GLN GLP GLu aty Hcy HIS w Unmodified Chemically Modified HSE ILE WA LEU LYS MET NLE nva orn PHE PRO SAR Either SER THR TRP TYR VAL ANY Any residue
197. peptides containing the see PEPTIDE sequence ALA PRO PHE SEARCHES page 108 Author Journal Bibliographic Find structures published by see AUTHOR AND J D Dunitz in J Am Chem Soc Name Class see COMPOUND NAME and Chemical class SEARCHES page 116 Chemical name CSD Class Find morphine Find all entries within the Steroid class Elements see CHEMICAL ELEMENT SEARCHES page 120 Chemical elements Find structures containing Au and Os Formula see CHEMICAL FORMULA SEARCHES page 123 Chemical formula Find molecules with the formula C6 7 Os Space Group see SPACE GROUP AND CRYSTAL SYSTEM SEARCHES page 126 Crystallographic space group and crystal system Find structures crystallising in space group Fdd2 ConQuest User Guide Unit Cell Cell dimensions Find structures with a 10 0 see UNIT CELL b 20 0 c 30 0 alpha SEARCHES page 129 beta gamma 90 0 Z Density Density and unit cell Find structures with Z 16 see CRYSTAL contents DENSITY AND UNIT CELL CONTENT SEARCHES page 131 Experimental Experimental details Find structures solved at low see SEARCHES FOR temperature EXPERIMENTAL DETAILS page 133 All Text General text Find entries containing the see GENERAL TEXT word green SEARCHES page 135 Refcode entry ID CSD refcode entry Find CSD entry BAJCOE see REFCODE identifier SEARCHES page 140 C
198. ps GROUP GRPI GROUP GRP2 Defined Groups Centroid Centroid Define Closest Atom v Closest Atom Delete Close Define Current Selection 103 Click on the Define button and specify the distance required between the two group centroids In the above example the centroids will be a that of the N and H atom and b the centroid of the N and O atoms of the ring By default the search will find all intermolecular contacts in the specified distance range To accept this default hit Done and then Search To allow intramolecular contacts hit Edit 5 3 3 Searching for Chemical Groups whose Closest Atoms are Separated by a Specified Distance Define the two groups see Defining Groups for Use in Nonbonded Searching page 101 e Select both the groups in the Defined Groups list box and ensure that the Closest Atom check buttons are switched on CONTACT lt new gt Hit Define to create contact or deselect atoms groups GROUP GRP3 GROUP GRP4 Defined Groups Closest Atom Closest Atom Define Delete Close Define Current Selection w Centroid w Centroid e Click on the Define button This specifies a search that will find all pairs of groups in the above example an N H group and the N O atoms of an isoxazole ring whose closest atoms lie in a specified distance range e By default the search will find intermolecular contacts shorte
199. publication Most journal pages are numeric but sometimes they contain letters e g L25 1238 For about 20 journals mostly Russian and Chinese each issue starts at page 1 To provide an unambiguous reference we store the issue number as well as the page number in the journal page field separating them by a hyphen e g 89 3 indicates page 89 of issue 3 Since 1997 Acta Cryst Sect C Cr Str Comm has reported so called CIF access papers These are represented in the Table of Contents of each issue by a brief abstract and diagram The actual paper does not appear in the printed issue but can be retrieved from the IUCr archive using the printed journal data validation number An example of such a number is IUC9900004 In this case the journal page in the CSD would contain 9900004 J Chem Res is published in two parts the synopsis S and the miniprint M Since this journal has no volume number the page number for part S is stored in the journal volume field and the page number for part M is stored in the journal page field To Search e Select the Author Journal button in the Build Queries pane see Journal Page page 115 Related Topics e Journal Name see page 229 e Journal Volume see page 230 Journal Volume The journal volume is normally numeric but may occasionally contain letters e g C471 However in other cases the alphabetic part of a volume number is absorbed into the journal name e g Acta Cryst Section B vo
200. r and then select the points of attachment The selected bond type from the atom to all in this case two attachment points will be the same e Hit OK and start the search e This will retrieve hits containing both o bromo chlorobenzenes and m bromo chlorobenzenes 3 10 Finding Molecules Containing Two or More Substructures If you construct a query in the Draw window containing two or more disconnected substructures you can ensure that these substructures are located in the same chemical molecule by selecting Atoms from the top level menu in the Draw window and All Atoms in Same Molecule from the resulting pull down menu 3 11 Using Chemical Groups and Substructure Templates Substructure drawing can be made easier by using chemical groups and templates both of which are pre drawn substructural fragments Chemical groups are substituents such as CF3 which have a 68 ConQuest User Guide specific point by which they must be attached to the rest of a query substructure e g Templates are complete stand alone substructural fragments e g OH CH OH CH OH CH N c o c o c o f c C 0 C 0 C c f f c c c c C C f f b f OH OH OH OH OH OH o o OH OH OH OH OH OH f f c c c c c c f N f c c o c c o c c if f o c Oo c c CH OH CH OH CH OH It is possible to e Adda chemical group to an existing substructure e Replace a termina
201. r more information about hit highlighting manipulation in Mercury please refer to the Mercury documentation 2 13 8 Displaying 3D Parameters and Objects e If3D geometric parameters or objects were defined in a substructure search see Geometric Parameters page 82 and the check box labelled Show substructure matches is switched on the visualiser will highlight the hit fragment and display the values of the defined parameters and objects CCDC ConQuest 1 search2 Search Eile Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists gt View Results ___ All Text Refcode ABORAK CSD version 5 30 November 2008 mE Author Journal Analyse Hitlist Chemical Crystal ___ Experimental Diagram 3D Visualiser CSD Internals Search Overview M Show substructure matches gt 1 Hit Show ai gt of 2 Gomi param EA gt Objects afan gt The arrows on either side of the boxes labelled Param and Objects can be used to control whether or not individual distances angles centroids and planes etc are displayed e To change the display style of the parameter or object right click anywhere in the visualiser area to get the pull down menu select Settings and either Show Parameters as Solid or Show Objects as Solid from the resulting pull down menu e Ifyou are using a display style other than wireframe you have the option of making the hit fragment transparent sele
202. r than the sum of the Van der Waals Radii see page 243 of the atoms involved To accept this default hit Done and then Search Distances based on van der Waals radii are only meaningful for contacts between non metals e If you are searching for contacts to C H N H or O H groups you may wish to normalise the H atom positions which corrects for systematic errors in the location of hydrogen atoms by X ray diffraction This cannot be done in the Draw window Instead it must be done in the Search Setup dialogue box which is displayed whenever you hit a Search button 104 ConQuest User Guide 5 4 To allow intramolecular contacts see Searching for Intramolecular Contacts page 97 or to alter the distance constraint see Specifying Distance Limits for Nonbonded Contacts page 99 hit Edit Correcting the Positions of Hydrogen Atoms Hydrogen atom positions determined by X ray diffraction are unreliable because hydrogen has a low scattering power for X rays In addition the lengths of covalent bonds involving hydrogen are almost invariably too short when measured by X ray diffraction because the centroid of the hydrogen atom electron density is displaced towards the heavy atom to which the hydrogen is bonded It is desirable to correct for these errors when searching for nonbonded contacts to hydrogen atoms such as hydrogen bonds Otherwise parameters such as hydrogen bond distances will be systematically incorrect The errors can
203. rance 1 5 of longest cell dimension Lattice Type notdefined Cell Parametere a A alpha a sj o z beta r a Ej s gamma Because of the possibility of different space group settings it may be necessary to set up store and combine more than one query For example finding all crystal structures with a repeat distance below 4 0A requires three queries one for a lt 4 0 one for b lt 4 0 and one for c lt 4 0 These must be combined see Complex Query Combinations page 21 to find all structures that satisfy at least one of the criteria Hints for Unit Cell Searching Since the choice of cell axes is often arbitrary it is normally better to search on the Reduced Cell Parameters see page 238 Reduced cell parameters are subject to experimental uncertainties Thus all searches should specify a reasonable tolerance value The default tolerance has been chosen carefully and will normally be suitable It is essential to specify correctly the Lattice Type see page 231 of your crystal when doing reduced cell parameter searching When viewing the results of a reduced cell search do not be surprised if the reduced cell dimensions of hit structures are different from the cell parameters you typed in This will be because your parameters have themselves been reduced to standard form Reduced cell searching only involves comparison of cell lengths not angles This is because the angles can
204. rch File Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results All T ABEKEX pd Refcode ABEKEX CSD version 5 30 November 2008 Author Journal SS SS SSS Analyse Hitlist e If Detach is selected the 2D diagram will be detached into its own window enabling the 2D diagram and any other panes in View Results to be viewed simultaneously e Selection of Use as Query from either the detached window or from the Diagram tab allows you to use the 2D chemical diagram of the current hit as the starting point for a new search A Use as Query Options dialogue box is generated for the query allowing you to e Include exclude hydrogen atoms e Select only the largest chemical unit e Make each chemical unit into a separate query e Include all chemical units in a single query The 2D image can be copied and pasted into other Windows applications Please note that this is a Windows only feature Ensure the complete diagram is visible on the screen and select Edit from the top level menu then click on Copy Alternatively the keyboard shortcut Ctrl C can be used 2 12 5 Setting the Default Results Pane Information for the currently selected entry i e the one highlighted in orange in the View Results hit list is divided into sections Each section can be displayed by clicking on the appropriate tab at the left hand side of the View Results screen 32 ConQuest
205. re below 273K Build each query separately and store see Closing and Resetting Dialogue Boxes page 18 Hit the tab labelled Combine Queries The three boxes on the left hand side of the Combine Queries screen labelled must have must not have must have at least one of represent the logical operations required to define complex searches Drag query icons into the boxes to set up the desired search The text above each of the logical operator boxes explains its function An icon can be dragged by clicking on it with the left hand mouse button and moving the mouse keeping the button depressed so that the icon drops into the desired box Icons may also be dragged from box to box Once the required search has been defined hit Search bottom left hand corner to start the search ConQuest User Guide 21 22 e The example below will find structures which contain magnesium or a benzene ring do not crystallise in space group P21 c and were determined at a temperature below 273K Query 5 Z 4 is ignored as it has not been dragged into a box Fle Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitists View Results Find entries that must have Elements Mg i Search on Sum of molecules boolean AND i Allow other elements Yes Query 4 r must not have Query 3 Space Group P21 c and equivalent space groups must have at least one of 2A Query 1 Temperature lt
206. re than one chemically discrete entity e g an ion pair or a solvated structure Number of Atoms with 3D Coordinates see page 234 Select the required mathematical operator see Mathematical Operators page 18 and type a number into the input box Calculated Density see Density page 223 Select the required mathematical operator see Mathematical Operators page 18 and type a number into the input box The example below would find all structures with density gt 2 0 g cc Calculated Deneity ig cars gt Number of Chemical Units molecules ions etc see page 234 Select the required mathematical operator see Mathematical Operators page 18 and type a number into the input box ConQuest User Guide 131 13 3 Hints for Density and Unit Cell Content Searching 132 Measured densities are sometimes reported in papers but tend to be unreliable and are no longer stored in the CSD Any search for a density should allow a reasonable tolerance i e use range rather than Number of Atoms with 3D Coordinates see page 234 This number might not match exactly the number of atoms in the chemical formula if for example not all of the H atoms were located experimentally Structures with Z gt 1 are interesting because they contain two or more crystallographically independent molecules i e molecules which have the same chemical structure but are not forced by symmetry to have identical geometries Comparing such molecules oft
207. ree choices are possible If Distance Range and Range are both switched on you may type in the minimum and maximum distances between the interacting atoms The example below specifies a distance range of 1 8 22A Distance range From ha to 22 A Range w Value tolerance w Shorter than sum of VdW radii e If Distance range and Value tolerance are both switched on you may type in a target value with a tolerance allowed either side The example below specifies that the minimum interatomic distance is 2 0 0 2 1 8A and the maximum is 2 0 0 2 2 2A Distance range Value 2 0 f 0 2 A Range Value tolerance Shorter than sum of VdW radii If Shorter than sum of VdW radii is switched on the van der Waals radii of the interacting atoms are added together to give a quantity V The search will then find all contacts shorter than V x where x is the value typed in the input box The example below will find all contacts shorter than V 0 1A where V is the sum of the van der Waals radii of the interacting atoms Thus for a contact between O vdw radius 1 52A and H vdw radius 1 20A contacts shorter than 1 52 1 20 0 1 2 62A would be found ConQuest User Guide 99 w Distance range a Shorter than sum of VdW radii J 0 1 Set Radii User Defined Radii None Setting of van der Waals radii is possible by selecting Set Radii which generates the VdW Radii Se
208. rom this menu opens up the Periodic Table There are then two ways to create a variable element type Method 1 e Select Single Pick and click on one of the orange pre defined element groups see Element Group Symbols page 225 e g 4B means any of Ti Zr Hf Then hit Apply or OK Method 2 e Select Multi Pick click on the required elements e g O and S 56 ConQuest User Guide Other Atom Type 1M 2M aM am nn Not H any sa Previous Selections Banga 88 B C N o F nel 4 se e 7 ax ov z 18 28 Al Sij P E CI Ar ie Ti Cr Mn Fe Co Ni Cu Zn Se Ga Ge As Br Y Zr Nb Mo Tc Ru Pd Ag Cd In Sn Sb Tej Laj Hf Ta W Re Os Pt Au Hg Tl Pb Bi Po At f Ac Picking Mode UN Ce w Single Pick Multi Pick E Reset Cancel Apply OK then hit OK closes the window or Apply leaves the window open The resulting variable element type is called QA if it is the first variable type created OB if it is the second etc Current Selection O 3 6 3 Changing the Element Types of Existing Atoms This can be done in several ways including In DRAW or EDIT modes click on the atom with the right hand mouse button and select Element from the resulting pull down menu Then select the required element type More allows selection of some common variabl
209. romatic Bonds see page 211 Azides see page 214 Chemical Diagram see page 217 Delocalised Double Bonds see page 223 Metal Carboxylates see page 232 Metal Metal Bonds see page 232 Pi Bonds see page 236 Polymeric Bonds see page 236 Variable Bond Type see page 246 ConQuest User Guide Centroids Centroids can be calculated for sets of atoms Chemical Diagram The chemical diagram is stored as a set of atom and bond properties This representation forms the basis for 2D chemical substructure searches and in combination with geometrical constraints is also used in 3D searching Because the structures in the CSD cover a wide range of chemistry a number of conventions have been employed in coding some of these properties particularly chemical bond types Information about these conventions and their implications for the coding of substructure queries can be found in the list of related topics Atom properties e Atomic Charge see page 212 e Cyclicity see page 222 e Element symbol e Number of bonded atoms excluding terminal hydrogens e Number of terminal hydrogens Bond properties e Bond type see Bond Type Conventions page 216 e Cyclicity see page 222 To Search Queries involving substructures are drawn in the Draw window see Layout of the Draw Window page 47 Related Topics Aromatic Bonds see page 211 Atomic Charge see page 212 Azides see page 214 Cyclicity see page 222
210. rrent Atom Selection c c3 c6 C Select All Deselect All e This query would find T N H c H c Dera D H because the specified atoms are not directly bonded to each other but would not find 64 ConQuest User Guide 3 8 2 Avoiding Unwanted Cyclic Bonds to Atoms outside the Substructure e Select Bonds from the top level menu and Exclude from the pull down menu e Select Ring Closure e Click on the atoms which must not form cyclic bonds to atoms outside the substructure e Hit OK e In the example below atom 5 has been selected to form no additional cyclic bonds Ring Closure Direct Links Disallow additional cyclic bonds from selected atoms Note this will not apply to direct links to other atoms in the query Current Atom Selection Select All Deselect All c5 ConQuest User Guide 65 e This query would find a E aa but would not find CH H se os ee a See ean 3 j CH H CH 3 3 8 3 Ensuring that a Ring System has no Additional Bridging or Fusion e Select Bonds from the top level menu and Exclude from the pull down menu e Select Ring Closure e Click on all of the atoms in the ring system e Select Direct Links e Click on all of the atoms in the ring system e Hit OK e In the example below the 6 membered ring system has been isolated i e prevented from being part of a larger fused or bridged ring system 66 Con
211. ry Combinations page 20 e Hitting Search on the Combine Queries screen starts a search for the logical combination of queries defined by the contents of the three ogical operator boxes on the left hand side see Complex Query Combinations page 21 If a Search button is hit by accident click on Cancel in the resulting Search Setup dialogue box ConQuest User Guide 27 2 11 Naming Searches and Setting Filters Whenever a Search button is hit the Search Setup dialogue box is opened before the search is actually started OLX Filters Advanced Options T 3D coordinates determined Search Setup Search Name search2 Available Databases I Rfactor lt 0 05 lt 0 075 M CSD version 5 30 November 2008 lt 0 1 F Not disordered M No errors You can search complete database s or a subset e g hits found in a previous search Select Subset Clear Subset Single query being used Search will find structures I Not polymeric I Noions T No powder structures where this query is true i Only Organics C Organometallic Start Search This box shows the version of the CSD that will be searched summarises the query and enables you to e Name the search by typing into the input box at the top left This name is used throughout the ConQuest session but a new name may be chosen if the search is saved as a file see Saving and Read
212. s This section describes how to search for intramolecular contacts between two atoms e Start by defining the contact as if it were an intermolecular search see Searching for Intermolecular Contacts page 96 e Once the contact has been defined it can be edited by hitting the Edit button in the Nonbonded Contact Definition dialogue box In the resulting pop up use the check boxes to control whether the search is for intermolecular contacts intramolecular contacts or both If intramolecular contacts are requested you may specify the number of chemical bonds ConQuest User Guide 97 separating the atoms which are in nonbonded contact e For example if the following is specified J Inter molecular E Intra molecular separated by 4 to ja bonds the search would find O H contacts like H where the O and H atoms are separated by four chemical bonds but not fT N C C n a a iin where the O and H atoms are separated by six bonds 98 ConQuest User Guide 5 2 3 Specifying Distance Limits for Nonbonded Contacts Once a contact between two atoms has been defined see Searching for Intermolecular Contacts page 96 it can be edited by hitting the Edit button in the Nonbonded Contact Definition dialogue box In the resulting pop up use the check boxes to control whether the distance between the interacting atoms is to be specified relative to the Van der Waals Radii see page 243 of the atoms Th
213. s accents etc However some journals express an umlaut by a following e thus M ller Sanger etc may sometimes appear as Mueller Saenger etc ConQuest User Guide 213 in the CSD Chinese Korean and Malaysian names are usually stored in full e g Bing Bing Chang Jung Mi Shin Occasionally however Oriental names are recorded with initials e g H S Kim These variations are due to different journal conventions Names from non Roman alphabets are not always transliterated in the same way in different papers e g Belskii Belsky Belskij query strings should be restricted to the root of the name Belsk There is some inconsistency in the database in the handling of 2 letter initials e g Yu T Struchkov might occasionally be stored as Y T Struchkov To Search e Select the Author Journal button in the Build Queries pane see AUTHOR AND JOURNAL SEARCHES page 113 Average e s d of C C Bonds The average estimated standard deviation e s d standard uncertainty s u of the carbon carbon bond lengths in a structure provides a rough measure of precision In searching the CSD you can either accept any value or restrict hits to values lt 0 005A The latter option limits hits to more precise structure determinations In certain entries if no carbon carbon e s d s are available then the value may be derived from C N C O N N N O O O e s d s To Search e Select the Experimental button in the Build Queries pane see Usi
214. s used 2 4 3 Greyed Out Buttons e Buttons are greyed out when they cannot be used This is usually because the user has not defined sufficient information for the button to be useable In the example below the Search button is greyed out because the user has not specified all the information required for a reduced cell search specifically the lattice type has not yet been defined Do you want to eearch on the reduced cell You should search on reduced cell if you want to find structures which match a particular set of cell dimensions a b c alpha beta gamma Yes do a reduced cell search w No do not do a reduced cell search Tolerance 1 5 of longest cell dimension Lattice Type notdefined Tell Parametere a A ji2143 alpha jo b A 14 126 beta jo c A fig 294 gamma Cancel Reset ConQuest User Guide 17 2 4 4 Mathematical Operators e Some queries involve testing the values of numbers e g to find out whether a density is greater than a certain value In such cases the input box into which the number is typed is preceded by a button labelled with a mathematical operator such as Calculated Deneity ig cars e Clicking on this button will produce a pull down menu from which the required mathematical operator not gt lt etc can be chosen e Using the operator to test the value of a non integral number can be unreliable e
215. s possible to search a subset of the database or a subset of both the CSD and in house databases should you have any of the latter You can restrict a search to Entries added modified before after a particular CSD release or a specific date see Searching CSD Entries Added or Modified Before or After a Particular Release or Date page 147 e Entires in a pre defined hitlist This allows you to search against the only best representative of each unique polymorph in the CSD or to restrict searches to the Classroom subset see Searching on entires in a pre defined hitlist page 148 e The hits found in a search you have already run during the current ConQuest session see 146 ConQuest User Guide Searching Hits from a Previous Search in the Current ConQuest Session page 149 e The hits found in a search that has been saved to disk either in native ConQuest format cqs a hitlist combination ch or as a refcode list gcd see Searching the Hits from a Search Previously Saved to Disk page 149 18 3 1 Searching CSD Entries Added or Modified Before or After a Particular Release or Date e Build the query as usual and hit Search Then hit the Select Subset button in the Search Setup dialogue box e Click on the CSD Version button at the bottom left of this window This will launch the Select Previous CSD Version window To view the database scrolling list click on the Restrict based on CSD version radio button The window w
216. s the entire CSD to be loaded A particular entry may then be viewed by typing its Refcode into the grey box at the top of the Refcode list in View Results or by scrolling down the list and clicking on the desired Refcode 140 ConQuest User Guide BAJFIB Analyse Hitlist BAJCAQ10 BAJCEU _ BAJCIY BaAJCIYO1 BAJCOE BAJCOE10 BAJCUK BAJDAR BAJDAR10 BAJDEY BAJDIZ BAJDOF BAJDOFIO BaAJDUL BAJDULIO BAJFAT BAJFEX BAJFIB1O BAJFOH BAJFOH10 RAIFIIN 16 2 Searching for Refcode Families and Multiple Structure Determinations It is possible to search for Refcode families or structures in the CSD that have been determined multiple times e Hit the Refcode entry ID button and enter e g SELHAS View Refcode ala Enter Refcode CSD entry code below Search for Refcode in the following Databases SELHAS v Go to entry in Database Find all Refcodes that begin with query text CSD version 5 27 November 2005 Altematively view full database s using the View Databases options on the top menu Ensure the Find all Refcodes that being with query text radio button is activated and click Find This will return all CSD entries with the query Refcode i e a refcode family ConQuest User Guide 141 JSELHAS Analyse Hitlist The results of these Refcode searches can be combined in the Manage Hitlists window of ConQuest see Managing Hitlists page 23 It is also possible to searc
217. s turned on and select Drawing Options to change the value the Default bond length is 60 e To change the minimum increment that will be made to a bond angle as the cursor is moved when drawing a new bond from an existing atom ensure Snap to Grid is turned on and select Drawing Options to change the value the Default bond angle is 15 degrees e To draw bonds freehand i e to the exact position specified by the cursor movement turn off the Snap to Grid check button e To change the tolerance for determining how close two atoms must be before they are judged to be overlapping and how close the cursor must be before it is considered to be on an atom select Drawing Options and change the value the default Tolerance is 15 increase to make the effective size of an atom bigger 3 14 Pasting in Substructures from Isis Draw ConQuest offers the ability to copy and paste substructure queries from ISIS Draw MDL Information Systems Inc into either the Build Queries area or the Draw window Windows only In order to use this facility ISIS Draw must be configured to copy a MOL file to the Windows clipboard ConQuest User Guide 75 e In ISIS Draw select Options from the top level menu and Settings from the resulting pull down menu Hit the General tab switch on the Copy Mol Rxnfile to Clipboard check box e Hit Save if you wish this change to be applied to subsequent ISIS DRAW sessions e Hit OK to close the dialogue box and
218. session by picking File from the top level menu followed by Open and then select Recent Files from the resulting pull down menu 2 9 3 Renaming Annotating Viewing and Deleting Hitlists Various options are available for renaming annotating viewing and deleting either searches or hitlists including combinations some of these options also apply to Refcode lists To rename a search or hitlist combination Select it from list of hitlists bottom right hand side of the screen Hit the Rename button underneath this list Type the new name into the Edit hitlist name input box Hit OK Alternatively it is possible to provide a name for the combination in the Combination Name entry box on the top left hand side of the screen The name changes will appear immediately in the Manage Hitlists screen To annotate a search or hitlist combination with additional information Select it from the list of hitlists bottom right hand side of the screen Hit the Notes button underneath this list Type any additional information into the Hitlist Details input box Hit OK to include the additional information Reset to clear any changes or Cancel to exit without making any changes To view a search hitlist combination or Refcode list from within the Manage Hitlists screen Select it from list of hitlists bottom right hand side of the screen Hit the View button underneath this list You will be presented with the requested information in the View Results s
219. splayed under the Author Journal Chemical Crystal and Experimental tabs see below Note that not all of the possible CSD information fields are present in all entries 30 ConQuest User Guide e Author Journal bibliographic information including deposition number where available see Deposition Numbers page 224 e A deposition hyperlink may be displayed for recent CCDC numbers 200000 or greater The hyperlink indicates that original supplementary structure data have been deposited in the CCDC electronic archive These CIFs may contain data not included in a CSD entry They have not been subjected to editorial checks The CIF can be obtained by following the hyperlink to the CCDC CIF Repository Request Form www ccdc cam ac uk products csd request Ifan entry does not contain coordinates and another publication by the same author s of the same data set exists with coordinates a hyperlink is provided in Notes to this entry However if no hyperlink is present from the CCDC deposition number of that entry coordinates can be obtained by exporting a CIF from ConQuest see Saving Individual Structures and Lists of Structures page 41 e A CrossRef button will be present when it is possible to link through via CrossRef to the original citation e An IUCr button will be present when it is possible to link from the CSD entry to UCr s Crystallography Journals Online where the original article will be available e Chemical compound name
220. st underneath the Journal Name box e Type the three letters Che into the Journal Name box The list underneath this box scrolls down to show journals which begin with these three letters Journal Name Type part of Journal name above to narrow list displayed Select required journal in list below Chem Ber 1940 1997 Chem Biol Interactions 1981 1985 ii Chem Comm 1965 1970 Chem Commun 1972 2000 Chem Commun Univ Stockholm 1976 1994 Chem Ind Dekker 1997 Chem Ind London 1934 1987 Chem Lett 1972 2000 e Select Chem Ber from the list e Type 23 into the Volume box e Type 485 into the Page box e Type 1990 into the Year box 5 Run the search Hit Search in the Author Journal window then Start Search in the next window e Click on the Author Journal tab in View Results to display the literature citation of the hit entry ConQuest User Guide 199 This ends the tutorial 200 ConQuest User Guide 21 9 Tutorial 9 Combined Compound Name and Keyword Search Objectives e To create a compound name query e To create a keyword query To combine them so as to search for entries containing both the compound name and the keyword Steps Required e Construct and store a compound name query e Construct and store a keyword query e Select both queries e Run the search The Example Find di molybdenum structures which are air sensitive Menu Commands Required 1 Start ConQues
221. sumed from the position at which it was stopped However it can be saved and retrieved see Saving and Reading Searches page 41 in the same way as searches that have run to completion 2 17 Suppressing Unwanted Entries e Clicking on the green tick next to a Refcode entry ID see page 238 in the View Results hit list will suppress that structure indicated by a red cross Four entries are suppressed in the example below BASLIG Analyse Hitlist y AECLPAOI ry y AECLPAIO VY ANAPHS VY AQFYMG y AQMEDA y BACSON X BACSON10 y BADTEX VY BADTEX01 X BADTEX10 Vv BALMGT y BASLIGOI X BASLIGIO y BAWGOV e Suppressed structures will not be written out if results from the search are saved in any format other than the native ConQuest cqs format see Saving and Reading Searches page 41 However they can still be viewed in ConQuest 40 ConQuest User Guide e Click on the red cross to reinstate a suppressed structure e To suppress all entries right click anywhere in the box containing the hit list and pick Deselect All from the resulting pull down menu e To unsuppress all entries i e reinstate any that you have suppressed right click anywhere in the box containing the hit list and pick Select All from the pull down menu e To reverse the suppression status of all entries right click anywhere in the box containing the hit list and pick Invert Selection 2 18 Saving and Reading Searches e To save a search ensure tha
222. symbol in this case P aa There are 127 aspect symbols having CSD space group numbers in the range 502 765 To Search e Select the Space Group button in the Build Queries pane see Using the Space Group Dialogue Box page 126 Related Topics e Crystal Systems see page 222 e Unit Cell Parameters see page 242 Temperature Factor Temperature factors are not currently available in the CSD Temperature of Structure Determination A comment is included in the Temperature section under the Experimental tab in the View Results window if a structure has been determined at a temperature other than room temperature Any structure determined in the range 283 303K is considered to be a room temperature structure To Search e Select the Experimental button in the Build Queries pane see Using the Experimental ConQuest User Guide 241 Dialogue Box page 133 Torsion Angles Torsion angles are used to describe conformations around rotatable bonds The torsion angle between 4 atoms A B C D is the angle by which the vector A B must be rotated in order to eclipse the vector C D when viewed along the vector B C Crystallographers usually express torsion angles in the range 180 to 180 degrees According to convention Klyne and Prelog Experientia 16 521 1960 a clockwise rotation is positive and an anti clockwise rotation is negative Torsion angles may be calculated for any set of four objects including atoms centroids and dummy poin
223. t a cqs file is always written to the working directory at the end of a search The name of this file will be lt jobname cqs gt i e the jobname supplied using the j command The jobname defined after j will also be used as the root for all other output filenames Hit entries will be automatically exported if one or more export format is specified after the export command ConQuest s default export settings are used unless an alternative is given using the export opts command Available options depend on the file type being exported Valid commands are the following export Cif Exports the search results in CIF Crystallographic Information File format see CIF Format page 218 export opts structure only Only the structure not the additional text and numeric fields contained in CIFs will be exported export opts include bonds Connectivity information is written export opts include parameters ConQuest User Guide 157 Data associated with geometric parameters defined in the search query are output export endnote Exports the search results as tab separated values which can be used to import references into the EndNote software for publishing and managing data export res Exports the search results as a simulated SHELX res file export mol2 Exports the search results in mol2 format Tripos Inc f
224. t Cell see page 246 Z Number of Molecules per Asymmetric Unit see page 247 Absolute Configuration The phrase absolute configuration is included in an entry if the absolute configuration of the structure has been determined by X ray methods This can only be done if the compound crystallises in one of the 65 Sohncke Groups Chiral Space Groups see page 240 To Search e Select the All Text button in the Build Queries pane see GENERAL TEXT SEARCHES page 135 Related Topics e Flack Parameter see page 227 e Internal Comparison see page 229 e Rogers Parameter see page 239 Angles in degrees can be calculated between atoms dummy points centroids planes or vectors Related Topics e Distances see page 225 e Torsion Angles see page 242 ConQuest User Guide Aromatic Bonds An aromatic bond type is used for the ring bonds of benzenoid systems 6 membered aromatic heterocycles and cyclopentadienyl systems However 5 membered heterocycles such as thiophene furan etc are normally coded with single and double bonds as are annulenes A few hundred entries contain the 6 membered carbon ring with alternating single and double bonds These structures are of 3 main types e Metal complexes where pi bonding between the metal and the 6 membered carbon ring involves only 2 or 4 of the 6 carbon atoms e Phthalocyanines and other benzoporphines e Fullerenes these structures always contain the root fuller in
225. t Subset and Clear Subset buttons are inactive Search Setup Fala Eq Search Name search Filters Advanced Options Available Databases I 3D coordinates determined M Rfactor lt 0 05 M CSD version 5 27 November 2005 C lt 0 075 V Restricted to 11181 refcodes C lt 01 M Notdisordered T No errors You can search complete database s or a subset e g hits found in a previous search T Not polymeric F Noions Select Subset Clear Subset T No powder structures o ENEG PEES heee Feee T Only Organics where this query is true Organometallic SRST R ee Ae Aa eee EEES Start Search 19 3 Choosing a Subset The subset used by Classroom ConQuest is specified by a file containing a list of CSD refcodes The default refcode list is classroom default gcd which is located in the user defaults directory You can elect to use a different subset containing up to one fifth of the current size of the entire database This can be done by e Replacing the default file with a new one that has the same name e Editing user defaults conquest options so that the line beginning classroom refcode list indicates the location of the refcode list to be used specify the full path For PC Windows use forward slashes in the path instead of back slashes e Selecting a different subset using the Select New Subset button to select a different refcode list This button is displ
226. t User Guide 79 e When you define each parameter constrain it as required e g specify a range of distances for a bond length see Applying Geometric Constraints page 88 e Run the search 4 4 Geometric Objects Geometric objects centroids planes etc may be defined when drawing a substructure in the Draw window These objects can then be used for computing geometric parameters e g the angle between two planes 4 4 1 Valid Geometric Objects Valid objects are e Centroids see page 217 e Dummy Points see page 225 e Vectors see page 246 e Planes see page 236 4 4 2 Defining Geometric Objects There are two ways to define geometric objects centroids vectors etc when drawing a substructure Method 1 e Open up the Geometric Parameters dialogue box by clicking on the ADD 3D mode button or by hitting 3D in the top level menu and then Add Constraints in the resulting pull down menu The dialogue box can only be opened when there is a substructure in the white drawing area e Select the atoms that are needed to calculate the object by clicking on them with the left hand mouse button click again on an atom to deselect e As the number of selected atoms varies the dialogue box will list the objects that can meaningfully be defined e Hit the appropriate Define button in the dialogue box e g next to the word Centroid to define a centroid e The defined object is listed in the box labelled Defined Objects In the
227. t and hit the Name Class button 2 Specify the required compound name e You don t need to type in a complete compound name part of a name will do Type dimolybdenum into the Compound Name box e You cannot be certain whether names in the CSD contain a hyphen or not i e CCDC editors might have used dimolybdenum or di molybdenum Therefore click on the check box Ignore non alphabetic character to ensure that you would find both of these e Click Add to add the compound name to the Contains dialogue Compound Name Contains l dimolybdenum ignore non alphabetic characters e g butadiene will match buta 1 3 diene aj ee ConQuest User Guide 201 e Hit Store The query is transferred to the Build Queries page but a search is not started File Edit Options View Databases Results Help Build Queries Combine Queries Manage Hitlists View Results I D ofits use this j avery G Name dimolybdenum alphabetic Peptide a Author Journal 3 Specify the keyword search e Hit the All Text button e Select air sensitive from the list e Hit Store 4 Search for both queries e Both of the queries you have built will be coloured green in the Build Queries display This means they are both selected e If you click on a query icon it will turn white which means that it is de selected If you click on it again it will turn green and be selected e We want to search for entries containing
228. t it is currently on display in View Results if it is not display it by using the Results top level menu option then select Searches from the resulting pull down menu to display the search of your choice see Switching between Searches page 40 e Then pick File from the top level menu and Save Search or Save Search as in the resulting pull down menu The first of these options will only be available if the search has already been saved in which case the only point in saving it again would be if one or more hit entries had been suppressed or unsuppressed since the last save see Suppressing Unwanted Entries page 40 e Search files will be given the extension cqs e Search cqs files are binary and contain all the information necessary to read the search back into ConQuest and display it as if it had just been run e To read a previously saved search pick File from the top level menu followed by Open and then select Search from the resulting pull down menu e Alternatively you can read in a search Refcode list or hitlist combination saved from an earlier ConQuest session by picking File from the top level menu followed by Open and then select Recent Files from the resulting pull down menu 2 19 Saving Individual Structures and Lists of Structures Pick File from the top level menu followed by Export Entries as in the resulting pull down menu to save e the individual structure currently being displayed turn on Current
229. t the Define button next to Distance Accept the default i e Intramolecular Distance from the resulting pop up by hitting OK This will ensure that both fragments are in the same molecule e Hit Options type in the required distance limits and hit OK Repeat for any further distance constraints Other constraints e g angles may also be applied Hit Done in the Geometric Parameters dialogue box when you have finished setting up all the required constraints then Search in the Draw window to run the search 4 8 Types of Distances between Disconnected Substructures You may be given the following choice of distance types when defining a distance between two disconnected substructures ConQuest User Guide 93 4 9 94 CHOOSE DISTANCE TYPE Intramolecular Distance Select this option to calculate distances between these fragments but only if they are in the same molecule Contact Select this option to find non bonded interactions between these fragments Any If you select this option then the distance calculated may be arbritarily calculated for some entries unless you define a Contact or Intramolecular distance between these fragments Select Intramolecular Distance if you want the substructures to be in the same molecule This allows you to find molecules containing two different chemical groups you will have the option to specify the distance between them e g 4 6A or the number of chemical bonds
230. tails The symbol X indicates an atom that may have Any element type The symbol Z indicates an atom that can be any element type except hydrogen A superscript beginning with the letter 7 indicates the total coordination number of the atom e g 74 indicates that the atom must be 4 coordinate H next to an atom indicates that the atom is bonded to a variable number of hydrogen atoms Put the cursor over the atom to get a help message giving further details Chemical groups accessed via buttons such as Groups Add Group and Chemical Groups are displayed as special symbols e g Et for ethyl The letter a indicates acyclic c indicates cyclic Various conventions are used to display unusual and variable bond types If in doubt place the cursor over the bond to get a help message giving further details If an atom is surrounded by a circle it is close to or on top of another atom Change to EDIT mode select the atom and move it away see Moving Atoms page 73 3 13 Advanced Drawing Options 3 13 1 Moving Atoms In EDIT mode select see Selecting Atoms and Bonds page 50 the atom s to be moved move the cursor onto one of the selected atoms press the left hand mouse button and move the cursor while keeping the button depressed If two atoms overlap coloured red when the mouse button is released they will be fused ConQuest User Guide 73 3 13 2 Rotating Substructures e Itis only possible to rotate complete substru
231. tally located crystallographically independent atoms in the Asymmetric Unit see page 211 plus any atoms that are symmetry related and bonded to these To Search e Select the Z Density button in the Build Queries pane see Using the Z Density Dialogue Box page 131 Number of Chemical Units molecules ions etc The number of chemical units refers to the number of molecules or ions etc which are present in the crystal structure e g selecting a value of 1 would retrieve all entries containing just one chemical unit To Search e Select the Z Density button in the Build Queries pane see Using the Z Density Dialogue Box page 131 Occupancy Factor A parameter that defines the partial occupancy of a given site by a particular atom It is most frequently used to describe disorder in a portion of a molecule Related Topics e Disordered Structures see page 224 234 ConQuest User Guide Only Organics Selecting this filter eliminates from the search any structure that contains a transition metal lanthanide actinide or any of Al Ga In Tl Ge Sn Pb Sb Bi Po To Search e Select the appropriate filter in the Search Setup dialogue box see Applying Filters page 143 Only Organometallics Selecting this filter restricts the search to structures containing at least one transition metal lanthanide actinide or any of Al Ga In Tl Ge Sn Pb Sb Bi Po To Search e Select the appropriate filter in the Search Se
232. te list of groups can be obtained by selecting the View option which appears in the menu that is displayed whenever an Add Group or Groups button is hit Groups may be selected from the resulting dialogue box and added to the query substructure 3 11 2 Changing an Atom to a Chemical Group This can be done in several ways including 70 In DRAW or EDIT mode right click on an atom select Element and then Chemical Groups and then pick the desired group from the subsequent pull down menus In DRAW or EDIT mode select Atoms from the top level menu then hit Element followed by Chemical Groups and pick the group you want from the subsequent menus You will then be asked to pick the atom s which are to be replaced by the group Select the atoms which you want to replace Then hit Atoms in the top level menu followed by Element and Chemical Groups in the resulting pull down menus and then pick the group you require In DRAW mode change the current element type to a chemical group by hitting the Groups button at the bottom of the window and selecting the required group from the subsequent menus Then left click on the atom s you wish to replace A complete list of groups can be obtained by selecting the View option which appears in the menu that is displayed whenever a Chemical Groups or Groups button is hit Groups may be ConQuest User Guide selected from the resulting dialogue box and added to the query substructure
233. ternative space group settings are allowed see Including or Excluding Alternative Space Group Settings page 127 e Search for a range of space groups see Searching for a Range of Space Groups page 127 e Limit the search to Sohncke chiral space groups see Restricting the Search to Sohncke or Chiral Space Groups page 128 e Search for a particular crystal system see Searching for Crystal Systems page 128 11 2 1 Searching for a Space Group e Open the Space Group dialogue box e Type the space group number valid range 1 230 or the space group symbol see Space Group page 240 into the input box e Alternatively pick the space group symbol from the top list box either by scrolling down the list with the scroll bar or by typing the first character or two of the space group symbol into the input box As the symbol is typed the list in the box is narrowed down Space Group Enter full or partial space group P2 symbol or number Or pick from list Click on symbol to select e Pick the required symbol with a single mouse click 126 ConQuest User Guide 11 2 2 Including or Excluding Alternative Space Group Settings e Ifthe check box Include alternative settings of selected space group is switched on the search will find all occurrences of the space group that has been defined even those with a different setting 1 e different choice of axes see Space Group page 240 e The different settings of the space gr
234. th directions move the cursor to one of the solid pink squares at a corner of the fragment s bounding box press the left hand mouse button and move the cursor keeping the mouse button and the Shift key depressed If atoms overlap when the mouse button is released they will not be merged 74 ConQuest User Guide 3 13 4 Duplicating Substructures Copy Cut and Paste To make a copy of all or part of a substructure select see Selecting Atoms and Bonds page 50 the atoms and bonds to be copied and either e Click ona blank point in the white area with the right hand mouse button and select Copy or Cut they both make a copy of the fragment in addition Cut will delete the selected atoms and bonds or e hit Edit in the top level menu and Copy or Cut in the resulting pull down menu To paste a copy of a substructure into the same Draw window or another Draw window in the same ConQuest session either e Click on a blank point in the white area with the right hand mouse button and select Paste the option will be greyed out if there is nothing available to paste or e hit Edit in the top level menu and Paste in the pull down menu 3 13 5 Changing Default Drawing Options By default all bonds drawn from an atom have a fixed length and other drawing options are also preset These defaults may be changed using check buttons under the top level menu item Options e To change the default length of bonds ensure Snap to Grid i
235. the atoms in the molecule In this situation the atoms in the asymmetric unit plus the symmetry generated atoms forming the other half of the molecule collectively form the crystal chemical unit If you request output of such a structure the coordinates of the entire molecule i e the crystal chemical unit will be written out not just the coordinates of the asymmetric unit The symmetry generated atoms can be distinguished from the atoms in the asymmetric unit because their atom labels will end in a letter The letter indicates which symmetry operation was applied to generate the atom Related Topics e Asymmetric Unit see page 211 e Atomic Labels see page 213 e Molecule see page 233 e Z Number of Molecules per Unit Cell see page 246 e Z Number of Molecules per Asymmetric Unit see page 247 ConQuest User Guide 221 Crystal Systems Any crystal must belong to one of seven crystal systems the symmetry of which introduces constraints on the possible values of the Unit Cell Parameters see page 242 The seven crystal systems and the distribution of space groups in them are Crystal System Space Groups Triclinic Anorthic 1 2 Monoclinic 3 15 Orthorhombic 16 74 Tetragonal 75 142 Trigonal Hexagonal trigonal 143 167 with hexagonal axes hexagonal 168 194 Rhombohedral trigonal 146 167 with rhombohedral axes Cubic 195 230 To Search e Select the Space Group button in the Bui
236. the compound name so it is safer to search for them with a compound name search see Using the Compound Name and Chemical Class Dialogue Box page 116 it is also easier than trying to construct a fullerene diagram Related Topics e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Delocalised Double Bonds see page 223 e Pi Bonds see page 236 e Variable Bond Type see page 246 Asymmetric Unit A crystal structure consists of a basic motif that is repeated in 3D space by the symmetry operators of the crystallographic space group A crystallographer determines the coordinates of the atoms in this basic motif called the asymmetric unit It is the smallest part of a crystal structure from which the complete structure can be built using space group symmetry The asymmetric unit may consist of only one molecule or ion part of a molecule or several molecules that are not related by crystallographic symmetry This is why you sometimes see more than one molecule in the ConQuest 3D visualiser when you view results For example consider structures of formula Ci2 Hig N4 Oo e Ifthe asymmetric unit contains one molecule the crystallographer must determine the coordinates of 36 atoms e Ifthe asymmetric unit contains two molecules the crystallographer must determine the coordinates of 72 atoms ConQuest User Guide 211 e Ifthe asymmetric unit is half a molecule this implies that the molecule possesses symmetry
237. tion specified CSD will add CSD and UPDATES will add updates if these can be found 154 ConQuest User Guide dbdir One or more database_directory All databases found in the directories specified will be searched along with any specified by db or dblist assuming dbfilter does not dictate otherwise dblist One or more database _list_file A database _list_file should contain a list of database paths one per line If this is the only option specified then only the databases listed will be searched dbfilter One or more database_names Will filter the list of databases defined by other database options including none so that it only includes those that match the names listed CSD will keep CSD and UPDATES will keep updates if these are present in the list defined by other options allcsd Force previous versions of the CSD to be included By default ConQuest will not include versions of the CSD that are older than the current version unless e the current version is not specified by other database related options in which case all old versions are included e theold databases flag in csds_defaults is set to something other than 0 e this command line option is specified 20 4 Restrictions e A saved search cqs hitlist combination ch or refcode list gcd can be used to restrict searches to a subset of entries via the restrict command line option For examp
238. tivity are included if the author indicates that the compound or a near relative is a drug or has biological activity e g anticancer drug derivative of cholinergic agent antidepressant activity Searches can be restricted to entries with Bioactivity comments see Specifying Required Fields page 137 Related Topics e Buioactivity see page 215 To Search e Select the All Text button in the Build Queries pane see All Text Searching page 135 e Select Bioactivity from the scrolling list in the Required Fields tab of the A Text dialogue box see Specifying Required Fields page 137 Dummy Points A dummy point is defined as the point lying on the extension of the vector from atom A to atom B at a distance d A from atom B Element Group Symbols The following preset element group symbols can be used for specifying substructures containing variable atom types For example a search for the substructure B C7 would find structures containing any of the bonds Cu Cl Ag Cl or Au Cl Element group symbols can also be used to generalise element and formula searches ConQuest User Guide 225 Element group symbol Elements contained in the group HD HD 1A Li Na K Rb Cs Fr 2A Be Mg Ca Sr Ba Ra 3A B Al Ga In T 4A Si Ge Sn Pb 5A N P As Sb Bi 6A O S Se Te Po 7A FCIBrIAt 8A He Ne Ar Kr Xe Rn 1B Cu Ag Au 2B Zn Cd Hg 3B Sc Y La Ac 4B Ti Zr
239. toms or bonds ERASE Click on this button when you want to delete atoms or bonds ADD 3D Click on this button to specify geometric objects parameters and constraints CONTACT Click on this button to set up a nonbonded contact search you must already have drawn two unconnected substructures Fundamentals of Drawing All drawing takes place in the central white area of the Draw window 3 4 1 Drawing a Bond ConQuest User Guide Ensure you are in DRAW mode Move the cursor into the white area of the Draw window Press down the left hand mouse button move the cursor while keeping the mouse button depressed and then release the button This draws a bond using the current element type see Changing the Current Element Type page 56 and bond type see Changing the Current Bond Type page 61 49 3 4 2 Drawing an Isolated Atom e Ensure you are in DRAW mode e Move the cursor into the white area of the Draw window e Click the left hand mouse button and release it again without moving the mouse 3 4 3 Drawing a Bond from an Existing Atom e Ensure you are in DRAW mode e Move the cursor onto the atom the atom will go red e Press down the left hand mouse button e Move the cursor while keeping the mouse button depressed then release the button 3 4 4 Drawing a Bond to an Existing Atom e Ensure you are in DRAW mode e Move the cursor into the white area of the Draw window e Press down the left hand mouse button e Move
240. ts Related Topics e Angles see page 210 e Distances see page 225 Unit Cell Parameters The unit cell is the basic building block of a crystal repeated infinitely in three dimensions It is characterised by e three vectors a b c that form the edges of a parallelepiped e the angles between the vectors alpha the angle between b and c beta the angle between a and c gamma the angle between a and b Depending on the crystal system see Crystal Systems page 222 there are sometimes restrictions on the values that unit cell parameters can take Triclinic Anorthic no restrictions Monoclinic alpha gamma 90 Orthorhombic alpha beta gamma 90 Tetragonal a b alpha beta gamma 90 Trigonal Hexagonal a b alpha beta 90 gamma 120 Rhombohedral a b c alpha beta gamma Cubic a b c alpha beta gamma 90 In the above table alpha gamma 90 for monoclinic corresponds to the b axis unique setting Two other settings are possible 242 ConQuest User Guide a axis unique beta gamma 90 c axis unique alpha beta 90 To Search e Select the Unit Cell button in the Build Queries pane see Using the Unit Cell Dialogue Box page 129 Related Topics e Crystal Systems see page 222 e Reduced Cell Parameters see page 238 e Space Group see page 240 Unresolved Errors When a new entry is added to the CSD checks are carried out to test for consistency between atomic
241. tup dialogue box see Applying Filters page 143 pdb Format pdb is the Protein Data Bank format for 3D structures and is a ConQuest output option Related Topics e Protein Data Bank see page 237 Physical and Chemical Properties Physical and chemical properties are sometimes recorded e g hygroscopic air sensitive piezoelectric phase transition at 123K isomorphous with the Co analogue For a more complete list of possible search terms see the scrolling list in the AJI Text dialogue box or the Required Fields scrolling list also available from the A Text dialogue box To Search e Select the All Text button in the Build Queries pane see All Text Searching page 135 e Select the All Text button in the Build Queries pane then click on the Required Fields tab and select the relevant field from the scrolling list see Specifying Required Fields page 137 ConQuest User Guide 235 Pi Bonds Pi bonds in the CSD refer to bonds between a metal and a ligand For a cyclopentadienyl ring with no substituents or just acyclic substituents a pi bond is recorded between the metal atom and each of the ring C atoms Similarly butadiene would have 4 pi bonds recorded to the metal atom Related Topics e Aromatic Bonds see page 211 e Bond Type Conventions see page 216 e Chemical Diagram see page 217 e Delocalised Double Bonds see page 223 e Polymeric Bonds see page 236 Planes Planes can be calculated through sets
242. tup dialogue box showing the current values and providing boxes for you to enter the element symbol and new van der Waals radius this is particularly important when searching for contacts involving metal atoms where CCDC default radii are not well defined Enter element symbol and VdW Radius Current Settings Angstroms Element E k vaw Radius Eaa 5 3 Nonbonded Contacts between Chemical Groups e Itis possible to search for nonbonded contacts between chemical groups each of which may contain any number of atoms The two groups are considered to be in contact if the closest pair of atoms one from one group one from the other are within a user specified distance or if the distance between the centroids of the two groups is in a specified distance range 100 ConQuest User Guide 5 3 1 Defining Groups for Use in Nonbonded Searching e Draw two unconnected substructures in the Draw window see Layout of the Draw Window page 47 e Either select Define Nonbonded Contact from the top level 3D menu or hit the CONTACT button located at the left hand side of the drawing area Hit Groups in the resulting pop up window e Pick all the atoms that you wish to be included in the first group CONTACT lt new gt Hit Define to create a group or deselect atoms ATOM ATOM Defined Groups f E Define Delete Close f f E Current Selection N7 H6
243. u have defined can be saved by selecting File from the top level menu then Export Parameters and Data from the pull down menu This ends the tutorial 184 ConQuest User Guide 21 5 Tutorial 5 Search for Nonbonded Interactions Objectives e To draw two chemical fragments e To specify that an intermolecular nonbonded interaction must occur between the fragments e To find such nonbonded interactions in the CSD e To tabulate some geometrical parameters Steps Required e Draw the fragments e Define the required nonbonded contact e Define the geometrical parameters that are to be tabulated e Run the search e Save the file of geometrical parameters The Example e ConQuest can find intramolecular or intermolecular contacts between individual atoms pre defined groups of atoms or between the centroids of pre defined groups of atoms The tutorial explains how to search for the following intermolecular contact where N is bonded to exactly 3 atoms and there is an intermolecular contact lt 2 1A between O and H The following parameters will be saved O H O N nonbonded distances e O H N and C O H angles e O and H atom labels e Orthogonal coordinates of the hit fragments ConQuest User Guide 185 Menu Commands Required 1 Start ConQuest and hit the Draw button to open the Draw window 2 Draw the two fragments ca T bE 3 Constrain N to be 3 coordinate e Right click on the N
244. uctures containing both nitrogen and chlorine Elements Required to be Present N Cl Use the buttons to specify whether the chosen elements must be present in the same molecule or ion or in the same crystal structure For example acetylcholine perchlorate contains two ions acetylcholine C7 H N O2 and perchlorate C104 It would be found by the example search above if the same structure option were chosen but not if the same molecule option were chosen since the structure contains both N and Cl but not in the same ion ConQuest User Guide e Ifthe check button Other elements allowed in molecule structure is turned off then no element other than those specified may be present The example below would find benzene Cs Ho but not aniline Cg H7 N or glucose Cg H Oo Elements Required to be Present Type in elements e g C H Se or Select from Table Elements must be in same molecule C same crystal structure I Other elements allowed in molecule structure 9 2 2 Searching for Any of a Group of Elements e To find structures containing e g either N or C create and store two separate queries one for Element N one for Element C and then combine them see Complex Query Combinations page 21 Alternatively some pre defined groups of elements may be specified by typing Element Group Symbols see page 225 or by hitting Select from Table and picking the orange buttons The example below would
245. ueries pane see Using the Experimental Dialogue Box page 133 e Select the appropriate Filter in the Search Setup dialogue box see Applying Filters page 143 Rogers Parameter This is a parameter eta Rogers Acta Cryst A37 734 1981 that can be used in the determination of Absolute Configuration see page 210 Related Topics ConQuest User Guide 239 e Absolute Configuration see page 210 SD Format SD is a molecular file format produced by MDL Information Systems Inc 14600 Catalina Street San Leandro CA 94577 USA and is a ConQuest output option Sohncke Groups Chiral Space Groups These 65 space groups contain only rotation or screw axes and are the only space groups in which chiral structures can crystallise They are space group numbers 1 3 5 16 24 75 80 89 98 143 146 149 155 168 173 177 182 195 199 and 207 214 Related Topics e Space Group see page 240 e Absolute Configuration see page 210 Source of Crystal Comments are sometimes included to indicate how crystals were prepared e g from the melt dichloromethane hexane if there are comments these can be found in the Additional Information section under the Crystal tab of the View Results window Comments to indicate the source of natural products are also occasionally given and can be found in the Source field under the Chemical tab in the View Results window e g Leaves of flemingia fruticulose wall Leguminos ae To Search e S
246. uest which has been designed for group teaching activities e Anyone with at least one normal ConQuest licence can install as many copies of Classroom ConQuest as they require e It has all the functionality of normal ConQuest with the limitation that searches can only be done on a subset of entries The subset of entries can either be the default selection supplied with Classroom ConQuest or one derived by the user from the main CSD 19 2 Basics of Using Classroom ConQuest Each time a classroom registered version of ConQuest is started it will produce a dialogue box similar to the following Classroom Options o x Valid Classroom Licence Ifyou are happy with the default subset file just select Continue below Current Subset C Program Files CCDC ConQuest 1 8 user_defaults classroom_default qed Use the button below to select a different subset Select New Subset Continue Exit The aim of this dialogue box is to e Tell you when the Classroom licence has expired e Allow the selection of a different subset for the duration of the session see Choosing a Subset page 152 Within ConQuest everything is normal except for the Search Setup dialogue box which indicates that e Only the main CSD is available e Searches are restricted to a subset of refcodes the associated check button is disabled so that it cannot be changed ConQuest User Guide 151 e The Se
247. uired coordination number 3 6 8 Defining Cyclic or Acyclic Atoms It is possible to specify that a particular atom must be cyclic i e part of a ring or conversely that it must be acyclic i e not part of a ring This can be done in several ways including In DRAW or EDIT mode click on an atom with the right hand mouse button pick Cyclicity from the resulting pull down menu then select the required option from the second pull down menu Unspecified in this menu means the atom may be either cyclic or acyclic If the atom is already part of a ring the Acyclic option will be greyed out In DRAW or EDIT mode click on Atoms in the top level menu select Cyclicity from the resulting pull down menu then select Cyclic Acyclic or Unspecified Click on the atom s to which the option is to be applied and hit Done e In EDIT mode select see Selecting Atoms and Bonds page 50 the required atom s Then pick Atoms from the top level menu Cyclicity from the resulting pull down menu and select Cyclic Acyclic or Unspecified as required 3 7 Bond Properties 3 7 1 Changing the Current Bond Type e The current bond type determines the type of any new bond created when drawing see Bond Type Conventions page 216 The current setting is shown on the button next to the word Bond at the bottom of the Draw window Bond Single The current bond type may be changed by clicking on this button and selecting from the resulting p
248. ull down menu 3 7 2 Setting Variable Bond Types e Bonds in a substructure may be variable e g double or aromatic see Variable Bond Type page 246 The current bond type see Changing the Current Bond Type page 61 can be made variable by ConQuest User Guide 61 clicking on the button next to the word Bond at the bottom of the Draw window Select Variable from the pull down menu click on the required bond types in the resulting pop up window then hit OK closes window or Apply leaves window open e The example below shows the setting required to create a variable bond type of single double or aromatic Variable Bond Type W Single W Double i Triple OK Quadruple E Aromatic _ Polymeric Cancel _j Delocalised _ Pi Current Definition 1 2 ar 3 7 3 Changing the Types of Existing Bonds This can be done in several ways including In DRAW or EDIT modes click on the centre of the bond with the right hand mouse button and select Type from the resulting pull down menu Then pick the required bond type this may be Variable see Variable Bond Type page 246 e In DRAW mode change the current bond type and then click on the bond with the left hand mouse button In DRAW or EDIT mode click on Bonds in the top level menu select Type from the resulting pull down menu select the required bond type this may be Variable see Variable Bond Type page 246 The Select Bonds pop up appears
249. umber of non hydrogen attachments with Any bond type if as drawn or zero e Ring bond count if as drawn or zero no ring bonds if chemically sensible e Bond Topology e A number of geometric objects such as planes and centroids and defined geometric parameters such as distances angles and dihedrals More information is available on what is translated and what is not elsewhere see Saving and Reading Queries page 19 76 ConQuest User Guide It is also possible to copy and paste structures from ChemDraw CambridgeSoft Corporation which can also include query features and these are handled in a similar way to ISIS query features 3 15 Reading MDL MOL Files MDL MOL files can be read into ConQuest in the same way as a query qry file see Saving and Reading Queries page 19 3 16 Starting Searches and Closing the Draw Window The Draw window can be closed down by 3 17 Hitting the Search button this starts a search for the substructure s in the white drawing area Hitting the Store button this transfers the substructure to the list of queries in Build Queries Hitting the Cancel button or selecting File from the top level menu and Close from the resulting pull down menu Both of these options will discard the current contents of the drawing area Hints for Substructure Searching The key to successful substructure searching is to understand the CSD bond type conventions see Bond Type Conventions page 21
250. unit e g both the metal containing moiety and the water molecule in a compound of formula Czo Hjo Fe N O2 HO To Search e Select the Z Density button in the Build Queries pane see Using the Z Density Dialogue Box page 131 Related Topics e Z Number of Molecules per Unit Cell see page 246 ConQuest User Guide 247 23 APPENDIX B CHANGES IN JOURNAL NAMES Some journals have been split into separate parts at a certain date or in other cases multiple parts of a journal have been merged together This means that a particular journal name may only be valid for a certain period of time The most important of these in the CSD are 248 Acta Crystallogr Acta Crystallogr Sect A Cryst Phys Diffr Theor Crystallogr 1968 1982 Acta Crystallogr Sect B Struct Crystallogr Cryst Chem 1968 1982 Acta Crystallogr Sect A Found Crystallogr Acta Crystallogr Sect B Struct Sci Acta Crystallogr Sect C Cryst Struct Comm Acta Crystallogr Sect D Biol Crystallogr Acta Crystallogr Sect E Struct Rep Online J Chem Soc J Chem Soc A J Chem Soc B J Chem Soc C Dalton Transactions J Chem Soc Dalton Transactions J Chem Soc Perkin Transactions 1 J Chem Soc Perkin Transactions 2 Org Biomol Chem Proc Chem Soc London Chem Comm J Chem Soc D J Chem Soc Chem Commun Chem Commun Acta Chem Scand Acta Chem Scand Ser A Acta Chem Scand Ser B Acta Chem Scand J Phys Chem J Phys Chem J Phys Chem B C R
251. user Inorganic Crystal Structure Database ICSD This is the inorganic counterpart of the Cambridge Structural Database Bergerhoff Hundt Sievers and Brown J Chem Inf Comput Sci 23 66 1983 The ICSD is produced by FIZ Karlsruhe D 7514 Eggenstein Leopoldshafen Germany in conjunction with the National Institute of Standards and Technology U S A Internal Comparison This is a method of determining Absolute Configuration see page 210 by preparing a derivative in which a carbon atom of known chirality is introduced into the molecule during synthesis of the derivative For example the absolute stereochemistry of 3 camphor is well known so the formation of the 3 camphor sulfonate derivative yields a new compound in which carbon centres of known chirality are present The technique is rarely used Related Topics e Absolute Configuration see page 210 Journal Name Journal names in the CSD are normally the abbreviations adopted by the International Standards Organisation Some journals have changed their names over time often by dividing into two or more sections significant examples are listed in APPENDIX B CHANGES IN JOURNAL NAMES see page 248 ConQuest User Guide 229 To Search e Select the Author Journal button in the Build Queries pane see Journal Name page 114 Related Topics e Journal Page see page 230 e Journal Volume see page 230 Journal Page The page number is the starting page of the
252. xplicitly defined in the Draw window in order to be displayed in View Results see Displaying the Values of Defined Geometrical Parameters page 38 or to be passed to Excel or Vista for tabulation and statistical analysis see Transferring Data to Other Programs for Analysis page 44 Open up the Geometric Parameters dialogue box by clicking on the ADD 3D mode button or by hitting 3D in the top level menu and then Add Constraints in the resulting pull down menu The dialogue box can only be opened when there is a substructure in the white drawing area Select the atoms that are needed to calculate the required parameter by clicking on them with the left hand mouse button click again on an atom to deselect As the number of selected atoms varies the dialogue box will list the parameters that can meaningfully be defined In the example below two atoms have been selected so it is possible to define their labels or the distance between them ConQuest User Guide To construct Parameter Object Select atoms from main window Hit Define to construct Parameter Object Current Selection N1 05 Valid Parameters Define Define Defined Objects Valid Objects Define penai Reset Done e Hit the relevant Define button e g next to the word Distance to define an interatomic distance The defined parameter will be listed in the box labelled 3D Parameters in the top right hand corner of t
253. y creation valid only with use as query stop lt n gt This option indicates that the search should stop after lt n gt hits If lt n gt equals zero this overrides a stop limit set anywhere else e g in an instruction file or saved search cqs lt filename gt The cqs output file is assigned the name lt filename gt ConQuest User Guide 163 21 TUTORIALS The easiest way to learn how to use ConQuest is to do the tutorials 21 1 Tutorial 1 Basic Substructure Search Objectives e To draw a chemical fragment substructure e To search the CSD for entries which contain the fragment e To obtain a list of journal references for the hit entries e Transfer the results to Mercury Steps Required e Draw the fragment in the substructure drawing window e Start the search e Decide which hit entries to keep e Write out the journal references The Example e The tutorial explains how to search for the following fragment Oo t i Be a where 7A F Cl Br or I Menu Commands Required 1 Start ConQuest and hit the Draw button to open the Draw window 2 Draw a chain of atoms e Move the cursor into the white drawing area press the left hand mouse button and move the 164 ConQuest User Guide mouse while keeping the button depressed Release the mouse button and you should have drawn a C C bond Keep the cursor where it is i e on one of the carbon atoms Press the l
254. y to convert each set of dimensions to a standard form This is called cell reduction 3 Enter the lattice type and cell dimensions of your crystal e It is essential to specify correctly the lattice type of your crystal In this example set the Lattice Type to Primitive e Type in the values of a b c alpha beta and gamma In this example they are ConQuest User Guide 195 Do you want to search on the reduced cell You should search on reduced cell if you want to find structures which match a particular set of cell dimensions a b c alpha beta gamma Yes do a reduced cell search w No do not do a reduced cell search Tolerance 1 5 of longest cell dimension Lattice Type Primitive P Cell Parameters 6 538 alpha jo 7 550 beta 95 98 23 180 gamma po 7 Search Store Cancel Reset All the cell parameter boxes must be filled in before you can do the search even though in this case the alpha and gamma angles must be 90 by symmetry Accept the default tolerance This defines how closely the reduced cell dimensions of a database structure must match the reduced cell dimensions of your crystal in order to be considered a match The default value has been carefully chosen so is usually best left unchanged 4 Run the search 196 Hit Search in the Unit Cell window then Start Search in the next window Click on the Crystal tab in View Results to display th

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