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MultipleAttachmentPoints
YoucanuseR-groupsthatcontainmorethanoneattachmentpoint,forexample:
ForthistypeofR-group,youmustindicatetheattachmentpointorderinyourtable.Ifyouhavewell-definedmultiple
attachmentpointsonyourstructurefragments,youcansearchforspecificmaterials.Thistypeofsearchisusefulfor
findingsimilarstructuresthatconform.
Forexample,assumeyouwanttofindcompoundsinfigureAbelow,butnotcompoundsinfigureB.
Figure14.12:Multipleattachmentpoints
Byspecifyingtheattachmentpointorder,youcanexcludetheunwantedcompounds.
Tospecifytheattachmentpointsorder:
1. Drawthestructureshownbelow
2. Createanalternativegroupboxlabeled“R1”.
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3. Drawthestructurefragmentsandlabelthemwithattachmentpoints.
Whenthealternativegroupdefinitioniscomplete,theattachmentpointsymbolsappearintheparentcompound.
Figure14.13:R-groupswithmulti-attachmentpoints
Bynumberingyourattachmentpoints,youspecifythatthemethylgroupmustbeadjacenttotheaminegroup.The
conformationsthatarenotofinterestareexcluded.
AttachmentPointNumbering
Numberedattachmentpointsletyouspecifyhowthestructurefragmentsconnecttoyourparentstructure.
Tosettheorderoftheattachmentpoints,usetheAttachmentPointtooltoclicktheendsofthebondsintheorderyou
want.
Tochangeattachmentpointorder:
ClicktheattachmentpointswiththeAttachmentPointtool.
HidingRankIndicators
Youcanhidetheattachmentrankindicatorsifrequired.Forexample,inpublication-qualitydrawingsthenumberingof
attachmentpointsisimplicitandthenumberedattachmentrankindicatorsaresuperfluous.
Tohidetheattachmentrankindicatorsandremovethenumbersfromtheattachmentpoints:
1. NavigatetoFile>Preferences.
2. InthePreferencesdialog,clickBuilding/Display.
3. DeselectShowAttachmentRankIndicators.
Thischangeaffectsalldocuments.
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Thefigurebelowshowsanalternativegroupdefinitionandaparentstructurewiththeattachmentrankindicatorshid-
den.
Figure14.14:Hiddenattachmentindicators
R-groupreactionqueries
Youcansearchandstorereactions.Inareaction,oneorseveralcompounds(reactants)aretransformedintoother
compounds(products).Individualreactants(orproducts)areseparatedfromeachotherwithplussigns.Thereact-
antsareseparatedfromtheproductswithanarrow.
Youcanalsosearchforchemicalreactionscontainingr-groups.Anexampleofachemicalreactioncontainingr-
groupsisshownbelow:
Searchingforreactants
Searchingforreactantsisusefulifyouhaveaknownstartingmaterialandyouareinterestedinlearningmoreabout
whatsubstancesitcanproduce.Areactantsqueryisverysimilartoareactionsearch,exceptthatthereisnothingto
therightofthearrow.Forexample,considerthequery:
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Figure14.15:Sampler-groupreactantquery
Alikelyhitfortheabovequeryisshownbelow:
Searchingforproducts
Ifyouknowthedesiredendproductbutnothowtogetthere,youcandoaproductsquery.Aproductsqueryissimilar
toareactionsearch,exceptthatthereisnothingtotheleftofthearrow.Forexample,considerthequery:
Figure14.16:Sampler-groupproductquery
AnonymousAlternativeGroups
Anonymousalternativegroupsareacrossbetweenanelementlistandanalternativegroup.Elementlistscomprise
singleelements,butanonymousalternativegroupscancontainanystructurethatcanberepresentedbytext,suchas
nicknamesandgenericnicknames.Anonymousalternativegroupsareshortcutnotationsforregularalternative
groups,eliminatingtheneedtospecifyaname,suchas“R1”.
Youcanconciselydefineyoursearchqueryusinganonymousalternativegroups.Bylabelinganatompositionasa
listofsubstructuresyouspecifythatoneofthesesubstructuresmustmatchinthestructureforwhichyouaresearch-
ing.Commasmustseparatetheitemsintheanonymousalternativegroup.Aspaceaftereachcommaandthebrack-
etsareoptional.Examplesofanonymousalternativegroupsareshownbelow.
Figure14.17:Anonymousalternativegroups.
Tocreateanonymousalternativegroups:
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1. Openanatomlabeltextbox.
2. Typeanopenbracket“[”followedbyalistofelements,fragments,nicknames,orgenericnicknamesseparatedby
commas,followedbyaclosebracket“]”.
ExpandGenericStructures
YoucangeneratemultiplestructuresfromanabbreviatedcombinatorialstructurewiththeExpandGenericStructure
tool.Thetoolislimitedto500generatedstructures.Forlargecombinatorialexpansions,useCombiChemforExcel.
Fourkindsofabbreviatedcombinatorialdefinitionsmaybeused:
Definition
Example
AlternativeGroupsand
R-tables
AnonymousAlternativeGroups
Element
Lists
Variable
Attachment
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Definition
Example
Definitionsareexpandedintomultiplecompletemolecules.Ifmorethanonesiteispresentintheselection,theexpan-
sionincludesallpermutationsofsubstitutions.Expansionsaregeneratedinanewdocument.
Toexpandagenericstructure:
1. Selectoneormoregenericstructurestoexpand.
Note:Foralternativegroup/R-tables,youmustselectthealternativegrouplabelandthetablemustbeselected.If
thelabelisselectedbutnotthetable,thelabelwillnotchangeintheexpansion,andwillappearasalabelinallgen-
eratedstructures.
2. NavigatetoStructure>ExpandGenericStructure.
Thestructuresaregeneratedinanewdocument.
R-LogicQueries
AfteryouhaveyourgenericstructureandasetofR-groups,youcanusethemtorunqueriesagainstastructuredata-
base.ThisiscalledanR-Logicquery.
WhenyourunanR-Logicquery,yousearchforstructuresthatallhavethegenericstructureandacombinationofyour
R-groups.ThecombinationsarebasedonaBooleanexpressionthatyoudefine.ToprepareanR-Logicsearch,nav-
igatetoStructure>R-LogicQuerytoopentheR-LogicQuerydialog.
Todefineaquery,selectoneormoreR-groupsinyourstructureandhowmanytimesitmustoccur.Youcanindicate
thatifthefirstR-groupconditionismet,anotherR-groupmustalsobefoundbeforethestructureisreturnedasares-
ult.Forexample,considerthisquerystructure:
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ThisstructureindicatesthatbothR
1
sitesmustconsistofeitherafluorineorchlorineatomandthattheR
2
sitemust
beeitherabromineoriodineatom.
AssumeyouwanttofindallstructuresinyourdatabasethathaveeitheraForClatomatbothR
1
locationsandeither
BrorIatR
2
:
1. NavigatetoStructure>R-LogicQuery.
2. IntheR-Groupdropdownlist,selectR
1
.
3. ForOccurrencerange,select2.ThisindicatesthattwoinstancesofanR
1
groupmustoccurinastructureforitto
bereturnedasaresult.
4. ForIfR(i),selectR
2
.ThisindicatesthattheR
2
locationmustconsistofeitherBrorI.
5. ClickAdd.
6. ClickOK.
RestH
SelectRestHintheR-LogicQuerydialogtoindicatethatifyouhavetwopossibleR-grouplocations,andonlyoneis
filled,theothermustbeahydrogentoreturnapositiveresult.
Atom-to-AtomMapping
Youcancreatecorrespondencesbetweenatomsindifferentstructuresforsearchingareactiondatabase.Thereac-
tionsmappedcanbesingleormulti-step.Adrawingthatincludesatom-to-atommappingcanbeaddedtoadatabase
orbeusedtosearch.
Youcanassignatommappingintwoways:
Automaticmapping(navigatetoStructure>MapReactionAtoms).
Manualmapping,usingtheReactionAtom-AtomMaptoolonthemaintoolspalette.
Usingeithermethod,ChemBioDrawassignsareactioncenterforthereactantsandproducts.
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Whenareactionmapisestablished,youcanpointtoanatominonestructurewiththeReactionAtom-AtomMaptool
tohighlightthemappedatomintheotherstructure.
DisplayingandPrinting
Todisplayreactionmappingsymbolsonscreenandinprint:
1. NavigatetoFile>Preferences.
2. InthePreferencesdialog,clicktheBuilding/Displaytab.
3. SelectAlwaysDisplayandPrintReactionMapping.
4. ClickOK.
DeselectAlwaysDisplayandPrintAtomMappingtoshowthesymbolsonlywhenyouselecttheReactionAtom-
AtomMaptool.Thesymbolsdonotprint.
AutomaticMapping
Tocreateareactionmap:
1. Selectthereaction.
Tip:Double-clickthearrowwithaselectiontooltoselectthereaction.
2. NavigatetoStructure>MapReactionAtoms.
ThesymbolRxnappearsnexttothebondsinthereactantandproductthataremodifiedbythereaction.Formore
informationabouttheReactionCenterbondproperty,see"BondProperties"onpage239.
Figure14.18:Automaticreactionmapping
ManualMapping
Whenmanualatom-to-atommappingisrequired,youcanusetheReactionAtom-AtomMaptool.Thismightbeneces-
sarywhentheautomaticmappingisappliedtocomplicatedreactions,butgivesincorrectresults.Inthesecasesyou
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canmanuallyreadjustthereactionmapping.
ThefigurebelowshowstheinitialmappingbeingamendedbyusingtheReactionAtom-AtomMaptool.
Figure14.19:Automaticmappingtobeamended
WhenyoumanuallymapreactionswiththeReactionAtom-AtomMaptool,youcansuppressautomaticre-mapping
ofatomsotherthanyourtargetatom.
Tosuppressautomaticremapping:
1. NavigatetoFile>Preferences.
2. OntheGeneraltab,de-selectAutomaticReactionMapping.
3. ClickOK.
TousetheReactionAtom-AtomMaptooltosupplementtheautomaticmapping:
1. ClicktheReactionAtom-AtomMaptoolontheQuerytoolbar.
2. Pointtotheatominthereactantwhosemappingyouwanttoestablish.Forexample,inthefollowingdrawingyou
wouldpointtotheacycliccarbonadjacenttotheetheroxygen.
3. Dragfromthereactantatomtothecorrespondingproductatom.
Theremainingatomsaremappedbasedonthemanualmapping.
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Figure14.20:Finalizedmapping
Youcansetorchangethemappingforotheratomsinthereaction.
ClearingReactionMapping
Toclearreactionmapping:
1. Selectthestructureswhosemappingyouwanttoclear.
2. NavigatetoStructure>ClearReactionMap.
ClickinganddraggingfromanyatomtoanemptyspaceintheChemDrawwindowusingtheReactionAtom-Atom
Maptoolwillclearthemappingfromthatatom.
ExportingReactionMapping
Reactionmappingandreactioncenterperceptioninformationarestoredinthe*.cdxfileformat.Youcanopenthefile
inChemBioDrawfortransfertootherapplicationsthatreadatommapping,suchasChemBioFinder.Youcanalso
copymappedreactionstothesesameapplicationsusingtheClipboard.
StereochemicalSymbols
Therearethreetypesofflagsthatindicatestereochemistry:
Racemic.Aracemicmixture.
Absolute.Apureenantiomerofknownconfiguration.
Relative.Apureenantiomerofunknownconfiguration.
Thedefaultatomlabelsizeforthedocumentdeterminesfontandsizeforstereochemicalflags.
Todrawastereochemicalflag:
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