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3. ClickUseDefaults.
Toremovespecificbondproperties:
1. Selectthebond.
2. Dooneofthefollowing:
Right-clicktoopenacontextmenu,pointtotheappropriateproperty,andclickthepropertytoremove.
NavigatetoStructure>BondPropertiesandclickthebondpropertytoremove.
BondPropertyOptions
Thepropertiesyoucanassigntobondsaredescribedbelow.
BondTypes
Thispropertyspecifiesthebondtypeoftheselectedbonds.
TheDefaultbondtypecorrespondstothecurrenttypeofthebond(single,double,andsoon.)asdrawn.
Single(all)andDative.Findscompoundswiththebondtypeyouselectfortheselectedbonds.
DoubleorDoubleBold.Findscompoundswhoseselectedbondsaredouble.
DoubleEither.Findscompoundswhoseselectedbondsaredoublebondsandhaveeithercis/transstereochemical
configuration.
Aromatic.Findscompoundswhoseselectedbondsarearomatic.
Tautomeric.Findscompoundswhoseselectedbondsaretautomeric.
Triple.Findscompoundswhoseselectedbondsaretriple.
Quadruple.Findscompoundswhoseselectedbondsarequadruple.
Any.Findsanycompound,regardlessofthebondtypeoftheselectedbonds.
S/D.Findscompoundswhoseselectedbondsaresingleordouble.
D/A.Findscompoundswhoseselectedbondsaredoubleoraromatic.
S/A.Findscompoundswhoseselectedbondsaresingleoraromatic.
Note:Notallbondtypesaresupportedinallfileformats.Whenanunsupportedbondtypeissavedtoagivenfile
format,itisconvertedtotheclosestequivalentthatissupported.
Topology
TheTopologypropertyspecifiestheringenvironmentoftheselectedbonds.
Unspecified.Default.Findscompoundsregardlessoftopology.
Ring.Findscompoundswheretheselectedbondsarepartofaring.
Chain.Findscompoundswheretheselectedbondsarepartofachain(butnotpartofaring).
RingorChain.Findscompoundswheretheselectedbondsarepartofeitheraringorachain.
ReactionCenter
TheReactionCenterpropertyspecifieshowtheselectedbondsareaffectedinareaction.Thispropertyismeaningful
onlywhensearchingadatabasecontainingchemicalreactions.
Unspecified.Default.Findscompoundsregardlessofwhethertheselectedbondsareaffectedbythereaction.
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Center.Findscompoundswheretheselectedbondsareaffectedbyareaction,butthetypeofchangeisunspecified.
Make/Break.Findscompoundswheretheselectedbondsareeitherbrokenorcreatedinareaction.
Change.Findscompoundswherethebondorderoftheselectedbondschangesinareaction.
Make&Change.Findscompoundswheretheselectedbondsareformed,broken,orundergoachangeinbond
order.
NotCenter.Findscompoundswheretheselectedbondsarenotpartofthereactioncenter.
NotModified.Findscompoundswheretheselectedbond’sordersdonotchange,butmay(ormaynot)bepartofthe
reactioncenter.
Unmapped.Findsallcompounds.
ElementLists
Anelementlistisalistofatomsallowedataspecifiedlocation.Forexample,thequerystructurebelowallowsbro-
mobenzene,Iodobenzene,orchlorobenzenetobereturned.Anexampleofanelementlistis:
Figure14.4:Anelementlistasanatomlabel
Theelementsinthelistmustbeseparatedbycommas.Aspaceaftereachcommaandbracketsareoptional.
Note:Anelementlistmaycontainonlyatomicsymbols,plusD(deuterium)andT(tritium).
Tocreateanelementlist:
1. Openanatomlabeltextbox.
2. Typeanopenbracket("[")followedbyalistofelementsseparatedbycommas(“Cl,Br,I”),followedbyaclose
bracket("]"),forexample:[Cl,Br,I].
3. Closethetextbox.
Thefigurebelowshowsaquerystructurecreatedtofindcompoundsmatchingthefollowingcriteria:
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(A)indicatesthattheatommustmatchanyatomexcepthydrogen.
TheIndicator(B)nearthebondindicatesthatthebondmustbesingleordouble,S/D.
Theelementlist(C)specifiesthatoneoftheseelementsmustmatchinthetargetstructures.
ElementNOTLists
Theelementnot-listspecifiesthattheelementsinthelistarenotallowedinthesearchresults.Commasmustsep-
aratetheelementsintheelementnot-list.Aspaceaftereachcommaandbracketsareoptional.
ThewordNOTmustbeinall-capsandmustbefollowedbyaspace.Alternatively,youcanreplacethewordNOT
withaminussign.
Forexample:
Figure14.5:ElementNOTlists
Note:Anelementnot-listmaycontainonlyatomicelements,plusD(deuterium)andT(tritium).
TocreateanelementNOTlist:
1. Openanatomlabeltextbox.
2. Typeanopenbracket"[",thewordNOT,andaspace,forexample:[NOT,followedbyalistofelementssep-
aratedbycommas(“Cl,Br,I”),followedbyaclosebracket,“]”,forexample:[NOTCl,Br,I].
Polymers
Youcanindicatepolymersusingeitherbrackets,parentheses,orbracesthatencloserepeatingstructures,orstruc-
turalfragments.Thebracketpropertiesletsyouspecifythecontextandorientationoftherepeatingunits.
Forexample:
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Toenclosestructureswithbrackets:
1. TodisplaytheBrackettoolbar,navigatetoView>OtherToolbars>Bracket.
2. OntheBrackettoolbar,selectoneofthedoublebrackettools.
3. Todrawthebrackets,clickanddragacrossthestructuretoenclose.
Thisgivesdefaultvalueforcomponentorder,multiplegrouprepeatcount,orsinglerepeatingunitlabel.
SettingBracketProperties
TosettheBracketProperties:
1. Selectabracket.
2. NavigatetoStructure>BracketProperties.TheBracketPropertiesdialogappears.
TheFlipTypeoptionappearsonlyforladderpolymers.See"FlipType"onpage248.
Youcancustomizethetextthatappearstothebottomrightofthebracketforthesebrackettypes:
Component(c#)—thecomponentordermustbeanon-negativeinteger,andisdisplayedastheletter“c”followed
byaninteger(or“c”aloneifanorderofzeroisspecified).
MultipleGroup(#)—therepeatcountmustbeapositiveinteger.
SRU(n)—theSRUlabelcanbeanytext.
YoucanalsoeditthetextforthesebracketusagetypesinthedocumentusingtheTexttool.Youcannoteditthetext
displayedforotherbracketusagetypes.
BracketUsage
PolymerRepresentationsareeitherstructure-basedorsource-based.Thetypeofbracketyouusedependsonthe
typeofrepresentation.
Structure-basedPolymers
Structure-basedrepresentationsencloseonlypartofastructurewithinbrackets.Oneormorebondscrosseachofthe
enclosingbrackets.Thecrossingbonds“matchup”,makingthepolymerstructuremoreexplicit.
Yourepresentastructure-basedpolymerbyenclosingaportionofastructureinbracketswithabrackettypeofSRU
(n).IUPACrecommendsthesubscript“n”todenotestructure-basedrepresentationsofunknownsize,butyoucan
editthetextusingthetexttool.
Astructure-basedrepresentationofpoly(vinyl chloride)isshownbelow:
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Youcanalsousethebracketusagetypes“Crosslink (xl)”,“Graft(grf)”,and“Modification(mod)”torepresenttypesof
repeatingunitsinastructure-basedrepresentation.
Source-basedPolymers
Source-basedpolymerrepresentationsencloseadiscretechemicalsubstanceinbrackets.Themodeofpoly-
merizationmaybeobviousfromcontextorbeunknown.Source-basedrepresentationsareusefulwhendescribing
processeswherethestartingmaterialsareknown,buttheexactstructureofthereactionproductisnot.
Youcancreateasource-basedrepresentationbyenclosingastructurein“Monomer(mon)”brackets.
Asource-basedrepresentationofpoly(vinylchloride)isshownbelow:
Youcanuse“Mer(mer)”bracketsforcomponentsofacopolymerwherethoseindividualcomponentsareknownnot
torepeatthemselvesortheyalternatewithothercomponents.Forexample:
Copolymersrepresentsubstanceswithmorethanonerepeatingunit.Ingeneral,youcanusebrackettype“Com-
ponent(co)”.Youcanalsouse“Copolymer,alternating(alt)”,“Copolymer,random(ran)”,and“Copolymer,block(blk)”
torepresentdifferentcopolymertypesinasource-basedrepresentation.
Thebrackettype,“Mixture,unordered(mix)”maybeusedtorepresentacollectionofsubstancesthatmayallbe
present,butnotnecessarilyinknownamounts.Brackettype“Component(c)”indicateseachmixtureelement,as
shownbelow:
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Figure14.6:Bracketsusedtoindicatemixtures
Brackettype“Mixture,ordered(f)”isprimarilyusedtodescribemanufacturingprocesses,wherecomponentorderis
critical.Aswithunorderedmixtures,individualelementsofanorderedmixtureshouldbesurroundedbybracketswith
abracketusageof“Component(c)”.However,componentsoforderedmixturesmustbenumberedtoshowtheir
order.Youcandothisbyeditingthe“c”labelwiththetexttooltoincludeanumber(“c1”,“c2”,andsoon.)
MultipleGroups
Youusethebrackettype,“MultipleGroup(#)”toindicatethattheencloseditemsarerepeatedaknownnumberof
times.Multiplegroupbracketsmayencloseentirestructures,orpartofthestructures.Someexamplesare:
Figure14.7:Bracketstoindicatemultiplegroups
Becausemultiplegroupbracketsrepresentaspecificrepeatcount,youcandisplaythemolecularweights(and
relateddata)fortheenclosedstructuresintheAnalysiswindow.
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RepeatPattern
Forsimplelinearpolymers,therepeatingunitsmayconnecthead-to-tailorhead-to-head(ortheirrepeatpatternmight
beamixtureorunknown).Youcanalsoassignthispropertytobrackets.
Thehead-to-tailtypeisthedefaultrepeatpattern,asshownbelow:
Figure14.8:Head-to-tailrepeatpattern.AandBrepresentthepolymersshown.CrepresentsamixtureofAandB.
RemovingBracketUsageLabels
Toremovethebracketusagelabels,dooneofthefollowing:
Hoveronthelabelandpress<delete>.
UsetheErasertooltodeletethelabel.
Note:Settingthebracketusagetypeto'Unspecified'removesanyspecificbracketusageassignment.
LinkNodes
Youcanspecifyavariable-lengthchain,orring,byindicatingthatoneoftheatomscanrepeatanumberoftimes
usinglinknodes.
Linknodesmusthaveexactlytwoconnectingbonds.
Theatomlabelmustmeettheseconditions:
Itmustconsistofagenericname,ornomorethanoneelementsymbol.
Thelastpartofthelabelmustbeintheform:numberhyphennumber,withthenumbersandhyphensubscripted.
Parenthesesorbracescanbeusedinsteadofbrackets.
Note:ChemBioFindersupportsonlybrackets,’[ ]’,forlinknodes.Parenthesesorbracescannotbeusedforlink
nodesinChemBioFinder.
Bracketscanbeomitted,ifnotrequiredforclarity,forexamplewithO
1-3
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Tocreatealinknode:
1. Openanatomlabeltextbox.
2. Typethelinknodeinthisformat:
[CH2]3-7
FlipType
Forladderpolymers(polymerswithtwoconnectingbondsoneachside)theconnectionordermaybeundefined.You
canassigntheFlipTypepropertytodefineit.Thispropertyisonlyforbracketswithexactlytwocrossingbonds.
Becauseofitsprevalence,theNoFliptypedoesnotreceivespecialannotation.Theexamplebelowillustratesaflip
typeinladderpolymers.
AlternativeGroups
Youcancreateasearchquerythatcontainsvariablefunctionalgroupsorsubstructures.Insteadofsubmittingmul-
tiplequeriesonstructuresthatshareacommonsubstructure,youcansubmitasinglequerywiththeparentstructure.
Theparentstructurecanhaveattachmentpointstoalistofalternativegroupsthatyoudefine.
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DefiningAlternativeGroups
Youcancreatealternativegroupdefinitions(R,G,andsoon.)thatrepresentasetofsubstituents,eachofwhichis
usedinthequery.
Todefinealternativegroups:
1. NavigatetoView>OtherToolbars>QueryToolstoopentheQuerytoolbar.
2. ClicktheAlternativeGroupquerytoolanddragwiththetooltocreateanarealargeenoughtodrawthealternative
groups.
3. Typeatitle,suchasR
1
,intheAlternativeGroupTitlebox,anddrawthesubstructurefragmentsintheAlternative
Groupbox.
Tip:Youcandrawtheboxafterwardtoenclosethelistofalternativegroups.
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Figure14.9:Defininganalternativegroup
Specifywherethefragmentsshouldbondtotheparentstructureonthealternativegrouplabelbydefiningattachment
Points.
1. Dooneofthefollowing:
Selectthediamond-shapedAttachmentPointtoolontheChemicalSymbolspalette(View>Other
Toolbars>ChemicalSymbols),andclickasubstructurefragmentwhereyouwanttoplacetheattachmentpoint.
Pointtoasubstructurefragmentwhereyouwanttoplacetheattachmentpointandpressthehotkey“.”(period).
Anattachmentpointsymbolappears.
2. Repeatforallfragments.
Figure14.10:Addingattachmentpoints.Anattachmentpointsymbolhasbeenappliedtothenitrogenatom.
Whenyoucreateastructurethatcontainsanalternativegroup,anattachmentpointsymbolappearsnexttothelabel.
Theattachmentpointnumbermatchesthatfoundinthedefinition.
Figure14.11:StructurewithR-grouptable
Thenumberdisplayedintheattachmentpointsymbolistheattachmentrankorder.Seetheexamplein"Multiple
AttachmentPoints"onpage251.
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