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ChemScript
ChemScriptisthecheminformaticsSoftwareDevelopmentKit(SDK).Itcontainstheprogrammingalgorithmscom-
monthroughoutPerkinElmerInformaticsproducts.Withenoughknowledgewritingsoftwarecode,youcanapply
ChemScripttocreateyourownscriptstousewithChemBioOfficeapplications.
ChemBioDrawUltraalsoincludesalibraryofsamplescriptsforyoutouse.NavigatetoFile>ChemScriptsand
selectanoption.
Torunascriptonthecurrentdrawing:
1. NavigatetoFile>RunChemScript.
2. IntheOpendialog,selectthescriptandclickOpen.
3. (Optional)Torunthescriptagain,navigatetoFile>Re-runPreviouslySelectedChemScript.
ChemScriptIntegration
Note:ChemScriptisanadvancedfeatureintendedforuserswithsomeprogrammingexperience.
ChemScriptletsyouaddcustomfunctionstoChemBioDraw.Customscriptscanbelaunchedfromtheapplication,
andtheresultsofthescriptarereturnedtoanewChemBioDrawdocument.Scriptsmustbewrittenusingeither
PYTHONor.NET.Youusecustomscriptsto:
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ApplycustomdrawingrulesusingChemScript
LaunchexternalapplicationsfromChemBioDraw
AutomateworkflowfromChemBioDraw
TheinputdataforthescriptconsistsofCDXMLdatafromthecurrentlyactivedocumentinChemDraw.Ifyouselecta
portionofthedocument,onlytheselectedpartofthedocumentisusedasinputtothescript.
Youcanapplyscriptstochemicalstructuresandreactions.
YoucanplacescriptsintheScriptsdirectoryforeasyusage.TheScriptsdirectoryisinthesamedirectoryasthe
ChemDrawitemsdirectory.
Tolaunchascript,dooneofthefollowing:
NavigatetoFile>ChemScripts,andselectascriptfromtheScriptsdirectory.
NavigatetoFile>RunChemScript,andselectascriptfromadirectoryotherthantheScriptsdirectory.
YoucanalsousethesamplescriptsavailableinChemDrawunderFile>ChemScripts.Oneexampleisgivenbelow:
1. Drawaminimumofthreestructuresinthedocumentwindow.
2. NavigatetoFile>ChemScripts>LayoutMoleculesinaCircle.Anewdocumentwindowappearswiththestruc-
turesarrangedinacircle.
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Struct=Name (Ultra Feature)
ChemBioDrawincludestwofeaturesforgeneratingstructuresandchemicalnames—Name>Structand
Struct>Name.Collectively,thesefeaturesarecalledStruct=Name.
Struct>NamegeneratesthenamesofchemicalstructuresusingtheCahn-Ingold-Prelogrulesforstereochemistry.
Usingthisoption,youcangeneratethenameofstructuresyouhavedrawn.
Name>Structletsyouconvertchemicalnamesintotheircorrespondingchemicalstructures.Itisdesignedtointerpret
chemicalnamesastheyareusedbychemists.Inotherwords,itrecognizestheshorthandandslangofeveryday
usage,inadditiontorecognizingmostoftheofficialIUPAC,IUBMB,andCASrulesandrecommendations.
Struct>Name
Struct>Namecaninterpretavarietyofchemicalstructures.Thismeansthatyoucandrawastructureand
Struct>Namewillprovideitsname.Italsoupdatesthenamewhenyoumodifythestructure.
UsingStruct>Name
Togeneratethenameofyourstructure:
1. Selectthestructure.
2. NavigatetoStructure>ConvertStructuretoName.Thenameappearsunderthestructure.
SupportedStructures
However,Struct>Namewillinterpret:
Stereochemistry
PrincipalGroupinRingsandChains
CarboxylicAcids
S,Se,andTeAcids
Peroxyacids
S,Se,andTeEsters
Amidederivativesofacids
S,Se,andTeAcidHalides
Carbonicacids
S,Se,andTeAmides
Nitricacids
Sulfidesandchalcogenanalogs
AcidHalides
Sulfoxidesandchalcogenanalogs
CarboxylicEsters
Heteroatomicacids(P,B,As)
Salts
Heteroatomicesters
Anhydrides
Heteroatomicacidhalides
Hydrazides
Aldehydesandchalcogenanalogs
Imides
Ketonesandchalcogenanalogs
Amides
Alcoholsandchalcogenanalogs
Hydrazines
Hydroperoxides
Nitriles
Peroxides
AminesandImines
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Non-RingedStructures
Isolatingandnamingthefunctionalgroups
Identifyingthebasechainofthemolecule
Identifyingandbuildingsubstituents
Nomenclatureofgroupscitedonlybyprefixes
Heteroacycliccompounds
Namingofsubstituentgroups
Locants
Namegeneration(alphabetization,punctuation,etc.)
RingedStructures
Struct>Namesupportsthethesetypesofringedstructures:
Carbomonocyclicstructures
Heteromonocyclicstructures
Fusedpolycyclicstructures:
Fusedpolycyclictrivially-namedstructures
Ringfusionsofmultiplerings
Ringfusionsoftwomultipleringsystems
Ringfusionsofmorethantworingsystems
Bridgedmonocyclicstructures
Spiroringsystems
Someoftheseringstructuresaredefinedbelow.
RingAssemblies
Aringassemblyhastwoormoreidenticalcyclicsystemsjoinedtogetherbysingleordoublebonds.Allthecyclicsys-
temsareeitherasinglering,fusedsystem,alicyclicvonBaeyersystem,spirosystem,phanesystem,orfullerene.
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Figure10.1:Anexampleofaringassemblystructure:1,1':2',1''-terphenyl.
FusedRingSystems
Struct>Namesupportsfusedringsystemsoftwoormorerings,suchasthestructurebelow.
Figure10.2:cyclopenta[ij]pentaleno[2,1,6-cde]azuleneisafusedringsystem.
BridgedFusedRingSystems
ChemBioDrawsupportsbipodal(bothbivalentandpolyvalent)simpleacyclic(chained)homogeneous(atomsofonly
oneelement)independentbridgedfusedringsystems.Forexample:
Figure10.3:Thebridgedfusedringsystem9,10-epidioxyanthracene.
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Polymers
PolymerstructurescannotbeexpressedbySMILES.However,Struct>Namesupportsmanyhomopolymers,copoly-
mers,andalternatingpolymers.Forexample:
Figure10.4:polyaziridinecompoundwithsulfamicacid(1:1)
OtherCompounds
PhosphorousandArseniccompounds
Si,Ge,Sn,andPbcompounds
Boroncompounds
Organometalliccompounds
Struct>NamegeneratesnameswithproperCIPstereochemistrydescriptors.
Struct>Nameprovidesdirectsupportforstoichoimetryspecifiedasbracketproperties,includingfractionalstoi-
chiometry.Also,themannerinwhichthestoichiometryof0.5("hemi")and1.5("sesqui")ishandledisimproved.For
example:
Figure10.5:2-(aminooxy)aceticacidhemihydrochloride
Struct>NamefollowsIUPACrulesascloselyaspossiblewhengeneratingchemicalnames.However,whilehandling
indicatedhydrogens,itconformstoCASnomenclaturerecommendations.Forexample,thecarbonatombetween
twooxygenatomsin1,3-dioxolecanneverformdoublebondsasitstwoneighbors(oxygenatoms)havenofree
valences.WhilepreferredIUPAC(PIN)nameforthatstructureis2H-1,3-dioxole,Struct>Namegeneratesthename
1,3-dioxole.ThenameproducedbyStruct>NameconformstoCASnomenclaturerecommendationsinthisregard.
UnsupportedStructures
Thisfeaturehasafewlimitationsforinterpretingsomestructuressuchas:
Sulfonesandchalcogenanalogs
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Isotopicallymodifiedcompounds
Radicals,ions,andradicalions
AutoUpdate
Youcanincludechemicalproperties,includingthechemicalnameandanalysis,inacaption,andthecaptioncontent
willupdateautomaticallywhenyoumodifythestructure.Formoreinformationonaddingchemicalpropertiestocap-
tions,see"AnalysisData"onpage66.
Totoggletheauto-updatefeature:
1. Pointtothecaption.
2. Right-clickandselectAuto-update.Acheckmarkappearsnexttothecommandwhenitisselected.Successive
clickstogglethecommandonandoff.
Whenauto-updateison(default)thelabelupdateseachtimeyoumodifythestructure.
Note:Forlargestructures,thenewlabelmaynotappearforafewseconds.Youdonothavetowaitforthenew
labeltoappearbeforecontinuingtomodifyyourstructure.
Name>Struct
YoucantypeachemicalnameandName>Structwilldrawthestructure.
Althoughsometradenamesaresupported,Name>Structisnotintendedtointerprettradeorcommonnames.Achem-
icaldatabase,suchasChemBioFinder.com,ismoreappropriateforobtainingthesestructures.
Note:Usethewords‘alpha’and‘beta’whenenteringformsofaminoacids.Forexample,‘alphaalanine’and‘beta
alanine’arevalidname>structchemicalnames.
Note:Name>StructcanalsointerpretmanyGermannames.
ConvertingNamestoStructures
Toenterthenameandconvertittoitsstructure:
1. NavigatetoStructure>ConvertNametoStructure.
TheInsertStructuredialogboxappears.
2. Typethename(example:2-bromobenzoicacid)orpastethecopiednamefromtheclipboard.
Tip:Youcanpastethenameusingkeyboardcommands:<CTRL>+<V>.
3. Toplacethenamebelowthestructure,selectPastenamebelowstructure.
4. ClickOK.
ConvertingClipboardNames
Topasteanameontheclipboardasastructure:
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1. Clickinthedocumentwindow.
2. NavigatetoEdit>PasteSpecial>NameasStructure.Thestructureappearsinyourdocument.
ConvertingCaptions
Youcanconvertacaptiontoastructure.
1. Selectthecaption.
2. NavigatetoStructure>ConvertNametoStructure.
SupportedStructures
Struct>Namecannamecompoundsinclassesofstructures:
PrincipalGroupsinRingsandChains
AcidHalides
Amidederivativesofacids
Alcoholsandchalcogenanalogs
Anhydrides
Aldehydesandchalcogenanalogs
Carbonicacids
Amides
Imides
AminesandImines
Nitricacids
CarboxylicAcids
Peroxyacids
CarboxylicEsters
Salts
Heteroatomicacidhalides
Sulfidesandchalcogenanalogs
Heteroatomicacids(P,B,As)
Sulfoxidesandchalcogenanalogs
Heteroatomicesters
Peroxides
Hydrazides
S,SeandTeAmides
Hydrazines
S,Se,andTeAcidHalides
Hydroperoxides
S,Se,andTeAcids
Ketonesandchalcogenanalogs
S,Se,andTeEsters
Nitriles
RingedStructures
Bridgedmonocyclicstructures
Heteromonocyclicstructures
Carbomonocyclicstructures
Ringfusionsofonlytworings
Fusedpolycyclictrivially-namedstructures
Ringfusionsoftwomultipleringsystems
OtherCompounds
Boroncompounds
Si,Ge,Sn,andPbcompounds
Organometalliccompounds
PhosphorousandArseniccompounds
Name>Structrecognizesmostorganicandinorganicnomenclature.However,sometypesarenotsupported:
Coordinationcomplexes
Polyboranes
Polymers
Somehighly-bridgedringsystems,includingfullerenesandporphyrins/porphines
Somestereochemistrydesignators:+,-,+/-,+-,
D
,l,dl,endo,exo,syn,anti,r,t,c
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Chemistry Features
StructureAnalysis
Youcandisplaythechemicalformula,exactmass,molecularweight,m/z,andelementalanalysisfortheentiredoc-
ument,astructure,orapartofastructureusingtheAnalysiswindow.
Valuesforselectedobjectsinthedocumentwindowareshown.Ifnostructureisselectedinyourdocument,values
fortheentiredocumentareshown.
Youcanhavethiswindowopenasyoudrawinthedocument.Itshowsthecurrentvaluesasyoudraw,seeexample
below:
TheDecimalssettingappliestoExactMass,MolecularWeight,andm/zonly.ThevaluesdisplayedintheAnalysis
windowincludes:
Formula.Themolecularformulashowingtheexactnumberofatomsofeachelementinthemoleculeandcharges,
radicals,andisotopes.
ExactMass.Theexactmolecularmassofthestructure,whereatomicmassesofeachatomarebasedonthemost
commonisotopefortheelement.
MolecularWeight.Theaveragemolecularmassofthestructure,whereatomicmassesarebasedonthenatural
abundanceofallisotopesoftheelement.
m/z.Mass/charge.Theweightsofthemostcommonisotopesandagraphicalrepresentationoftheisotopicabund-
anceisshown.
Themolecularweightaccountsfortheisotopesforeachatomandtheirnaturalabundance.Wherethereismorethan
oneabundantisotope,thisfeaturecomputesmultiplemolecularweights.Lowabundancecombinations(whether
becausetheisotopeisinlowabundanceorbecauseitincludesmanymoderate-abundancecontributions)arenot
takenintoaccount.
ElementalAnalysis.Thepercentbyweightofeachelementinthestructure.
Toopentheanalysiswindow:
1. Selecttheentirestructure,orpartofthestructure.Ifnothingisselected,theanalysiswindowdisplaysvalueforthe
entirestructure.
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2. NavigatetoView>ShowAnalysisWindow.Theanalysiswindowsdisplaysvaluesforthepartsofthedrawing
youselect,ortheentiredrawingifnothingisselected.
3. (Optional)SelectPastetoaddtheanalysisinformationtoyourdrawing.Theinformationappearsasacaptionthat
youcanedit.
Figure11.1:Structuralanalysis
Theinformationupdatesasyoueditthestructure.Youcanshoworhidetheinformation:
1. Usinganytool,right-clickthecaption.
2. PointtoAnalysis,andselectordeselecttheitemtoshow/hide.
ChemBioFinderhotlink
PerkinElmerInformaticsmaintainsavastdatabaseofcompoundsandtheirproperties.ChemBioDrawprovidesalive
Internetconnectiontoadatabase,thatincludes:
LinkstoavailabledataresourcessuchasthePerkinElmerInformaticsChemIndex.
LinkstoChemSpiderdatabase.
Namesandsynonyms.
ChemicalidentifierssuchasCASRegistryNumbersandChemACXIDs.
TheHotLinkinformationandthedataitselfarecontinuallyupdated.
TheHotLinkdisplaysinformationforthestructureinthedocumentwindow.
ToopentheChemBioFinderHotLink:
1. Selectastructure.
2. GotoView>ShowChemBioFinderHotLinkWindow.
Note:ToaccessChemSpiderdatabase,clickonthevalueofeitherInchiKeyorStdInchiKeyintheProperties
tableintheChemBioFinderHotlinkwindow.
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