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methylethylketoneandMeOHisrecognizedasmethanol.Ontheotherhand,C
6
H
6
mightmeanbenzene,oranother
isomer.Generally,empiricalformulas(C
2
H
6
andH
2
SO
4
)arenotrecognized,butstructuralformulas(CH
3
CH
3
and
HOSO
2
OH)are.
Molecularweightandelementalanalysesofempiricalstructuresarepossible,buttheExpandLabelcommanddoes
notworkwiththem.Empiricalstructuresarediscardedwhentheyaretransferredtootherapplicationsthatrequire
unambiguousstructures.
Chemically-significanttextmustbeentirelyinformulaor,forisotopesandcharges,superscriptstyle.ChemBioDraw
doesnotrecognizeachemicalformulaembeddedwithinalargerblockoftext.
Ifyoudrawabond,addanatomlabel,andthendeletethebond,you
haveachemicallymeaningfultextblockwhosefont,size,andstyle
matchotheratomlabels.
IfyoucreateacaptionwiththetexttoolandsetittoFormulastyle,
youhaveachemicallymeaningfultextblockwhosefont,size,and
stylematchothercaptions.
Charges
YoucancreatechargesaspartofaatomlabelorwiththeappropriatesymbolfromtheChemicalSymbolstoolbar.
Chargesarealwaysassignedtoaspecificelementintheatomlabel,whoseacceptablevalencesbecomethoseof
thesimilarisoelectronicneutralelement
.
Achargefollowinganelementisassignedtothatelement.
Achargethatdoesnotfollowanelementisassignedtothenextelement.
Chargesthatfollowamonovalentelementwitharepeatcountare
assignedtotheelementbeforethatelement.
Chargesthatfollowotherrepeatingunitsaredistributedamongthose
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units.
Chargesmaybesuperscripted.
Multiplechargesarerecognizedappropriately.
Chargesmayhaverepeatcountsaslongasboththechargeandthe
repeatcountaresuperscripted.
A“floating”chargeplacedwiththeChemicalSymbolsToolisassignedto
thenearestatom.IfnoatomiswithinthedistancesetastheFixedLength,
thechargeisignoredandnotassignedtoanyatom.
A“floating”chargeplacedwithinadelocalizedsystemisrecognizedbythe
AnalyzeStructurefunction,butisdiscardedwhensavedtoformatsthat
requireallchargestobeassociatedwithspecificatoms.
IsotopesandElements
Bydefault,allisotopesarerecognizedinthefullTableoftheElements.ThisdataisprovidedbyCRCPress,Inc.Iso-
topesaredefinedintheIsotopesTablefile.Youcaneditthisfileinanytexteditortoaddnewisotopes.
Asuper-scriptednumberbeforetheelementsymbolindicatesisotopenum-
bers.
Isotopescanbeincludedanywherethatregularelementscan.
DeuteriumandTritiumappearasone-lettersymbols.
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Radicals
RadicalsareindicatedwiththeappropriatesymbolfromtheChemicalSymbolspalette.Aswithcharges,theyare
assignedtothenearestatom.Radicalsalwaysoccupyonefreevalence,inadditiontoanychargeeffects.Two
examplesare:
Note:Thelonepairsymbolisinterpretedasadiradicalwhenitisplacednexttoanunlabeledcarbonatom.
H-Dot/H-Dash
H-DotandH-DashsymbolsfromtheChemicalSymbolspaletteindicatethestereochemistryofasinglehydrogen
atom.Thesesymbolsaremostcommoninfusedsystems,suchasbelow:
Complexes
CompoundswithelectronpairscanactasLewisbases,bondingwithLewisacidsthatareelectron-deficient.Similar
behaviorcanbeseenbetweenlonepairsandmetals.
Thebestrepresentationofthesetypesofinteractioniswithadativebondfromtheelectron-pairdonortotheacceptor.
Usingaplainbondinsteadofthedativebond,willcauseavalenceerror.Thedativebondmoreaccuratelyrepresents
theelectrondonation.
Complexesmayalsoberepresentedwithexplicitlonepairsandwithoutanybonds.
Ifyouuseasimplebondtoindicateacomplex,youmaywanttosetAbnormalValencetoAllowedintheAtomProp-
ertiesdialog.
Multi-centerAttachments
Multi-centerattachmentsaremeaningfulonlywhencreatedusingStructure>AddMulti-CenterAttachment.Multi-
centerattachmentscreateapseudo-atomthatisdisregardedduringchemicalcalculationsbutstillletsyoucreate
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diagramsthatlookmeaningfultoanexperiencedchemist.Afewexamplesareshownbelow:
h
3
or
p
-Allylcomplex:
Ferrocene,a
p
-Arylcomplex:
Cp
2
TiCl
2
,another
p
-Arylcomplex:
h
-C
5
H
5
Mn(CO):
Cahn-Ingold-Prelog
AbsolutestereochemistryiscalculatedfortetrahedralatomsanddoublebondsaccordingtotheCahn-Ingold-Prelog
(CIP)priorityrules.
TheCIPrulesaredesignedtoorderligandsbytheirpriorityanddetermineadescriptorbasedontheorientationofthe
orderedligandsinspace.
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Aligandisanentityattachedtoastereocenter.Forexample,atetrahedralcarbonhasfourligandscorrespondingtoits
foursubstituents.Whenatetrahedralcarbonisinaring,itstillhasfourligands:thetwoligandsoutsidethering,athird
consistingofthering“unpeeled”clockwise,andafourthconsistingofthering“unpeeled”counterclockwise.
Fiverulesusedtodeterminethepriorityofligandsaresummarizedbelowinsimplifiedform.Formoredetailedinform-
ation,seethereferences.
Rule1.Higheratomicnumberprecedeslower
Rule2.Higheratomicmassprecedeslower
Rule3.cisprecedestrans
Rule4.Likepairsofdescriptorsprecedeunlikepairs
Rule5.RprecedesS
ChemBioDrawchecksdifferencesupto15atomsdistantfromthestereocenter.
StereochemicalIndicators
Aftertheligandsareranked,anindicatorisassignedasshowninthefollowingtable.
Stereocenter
Indicator
Doublebond
Zifthehighestrankingligandofeachpairareonthesamesideofthebond;otherwiseE.
Tetrahedralatom
Whenthelowest-rankingligandislocatedbehindthecentralatom:
Rwhenremaining3ligandsarearrangedclockwiseindescendingorder
Swhenremaining3ligandsarearrangedcounterclockwiseindescendingorder
rorsisusedforpseudoasymmetricatoms
StereochemicalFlags
Whilethechiralityofaspecificstereocentercanbeindicatedwiththeappropriatewedged,hashed,orplainbond,
sometimesitisusefultoindicatetherelativestereochemistryofamoleculeasawhole,consideringtherelationship
betweenallstereo-centers.Stereochemicalflagsapplytotheneareststructure;ifnostructureiswithinthedistance
specifiedbytheFixedLengthvalue,thestereochemicalflagisnotassignedtoanystructure.
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Figure16.2:TheAbsoluteflagindicatestheexactstereoisomerasdrawn.
Figure16.3:Therelativeflagindicatestheexactstereoisomerasdrawn,oritsenantiomer.
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Figure16.4:Theracemicflagindicatesamixtureoftheexactstereoisomerasdrawnanditsenantiomer.
PolymerRepresentations
Polymersarerepresentedbybracketsusedtoencloserepeatedstructuresorstructuralfragments.Bracketproperties
specifytheorientationandcontextoftherepeatingunits.Foranexplanationofthebracketproperties,see"Setting
BracketProperties"onpage244.
Note:ThepolymerdrawingfeatureisavailableonlyinChemBioDrawUltra,andChemDrawPro.
References
“GraphicRepresentations(ChemicalFormulae)ofMacromolecules(Recommendations1994)”PureAppl.Chem.,66,
2469-2482(1994).
“Source-BasedNomenclatureforCopolymers(Recommendations1985)”PureAppl.Chem.,57,1427-1440(1985).
Alsoavailableat:http://www.iupac.org/publications/books/pbook/PurpleBook-C7.pdf.
“BasicDefinitionsofTermsRelatingtoPolymers(1974)”PureAppl.Chem.,40,479-491(1974)Alsoavailableat:
http://www.iupac.org/reports/1996/6812jenkins/index.html.
AlsoseetheGuidefortheauthorsofpapersandreportsinpolymerscienceandtechnologyfromIUPAC.
AnalysisMessages
Whenastructurecannotbefullyanalyzed,twogeneraltypesofmessagesaredisplayed:
Statusmessagesthatreportaproblemthatmaynotaffectthefinalanalysis
Criticalmessagesthatmayaffectthefinalanalysis
Message
Description
Therearetoomanybondstothis
unlabeledCarbon.
Displayedforeveryunlabeledatomwithmorethanfourfilledvalences.
Filledvalencesincludesumofbondorders,charge,radicals,andfreesites.
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Message
Description
Aromaticbondscount1.5each,roundeddownunlessitistheonlybondto
theatom.Chargeissignedandincludeschargeimpliedbydativebonds.
TheSubstituentsquerypropertytreatsfreesites,uptoandexactlythe
sameway:anatomwithtwoexplicitbondsand“Substituents:UpTo3”or
“Substituents:Exactly3”or“Substituents:FreeSites1”hasthreefilled
valences.
Anatominthislabelhasaninvalid
valence.
Displayedincaseswhereaplacecannotbefoundtoplaceabondorabond
cannotbefoundtoplaceanatom.Validvalencesforeachelementarelis-
tedintheIsotopesTablefile.
ChemDrawcan’tinterpretthis
label.
Displayedwhentextisfoundthatcannotbeidentifiedasanelement,nick-
name,genericnickname,oralternativegroupname.
Parenthesesdon’tmatch.
Displayedwhenparenthesescannotbematchedintonestedopen-close
pairs.
Thislabelhasconflictingorunas-
signablecharges.
Displayedwhenaplusandminuschargehavebeenassignedtothesame
element,chargeshavebeenassignedinmorethanoneway,oracharge
hasbeenassignedtoanickname,genericnickname,orAlternativeGroup
name.
Formulacannotbecomputedfor
queries.
Displayedforeverylabelthatcontainsagenericnickname,anelementlist
oranalternativegroup.Thisisastatusmessageonly;analysiscontinues
asiftheproblematiclabelwerenotselected.
TextnotinFormulastylewon’tbe
interpreted.
DisplayedforthefirstcaptionthatisnotanatomlabelorAlternativeGroup
name,andwhichcontainsanytextnotinFormula,Subscript,orSuper-
scriptstyle.Thisisastatusmessageonly,andappearsonlyonceregard-
lessofhowmanycaptionsareintheselection.
Thisnamedalternativegroupcon-
tainsnoattachmentpoint.
DisplayedforanystructurewithinanAlternativeGroupBoxwherethestruc-
turelacksanattachmentpoint.Thisisastatusmessageonly.
Thisnamedalternativegroupcon-
tainsfragmentswithinconsistent
valences.
DisplayedforanyAlternativeGroupBoxwhosecontainedstructureshave
varyingnumbersofattachmentpoints.SinceallstructureswithinanAltern-
ativeGroupBoxaretobeusedinterchangeably,theymusthavethesame
numberofattachments.Thisisastatusmessageonly.
Thisnamedalternativegroupcon-
tainsnofragment.
DisplayedforanyAlternativeGroupBoxthatisempty.Thisisastatusmes-
sageonly.
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Message
Description
Partofamoleculeisoutsideofthe
alternativegroupdefinition.
DisplayedforanyAlternativeGroupBoxwhosebordercrossespartofa
structure.Thisisastatusmessageonly.
Thisisolatedbondisprobablynot
intendedtohavechemicalsig-
nificance.
Displayedforunlabeledsinglebondsunattachedtootherbonds.Allbonds
areinterpretedchemically,usuallyasC
2
H
6
,andmaycauseunexpected
resultsifintendedasagraphicallineonly.Thisisastatusmessageonly.
Theatomisveryclosetoanother
atomorbond.
Displayedforanyatomthatisnearlytouchinganotheratomorbondbutnot
boundtoit.Ifabondreallywasintended,theanalysisofthestructurepro-
ducesincorrectresults.Thisisastatusmessageonly.
Thestereocenterhasnoste-
reobondsspecified.
Displayedforanyasymmetriccenterwithoutattachedwedged,hashed,
dashed,orboldbonds.Thisisastatusmessageonly,andappearsonly
whenShowStereochemistryistunedonandthereisatleastoneother
wedged,hashed,dashed,orboldbondinthestructure.
Thereisavalenceandchargeerror
somewhereinthisaromaticsys-
tem.
Displayedforanyodd-memberedringdrawnasadelocalizedsystem(with
acircleinthemiddle),wherethereisnocorrespondingassociatedcharge.
Forexample,adelocalizedrepresentationofcyclopentadienemustinclude
eitheranegativechargeoramulticenterattachment.
Thestereocenterhasconflictingor
ambiguousstereobondsspecified.
Displayedforanystereocenter(tetrahedralatom,asymmetricdoublebond,
etc.)wheretheabsolutestereochemistrycannotbedeterminedfromthe
structureasdrawn.Forexample,thismessagewouldbeshownforacar-
bonatomattachedbyboldbondstofourdifferentligands.Thismessageis
displayedonlywhenShowStereochemistryisalsoturnedon.
Thislabelhasanunrecognizediso-
topicmass.
Displayedforeverylabelthathasanumericsuperscriptimmediatelypre-
cedinganatomicsymbol,wherethesuperscriptednumberdoesnotcor-
respondtoarecognizedisotope.Forexample,
24
CH
3
.
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Property Calculations
Youcancalculatepredictedvaluesofselectedphysicalandthermodynamicpropertiesforstructuresofupto200
heavyatoms.Thissectiondescribeshowthevaluesaredetermined.
LogP
ThreefragmentationmethodsareusedtopredictthelogPvalues:
MethodOne:Basedon94atomiccontributionsevaluatedfrom830moleculesbyleastsquaresanalysis.This
methodworkswithastandarddeviationof0.47logPunitsandcanhandlemoleculescontaininghydrogen,oxygen,
nitrogen,sulfur,andhalogens.
MethodTwo:Anextensionofmethodonebutisbasedon120atomiccontributionsevaluatedfrom893molecules
byleastsquaresanalysis.Inadditiontotheatomsintroducedformethodone,itcanhandlemoleculesthatcontain
phosphorusandseleniumatoms.Thismethodworkswithastandarddeviationof0.50logPunits.
MethodThree:Basedon222atomiccontributionscalculatedfrom1868moleculesbyleastsquaresanalysis.This
methodallowsacalculationoflogPwithastandarddeviationof0.43logPunitsandcanhandlemoleculescon-
taininghydrogen,oxygen,nitrogen,sulfur,halogens,andphosphorusatoms.Ifthismethodisappliedtomolecules
withinternalhydrogenbonds,thestandarddeviationis0.83LogPunits.
Henry’sLaw
TwomethodsareusedtopredictHenry’sLawconstant:
MethodOne:Anapproachbasedonthebondcontributionmethod,thismethoduses59bondcontributionvalues
and15correctionfactors.Thecontributionswerecalculatedbyleastsquaresanalysisusingadatasetof345chem-
icals.Thismethodestimateswithameanerrorof0.30unitsandastandarddeviationof0.45units,andcanhandle
moleculescontainingcarbon,hydrogen,oxygen,nitrogen,sulfur,phosphorusand,halogens.
MethodTwo:Henry’sLawconstantisestimatedfromanequationfoundusinglinearregression.Multifunctional
compoundswereomittedfromthisstudy.Thismethodshouldnotbeusedforcompoundswheredistantpolarinter-
actionispresent.
MolarRefractivity
Twofragmentationmethodsareusedtoestimatethemolarrefractivityvalue:
MethodOne:Includes93atomiccontributionsevaluatedfrom504moleculesbyusingaconstrainedleastsquares
technique.Thismethodworkswithastandarddeviation1.27cm
3
/molandcanhandlemoleculescontaininghydro-
gen,oxygen,nitrogen,sulfur,andhalogens.
MethodTwo:Isanextensionofmethodonethatincludes120atomiccontributionsevaluatedfrom538molecules
byusingaconstrainedleastsquaresanalysistechnique.Inadditiontotheatomsintroducedformethodone,this
methodcanhandlemoleculeswithphosphorusandseleniumatoms.Thismethodworkswithastandarddeviation
of0.77cm
3
/mol.
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