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Stereochemistry
ChemBioDrawcalculatestheabsolutestereochemistryaccordingtotheCahn-Ingold-Prelog(CIP)priorityrules.For
moreinformation,see"Cahn-Ingold-Prelog"onpage284.
Onlytetrahedralanddouble-bondstereochemistryaresupported,andonlynon-racemicstereochemistryisinter-
preted.Stereochemicalindicatorsforaromaticbondsarenotdisplayed.
ChemBioDrawusesthisnotation:
(R),(S)
Standardtetrahedralstereochemistry
(r),(s)
Tetrahedralstereochemistrydeterminedbyotherstereochemicalcenters.Forexample:cis-decalinandmyo-inositol
(E),(Z)
Standarddouble-bondstereochemistry
StereochemistryIndicators
ChemBioDrawupdatesstereochemistryindicatorsasyouchangeyourdrawing.
Toincludestereochemistryindicatorsinyourdrawing:
1. Selectthestructure.
2. Right-clickandselectObjectSettingsfromthecontextmenu.
3. FromtheDrawingtab,underAtomIndicatorsandBondIndicators,selectShowStereochemistry.
Thestereo-centersaremarked,asshowninthisexample:
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HidingIndicators
1. Selecttheindicatoryouwanttohide.
2. Right-clickandselectHideIndicatorfromthecontextmenu.
FormattingIndicators
Tochangethefontstyle:
1. Selecttheindicatoryouwanttomanipulate.
2. Right-clickandselecttheStylefromthecontextmenu.
ApplyingParenthesis
Toapplyparenthesestostereochemistryindicators:
1. NavigatetoFile>Preferences.
2. FromthePreferencesdialog,undertheBuilding/Displaytab,selectIncludeParenthesesWhenShowingSte-
reochemistry.
RemovingIndicators
Toremoveanindicator,clickonitusingtheErasertool.
PositioningIndicators
Youcanpositionaqueryindicatorbyeitherdraggingitorenteringanumericvalueforthenewlocation.
Toindicateanexactlocation:
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1. Selecttheindicatoryouwanttore-position.
2. Right-clickandchoosePositionfromthecontextmenu.ThePositionIndicatordialogappears.
3. Clicktheappropriateoption,andtypeavalue,asdescribedinthetablebelow:
ToPosition
TypeaValueforthePositionby
Fromtheatomorbondcenter
toindicatorcenter
Angle,indegrees
or
Clock,inclocktime
Fromtheatomorbondcenter
tobottomleftofindicator
baseline
Offset,horizontal,andvertical
Atspecifiedcoordinates
Absolute,horizontal,andvertical
Relativestereochemistry
Youcanspecifyrelationshipsbetweengroupsofstereocenterswithinamolecule.
Thisnotationenablesyoutodescribestereochemicalpropertiesandindividualstereocentersratherthantheentire
molecule.Asaresult,youcanillustratepropertiesofseveralenantiomersusingonlyafew(orjustone)structures.
Thenotationisillustratedbelow:
Toaddstereochemicalnotationtoastructure,gotoStructure>EnhancedStereochemistry.
Thepowerofthisnotationbecomesclearwhenyoudrawcomplexenantiomers.Forexample,beta-cypermethrinisa
mixtureoffourdistinctstereoisomersconsistingoftwoenantiomericpairs.However,drawingthisrequiresonlyone
structure:
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Figure11.2:beta-Cypermethrin
Twostereo-centershavethe&1designationbecauseoftheirfixedrelativeconfiguration:whenoneis(R)theother
mustbe(S).Asaresult,theyformagroup.Thethirdstereocentervariesindependentlyandisdesignated&2.Group
numbersareincrementedautomatically.Toseeallthebeta-cypermethrinstereoisomers,gotoFile>Open
Samples>b-Cypermethrin.
Toindicatestereochemistryforagroup:
1. SelectallatomsinthegroupusingSHIFT+click.
2. GotoStructure>EnhancedStereochemistryandselectastereochemistrymarker.
See"Relativestereochemistry"onpage153forinformationonshowingandhidingindicators.
Youcansaveenhancedstereochemistrynotationinanyoftheseformats:CDX,CDXML,MOLV3000,RXNV3000,
SKC,TGF.
WhensavingtoSKCorTGFformat,theindicatorsareconvertedintocorrespondingDataSGroups.Wheneveryou
openSKCorTGFfilescontainingsuchDataSGroups,theyareconvertedintotrueEnhancedStereochemistryval-
ues.
ChemicalAnnotations
ChemBioDrawprovidesthefollowingtoolsandtoolpalettesthatenableyoutoaddchemicalannotationstoyourdoc-
uments:
Orbitaltoolspalette.Draworbitals
ChemicalSymbolToolspalette.Drawcharges,radicals,andothersymbols
Orbitals
Youdraworbitalssothatthenodeappearsfirst.Thenyoucanchangethebackgroundcolor,shading,andsolidcolor
usingtheColormenu.
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DisplaytheInfowindowtoviewtheorbital’slengthandanglerelativetotheX-axiswhileyoudrawit.Toconstrainthe
lengthandangleofanorbital,navigatetoObject>FixedLengthsorFixedAngles.
Note:Orbitalsarenotnormallyapartofthestructuretheyaredrawnnearandarenotselectedwhenyou
double-clickabond,atom,oratomlabelwithaselectiontool.Togrouptheorbitalswiththestructure,navigateto
Object>Group.See"GroupingObjects"onpage85.
S-orbitals
Thes-orbitalisshownbelow:
Todrawansorbital:
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthes
-orbital
toolfromthepalette.
2. Clickanatominthedrawingwheretheorbitalwillbecentered.
SigmaOrbitals
Thesigma-orbitalisshownbelow:
Todrawa
s
-orbital:
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthe
s
-orbitaltoolfromthepalette.
2. Clickanatominthedrawingwheretheorbitalwillbecentered.
SingleLobeOrbitals
Todrawasinglelobeorbital:
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthesinglelobeorbitaltoolfromthepalette.
2. Clickanatomwherethenarrowendoftheorbitalwillbeattached.
P-orbitals
Thep-orbitalisshownbelow:
Todrawaporbital:
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthe
p-orbital
toolfromthepalette.
2. Clickanatomwherethenodeoftheorbitalwillbeattached.
HybridOrbitals
Thehybridorbitalisshownbelow:
Todrawahybridorbital(‘sp3’):
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthe
hybrid-orbital
toolfromthepalette.
2. clickanatomwherethenodeoftheorbitalwillbeattached.
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D-orbitals
Thed-orbitalisshownbelow:
Todrawadorbital(‘dxy’):
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthed-orbitaltoolfromthepalette.
2. Clickanatomwherethenodeoftheorbitalwillbeattached.
Todrawad
z
2-
orbital:
1. HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthed
z
2-orbitaltoolfromthepalette.
2. Clickanatomwherethenodeoftheorbitalwillbeattached.
ChemicalSymbols
Youcanmoveanyattachedchemicalsymbol(otherthanH-dotandH-dash)anydistancefromitsrelatedatom.The
availablechemicalsymbolsare:
Figure11.3:ChemicalSymbols:A)CirclePlus;B)Plus;C)Radicalcation;D)Lonepair;E)ElectronPushing;F)H-
dot;G)Attachmentpoint;H)Polymerbeadattachmentpoint;I)Attachmentpoint;J)Attachmentpoint;K)H-dash;L)
RadicalPushing;M)Radical;N)Radicalanion;O)Minus;P)Circleminus.
Youcanplaceunattachedsymbolsanywherewithinyourdocumentandresizethem.
H–dotandH–dash
TorepresentahydrogenatomthatiscomingoutoftheplanetowardyoualongtheZaxis,usetheH–dotsymbol.
TorepresentahydrogenatomthatisdirectedbackwardsintotheplaneawayfromyoualongtheZaxis,usetheH–
dashsymbol.ToinsertH–dotsandH–dashes,clickanatom.
LonePair/Diradical
UsethelonepairsymboltoindicatealonepairofelectronscommoninLewisstructures.
Tousethelonepairsymbol:
1. HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthelonepairfromthepalette.
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2. Clickanddragtheatomtowhereyouwantthelonepair.Thelonepairisoffsetfromtheatomatafixedposition.
ElectronandRadicalPushing
ChemBioDrawprovidestheElectronPushingandRadicalPushingtoolsforillustratingelectrontransfer.Electron
transferscanbedrawnbetweenatoms,bonds,andorbitals.Formoreinformation,see"ElectronandRadicalPush-
ing"onpage132.
Radical
Usetheradicalsymboltoindicateasinglenon-bondedelectron.
Tousetheradicalsymbol:
1. HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselecttheradicalfromthepalette.
2. Clickanddragtheatomtowhereyouwanttheradicalsymbol.
Note:Thelonepairsymbolisinterpretedasadiradicalwhenitisplacednexttoanunlabeledcarbonatom.
RadicalCationandRadicalAnion
Usethechargeradicalsymbolstorepresentradicalsthatarecharged.
Tousethechargeradicalsymbols:
1. HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthesymbolfromthepalette.
2. Clickanddragtheatomtowhereyouwantthesymbol.
3. Clickanatomtoaddaradicalcationorradicalanionsymbolinahorizontalorientation.
ChargeSymbols
Todrawachargeandassociateitwithastructure:
1. HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthechargesymbolfromthe
palette.
2. Clickanddragtheatomtowhichyouwantthechargetocorrespond.
Thenumberofhydrogenatomsincreasesordecreasesasappropriatefortheadditionofthecharge.
AttachmentPoints
Indicatinganattachmentpointisusefulinpolymer-boundcombinatorialsynthesis,proteinchemistry,andothersitu-
ations.TheChemicalSymbolstoolbarincludesattachmentpointdrawingtoolsthatindicateapointofattachment
whilemaintainingchemicalmeaning.
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Thebeadtoolsareintendedtoindicateattachmenttoaresin.Anyofthesetoolsmaybeusedforvariableattach-
mentsinqueries(see"AttachmentPoints"onpage122);but,onlythediamondtoolshowsranknumbers.Thismeans
that,asyouadddiamondsymbolstoastructure,thepointswillhavesequentialnumbers.
Note:Youcanresizeapolymerbeadbyselectingitwithamarquetool,anddraggingtheresizedraghandles.
RotatingaSymbol
Youcanrotatetheradicalanion,cation,andlonepairsymbolsaroundthesameendfromwhichtheywereoriginally
drawn.Forexample,theradicalcationsymbolisrotatedandresizedfromthecharge.TheInfowindowshowsthe
anglethatoneoftheendsofasymbolmakeswiththeX–axisasyourotate.
Torotateachemicalsymbol:
1. Selectthechemicalsymbol.
2. Dragtherotationhandleonthechemicalsymbol.See"RotatingObjects"onpage82.
ChemicalProperties
ChemicalPropertyPredictionisafeaturesupportedbyChemBioOffice.Itenablesyoutocalculatevaluesforawide
rangeofmethodologies;forexample,topologicaldescriptorssuchastheWeinerindexandBalabanindex,ther-
modynamicdescriptorssuchassolubility,meltingandboilingpoints,andpartitioncoefficientssuchasCLogP,prop-
ertiesrelatedtothethree-dimensionalshapeandvolumeofachemicalsuchastheConnollysurfaceareaand
volume.Intotal,youcancalculatemorethan100chemicalpropertiesforagivenstructure.
Foralistofpropertiesavailableinaspecificapplication,clicktherespectivelinkbelow,orvisitthePerkinElmer
Informatics
website
.
"PropertyPredictionsinChemBioDraw"onpage158
"PropertyPredictionsinChem3D"onpage163
"PropertyPredictionsinChemDraw/Excel"onpage162
"ChemBioFinderProperties"onpage164
PropertyPredictionsinChemBioDraw
Youcanenterpredictedvaluesforthephysicalandthermodynamicpropertiesofachemicalstructureofupto100
atoms.
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Thepropertiesarecalculatedusingthemostreliablemethodsforthegivenstructure.Log P,andCMRvaluesbased
onliteraturevaluesratherthanacalculationareincludedinthereportfile.Thereportisproducedasatextfileandthe
informationinitcanbecutandpastedtootherdocumentslikeaworddocument.
Alistofallthepropertiescalculatedisasfollows:
B
H
P
BoilingPoint
HeatofFormation
pKa
C
Henry’sLawConstant
T
CriticalPressure
L
tPSA
CriticalTemperature
LogP
CriticalVolume
LogS
CLogP/CMR
M
G
Meltingpoint
GibbsFreeEnergy
MR
AboutMolecularNetworks
*MOSES.pKa,MOSES.logSandMOSES.logPforpredictingaciddissociationconstants,aqueoussolubilityand
octanol/waterdistributioncoefficientsofchemicalcompoundsarecomputationalcalculatormodulesbasedonMolecu-
larNetworks'cheminformaticsplatformMOSES.MOSESisdeveloped,maintainedandownedbyMolecularNet-
worksGmbH,Erlangen,Germany.Forfurtherinformationpleasevisitwww.molecular-
networks.com/moses
.All
rightsreserved.MolecularNetworksGmbH,Erlangen,Germany(www.molecular-
networks.com
).
Limitations
Onlythefollowingatomtypesandhybridizationstatesareparameterized:
C
sp
3
C
sp
2
C
aromatic
C
sp
N
sp
3
N
sp
2
N
amide
N
aromatic
N
sp
O
sp
3
O
sp
2
P
sp
3
S
sp
3
S
sp
2
S
sulfoxide
S
sulfone
F
Cl
Br
I
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BoilingPoint
TheboilingpointisreportedinKelvin.
Asolutionboilsataslightlyhighertemperaturethanthepuresolvent.Thechangeinboilingpointiscalculatedusing
theformula:
WhereK
b
isthemolalboilingpointconstant,mistheconcentrationofthesoluteexpressedasmolality,and
D
T
b
is
thechangeintemperature.
CriticalPressure
Reportedinbars,thisistheleastappliedpressurerequiredatthecriticaltemperaturetoliquefyagas.
CriticalTemperature
ReportedinKelvin,thisisthetemperatureabovewhichagascannotbeliquefied,regardlessofthepressureapplied.
CriticalVolume
Reportedincm
3
/mol,thisisthevolumeoccupiedbyonemoleofasubstanceatthecriticaltemperatureandpres-
sure.
CLogP/CMR
UseCLogPtocalculaten-octanol/waterpartitioncoefficient(logP
ow
).LogPvaluesbasedonliteratureratherthancal-
culationsareincludedinthereportfile.
UseCMRtocalculateMolarRefractivity.MRvaluesbasedonliteratureratherthancalculationsareincludedinthe
reportfile.
Note:CLogPandCMRvaluesappearonlyinChemBioDrawUltraandChemDrawUltra.
GibbsFreeEnergy
Gibbsfreeenergyisdefinedas:
Whichissameas:
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