ChemBioDraw 14.0UserGuide [628824]

ChemBioDraw 14.0UserGuide

TableofContents
RecentAdditions vi
Chapter1:Introduction 1
AboutthisGuide 1
Chapter2:GettingStarted 4
AboutChemBioDraw Tutorials 4
ChemBioDraw UserInterface 4
Toolbars 5
Documents 6
Chapter3:PageLayout 10
TheDrawingArea 10
TheDocument Type 10
Printing 12
SavingPageSetupSettings 13
35mmSlideBoundaryGuides 13
ViewingDrawings 14
Tables 16
Chapter4:Preferences andSettings 20
SettingPreferences 20
Customizing Toolbars 23
Document andObjectSettings 23
Customizing Hotkeys 33
WorkingwithColor 35
Document Settings 38
Chapter5:Shortcuts andHotkeys 44
AtomKeys 44
BondHotkeys 45
FunctionHotkeys 46ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. i

Shortcuts 47
Nicknames 50
Chapter6:BasicDrawings 52
Bonds 52
Atoms 57
Captions 58
DrawingRings 67
Chains 69
Objects 71
CleanUpStructure 88
CheckingStructures 89
ChemicalWarnings 89
Chapter7:BioDraw(Ultrafeatureonly) 92
BioDrawTemplates 92
Customizable Objects 95
Chapter8:DrawingBiopolymers 101
Biopolymer Editor 102
Protecting Groups 103
PastingSequences 104
Expanding Sequences 106
Contracting Labels 106
Modifying Sequence Residues 107
MergingSidechains withResidue 107
HybridBiopolymers 110
IUPACCodes 111
DisulfideBridges 115
LactamBridges 116
Chapter9:Advanced DrawingTechniques 118
ColoringObjects 118ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. ii

Labels 119
Attachment Points 122
AtomNumbering 124
StructurePerspective 125
MassFragmentation 126
DrawingReactions 127
Stoichiometry Grid 133
Templates 136
DefiningNicknames 138
ChemScript 141
Chapter10:Struct=Name (UltraFeature) 143
Struct>Name 143
Name>Struct 147
Chapter11:Chemistry Features 149
StructureAnalysis 149
ChemBioFinder hotlink 150
Stereochemistry 151
ChemicalAnnotations 154
ChemicalProperties 158
3DViewing 165
TLC 168
ChemNMR (UltraFeature) 173
Chapter12:ChemDraw/Excel andCombiChem 180
SettingUpChemDraw/Excel 180
Importingtables 180
Importinghitlists 181
Exportingtables 181
Synchronizing Tables 182
Addingstructures 183ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. iii

Searching 184
R-Groupanalysis 185
WorkingwithStructures 186
ChemDraw/Excel Functions 188
ChemicalProperties 202
GeneralPreferences 210
CombiChem 212
Chapter13:ChemScript 220
WhyuseChemScript? 220
HowChemScript works 221
GettingStarted 221
EditingScripts 222
Introducing theChemScript API 223
Tutorials 224
UsefulReferences 227
Chapter14:QueryStructures 228
SearchLimitations 228
GenericLabels 228
AtomProperties 231
BondProperties 239
ElementLists 242
Polymers 243
LinkNodes 247
Alternative Groups 248
Anonymous Alternative Groups 254
ExpandGenericStructures 255
Atom-to-AtomMapping 257
Stereochemical Symbols 260
3DProperties 261ChemBioDraw 14.0
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ExportCompatibility 262
Chapter15:SharingInformation 267
TheClipboard 267
Transferring Objects 270
Embedding Objects 271
Exporting 271
Importing 272
Transferring AcrossPlatforms 276
Chapter16:Chemical Interpretation 277
Database Conventions 277
Chapter17:PropertyCalculations 290
Chapter18:ChemBioDraw WebResources 293
Registering Online 293
User’sGuide 293
Technical Support 293
QueryingSciFinder® withChemBioDraw (UltraFeature) 295
Chapter19:Tutorials 298
Tutorial1:DrawingaStructure 298
Tutorial2:Drawingrings 299
Tutorial3:Fischerprojections 301
Tutorial4:Perspective Drawings 304
Tutorial5:Newmanprojections 308
Tutorial6:Stereochemistry 311
Tutorial7:Templates 314ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. v

RecentAdditions
Windows 8.1,Microsoft Office2013,andMacOSX10.9.x.
ChemDraw strivestobeavitalandpreferredtoolforillustrating chemicalandbiologicalconcepts. Compatibility with
thelatestoperatingsystemsandtoolsisanessentialpartofthat.HavingtheChemDraw Active-Xcontrolfunctional
withthelatestbrowsersonbothWindowsandMacplatformsispartofthisprocess,aswell.
ChemDraw toSciFinder Interface.
SendChemDraw structureandreactionqueriesdirectlytoSciFindertofindusefulinformation relevanttoyourcom-
pound/reaction. Formoreinformation, see"Querying SciFinder® withChemBioDraw (UltraFeature)"onpage295.
Biopolymer BuilderEnhancements .
Singleandmultiletteraminoacids-Letsyoucreatesingleletteraminoacidsandnucleotides eitherbyenteringthe
corresponding IUPACcode,orbyusingtheBiopolymer toolbar.TheBiopolymer Editorletsyoucreatethreeletter,
ornon-standardaminoacids,byenteringtheresiduename.
ToggleAminoAcidStyleAA1<->AA3command -Letsyouchangetheaminoacidrepresentation fromsingleto
multi-letter,andviceversa.Formoreinformation, see"DrawingBiopolymers" onpage101.
L-andD-aminoacids-LetsyoucreatestandardL-orD-aminoacidsbyenteringtherelevantIUPACcode.
ToggleL-andD-aminoacids-The‘ToggleAminoAcidStereoL<->D’command letsyouchangetheste-
reochemistry ofaminoacidsfromLtoDandviceversa.
Protecting groups-Letsyouaddprotecting groupssuchasTrtandFmoctoaminoacidscontaining additionalNH2orOHgroups(Arg,Aad).Youcanalsoexpandandcontracttheprotectedresidues.Formoreinformation, see"Pro-
tectingGroups"onpage103.
ChemBioDraw 14.0
©Copyright1998-2014CambridgeSoft Corporation, asubsidiaryofPerkinElmer, Inc.Allrights
reserved.vi

Cyclicandbranchedpeptides-Letsyoucreatecyclicpeptidesbybondingtogethertheterminalresiduesinapep-
tidesequence. Aloopedbondindicatesthatthepeptideiscyclic.Youcancreatebranchedpeptidesusingthe
sequence builderandbondtools.Formoreinformation, see"Cyclic,Crosslinked, andBranchedPeptides" onpage
113.
Lactambridges-Letsyouformlactambridgesbetweenresidueswithavailableaminoandcarboxylic acidleaving
groups,suchasLys-AspandLys-Glu.Formoreinformation, see"LactamBridges"onpage116.
Mergingsequences -Letsyoumergemultiplesequences intoonesequence bybondingtogethertheirterminal
residues.
Hybridbiopolymers -Letsyoucreatehybrid(alsocalled'chimeric') biopolymers containing peptide,nucleotide, and
linkerresidues,usingtheBiopolymer toolbar.Formoreinformation, see"HybridBiopolymers" onpage110.
Pastingsequences -Letsyoupastesequences intheFASTAformat.Youcanalsocopyatextstringdescribing a
biopolymer asaseriesofsingleormultiletterresidues,withvalidseparators (space,tab,dash),andpasteitasa
sequence. Thetextstringcanbegenerated withinoroutsideofChemBioDraw. See"PastingSequences" onpage
104.
Displaying expanded residues-Expanded residuescanappearineitherlinearmodeorzigzagmode.
Expanding andcontracting labels-Letsyouexpandtheentiresequence, oranypartofit.Thesequence isauto-
maticallycleanedfollowingexpansion.
Whenyoucontractasequence, theCleanUpBiopolymer command cleansandre-arrangesthesequence, so
thattheresiduesarealignedandwrapped.
Numbering residues-Letsyoudisplayresiduenumbersaboveanyresidue.Formoreinformation, see"Numbering
Residues" onpage110.
Hide/Show terminiandbonds-Letsyouhidebondsandterminiwithoutaffectingtheunderlying chemistry.
Nickname Enhancements .
InChemBioDraw 14.0,manynewresidues,forexample,non-standardaminoacids,non-standardnucleotides, linkers
havebeenaddedtothenickname library.Definingnicknames ismucheasierandmoreflexiblenow.Formoreinform-
ationonnicknames, see"DefiningNicknames" onpage138.
Struct>Name Enhancements .
Struct>Name inChemBioDraw 14.0isenhanced tosupportmanyhomopolymers, copolymers, andalternating poly-
mers,andstoichiometry specifiedasbracketproperties, includingfractionalstoichiometry. Formoreinformation, see
"Struct>Name "onpage143.
ElectronPushing.
ChemBioDraw 14.0introduces theElectronPushingtoolforillustrating electrontransfer.Formoreinformation, see
"ElectronandRadicalPushing"onpage132.ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. vii

GelElectrophoresis Tool.
Gelelectrophoresis separates molecules usinganelectricfieldappliedtoagelmatrix.Thegelelectrophoresis toolin
ChemBioDraw 14.0worksmuchliketheTLCtoolandletsyoueasilydrawandmarkbandsbasedonweightordis-
tance.Formoreinformation, see"TLC"onpage168.
TLCPlateEnhancements .
Letsyoucopyanddragspotsbetweenlanes.Formoreinformation, see"TLC"onpage168.
PolymerBeadEnhancements .
Letsyoure-sizepolymerbeads.Formoreinformation onpolymerbeadsandotherattachment points,see"Attach-
mentPoints"onpage122.
NewToolbars.
ChemBioDraw 14.0introduces severalnewtoolbars,including,Structure, Curves,Windows, andBiopolymer tool-
bars.YouaccessthesetoolbarsfromtheViewmenu.
ColorbyElement.
Letsyoucoloratomlabelsusingcolorsassociated withtheiratomicsymbols,asshownintheexamplebelow.
Formoreinformation, see"ColorbyElement"onpage36.
NewPropertyPredictions .
Incorporates newcalculations fromMolecular Networks forpredicting pKa,LogSandLogP.See"PropertyPre-
dictionsinChemBioDraw" onpage158.
JPEG/JPGfileexport.
LetsyouexportfilesoftypeJPEG.
CopyAs/Paste SpecialCDXML and MOLfilesastext.
LetsyousaveCDXML and MOLfilestotheclipboardastextandthenpasteinotherapplications astext.See"Creat-
ingCDXMLorMOLText"onpage269.ChemBioDraw 14.0
©Copyright1998-2014CambridgeSoft Corporation, asubsidiaryofPerkinElmer, Inc.Allrights
reserved.viii

CopyStructure toMS Word fromChemDraw/Excel .
Letsyoucopystructures fromChemDraw/Excel worksheets toMicrosoft Word throughasettingintheGeneralPrefer-
encesdialog.See"GeneralPreferences" onpage210.ChemBioDraw 14.0
©Copyright 1998-2014CambridgeSoft Corporation, asubsidiary ofPerkinElmer, Inc.Allrightsreserved. ix

Introduction
Designedforscientists, students,andscientificauthors,ChemBioDraw isapowerful,yeteasy-touse,toolforpro-
ducingchemicalandbiologicaldrawings. Youcancreateyourowndrawingsorusethoseprovidedinthelibraryof
availabletemplates.
Technical Support
TheonlinemenulinkTechnical SupportopenstheTechnical SupportWebpage.Hereyoucanfinddesktopsupport
resources, includingthePerkinElmer Informatics Knowledge Base,productdownloads, FAQ,anddocumentation.
ToreachthePerkinElmer Informatics Technical SupportWebpage:
1.NavigatetoOnline>BrowsePerkinElmer Technical Support.TheTechnical SupportWebpageopens.
2.ClickDesktopSupport.
AboutthisGuide
Thisguidedescribes thefeaturesinChemBioDraw. Sometasksdescribed inthisguidemustbeperformed incon-
junctionwithothersoftware.Forexample,instructions forChemDraw/Excel describetasksthatrequireMicrosoft
Excel.Forassistance, consultthe Microsoft Excelonlinehelporuser’sguide.
Conventions usedinthisGuide
Thisguideusesseveralbasicconventions tohelpyouquicklylearnChemBioDraw.
Instructions
Instructions aredesignedtohelpyounavigatethroughmenusandscreens.Menuitemsappearinbold.Forexample,
toopenanewdrawingtemplate:
1.GotoFile>OpenTemplates >AminoAcids.
ThisstepasksyoutoselecttheFilemenu,selectOpenTemplates (intheFilemenu),andthenselectAminoAcids
(intheOpenTemplates submenu).
Notes,Tips,andCautions
Theguideusesparticulariconsforvarioustypesofinformation:
Note:Noteshighlightimportantinformation.
Tip:Tipssupplyuseful,specific,“nicetoknow”,information, supplemental tothemaintext.
Caution:Cautionsindicateimportantinformation that,ifignored,mayleadtodataloss,orotherseriousproblems.
Additional Information
Theseresources areavailabletohelpyougetstartedwithChemBioDraw:
OnlineHelp
InChemBioDraw, press<F1>ornavigatetoHelp>Contents .ChemBioDraw 14.0
Chapter1:Introduction 1of315

ToolTips
Thisisthenameorashortdescription ofatool.Toviewatooltip,pointtoatool.Alongerdescription ofthetooltipis
availableinthestatusbar.
StatusBar
SeethelowerleftcorneroftheChemBioDraw windowforusefulinformation, asshownbelow.
Figure1.1:Statusbardisplaying information aboutsolidbond.
SerialNumberandTechnical Support
Formoreinformation onobtainingserialnumbersandregistration codes,seetheonlineServicesWebsite.
Technical supportisavailabletoregistered usersthroughtheInternetandourTechnical Supportdepartment.When
contacting Technical Support,alwaysprovidetheserialnumberofyourChemBioOffice application. OurTechnical
SupportWebpagescontainanswerstofrequently askedquestions (FAQs)andotherinformation.
ToaccessourTechnical SupportinChemBioDraw, navigatetoOnline>BrowsePerkinElmerTechnical Support.
IfyouareunabletofindasolutionontheWebsite,followthesestepsbeforeyoucontactTechnical Support:
1.Checkthesystemrequirements forthesoftware.
2.Readandfollowsuggestions outlinedin"Troubleshooting" onpage3.
3.Ifyourattemptstoresolveaproblemfail,contactTechnicalsupport.
Beforeyoucall:
Trytoreproduce theproblembeforecontacting us.Ifyoucanreproduce theproblem,pleaserecordtheexact
steps.
Recordtheexactwordingofanyerrormessages thatappear.
Recordyourattemptstocorrecttheproblem.
Additional sourcesofChemOffice information are:
ChemBioDraw onlineHelp
ThePerkinElmer Informatics Website.
PerkinElmer Informatics Services.ChemBioDraw 14.0
Chapter1:Introduction 2of315

Troubleshooting
Thissectiondescribes stepsyoucantakethataffecttheoverallperformance ofCSDesktopApplications, aswellas
stepstofollowifyourcomputercrasheswhenusingaCSsoftwareproduct.
Performance
Belowaresomewaysyoucanoptimizetheperformance ofChemBioOffice DesktopApplications:
FromthePerformance tabintheSystemcontrolpanel,allocatemoreprocessor timetotheapplication.
InstallmorephysicalRAM.Themoreyouhave,thelessChemBioOffice desktopapplications willhavetoaccess
yourharddisktouseVirtualMemory.
IncreasetheVirtualMemory(VM).VirtualmemoryextendsRAMbyallowingspaceonyourharddisktobeusedas
RAM.However, thetimeforswappingbetweentheapplication andtheharddiskisslowerthanswappingwithphys-
icalRAM.
Applications andDrivers
Aswithmostcomplexsoftwareapplications, theremaybeunusualcircumstances inwhichChemBioDraw may
becomeunresponsive. Belowaresomerecommended stepsforyoutofollowtotrytoresolvesoftwareanddriver
issues.
1.RestartWindowsandtrytoreproduce theproblem.Iftheproblemrecurs,continuewiththefollowingsteps.
2.Themostcommonconflictsconcernvideodrivers,printerdrivers,screensavers,andvirusprotection. Ifyou
doneedtocontactus,besuretodetermine whattypeandversionofdriversyouareusing.
VideoDriver-relatedissues:Ifyouexperience problemsdisplaying anyChemBioOffice DesktopApplication, first
tryswitchingtotheVGAvideodriverinthedisplayControlPanelorSystemSetup,andthenretesttheissues.If
usingadifferentdriverhelps,youroriginaldrivermayneedtobeupdated–contactthemakerofthedriverandobtain
themostup-to-datedriver.Ifyoustillencounter problems, contactuswiththerelevantdetailsabouttheoriginal
driverandtheresultingproblem.
PrinterDriver-relatedissues:Tryusingadifferentprinterdriver.Ifusingadifferentdriverhelps,youroriginal
drivermayneedtobeupdated–contactthemakerofthedriverandobtainthemostup-to-datedriver.Ifyoustill
encounter problems, contactuswiththerelevantdetailsabouttheoriginaldriverandtheresultingproblem.
3.Reinstallthesoftware.Beforeyoureinstall,uninstallthesoftware,anddisableallbackground applications,
includingscreensavers,andvirusprotection. Readcompleteuninstallinstructions ontheTechnical Support
webpage.
4.Iftheproblemstillpersists,useouronlinecontactformtoprovidedetailstoTechnical Support.ChemBioDraw 14.0
Chapter1:Introduction 3of315

GettingStarted
Thistopicscoveredinthischapterwillhelpyoubecomefamiliarwiththeuserinterface:
AboutChemBioDraw Tutorials
ThereareseventutorialsavailableintheTutorialschapter:
lTutorial1:DrawingaStructure
lTutorial2:UsingRings
lTutorial3:FischerProjections
lTutorial4:PerspectiveDrawings
lTutorial5: NewmanProjections
lTutorial6:Stereochemistry
lTutorial7:Templates
Thesetutorialsprovidestep-by-stepinstructions tohelpyouworkwiththeChemBioDraw tools.
ChemBioDraw UserInterface
Bydefault,theuserinterfacedisplayscommonly- usedtoolbars,themainmenu,anddocument statusbar.Theuser
interfaceappearsbelow:ChemBioDraw 14.0
Chapter2:GettingStarted 4of315

ChemBioDraw Ultrawindowsuserinterface
Toolbars
InChemBioDraw, severalnewtoolbarsareintroduced, suchasStructure, Curves,Windows, andBiopolymer tool-
bars.Todisplayorhideatoolbar,selectitintheViewmenu.Acheckmarkappearsnexttothetoolbarnamewhenit
isvisible.Youcanalsohidethetoolbarbyclickingonthe'X'iconontheupper-rightcornerofthetoolbar.
TheMainToolbar
Themaintoolbarincludesthetoolsmostcommonly usedfordrawingstructures. Theseincludeallselectionandbond
tools.Youcanopenothertoolbarsfromthemaintoolbar.NavigatetoView>ShowMainToolbar.
TearingoffToolbars
Sometoolsonthemaintoolbarhaveothertoolbarsassociated withthem.Theseareindicatedbyasmallblacktri-
angleinthelowerrightcorner.Forexample:ChemBioDraw 14.0
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Youcan“tearoff”thesesmallertoolbarsandplacethemanywhere onyourscreen.
Totearoffatoolbar:
1.Clickthearrowonthelowerrightofatoolinthemaintoolbar.
2.Whileholdingthemousebuttondown,pointtothetitlebar,andreleasethebutton.
Note:Ifthetoolbardoesnotopen,itislikelyalreadyopen,eitherdocked,orfloatingonthescreen.
DockingandFloating
Youcandockorfloatanystandardtoolbar.Whenyoudockatoolbar,itbecomesattachedtothedrawingwindow.The
floatingtoolbarsappearinfrontofthedocument windowandyoucanmovethemaroundinthedrawingwindow.
Double-clickingthetoolbarrestoresittothelast,ordefault,ordockedposition.
Todockatoolbar,dooneofthefollowing:
Clickanddragthetoolbartoanyedgeoutsidethedrawingwindow.
Right-clickthetoolbarandselectDockToolbar.
Tofloatatoolbar,dooneofthefollowing:
Double-clickthedockedtoolbar.
Clickanddragthedockedtoolbarintothedrawingwindow.
Right-clickthetoolbarandselectFloatToolbar.
BioDrawToolbar
TheBioDrawtoolbarcontainsdrawingtoolsforaddingbiologicalandbiochemical elementstoyourdrawings. See
"BioDraw(Ultrafeatureonly)"onpage92formoreinformation.
Documents
Adocument isaworkspace whereyoucreateandeditstructures. Adocument maycontainmultiplepages,orasingle
page.
CreatingDocuments
Youcancreateanewdocument usingeitherthedefaultsettings,oraStyleSheetwithcustomized settings.Tocreate
adocument, navigatetoFile>NewDocument .
UsingStyles
Tocreateanewdocument usingadifferentstylesheet,orstationery pad:ChemBioDraw 14.0
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1.NavigatetoFile>OpenStyleSheets.
2.ChooseaStyleSheetfromthelist.
ChemBioDraw providespre-defined stylesheetsintheChemDraw Itemsfolder.Forexample,theACSDocument
1996isconfigured tocreatedocuments setwiththebondlengths,bondwidth,spacing,andfontsusedinthe2-
columnformatofACSjournals.
Foralistofthesettingsinthesedocuments, see"Document Settings"onpage38.
OpeningDocuments
Toopenadocument, dooneofthefollowing:
NavigatetoFile>Open.FromtheOpendialog,selectthefilenameandlocationofthefileandclickOpen.
FromtheFilemenu,choosethedocument fromthelistatthebottom.
Selecting anOpenDocument
TheWindowmenulistsallopendocuments andtemplates. Thedocument youchoosefromthelistbecomestheact-
ivewindow.
Annotating Documents
Annotations areusefulforaddingtextinformation tohelpyouidentifydocuments inadatabasesearch.Annotations
arecategorized usingkeywords andanassociated datavalue.Thereareseveraldefaultkeywords: Name,Descrip-
tion,Type,andOtherInfo.Youcanalsoaddyourownkeywords.
Toannotateadocument:
1.NavigatetoFile>Document Annotations .TheAnnotatedialogopens.
2.Selectakeywordfromthekeywordlist,oraddyourownkeyword.
3.Toaddakeyword:
a.SelectAddNewAnnotation fromthekeywordlist.TheAddNewAnnotation dialogappears.
b.EnterakeywordintheNewKeywordtextfield.
c.IntheNewContenttextfield,enterthenotestoapplytothedocument andclickAdd.
4.ClickOK.
DeletingaKeyword
Whenyoudeleteakeyword,theannotation forthatkeywordisalsodeleted.
1.IntheAnnotatedialogbox,selectthekeywordfromtheKeywordlist.
2.ClickDeleteKeyword.ClickYeswhenpromptedforconfirmation.
3.ClickOK.
Discarding Changes
Toretrievethelast-savedversionofafile,navigatetoFile>Revert.ChemBioDraw 14.0
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Undo,Redo,andRepeat
ChemBioDraw tracksyouractions.Toundo,redo,orrepeatyourlastaction,selecttheappropriate optionintheEdit
menu.Thenumberofactionstrackedislimitedbytheamountofmemory(RAMandvirtualmemory)available.
Note:ChemBioDraw tracksonlythoseactionsyouhaveperformed sinceyoulastsavedthedocument.
SavingDocuments
1.NavigatetoFile>Save.
2.Chooseafolderinwhichtostorethefile.
3.TypeafilenameintheSaveAstextfield.
4.Selectafileformat.
5.ClickSave.
Note:ChemBioDraw usestheCDXfileformatbydefault.Someotherformatsstoreapictureofyourdrawingbut
maynotstorethechemicaldataassociated withastructureinitsentirety.Forexample,ifyousavea
ChemBioDraw drawinginthe.epsfileformat,youwillstoreonlyapictureofthestructurewithoutstoringthechem-
icalsignificance oftheconnections betweenatomsandbonds.
ChemBioDraw letsyouaddcomments, ordescriptions, tothedocument yousave.
Toenable/disable document comments:
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheOpen/Save tab.
3.CheckthePromptforComment checkbox.
Toadddocument comments:
1.ClickSave.TheSetDocument Comment dialogappears:
2.Enterthedescription andclickOK.
Autosave
YoucanconfigureChemBioDraw toperiodically saveanopendocument.ChemBioDraw 14.0
Chapter2:GettingStarted 8of315

1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheOpen/Save tab.
3.ChecktheAutosave Everycheckboxandenteratimeframe(inminutes),forexample5minutes.
Thetimestartsafteryoumakeyourfirstchangetothedocument.
DefaultFileFormat
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheOpen/Save tab.
3.ChecktheUseDefaultFileFormatcheckboxintheSavingFilessectionandchooseaformatfromthelist.ChemBioDraw 14.0
Chapter2:GettingStarted 9of315

PageLayout
Objectalignment, pagesize,orientation, andotherfactorsaffectthepresentation qualityofyourdocument.
TheDrawingArea
Thedocument windowmaynotbethesamesizeasthedrawingareaofthepage.Adocument window,maycover
onlyapartofthedrawingarea.
Theseoptionsletyousetthedrawingareaonyourscreen:
Document SettingsandPageSetupletyoumodifythepage,margins,headers,footers,document type,andsize.
Viewmenuoptions:ActualSize,ShowDocument, Magnify,andReduce.
Magnification Controls:enlargeandreduce
Draggingtoenlargethedrawingarea.
TheDocument Type
Youcansetupadocument aseitherapageoraposter:
Pages.Asingledocument containing oneormoresheets,eachofwhichisprintedonasinglepieceofpaper.
Posters.Asinglelargedocument, comprising asmanysheetsofpaperasnecessary.
PagedDocument Setup
Tocreateadocument withoneormorepages:
1.NavigatetoFile>Document Settings.TheDocument Settingsdialogappears.
2.OntheLayouttab,selectPages.
3.SpecifythenumberofpagesintheDocument Sizesection.ThePageSetupsettingsdetermines thesizeofthe
pages.Formoreinformation, see"PageSetup"onpage12.
4.TypetheMarginsettings.YousettheunitsofthemarginsinthePreferences dialog.Thepapersizeminusthemar-
ginsdetermines thedrawingarea.
5.CreateHeadersandFootersasdescribed in"HeadersandFooters"onpage11.
6.ClickOK.Anewdocument opens,usingyoursettings.
PosterDocuments Setup
Youcancreateaposterbycreatingasinglelargedrawingarea,whichwillbeprintedonasmanyseparatepagesas
necessary. Whenyousetthedocument sizeandhowmucheachpageoverlaps,ChemBioDraw calculates thenum-
berofpagesneededandthemarginsizes.Youcansetregistration marks,whichmarktheoverlapsettingoneach
page,touseasaguidewhenassembling theposterfromtheseparatepages.
Tocreateaposter:
1.NavigatetoFile>Document Settings.
2.OntheLayouttab,clickPoster.ChemBioDraw 14.0
Chapter3:PageLayout 10of315

3.EntertheHeight,Width,andPageOverlap.
4.SelectwhethertoPrintRegistration Marks.
5.CreateHeadersandFooters.
6.ClickOK.
HeadersandFooters
Forposters,onlyoneheaderandfooterappearfortheentiredocument.
Tocreateaheaderandfooter:
1.NavigatetoFile>Document Settings.
2.ClickHeader/Footer category.
3.Enterthepositionfromtheedgeofthepagefortheheaderorfootertoappear.
4.Typethetexttoappearintheheaderorfooter.
5.Typeadditionalinformation intheTextboxfromthefollowing:
filename&f
pagenumber&p
dateprinted&d
timeprinted&t
6.Positionthetexthorizontally bytypingtheappropriate characters listedbelow:
centered&c
right&r
left(default)&l
Forexample:
Figure3.1:A)Variablestodisplayfilenamecenteralignedintheheader;B)Variablestodisplaypagenumberaligned
rightintheheader.ChemBioDraw 14.0
Chapter3:PageLayout 11of315

Figure3.2:A)Thefilenameisdisplayedcenteralignedintheheader;B)Thepagenumberisdisplayedalignedrightin
thefooter.
PageSetup
Tosetupthepage,navigatetoFile>PageSetup.Pagesetupoptionsare:
Paper.Choosethesizeofthepaperonwhichtoprintthedocument andtheprintertray.
Orientation .SelecteitherPortraitorLandscape .
Margins.Bydefault,marginsaresetto0.5inches.
Printer.Clicktoselectaprinterandsetpreferences. YoucanalsochoosetheprinterinthePrintOptionsdialog.
Printing
ChemBioDraw usesthestandardsystemcommands toprintdocuments. Availableoptionsdependontheprinteryou
use.Refertoyourprinter’sdocumentation formoreinformation.
Ingeneral,toprintadocument:
1.NavigatetoFile>PageSetup.
2.Makeallappropriate selections foryourprinterandclickOK.
3.NavigatetoFile>Print.
4.Makeyourselections inthePrintdialogandclickOK.
Toprintadocument fromExplorer:ChemBioDraw 14.0
Chapter3:PageLayout 12of315

1.Selectthedocument toprint.
2.NavigatetoFile>Print.ChemBioDraw opensandthePrintdialogappears.
3.Makeyourselections inthePrintdialogandclickOK.
PrintOptions
SelectPrinter.Thiswindowlistsallprintersconnected toyourcomputer. Youcanusethedefaultprinterorselect
anotherprinter.
PrinttoFile.Thedocument issavedasa.prnfileandincludesyourprinterpreferences. Thedocument canthenbe
sentlatertoaprinter.
FindPrinter.ClicktomaptoaprinternotlistedintheSelectPrinterwindow.
PageRange.Selectthepagestoprint.Toprintpartsofyourdocument, selectthepartsandchooseSelection inthe
PrintOptionsdialog.
Numberofcopies.Bydefault,onlyonecopyisprinted.
Scaling
Withsomeprinters,youcanreduceorenlargeyourdrawingsbyavariablepercentage (25-400%).Thisoptionscales
allobjectsandtextinthedocument window.Thesizechangesrelativetothepapersize,margins,andorientation.
Theenlargeorreduceoptionisusefulforchangingthesizeofthedrawingarea,whilekeepingtheimagesize.Ifyour
document fillsthepageononeprinterandyouuseanotherprinterthatrequireslargermargins,thedrawingmaydis-
appearofftheedgeofthedocument window.Youcanreducethedrawingsizewiththereduceoptiontofitinthedoc-
umentwindow.
SavingPageSetupSettings
Youcansavepagesetupsettingsinastylesheet.Thesettingsaresavedwiththetextsettings,drawingsettings,
andthecolorpalette.
35mmSlideBoundary Guides
Ifyoucreate35mmslidesfromahardcopyofadocument orfromascreenshot,youcandisplayboundarylinesthat
appearonyourscreenpositioned at7inchesand10.5inchestomatchthe2:3ratioforthe35mmslideformat.These
guidesarenotprinted.Thedrawingareaofthepagemustbeatleast7x10.5inchesfortheseboundarylinestobevis-
ible.
Todisplaythe35mmslideboundarylines:
1.NavigatetoFile>Preferences .
2.SelecttheBuilding/Display tab.
3.SelecttheShow35mmSlideBoundary Guidescheckbox.
4.ClickOK.ChemBioDraw 14.0
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Two35mmSlideBoundaryGuidesappearintheorientation choseninthePageSetupdialog.Theseguidesappearin
everydocument.
ViewingDrawings
Magnification
Magnification changeshowlargeorsmallyourdrawingappearswithoutchangingitsdimensions. Youcaneither
selectavalueinthemagnification dropdownlistorenteryourownvaluebetween1%and999%.
Magnify
1.Selectanobjecttokeepinviewasyoumagnifythedrawing.
Note:Ifyoudonotselectanobject,thelastobjectdrawnisthecenterpointofthemagnification.
2.Selectanoptionbelow:
Toincreasethemagnification, navigatetoView>Magnify .
Toreducethemagnification, navigatetoView>Reduce .
Toreturnthedocument toitsactualsize,navigatetoView>Actual .
Todisplaythewholedocument, navigatetoView>Show Document .
Tosetthemagnification toaspecificvalue,selectorenterapercentage (enterOtherbetween1-999%)inthe
Generaltoolbar.
Rulers
Usetherulerstopositionobjectsameasured distancefromareferencepointorcreateobjectsofanapproximate
size.Tosettherulerunits,gotoFile>Preferences andselecttheGeneraltab.
Displaying Rulers
Totogglerulersonandoff,navigatetoView>ShowRulers.
Asyoumovethepointer,guidesappearoneachruler,indicatingthepositionofthepointer.ChemBioDraw 14.0
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Figure3.1:Howrulersindicateposition.A)Thecursor;B)Rulerguidesindicatingverticalandhorizontal locationof
thecursor.
Whenyouselectanobject,twoguidesappearineachruler.Thefourguidestogethershowtheheightandwidthofthe
selectedobject.
Note:Therulersadoptthesameunitsthatwereselectedforthedocument settings.
TheCrosshairs
Thecrosshairs arehelpfulforpositioning objects.
Totogglethecrosshairs onandoff,navigatetoView>ShowCrosshair .
Toassistyouinaligningobjects,thecrosshairs includegridlinesthatextendfromthemajordivisionmarksoneach
axis.
Youcanalsoshowtherulerswiththecrosshairs toviewtheunitmeasurement associated witheachdivisiononthe
crosshairaxes.
MovingtheCrosshair
1.PositionthecursorwheretheCrosshair axesintersect.
Thecursorchangestoanarrownearthecenterofthecrosshair.
2.Clickanddragthecrosshair.
ToconstraincrosshairtomoveintheX-orY-direction,<shift>+drag thecrosshair.
Positioning Objects
Toaligntwoormoreobjectsusingthecrosshairs, dothefollowing:
1.MovetheCrosshair axesandalignitwiththeobject.
2.Selectanobjectanddragituntilitisalignedwitheitheraxisofthecrosshairoragridline.
3.Selectasecondobject.ChemBioDraw 14.0
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4.Dragthesecondobjecttothecrosshairaxisorgridlineandalignittothefirst.
Youcanalsomoveselectedobjectsinsmallincrements toalignthemwiththecrosshairusingthearrowkeysavail-
ableonsomekeyboards: Tomove1point,selecttheobjectsandpressanarrowkey.Tomovein10ptincrements,
press<alt>whileyoupressthearrowkey.
Tables
Afteryoucreateatable,youcanadjustitsbordersandcolor.
CreatingTables
Tocreateatable:
1.SelecttheTabletoolontheMainToolstoolbar.
2.Dooneofthefollowing:
Clickanddraginthedocument windowtocreatethetable.Thetablehastworowsandtwocolumns.
Clickinthedocument window.TypethenumbersofrowsandcolumnsintheInsertTabledialog,andclickOK.
Thetableappearsinthedocument window.
ResizingTables
Toresizerowsorcolumns,clickanddragaborderusingthetabletool.
Note:Toproportionally resizeallrowsandcolumnsinthetable,clickanddragthetopandleftborderofthetable.
Customizing Borders
Tocustomize thebordersofthetable:
1.WiththeTabletoolselected,right-clickaborder.
2.ClickBordersonthecontextmenu.TheTableBordersdialogappears.ChemBioDraw 14.0
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3.UnderSetting,selectabordersetting.
4.UnderStyle,selectthestyle,colorandwidthofthebordertoapply.
5.Foracustomborder,selectthedesiredbordersinthetablediagram.
6.ClickOK.
Thetabletoolincludescommands toaligncellcontents;fit,addordeletecells,andclearcells.Ingeneral,tochange
thetable,workwiththerightorbottomborders.Tochangearoworcolumn,workwiththeleftortopborders.
Toresizeacelltofititscontents:
1.Pointtoaborderandright-click.
2.ChooseSizeToFitContents.Thecellsresizetofitaroundthecontents.
Toaddordeleterowsorcolumnsinthetable:
1.Pointtothetoporleftborderwhereyouwanttoaddordeletetheroworcolumn.Aborderappearsasshownbelow.
2.Right-clicktheborderandselecttheappropriate optionfromthecontextmenu.
Toalignalloftheobjectsinacolumnorrow,pointtoatoporleftborderusingtheTabletool,right-click,pointtothe
Aligncommand onthecontextmenu,andchoosethealignment youwant.
Thecellcontentsshiftandstayinafixedpositionrelativetothecell.Thedefaultalignment isunaligned.ChemBioDraw 14.0
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Toalignallobjectsinatable,pointtoabottomorrightborder,right-click,pointtoAlign,andchoosethealignment you
want.
UsingtheTextTool
ChemBioDraw letsyoucreatetablesoftextusingthe<tab>keywiththeTexttool.
Tocreatethefirstrowandestablishthecolumnsofatable:
1.UsingtheTexttool,clickinadocument windowwhereyouwantthetabletostart.
2.Typeacaption.
3.Press<tab>.Asecondcaptionboxappears.
4.Typeasecondcaption.Thesecondcolumnappears20pointstotheright.
5.Press<tab>againtocreateathirdcolumn,andsoon.
Note:Thestyle,font,andsizethatyousetineachcolumnaremaintained inalltherowsthatfollow.
Tochangethespacingbetweencolumnsonepointatatimewhileeditingacaption:
1.Selectthecaption.
2.Movethecaptionwiththearrowkeys.
Formoreinformation onmovingobjects,see"MovingObjects"onpage83.
3.Tocreateanothercolumnwiththissamespacingastheprevious,selecttheTexttoolandpress<tab>.Athirdcap-
tiontextboxappears.
CreatingNewRows
Tostartanewrowthatisalignedwiththefirst,press<tab>twiceattheendofarow.
Acaptiontextboxappearsunderthefirstcaptionpositioned exactly20pointsbelowthefirstcaptioninthefirstrow.
Tochangethespacingbetweenrowsasyoucreatethetable:
1.Selectallthecaptionsinarow.
2.Movethecaptionsusingthearrowkeys.
Formoreinformation onmovingobjects,see"MovingObjects"onpage83.
Adjusting RoworColumnSpacing
1.Selectallthecaptionsintheroworcolumnwithaselectiontool.ChemBioDraw 14.0
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2.<Shift>anddragthecaptions.
Themovement isconstrained totheX-axisorY-axissothatyoucanmaintaintheroworcolumnalignment.
Inserting NewRows
Toinsertarow:
1.Selectaselectiontoolandselectarowofcaptions.
2.<Shift>+drag theselectedrow.
3.<Shift>constrains themovement totheY-axistomaintainthecolumnalignment.
4.Selectthefirstcaptionintherowaboveorbelowthespaceyoucreated.
5.<Control>+<shift>+drag tocreateacopyofthecaptionandpositionitintheemptyspaceyoucreated.
6.Theplacement ofthiscopiedcaptionsetsthepositionoftheinsertedrow.
Tofillintheinsertedrowwithcaptiontext:
1.ClicktheTexttoolandselectthefirstcaptionintheinsertedrow.
2.Typenewtext.
3.Press<tab>tomovetothesecondcaptionintheinsertedrow,andsoon.ChemBioDraw 14.0
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Preferences andSettings
Youcancustomize ChemBioDraw byconfiguring Preferences andDocument Settingstomatchthewayyouwork.
Preferences allowyoutochangethedefaultbehaviorofcertainoptionsthatapplytoeveryopendocument. The
changesyouspecifyinthedocument settingsareapplicable onlywithinthedocument andisnotapplicable through-
outtheapplication. Thechangesyouspecifyintheobjectsettingsarespecifictotheselectedobject.
Formoreinformation, seethetopicsfoundinthischapter:
lSettingPreferences
lCustomizing Toolbars
lDocument ObjectsandSettings
lCustomizing Hotkeys
lWorkingwithColor
SettingPreferences
Preferences affecthowChemBioDraw works,regardless ofthedocument withwhichyouareworking.
1.ToopenthePreferences dialogbox,navigatetoFile>Preferences .
2.Torestorethedefaultsettings,clickUseDefaults.
ThemeOptions
Thethemedefinestheappearance oftheChemBioDraw GUIbutdoesnotaffectfunctions. Bydefault,ChemBioDraw
displaystheChemDraw theme.ThethemeChemDraw Largehaslargerversionsoftheicons,whicharemoreread-
ablebutwillrequirelargerscreenrealestate.However, otherthemes,suchasI/Drawarealsoavailable.
Tochangethemes:
1.NavigatetoFile>Preferences andselecttheGeneraltab.
2.SelectathemeintheThemedrop-downlist.
3.ClickOK.ChemBioDraw 14.0
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I/Draw
TheI/DrawthemechangesthelookoftheMaintoolbar.However, besideschangingthetoolbar,youcanselectthe
I/Drawmodetoactivatetwootherhelpfulfeatures:
Sproutrings(asopposedtospirorings).
ThedefaultstylesheetischangedtoI/DrawStyles.cds.
ToactivatetheI/Drawmode,navigatetoFile>Preferences andclickI/DrawMode.
DefaultDocument Location
Youcansetthedefaultfiledirectoryforeachtimeyouopenafile.
Tosetthedefaultfiledirectory:
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheDirectories tab.
3.ClicktheUseDocuments Locationcheckboxandtypeinorbrowsetothelocationtouse.
DefaultOpenFileFormat
TosetthedefaultfileformatintheOpendialogbox:
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheOpen/Save tab.
3.ClickUseDefaultFileFormatintheOpeningFilessection,andchoosethefileformat.
SettingtheDefaultTool
Youcanchoosewhichtoolisselectedwhenyouopendocuments.
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheOpen/Save tab.
3.UnderOpeningFiles,selectatool.
NewLinesandClosingTextBoxes
Tocreateanewlineinacaptiontextboxpresseither<Enter>or<Return>. Tocreateanewlineinanatomlabel
press<Alt>+<Enter> .Toclosethetextbox,clickoutsidethetextboxorselectanothertool.
Tochangethedefault:
1.NavigatetoFile>Preferences .
2.Choosetheappropriate optionontheBuilding/Display tab,tochangethedefaultfor:
AtomLabelText-Require<Alt>+<Enter> tocreatenewlineinAtomlabels.
CaptionText-Require<Alt>+<Enter> tocreatenewlineinCaptions.
3.ClickOK.ChemBioDraw 14.0
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Highlight BoxTolerance
Tolerance determines thesizeofthehighlightboxandhowcloseyoumovethecursortoanobjecttoactivateit.The
defaultsettingfortheTolerance is5pixels.Atthissetting,thehighlightboxappearsonbondsifthepointerislocated
5pixelsorlessfromanypointonthebond.
Tosetthetolerance:
1.NavigatetoFile>Preferences .
2.OntheGeneraltab,selectortypethetolerance. Thischangeaffectsalldocuments.
TheChemDraw ItemsFolder
Thefoldercontainsthepreferences, hotkeys,nicknames, andisotopesfiles;scripts,andthegenericnicknames file.
Italsocontainstemplatedocuments andtemplateStationery Pads.YoucanhavemultipleChemDraw Itemsfolders.
Thisisusefulincorporateinstallations formaintaining personalfilessuchasnicknames andstandardtemplates.
ThelocationoftheChemDraw Itemsfolderisbasedonyouroperatingsystem.IfyouareusingChemOffice 2014,the
folderisat:
C:\ProgramData\CambridgeSoft\ChemOffice2014\ChemDraw\ChemDraw Items
ToaddapathtoaChemDraw Itemsfolder:
1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.ClicktheDirectories tab.
3.ClickAddNew,browsetoalocation,andclickOK.Anewpathisaddedtothelist.
4.Torearrangethesearchorder,clickMoveUpandMoveDown.
5.Todeleteapath,clickRemove.Todeletealladdedpaths,clickDefaultPaths.
DefaultStyles
ChemBioDraw savesdefaultstylesasastylesheet.WhenyoulaunchChemBioDraw, thelaststylesheetyouuse
opensasthedefault.Ifyouchoosedifferentone,thatfilebecomesthedefault.
Youcansetadefaultthatisnotchanged:
1.NavigatetoFile>Preferences .
2.OntheOpen/Save tab,browsetothedefaultstylesheet.
3.DeselectOpeningAnyStyleSheetChanges Default.
4.ClickOK.
Toviewthedefaultstyle,clicktheFilemenu.TheNewmenuitemdisplaysthenameoftheStyleSheet.
SavingCustomized Styles
Everynewdocument youcreateusesastylesheetfileforitsdocument settings.Thesefilescanalsocontainpre-
definedobjects.Whenyoucreateanewdocument, youactuallycreateanuntitledcopyofthestylesheet.Changes
youmaketothecopydonotaffectthefile.ChemBioDraw 14.0
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Youcancreateastylesheetwithyourowncustomized settingbysavingitasaCDSfile.IfyoustoretheCDSfilein
theChemDraw Itemsfolder,itappearsintheOpenTemplates menu(undertheFilemenu).
Tosaveadocument’s settingasastylesheet:
1.NavigatetoFile>SaveAs.TheSaveAsdialogappears.
2.Namethefileandchangethetype(inOSX:format)toCDStyleSheet(cds)
3.TosavethefileintheChemDraw itemsfolder,clickGoToChemDraw Items.
4.ClickSave.
Customizing Toolbars
Thelookandarrangement oftoolbarsaredefinedbyasetofXMLfiles.IfyouarefamiliarwitheditingXMLfiles,your
canmodifythetoolbarforthewayyouwork.Youcanremove,rename,andresizebuttons;changebuttonicons,or
movethemfromonetoolbartoanother.Youcanalsocreateordeletetoolbars.
TheToolbarSchema
TheToolbars.xsd filecontainstheschemadefinitions forallthetoolbars.Theseincludedefinitions (butnotthecon-
tent)forthetoolbars,thepop-uptext,andthestatusbartext.
TheToolbarXMLFiles
TheToolbarsdirectoryatC:\Documents andSettings\All Users\Application Data\Cam –
bridgeSoft\ChemOffice2014\ChemDraw\GUI\Common\XML\Toolbars ,containsthesubdirectory where
thetoolbarsxmlfilesarestored.Thefilesarestoredaccording totheskinsinwhichtheyareused.Thesearethefiles
youwillmostcommonly edittocustomize thetoolbars.TheXMLfilewhenlaunched, validatesitselfagainsttheTool-
bars.xsdfilestoredonline.
EditingtheXMLFiles
Youcaneditthefilesusinganyxmlortexteditor.Afteryousavethefiles,exitandrestartChemBioDraw. Your
changeswilltakeeffect.
CreateabackupofallXMLfilesyouintendtoedit.
Note:Allimagesfilesyouuseasiconsmustbein.pngformat.
Document andObjectSettings
Youcanapplydocument andobjectsettingstothecurrentdocument. Thechangesyouspecifyinthedocument set-
tingsareapplicable onlywithinthedocument andarenotapplicable throughout theapplication. Thechangesyouspe-
cifyintheobjectsettingsarespecifictotheselectedobject.
Settingsinclude:
Drawingsettings.Setdrawingoptionssuchasthefixedlengthusedtodrawbonds.
Captionandlabeltextsettings.Settextoptionssuchasthefontusedforatomlabelsandcaptions.
Colorsettings.Setavailablecolorsforobjectsandthedocument background.ChemBioDraw 14.0
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Print/Page Setup.Setoptionssuchasthepagesizeusedandtextdisplayedinfooters.
Youcanapplydocument settingsinthefollowingways:
Customize settingsfortheentiredocument usingtheDocument Settingsdialog.
Applysettingstotheentirecurrentdocument fromanexistingdocument.
Applysettingstoselectedobjectsinthecurrentdocument fromanexistingdocument.
DrawingSettings
Drawingsettingsaffecthowbondsandotherobjectsaredrawn.Youcanconfigurethedrawingsettingsforanentire
document orforaparticularobjectasfollows:
Fortheentiredocument, navigatetoFile>Document SettingsandselecttheDrawingcategory.
Foranobject,usetheObjectSettingsdialogbox.
Changesyoumaketothedrawingsettingsaffecttheactivedocument windowonly.Youcansavedrawingsettingsin
stylesheets.
Toapplysettingsfromotherdocuments toyourdocument, navigatetoFile>ApplyDocument Settings.
ThevariousoptionsavailableunderDrawingcategoryincludes:
FixedLength.Constrain thebondsdrawntothelengthyouspecify.Thisalsoadjuststhepreferredbondlengthwhen
youusetheCleanUpStructurecommand. See"DrawingFixedLengthBonds"onpage56and"Attachment Points"
onpage122.
BondSpacing.Setthedistancebetweenthelinesindoubleortriplebonds.Thedistanceisseteitheras:
Thepercentofthelengthofthebond(between1and100).Thisallowsforproportional spacingifdifferentbond
lengthsareused.ChemBioDraw 14.0
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Anabsolutevalueyouchooseintheunitsspecifiedforyourdocument.
BoldWidth.Setthewidthofthelineusedwhenboldandwedgebondsaredrawn.TheBoldWidthsettingmustbe
greaterthantheLineWidthsetting.Theendofawedgeis1.5timestheboldwidth.
LineWidth.Setthewidthofallbonds,lines,andarrowheads inthedrawing.
MarginWidth.Changetheamountofspacesurrounding allatomlabelsthatwilleraseportionsofthebondstowhich
theyareattached.Themarginwidthalsodetermines theamountofwhitespacesurrounding thefrontbondsinabond
crossing.See"BondCrossing" onpage55.
HashSpacing.Setthespacingbetweenthehashedlinesusedwhenwedgedhashedbonds,hashedbonds,dashed
bonds,dashedarrows,ordashedcurvesaredrawn.
ChainAngle.Settheangle(from1to179degrees)betweenbondscreatedbytheAcyclicchaintoolormodifiedby
theCleanUpStructurecommand. See"Chains"onpage69and"Attachment Points"onpage122.
Units.SettheunitsusedintheObjectSettingsdialogboxtocentimeters, inches,points,orpicas.
AtomandBondIndicators .Setwhichindicators todisplay.See"AtomNumbering" onpage124.
Configuring Documents
1.NavigatetoFile>Document Settings.
2.ClicktheDrawingcategoryandconfigurethesettings.
3.ClickOK.
Terminal CarbonLabels
Bydefault,ChemBioDraw doesnotdisplayterminalcarbons.
Todisplayterminalcarbonlabels:
1.NavigatetoFile>Document Settings.ChemBioDraw 14.0
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2.SelecttheAtomLabelscategory.
3.SelectShowLabelsOnTerminal Carbons.Seefigurebelow:
Configuring Objects
Toconfigurethedrawingsettingsforaselectedobject:
1.Selecttheobject.
2.NavigatetoObject>ObjectSettings.
3.Configure thesettingsandclickOK.Thesettingsyouchoseareappliedonlytotheselectedobject.
AnalysisandProperties
Youcanpastefundamental structureproperties intoyourdrawing.Youcanalsorenametheseproperties when
desired.Forinstance,youmayconsiderrenaming“Molecular Weight”to“MW”tosaveroomonthepage.The
changesyoumakeapplyonlytotheproperties youpasteinyourdrawing.ThenamesintheAnalysisandChemical
Properties dialogboxesremainunaffected.
Tochangethenamesoftheproperties:
1.NavigatetoFile>Document Settings.
2.SelectthePropertyLabelscategory.Seefigurebelow:
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3.IntheAnalysiswindow,selectthepropertytorename.
4.ClickEditLabelandtypeanewnameintheEditLabeltextbox.ClickOK.
5.Typethenewname,andclickOK.
6.Repeatstep4forotherproperties.
7.ClickOK.
Formatting Captions
Textsettingsaffecthowcaptionsandatomlabelsforthecurrentdocument aredrawnandformatted.
Formatting optionsinclude:
Font(fonttype)
Size(fontsize)
Style(fontandbaselinestyle)
Linespacing
Alignment
SettingFontParameters
ChangingtextformatsintheDocument Settingsdialogaffectsthecurrentdocument only.Youcanalsochangeset-
tingsforindividualobjectsbyusingtheObjectSettingsdialog,theTextmenu,ortheStyletoolbar.
Toeditthedocument textsettingsforcaptionsandatomlabels:
1.ClickFile>Document Settings.
2.IntheDocument Settingsdialog,clickTextCaptions orAtomLabels.
3.Changethesettingsasdesired.Theoptionsaredescribed inthefollowingsections.
4.ClickOK.Theformatting isappliedtothecurrentdocument.
SettingtheBaseline Style
Youcanspecifythesebaselinestyles:
Normal.Usethisforstandardtext.
Superscript .Reducesthetextsizebyabout25 percent andraisesitsbaseline.
Subscript .Reducesthetextsizebyabout25 percent andlowersthebaseline.
Formula.Formatsinawaythatisappropriate formostchemicalformulas,thatis,numbersaresubscripted. You
must,however,manuallycapitalize.
Youcanalsoapplymultiplestylestodifferentportionsofasinglecaption.ChemBioDraw 14.0
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StyleIndicators
Selectanytextinthedocument windowandnavigatetoText>Styletoviewthestylesthathavebeenapplied.A
checkindicatesthestyleappliestoalltheselectedtext.Ahyphenindicatesthestyleappliestosomeoftheselected
text.
Specifying LineSpacing
Youcanspecifythesetypesoflinespacing:
Automatic .Consistently spacedlinesoftextbasedontheheightofthetallestcharacterinthecaption.Thisisthe
defaultlinespacing.
Variable.Linesoftextwithdifferentspacingbasedonthetallestcharacterandthelowestdescender ineachline.
Fixed.Consistently spacedlinesusingaspacingthatyouspecify.
Aligning Text
Youcanaligncaptionsandatomlabelstojustifytexttosuityourneeds.Theoptionsavailabledependonwhetheryou
arealigningcaptionsoratomlabels.ApplysettingsintheObjectSettingsdialog.
Toopentheobjectsettingsdialog:
1.Selectacaptionoratomlabel.
2.NavigatetoObject>ObjectSettings.TheObjectSettingsdialogappears.
Captions
Youspecifythecaptionjustification andlinespacingontheTextCaptionstaboftheObjectSettingsdialog.Alltextin
asinglecaptionmusthavethesamejustification andlineSpacing.
Therearefouravailablejustifications:
FlushLeft.Createsleft-justifiedcaptiontext.
Centered.Createscenteredcaptiontext.
FlushRight.Createsright-justifiedcaptiontext.
Justified.Createsright-leftjustifiedcaptiontext.
AtomLabels
UsetheCentered,FlushLeft,FlushRight,StackedAbove,orAutomatic justifications tocreatelabelsthat
identifyatomsandfunctional groupsinyourchemicalstructurewithoutobscuring bondsorotheratomlabels.ChemBioDraw 14.0
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Note:WhenusingStackedAbovejustification, enterthetokensfromtoptobottomusing<alt>+<enter> togotoa
newline.Ifyouchangethejustification afterthelabelisentered,warningmayappear.
Examples oftheatomlabeljustifications areshownbelow.
Figure4.1:Atomlabeljustification. A)stackedabove;B)centered;C)flushleft;D)flushright.
Automatic Alignment
Whenyoujustifyatomlabelsautomatically, ChemBioDraw breaksthelabelintotokens.Atokenconsistsofanupper-
caseletterfollowedbyanynumbersorlowercase letters.Thefirsttokenisattachedtotheatomandtherestofthe
labelappearswithoutobscuring otherpartsofthechemicalstructure.
Forexample,tocreateN-methylpiperidine, labelanatomincyclohexane asNCH3.Thislabelhasthreetokens,N,C
andH3.IfyoulabelC3,thetokensareplacedfromlefttorightbecausetherearebondstotheleftoftheatom.
IfyoulabelC5,thetokensappearfromrighttoleftbecausetherearebondstotherightoftheatom:
Youcanforceanentiremulti-atomlabeltobeatokenbydefiningitasanickname. Thispreventsthelabelfromflip-
pingwhenappliedtotheleftsideofastructure.
Forexample,ifyoudefinethenickname CH3,andlabelC5withthecombined labelandnickname NCH3,thefinalori-
entationisCH3NinsteadofH3CN.Inthiscase,thenickname, CH3,isatoken.ChemBioDraw 14.0
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IfyoulabelC1,thesecondandthirdtokensareplacedabovethefirsttokensincetherearebondsbelowtheatom.
IfyoulabelC4,thesecondandthirdtokensareplacedbelowthefirsttoken.
Changing DefaultFormats
Eachnewcaptionoratomlabelusesdefaultdocument settingsforthefont,font-size,andstyleofcaptionsandatom
labels.
Youcanchangetheformatby:
Changingthedocument settingsforsubsequent drawingsinthecurrentdocument.
ChoosinganewformatforanindividualcaptionorlabelfromtheTextmenuortoolbarbeforeyoutype.
Selectingtextandapplyinganewformattoanindividuallabelafteryoutype.
Settings forNewText
Tospecifythetextsettingsfornewcaptionsandatomlabelsinthecurrentdocument:
1.NavigatetoFile>Document Settings.
2.ClickTextCaptions orAtomLabelsintheDocument Settingsdialog.
3.Selecttheappropriate options.
4.ClickOK.
Thesesettingsaffectallnewcaptionsoratomlabelsinthecurrentdocument. Tousethesesettingsinnewdoc-
uments,savetheminastylesheet.Formoreinformation, see"Document andObjectSettings"onpage23.
Formatting aCaption orLabel
Youcansetthetextformatforanindividualcaptionoratomlabelbeforeyoutype.Theformatchangeisappliedonly
tothecurrenttext.
Tosetthetextformatbeforeyoutype:
1.SelecttheTexttoolandclickinthedocument window.Atextboxappears.
2.Tosetthetextformatdooneofthefollowing:ChemBioDraw 14.0
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NavigatetoText>Font,StyleorSize.
SettheformatoptionsontheStyletoolbar.
3.Typethetextinthetextbox.
Theformatisappliedtothetypedtext.Subsequent textyoutypeusesthedefaultdocument settings.
Changing TextSetting
Youcanchangethetextsettingsforaselectedcaptionoratomlabel.Youcanchoosetohavethesettingsappliedto
theselectedtextandtoallsubsequent textyoutype.
Tochangethetextsettingsforaselectedcaptionoratomlabel:
1.Selectthetexttochangewithaselectiontool.
2.Settheappropriate optionsontheTextmenu.
Tochangepartofacaption,selectthepartyouwanttochangeusingtheTexttool.
Tospecifyafontandsizeforselectedtext,dooneofthefollowing:
ChoosethefontandsizefromtheTextmenu.
Right-clickandchoosethefontandsizefromthecontextmenu.
Selectthefontandfont-sizefromthedrop-downlistontheStyleToolbar.
Biopolymer settings
Youcanspecifyhowthesequences andresiduesappearineithertheentiredocument orforaspecificsequence, as
follows:
Fortheentiredocument, gotoFile>Document SettingsandselecttheBiopolymer Displaytab.
Foranobject,usetheObjectSettingsdialogbox.
Inthebiopolymer Displaytab,selectfromtheseoptions:
Residues perline.specifythenumberofresiduestobedisplayedineachlineofthesequence.
Residueperblock.specifythenumberofresiduestobedisplayedineachblockofthesequence.
Amino-acidTermini.SeteitherNH2/COOH orH/OHastheterminiinthesequence.
Note:WhentheterminiaredisplayedusingtheNH2/COOH style,theunderlying atomsareactuallyHandOH.
ThelabelsareintendedtoconveywhethertheNorCterminusispresent.Sincethiscanbeconfusing orambigu-
ous,thisdisplayisnotrecommended, andisprovidedonlyforcompatibility withotherproducts.
Specifying themargin width
Youcanadjustthewhitespacesurrounding theatomlabelsothatsomeoftheattachedbondishidden.ChemBioDraw 14.0
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Toadjustthewhitespace:
1.GotoFile>Document Settings.TheDocument Settingsdialogboxappears.
2.ClicktheDrawingtab.
3.TypeanewMarginWidthvalue.
4.ClickOK.
Themarginwidthisappliedtoallsubsequent drawingsinthecurrentdocument.
Settingsfromotherdocuments
Toapplydocument settingstotheactivewindowthatarecontained inadifferentdocument, gotoFile>ApplyDocu-
mentSettingsfromandchoosethedocument fromwhichtoapplythesettings.
Thesettingsintheactivedocument windowchangetothosefoundinthestylesheetthatyouchoose.
Note:Appliedsettingsareforthecurrentdocument only.Tomakethemthedefaultsettingsforalldocuments you
open,gotoFile>OpenStyleSheets.
Toapplythedocument settingsfromadocument orstylesheetnotlistedinthemenu:
1.GotoFile>ApplyDocument Settingsfrom>Other.Theselectdocument dialogboxappears.
2.Opentheappropriate folderandselectadocument orStyleSheet.
3.ClickOpen.
Applying objectsettings
Youcanapplysettingsfromanotherdocument toselectedobjectsinthecurrentdocument. Youcanapplythechosen
settingstotheselectedobjects,ortoallnewobjectsdrawninthecurrentdocument.
Toapplyobjectsettings:
1.Selecttheobject.
2.GotoObject>ApplyObjectSettingsfromandchoosethedocument fromwhichtoapplythesettings.Adialog
boxappears.
3.Dooneofthefollowing:
Toselectedobjectonly,clickNo.
Toselectedobjectandanynewobjectsyoudraw,clickYes.ChemBioDraw 14.0
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Customizing Hotkeys
IfyouarefamiliarwithXML,youcanedittheChemBioDraw Hotkeys,orcreateyourown.
Tocustomize Hotkeys,opentheHotkeys.xml fileinatexteditor.Therearetwopaths–depending onwhetherthisisa
defaultinstallation oracustominstallation .Thepreferredmethodistoeditthisfilefromacustominstallation loc-
ation.
lIfaDefaultInstallation ,thepathis:
Go>Applications >Right-clickonChemBioDraw >ChooseShowPackage Contents >Con-
tents>Resources >SpecialPurpose >ChemDraw Items>Hotkeys.xml
lIfaCustomInstallation ,thepathis:
Customlocation folder>ChemDraw Items>Hotkeys.xml
Note:ItissafesttoedittheHotkeys.xml filefromacustominstallation location,ratherthanfromthedefaultinstall-
ationlocation.SincewheneditingtheHotkeys.xml fromthedefaultinstallation location,thiscanaffectthewhole
ChemBioDraw packagecontent.
TheHotkeyswithinthefileareorganized byobjecttype:
“Atom”:Hotkeysthatmodifyatoms.
“Bond”:Hotkeysthatmodifybonds.
"AA1":Hotkeysthatsetsthelabelforthesingleletteraminoacids.
"DNA":HotkeysthatsetsthelabelfortheDNAsequence.
"RNA":HotkeysthatsetsthelabelfortheRNAsequence.
“Generic”: Hotkeysthatselecttoolsandopendialogboxes.
EachHotkeyisencodedinthisformat:
<Hotkey key="{key}"command=" {command}"value=" {value}"description=" {description} ”/>
Key
Keyisthekeyboardkeythatinvokesthecommand. Youcanassignthesamekeytodifferentfunctionsaslongasthe
functionsaredefinedfordifferentobjecttypes.Forexample,‘b’changesanatomtoBoronintheAtomobjecttype,a
bondtoboldintheBondobjecttype,andcouldbeassignedtotheBenzenetoolintheGeneric objecttype.Youcan
useanykeyexceptthehard-codedkeys:functionkeys,ENTER,SPACE,BACKSPACE, andarrowkeys.
Note:Hotkeysarecasesensitve.Forexample,youcandefinethehotkeys"S"and"s"todifferentfunctions
withinanobjecttype.
Ifakeyappearsmorethanonceinthefileforthesameobjecttype,theoneclosesttotheendofthefiletakespre-
cedence.ChemBioDraw 14.0
Chapter4:Preferences andSettings 33of315

Command
Command isanyoneofthepredefined command names.Allavailablecommands aredescribed inthehotkeys.xml
file.Thecommand ID'saredefinedbasedontheobjecttypesasfollows:
Object Type Command ID Description
Atom LABELTEXT Setsthelabelfortheatomstext
SPROUT Additionofbondstoanatom
CHARGE Changesthechargeofanatom
FREE_SITE Increment/decrement freesitesofanatom
UPTO_SITEIncrement/decrement theUpTonumberofsub-
stituentsofanatom
EXACT_SITEIncrement/decrement thenumberofsub-
stituentsofanatom
ATOMNUMBER Show/hidetheatomnumbers
ATTACHMENTPOINT Setsthevalueoftheattachmentpoint
Bond BONDORDER Setsthebondorder
BONDDISPLAY Setsthebonddisplay
BONDPOSITION Setsthepositionofbonds
BONDDOUBLEPOSITION Setsthealignmentfordoublebonds
FUSERING Fusesaringtoabond
Generic DIALOG Displayadialog
TOOLMODE Changesthecurrenttool
AA1 AA1 Setsthelabelforthesingleletteraminoacids
DNA DNA SetsthelabelfortheDNAsequence
RNA RNA SetsthelabelfortheRNAsequence
Note:Youcannotaddtothecommand list.
Value
Thisistheparameter valueassociated withthecommand. Forexample,ifthecommand isLABELTEXT, thevalueis
thelabelthatappears.Ifthecommand isBONDDISPLAY, thevaluecorresponds tothebonddisplaytype.
Tocreateahotkeythatswitchestoaparticulartool,chooseTOOLMODE foracommand anduseanyofthesecom-
mandnamesforavalue:
LASSO TLCPLATE
MARQUEE BENZENE
3DTRACKBALL CYCLOPENTADIENE
MASSFRAG CYCLOHEXANECHAIR2
ERASER CYCLOHEXANECHAIR1
TEXT CYCLOOCTANEChemBioDraw 14.0
Chapter4:PreferencesandSettings 34of315

SOLIDBOND CYCLOHEPTANE
MULTIBOND CYCLOHEXANE
DASHEDBOND CYCLOPENTANE
PEN CYCLOBUTANE
HASHEDBOND CYCLOPROPANE
ARROW TEMPLATE
HASHEDWEDGEDBOND SNAKINGCHAIN
ORBITAL ACYCLICCHAIN
BOLDBOND QUERY
DRAWINGELEMENTS TABLE
WEDGEDBOND ARC
BRACKET WAVYBOND
HOLLOWWEDGEDBOND CHEMICALSYMBOLS
Note:ThefeaturesthatareavailabledependsonthelevelofChemBioDraw youhave.
Description
Thetooldescription explainswhateachhotkeydoes.
EditingtheHotkeys.xml file
ToeditChemBioDraw hotkeys:
1.Openthehotkeys.xml fileinatexteditor.
2.Navigatetotheappropriate hotkeylistinthehotkeys.xml file.
3.Eitheraddanewhotkeyentryusingtheappropriate formatandvaluesoreditanexistinghotkeyinthelist.
4.Savethehotkeys.xml file.
5.ExitandrestartChemBioDraw.
Caution:Exercisecautionwheneditinghotkeys.xml file,sinceiftheformatting isincorrect,itwillnotberead,and
somefunctionsofChemBioDraw mayceasetoworkcorrectly.Makeabackuptheoriginalcopyofthefilepriorto
makinganychanges.
WorkingwithColor
Youcancreatefullcolorpresentations ofyourchemicaldrawingstoappearonyourmonitor,printonacolorprinter,or
create35mmslidesusingafilmprinter.
Mostcomputers candisplayupto16millioncolors,butthenumberofcolorsmaybelimitedbyyourmonitoranddis-
playcard.
WhatYouCanColor
InChemBioDraw ,youcanchangethecolorofthebackground, foreground, orindividualobjectsandelements:
Background color.Thecolorofthedocument window.Bydefault,thebackground iswhite.
Foreground color.Thecolorofobjectsthatyoudraw.Bydefault,theforeground isblack.ChemBioDraw 14.0
Chapter4:Preferences andSettings 35of315

Individual objects.Youcanassigncolorstoobjectstohelpthenstandoutfromotherobjects.
Individual elements.Youcanassigncolorstospecificatomsorelementsinastructure.
Tochangethebackground andforeground colors:
1.NavigatetoFile>Document SettingsandselecttheColorstab.
2.Selectthebackground andforeground colors.
3.ClickOK.
ColorbyElement
Youcannowcoloratomlabelsusingcolorsassociated withtheiratomicsymbols.You canassigncolorstoelements
intheperiodictable.Whenever youuseaparticularelementinyourdrawing,theelementappearsinsamecoloryou
assignedtoitintheperiodictable.
Toassigndifferentcolorstoelementsinaperiodictable:
1.NavigatetoView>Show PeriodicTableWindow.Theperiodictableappears.
2.Double-clickanelement.Thecolorpaletteappears.
3.SelectacolorandclickOK.
Note:ThemodifiedcolorsaresavedwhenyouexitChemBioDraw.
Toapplyacolortoastructure:
1.Selectthestructure.
2.NavigatetoColor>By Element.
ChemBioDraw 14.0
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Note:Theatomcolorsarenotdynamically set,hencechangingthelabeldoesnotresetthecolor.
TheColorPalette
Usethecolorpalettetospecifythecolorofobjectsandtextinthedocument intheactivewindow.Apaletteisstored
ineverydocument andstylesheet.Youcanusestylesheetstocreateaseriesofdocuments withthesamecolor
scheme.
Customizing Colors
Changesyoumaketothecolorpaletteaffectthecurrentdocument only.Youcansaveupto20colors.Formore
information, see"Document andObjectSettings"onpage23.
Note:Ifyouselectanobjectorgroupthatcontainsmultiplecolors,acheckmarkappearsnexttoeachofthecol-
orsintheColormenu.Thecheckmarkalertsyouthatachangewouldaffectmorethanonecolor.
Tochangethecolorpaletteinthecurrentdocument:
1.NavigatetoFile>Document Settings.TheDocument Settingsdialogappears.
2.ClicktheColorstab.
3.Clickthecolortochange(eitherbackground orforeground) andselectOther.TheColordialogopens.
4.ClickthenewcolorintheBasicColorsortheCustomColorssection.
5.ClickOK.ThecolorchangestothenewcolorandappearsontheColormenu.
Toaddacustomized color:
Figure4.2:Settingcustomcolors.A)Colorrefinerbox;B)Luminosity box.
6.ClickacolorintheColorRefinerboxtosetthehueandsaturation.
Thepointerturnsintoacrosshairwhenyouclick.Youcandragtoadifferentregiontochangethehueandsat-
uration.ChemBioDraw 14.0
Chapter4:Preferences andSettings 37of315

7.ClickintheLuminosity boxtosetthecolorbrightness.
8.Ifnecessary, changethehue,saturation, luminosity, andRGBcomponents bytypingthevaluesinthetextboxes.
9.ClickAddtoCustomColors.
10.ClickOK.
Templates andColor
Thebackground andforeground colorsinatemplatefromthetemplatepop-uppalettearenotusedwhenthetemplate
isdrawninadocument window.However, othercolorsinthetemplateareaddedtothecolorpaletteofthedocument
iftheyarenotalreadypresent.Formoreinformation, see"Autoscaling" onpage270.
SavingColorPaletteSettings
Youcansavethecolorpaletteinastylesheet.Thecolorpaletteissavedwithotherdocument settingssuchaspage
setupsettings,textsettings,anddrawingsettings.
PrintingBackground Color
Tochangewhetherthebackground colorisprinted:
1.NavigatetoFile>Preferences .
2.Selectorde-selectPrintBackground ColorontheGeneraltab.
3.ClickOK.
DocumentSettings
ChemBioDraw includesalibraryofdocument settingsbasedonthosefoundinmanywell-knownscientificpub-
lications.Forexample,somejournalsmayrequiresubmitted articlesbeformattedwithspecificmargins,fonts,page
size,andsoon.Ifyouplantosubmityourdocument toaspecificjournal,openinChemBioDraw thestylesheetfor
thatjournal.Youcanalsocreatestylesheetsofyourown.
Note:Thechangesyoumaketothedocument settingsisreflectedonlyinthecurrentdocument andisnotavail-
ablethroughout theapplication.
Tocreateyourownstylesheet:
1.Createanewdocument.
2.EnterthesettingsinthePageSetup,Drawing,TextSettings,andColorpalettedialogboxes.
3.NavigatetoFile>SaveAs.
4.IntheSaveAsdialogbox:
a.SelecttheChemBioDraw stylesheetsfileformat.
b.Typeanameforthedocument.
c.SavethetemplateintheChemDraw Itemsfolder.
5.ClickOK.ChemBioDraw 14.0
Chapter4:PreferencesandSettings 38of315

ACSDocument 1996
FixedLength:14.4pt
BoldWidth:2pt
LineWidth:0.6pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:10pt
DrawingArea(WidthxHeight):540ptx720pt
PageSize:USLetter
Reduction (%):100
Adv.SynthCatal.
FixedLength:17pt
BoldWidth:2pt
LineWidth:1pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):540ptx720pt
PageSize:USLetter
Reduction (%):100
J.Chin.Chem.Soc.
FixedLength:18pt
BoldWidth:2.5pt
LineWidth:1pt
MarginWidth:2pt
HashSpacing:2.5pt
ChainAngle(degrees): 120ChemBioDraw 14.0
Chapter4:Preferences andSettings 39of315

BondSpacing(%oflength):20
AtomLabelFont:
AtomLabelSize:12pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):693ptx918pt
PageSize:USLetter
Reduction (%):80
J.Mol.Mod.(1column)
FixedLength:14.4pt
BoldWidth:2pt
LineWidth:0.6pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:TimesNewRoman
AtomLabelSize:10pt
CaptionFont:TimesNewRoman
CaptionSize:10pt
DrawingArea(WidthxHeight):8.5cmx25.4cm(1
column);17cmx25.4cm(2column)
PageSize:USLetter
Reduction (%):100
NewDocument
FixedLength:30pt
BoldWidth:2pt
LineWidth:1pt
MarginWidth:2pt
HashSpacing:2.7pt
ChainAngle(degrees): 120
BondSpacing(%oflength):12
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):7.5inx10inChemBioDraw 14.0
Chapter4:PreferencesandSettings 40of315

PageSize:USLetterorA4(asselected)
Reduction (%):100
NewSlide
FixedLength:30pt
BoldWidth:4pt
LineWidth:1.6pt
MarginWidth:2pt
HashSpacing:2.7pt
ChainAngle(degrees): 120
BondSpacing(%oflength):15
AtomLabelFont:
AtomLabelSize:12pt
CaptionFont:
CaptionSize:16pt
DrawingArea(WidthxHeight):7.5inx10in
PageSize:USLetter
Reduction (%):100
Phytomedicine
FixedLength:20pt
BoldWidth:1.33pt
LineWidth:1pt
MarginWidth:1.25pt
HashSpacing:3pt
ChainAngle(degrees): 120
BondSpacing(%oflength):8
AtomLabelFont:
AtomLabelSize:12pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):540ptx720pt
PageSize:USLetter
Reduction (%):100
RSC
FixedLength:0.43cm
BoldWidth:0.056cm
LineWidth:0.016cm
MarginWidth:0.044cm
HashSpacing:0.062cmChemBioDraw 14.0
Chapter4:Preferences andSettings 41of315

ChainAngle(degrees): 120
BondSpacing(%oflength):20
AtomLabelFont:
AtomLabelSize:9pt
CaptionFont:
CaptionSize:9pt
DrawingArea(WidthxHeight):8.9cmx25.4cm(1
column);19cmx27.7cm
PageSize:USLetter
Reduction (%):100
ScienceofSynthesis
FixedLength:17pt
BoldWidth:2pt
LineWidth:0.8pt
MarginWidth:2.25pt
HashSpacing:2.5pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:10pt
DrawingArea(WidthxHeight):19.79cmx27.15cm
PageSize:A4
Reduction (%):100
Synthesis, Synlett
FixedLength:17pt
BoldWidth:2pt
LineWidth:0.8pt
MarginWidth:1.3pt
HashSpacing:2.5pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:10ptChemBioDraw 14.0
Chapter4:PreferencesandSettings 42of315

DrawingArea(WidthxHeight):12cmx26.7cm
PageSize:A4
Reduction (%):100
VerlagHelvetica ChimicaActa
FixedLength:17pt
BoldWidth:2.9pt
LineWidth:0.54pt
MarginWidth:2pt
HashSpacing:2pt
ChainAngle(degrees): 120
BondSpacing(%oflength):14
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):368x720pts
PageSize:USLetter
Reduction (%):100
WileyDocument
FixedLength:17pt
BoldWidth:2.6 pt
LineWidth:0.75 pt
MarginWidth:2pt
HashSpacing:2.6pt
ChainAngle(degrees): 120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:12pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):19.79×27.15cm
PageSize:A4
Reduction (%):100ChemBioDraw 14.0
Chapter4:Preferences andSettings 43of315

Shortcuts andHotkeys
Hotkeysareorganized intoatomlabels,bondtypes,andfunctions(suchasaddingachargeordisplaying abond).
Shortcuts areorganized bythemenuonwhichthecommand isfound.
Note:Youcanmodifyhotkeysandnicknames. Thetablesinthissectionrefertothedefaultvalues.
AtomKeys
Useatomkeystoinsertatomsinadrawingusingyourkeyboard. Forexample,placeyourmouseoveranatomand
press<3>toaddatert-butylgroup.
AtomLabelKey
A a
F f
Ph Por4
Ac Aor5
H h
Q* q
Br b
I i
R r
n-Bu 1
K k
S s
s-Bu 2
Me m
Si S
t-Bu 3
N n
TMS tChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 44of315

AtomLabelKey
C c
Na N
X x
Cl Corl
O o
COOCH3 E
D d
OTs T
CH2OH 6
Et e
P p
B B
BondHotkeys
Tomodifyabond,placeyourmouseoverthebondandselectakeylistedbelow.
Function Key
Changetosinglebond 1
Changetodashedbond d
Changetodoublebond 2
Changetowavybond y
Changetotriplebond 3
Positionadoublebondtotheleft l
Changetoquadruple bond 4
Centeradoublebond c
Changetoboldbond bChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 45of315

Function Key
Positionadoublebondtotheright r
Changetowedgedbond w
Bringbondtofront f
Changetohashedbond H
Openabondproperties textbox /(slash)or?
Changetohashed-wedgedbond h
Fuse5membered ring 5
Fuse6membered ring 6
Fuse7membered ring 7
Fuse8membered ring 8
Createchairformofcyclohexane withtwodifferentori-
entations9or0
Function Hotkeys
Function Key
Addanattachment point .(period)
Addanatomnumber ‘ (singlequote)
Addanegativecharge –
Addapositivecharge +
Sproutonebond 0
Sprouttwobonds 9
Sproutthreebonds 8
DisplaytheAtomProperties dia-
logbox/(slash)or?
DisplaytheChooseNickname dia-
logbox=(equals)ChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 46of315

Function Key
Openanatomlabeltextbox <Enter>
Removeanatomlabel <Backspace>, <Delete>or
<space>
Shortcuts
Belowisalistofkeycombinations forcommontasks.
File
Command KeyCombination
Createanewdoc-
umentCTRL+N
Openadocument CTRL+O
Saveadocument CTRL+S
Saveadocument asSHIFT+CTRL+S
Printadocument CTRL+P
Pagesetup SHIFT+CTRL+P
Closeadocument CTRL+W
ExitChemBioDraw ALT+F4
Edit
Command KeyCombination
Cut CTRL+X
Copy CTRL+C
Paste CTRL+V
Selectall CTRL+A
Undo CTRL+Z
Redo SHIFT+CTRL+Z
Repeatlastcommand CTRL+YChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 47of315

Command KeyCombination
Clear Delete
View
Command KeyCombination
Actualsize F5
Reduce F8
Magnify F7
Fittowindow F6
Toggleruler F11
Togglecrosshair CTRL+H
Object
Command KeyCombination
Togglefixedlength CTRL+L
Togglefixedangles CTRL+E
Selectmultipleobjects SHIFT+Click (withLasso,Marquee,or
StructurePerspective tools
Groupselectedobjects CTRL+G
Ungroupobjects SHIFT+CTRL+G
Joinselectedobjects CTRL+J
Bringtofront F2
Sendtoback F3
Fliphorizontal SHIFT+CTRL+H
Flipvertical SHIFT+CTRL+V
Rotate180°horizontal ALT+SHIFT+CTRL+H
Rotate180°vertical ALT+SHIFT+CTRL+VChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 48of315

Command KeyCombination
Rotate…(opensRotateObjects
dialog)CTRL+R
Scale…(opensScaleObjectsdia-
log)CTRL+K
Structure
Command KeyCombination
Cleanupstructure SHIFT+CTRL+K
Convertnametostructure SHIFT+CTRL+N
Convertstructuretoname ALT+CTRL+N
Text
Command KeyCombination
Flushleft SHIFT+CTRL+L
Center SHIFT+CTRL+C
Flushright SHIFT+CTRL+R
Justified SHIFT+CTRL+J
Automatic justification SHIFT+CTRL+M
Plain CTRL+T
Bold CTRL+B
Italic CTRL+I
Underline CTRL+U
Formula CTRL+F
Subscriptselectedcharacter, or
nextcharactertypedF9(inalabel)
Superscript selectedcharacter, or
nextcharactertypedF10(inalabel)
Addsadegreesign(°) ALT+248(inalabel)ChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 49of315

Drawing
Command KeyCombination
Copyaselectedobject CTRL+drag
Copyaselectedobject
(constrained toXandY
axes)SHIFT+CTRL+drag
Distort(limitresizetoXor
Yaxis)SHIFT+drag (withresizehandle)
ToggletheLassoandthe
previousdrawingtoolCTRL+ALT+Tab
ChangedirectionofachainCTRL+Drag(withalkanechaintool)
Changeorientation of
doublebondsSHIFT+Click
(withsaturateddouble-bondringtools)
Createresonance delo-
calizedringCTRL+Click(withringtoolsexceptchairs)
Removeacurvesegment ALT+SHIFT+Click (withthepentool)
Nicknames
Ac Bz c-C7H13 cyclopropyl DPIPS i-C4H9
Ad BOM c-C8H15 Cys DPTBS i-C5H11
Ala Bs c-Hx Dan DTBMS i-Pr
Alloc Bt C10H20 DEAE DTBS Ile
Allyl Btm C10H21 DEIPS Et Im
Am Bu Cbz DMIPS Fmoc Leu
Arg Bzh cHx DMPM Gln Lys
Asn Bzl CoA DMPS Glu m-C6H4ChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 50of315

Asp BzOM Cy DMTr Gly m-Phenylene
Benzoyl c-C3H5 cyclobutyl DNP His m-Tolyl
Benzyl c-C4H7 cycloheptyl Dnp i-Am MDIPS
Bn c-C5H9 cyclooctyl Dns i-Bu MDPS
Boc c-C6H11 cyclopentyl DNS i-C3H7 Me
MEM n-Pr Phenyl s-Butyl TBDMS Thr
Mes N3 Pht s-C4H9 TBDPS TIPDS
Met neo-Am Piv s-C5H11 TBMPS TIPS
MMTr neo-C5H11 PMB SEM TBS TMS
MOM Np PMBM Ser TDS Tos
MPM o-C6H4 PNB SES Tf trans-Cin-
namyl
Ms o-Phenylene Poc t-Am Tfa Troc
MTM o-Tolyl PPi t-BOC TFA Trp
n-Am p-C6H4 Pr t-Boc Thexyl Trt
n-Bu p-Phenylene Pro t-Bu THF Ts
n-C3H7 p-Tolyl Pv t-Butyl Thf Tyr
n-C4H9 Ph s-Am t-C4H9 THP Val
n-C5H11 Phe s-Bu t-C5H11 Thp XylChemBioDraw 14.0
Chapter5:ShortcutsandHotkeys 51of315

BasicDrawings
ChemBioDraw providesavarietyoftoolsfordrawingeverything fromsimplechemicalstructures tocomplexreac-
tions.Inthissection,weintroducebasictechniques tohelpyoucreateyourfirststructures. Wealsoexplainhowto
addfeatures,suchasarrowsandshapes,toenhancestructures andreactions. Formoredrawingfeatures,see
"BioDraw(Ultrafeatureonly)"onpage92and"Advanced DrawingTechniques" onpage118.
Bonds
TheMaintoolbarandMultipleBondstoolbaroffernumerous optionsfordrawingbonds.Sometoolsarefordrawing
specifictypesofbonds,whileothersarefordrawingstructures fordatabasequeries.Foradditionalinformation onvari-
ousbondtypes,see"BondConventions" onpage278.
DrawingBonds
Todrawthefirstbondofyourstructure,selectthesolidbondtoolintheMaintoolbarandclickinthedocument win-
dow.Thebondappearsinthedrawingwindow.Todrawanotherbondattachedtothefirst,clickeitherendofthefirst
bond.Thesecondbondappearsinthedrawingwindow,asshownbelow.
Figure6.1:Addingabondtoanatom
Youcandrawabondinanydirection.Usingabondtool,clickanddragfromanexistingatomoranemptyareainthe
document window.Thebondisdrawninthedirectionyoudragthecursor.
Figure6.2:Addingabondbydragging
DoubleBonds
Therearefourwaystodrawadoublebond:
DrawabondusingtheDoublebondtool.
Drawasinglebondoveranexistingsinglebond.
Usinganybondorselectiontool,pointtoanexistingbondandtype‘2’.See"Shortcuts andHotkeys"onpage44.
Right-clickanybondandselectDouble>Plaininthecontextmenu.ChemBioDraw 14.0
Chapter6:BasicDrawings 52of315

DoubleEitherBonds
Doubleeitherbonds,orcrosseddoublebonds,indicateunspecified doublebondconfiguration, oramixtureofcon-
figurations. Todrawadoubleeitherbond,usethedoubleeitherbondtool
fromtheMultipleBondstoolbar,or:
1.DrawabondusingtheWavyBondtool.
2.Clickthecenterofthebondtocreateadoublebond.
3.Clickagaintocreateadoubleeitherbond.
TripleBonds
Therearethreewaystodrawatriplebond:
DrawabondusingtheTripleBondtool.
UsingtheSolid,Dashed,orBoldBondtool,dragfromoneendofanexistingdoublebondtotheotherend.
Usinganybond,orselectiontool,pointtoanexistingbondandtype‘3’onyourkeyboard.
Quadruple Bonds
Therearethreewaystodrawaquadruple bond:
DrawabondusingtheQuadruple Bondtool.
UsingtheSolid,Dashed,orBoldBondtool,dragfromoneendofanexistingtriplebondtotheotherend.
Usinganybondorselectiontool,pointtoanexistingbondandtype‘4’onyourkeyboard.
Tochangeaquadruple bondintoasinglebond:
1.Selectanybondtool.
2.Dragfromoneendofanexistingquadruple bondtotheother.
Youcanalsodrawmultiplebondsbyright-clicking abondandselectingthebondtypefromtheshortcutmenu,using
thebondproperties dialog,orusingHotkeys.See"BondProperties" onpage239.
Note:Toreducethebondorder,selecttheErasertoolandclickthebond.
DativeBonds
Dativebondsareaspecifictypeofcovalentbondinwhichthepairofelectronssharedbytheatomsintheformation
ofabondiscontributed byoneoftheatomsonly.Theatomcontributing thepairofelectronsisknownas"donor"
whiletheatomwhichdoesnotcontribute, butsharesthepairofelectrons, isreferredtoas"acceptor".
Todrawadativebond:
1.SelecttheDativeBondtool.
2.Dragfromthepositivetothenegativeend(arrowhead)ofthedativebond.
Dativebondsaredrawnwithafixedorientation inadocument window.
Tochangetheorientation ofadativebond:
Clickthebondusingthedativebondtool.ChemBioDraw 14.0
Chapter6:BasicDrawings 53of315

WedgedBonds
Todrawawedgedbond:
1.Clickoneofthewedgedbondtools.
2.Dragfromthenarrowendofthewedgedbondtothewideendofthewedgedbond.
Wedgedbondsaredrawnwithafixedorientation inadocument window.
Tochangetheorientation ofthewedgedbond:
Clickthebondusingthewedgedbondtool.
Note:ChemBioDraw treatshashedwedgedbondswiththenarrowendintheplaneofthescreenandthewideend
behindtheplane.
Changing Bonds
Youcanchangebondsby:
Changingbondtypes
Changingbondalignment andorientation
Movingatoms
Layeringbonds
Changing BondTypes
Changeasinglebondfromonetypetoanotherusingoneofthefollowingmethods:
Selectabondtoolandclickanexistingbond
Right-clickandselectthenewtypefromthecontextmenu
Withhotkeys.See"Shortcuts andHotkeys"onpage44.
Changing DoubleBonds
Tochangeonetypeofdoublebondtoanother:
1.SelecttheBold,Dashed,orSolidBondtool.
2.Clickadoublebond.
Thedoublebondchangestothenewbondtype.Oneofthebondsinthedoublebondisalwaysasolidordashedbond.
Note:Ifyouclickatautomeric bond(solid/dashed) againwiththedashedbondtool,youcreateanaromaticdouble
bond(dashed/dashed).
AligningDoubleBonds
Doublebondscanhaveoneofthreealignments relativetootherbonds—above,below,andcentered.
Above
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Centered
1.Clickthebondtoolusedtocreatetheexistingdoublebond.
2.Tochangethealignment, dooneofthefollowing:
Clickthecenterofthedoublebond.
Right-click,pointtoBondPositiononthecontextmenu,andchoosethealignment.
MovingAtoms
Tomoveanatominastructure,clickanddragitusingaselectiontool.Tomovetwobondedatomsinastructure,
clickanddragthebondbetweenthem.
Tomoveindividualatoms:
1.Clickaselectiontool.
2.Pointtotheatomyouwanttomove.Ahighlightboxappearsovertheatom.
3.<SHIFT>+drag theatom.
Note:Youcanalsomoveatomsusingaselectiontool.See"MovingObjects"onpage83.
Reducing RingSize
Youcanreducethenumberofatomsinaring.Forexample,youcanconvertcyclohexane tocyclopentane.
Toreducetheringsize,dooneofthefollowing:
Usingtheselectiontool,clickanddrag.
Usingabondtool,pointtoanatomand<SHIFT>+drag. Releasewhenoneatomisontopoftheother.Thebond
betweentheatomsdisappears.
BondCrossing
Whenonebondcrossesanother,youcanindicatewhichbondisinfront.Thebondwhichisbehindhasasmallsec-
tioncutout,soyoucanclearlydiscernwhichbondisfront-most.
Tomoveanobjecttothefrontposition:
1.Selecttheobjecttomovetothefront.
2.GotoObject>BringtoFront.Theselectedobjectnowappearsinfrontofallotherobjects.
Similarly,navigatetoObject>SendtoBacktopositionthebondbehindotherobjects.
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Note:Somefileformatsstore3Dcoordinates foratoms,whileothersonlystore2Dcoordinates. Forbondswith
3Dcoordinates, thosecoordinates determine thevisiblebondcrossings. BringToFrontandSendToBack
havenoeffect.Formoredetailsonconverting bondsandstructures into3Dview,see"3DViewing"onpage165
FixedBonds
Bydefault,ChemBioDraw drawsstructures withfixedbondlengthsandbondangles.Thevaluesofthoselengthsand
anglesisdetermined bythesettingsfortheparticulartypeofdocument. Formoreinformation, see"Document Set-
tings"onpage38.However, youcanmodifythebehaviorsothatyouarenotconstrained tofixedbondsandangles.
Note:Tosuppressfixedlengthsandfixedangles,presstheALTkeyasyoudragthebond.
DrawingFixedLengthBonds
Todrawbondsconstrained toafixedlength:
1.NavigatetoObject>FixedLengthsandensureacheckmarkappearsnexttoFixedLengths.
2.Drawabondusinganybondtool.
DrawingFixedAngleBonds
Bondanglesaregenerallyeithersettothedefaultchainangleof120degrees,orareconstrained toanglesof15
degreeincrements.
Todrawfixedanglebonds:
1.NavigatetoObject>FixedAnglesandensureacheckmarkappearsnexttoFixedAngles.
2.Drawabondusinganybondtool.
Thebondsinthenewstructureappearatstandard120°angles.
Changing FixedValues
Bydefault,bondlengthsare.4176inchesandbondanglesinachainare120°.
Tochangefixedvalues:
1.NavigatetoFile>Document SettingsandclicktheDrawingcategory.
2.EnteravalueintheFixedLengthtextfield.Usein,cm,pt,orpicasforunits.
3.EnteravalueintheChainsAngletextfield.
4.ClickOK.
Formoreinformation ondrawingsettings,see"DrawingSettings"onpage24.ChemBioDraw 14.0
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Atoms
Bydefault,whenyoudrawstructures withthevariousbond,ring,orchaintools,simplehydrocarbons arecreated.
YoucanaddatomlabelstotheatomsusingtheTexttool.YoucanalsousetheTexttooltoaddtextualcaptionstoa
document. Forexample,youcanaddtheatomlabel“OH”toadrawingoftoluenetocreatephenol:
1.Drawthetoluenestructure.
2.UsingtheTexttool,clickthemethylcarbon.Atextfieldappears.
3.TypeOHinthetextfield.
4.Clickoutsidethetextfield.
Toedittheatomlabel,clickinthetextfieldwiththetexttoolandbegintyping.
Youcaneitherentertheatomlabelinatextfieldortypethehotkeywhilehoveringoveranatom.Formoreinformation
abouthotkeys,see"Hotkeys"onpage61and"Shortcuts andHotkeys"onpage44.
PeriodicTable
Youcanusetheperiodictabletoinsertatomsintostructures. NavigatetoView>ShowPeriodicTableWindow.
ClickasymbolintheperiodictabletohighlighttheatomandactivatetheTexttool.Movethemouseacrossthetable
tohighlighteachatom.
Toaddanatom.Selectthedesiredelementintheperiodictableandclickanemptyspaceinthedocument. The
atomappearsinitschemically neutralform.Forexample,carbonappearsasCH4andhydrogenappearsasH2.
Tolabelanatom.Clickanexistingunlabeledatom.ChemBioDraw 14.0
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Tochangetheoxidation state.Usingthesymbolfortheatom,clicktheatominthedocument window.
Tochangetoadifferentatom.Selectthenewatomintheperiodictableandclicktheatominthedrawingyouwant
tochange.
Toeditalabel.YoucaneditanatomlabelusingtheTexttool.Highlightthetextandclickasymbolintheperiodic
table.Thehighlighted textisreplaced.
Repeating AtomLabels
Youcanrepeatanatomlabelusingthetext,bond,orringtools.
1.ClicktheTexttool.
2.Labelasingleatom.
3.Dooneofthefollowing:
UsingtheTexttool,double-clickanotheratom.
Usingabond,ring,oracyclicchaintool,triple-clickanotheratom.
DeletingLabels
Todeleteanatomlabel,dooneofthefollowing:
SelecttheErasertoolandclicktheatomlabel.
Withaselection, bond,orringtoolselected,pointtotheatomlabelandpressthe<spacebar>, <Backspace>, or
<Delete>key.Notethatifanatomislabeled,pressingthe<spacebar>, <Backspace>, or<Delete>keywilldelete
thelabel,butnottheatom.Todeletetheatomaswell,pressthe<Delete>keyasecondtimetodeletethe
unlabeledatom.
Captions
Youcanaddandeditcaptionstoyourstructures usingtheTexttool.Thefollowingexampleaddsthecaption'Phenol'
toaphenolstructure.
Toaddthecaption‘Phenol’toaphenolstructure:
1.Drawthephenolstructure.
2.UsingtheTexttool,clickbelowthedrawingandtype“Phenol”inthetextfield.
3.Clickoutsidethetextfield.
Toeditthecaption,clickinthetextfieldwiththeTexttoolandbegintyping.Formoreinformation, see"NewLinesand
ClosingTextBoxes"onpage21.ChemBioDraw 14.0
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Formatting
Eachnewcaption,oratomlabel,usesdefaultdocument settingsforfont,size,andstyleofcaptionsandatomlabels.
Youcanchangetheformatby:
Changingthedocument settingsforsubsequent drawingsinthecurrentdocument.
ChoosinganewformatforanindividualcaptionorlabelfromtheTextmenuortoolbarbeforeyoutype.
Selectingtextandapplyinganewformattoanindividuallabelafteryoutype.
Tospecifythetextsettingsfornewcaptionsandatomlabelsinthecurrentdocument:
1.NavigatetoFile>Document Settings.TheDocument Settingsdialogappears.
2.SelectTextCaptionsorAtomLabelscategory.
3.Selecttheappropriate options.
4.ClickOK.Thesesettingsaffectallnewcaptions,oratomlabels,inthecurrentdocument.
Youcansetthetextformatforanindividualcaption,oratomlabel,beforeyoubegintyping.
Tosetthetextformatbeforeyoutype:
1.ClicktheTexttoolandclickinthedocument window.Atextfieldappears.
2.Setthetextformatinoneofthefollowingways:
FromtheTextmenu,choosetheformatoptions.
FromtheStyletoolbar,choosetheformatoptions.
3.Typethetextinthetextbox.
Note:Theformatchangeisappliedtothecurrenttextonly.Anysubsequent textyoutypeisformattedaccording
tothedefaultdocument settingsforthecurrentdocument.
Tospecifyafont,style,andsizeforselectedtext,dooneofthefollowing:
ChoosethefontandsizefromtheTextmenu.
Right-clickandchoosethefontandsizefromthecontextmenu.
FromtheStyleToolbar,selectthefontandsizefromthedrop-downmenus.
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Coloring Text
Youcancolorcaptionsandatomlabelsbeforeorafteryoutypethem,andasawholeorinpart.
Tocoloracaptionoratomlabel:
1.SelecttheTexttool.
2.Clickinsidethedocument whereyouwanttoplacethetext.
3.ChooseacolorfromtheColormenu.
4.Typethecaptionoratomlabel.
Tocolorindividualcharacters:
1.Selectpartofanexistingcaption,oratomlabel,usingtheTexttool.
2.FromtheColormenu,chooseacolor.
Tocolorseveralcaptionsoratomlabelsatonce:
1.Selectthecaptionsorlabelsusingaselectiontool.
2.ChooseacolorfromtheColormenu.
CaptionWidth
Toeditthewidthofacaption:
1.SelectthecaptionusingtheTexttool.Aresizehandleappearsontherightsideofthecaption.
2.Dragtheresizehandletochangethewidthofthecaption.
AboutFonts
ChemBioDraw usesthefontsinstalledonyourcomputer. IfaChemBioDraw document containsfontsthatarenot
availableonaparticularcomputer, theyaresubstituted withtheavailablefonts.
Character Map
Thefloatingcharactermapwindowdisplaysthe256ASCIIcharacters inanyfont.ThedefaultfontisSymbol.ChemBioDraw 14.0
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Usethecharactermaptoaddsymbolstoyourdocument invariousfontstyles.Toshoworhidethemap,navigateto
View>ShowCharacter MapWindow.Thecharactermapisshownbelow.
Thecharactermapisactiveonlywhenatextfieldisopenforediting.Withatextboxopen,mouseoverthecharacter
maptoviewalargerversionofthecharacters inthetoprightcornerofthewindow.Clickanycharacterinthetableto
enteritinthetextfield.Theselectedfont(showninthecharactermapwindow)isappliedtothatcharacteronly.It
doesnotchangetheactivefontinthetextfield.
Theeightmost-recentlyusedcharacters appearatthetopofthewindow.Acharactermayappearmorethanoncein
thissectioniftheversionsusedifferentfonts.ClicktheBackbuttontotoggleamongallthedisplayedcharacters.
Hotkeys
Hotkeysarekeysonyourkeyboardthatarelinkedtospecificatomlabels.UseChemBioDraw hotkeystoquickly
labelatomsandapplyatomproperties. TheHotkeys.xml fileintheChemDraw Itemsfoldercontainsthehotkeys
providedwithChemBioDraw. Youcanaddorchangehotkeysbyeditingthisfileinatexteditor.
UsingHotkeys
Usinghotkeys,youcanaddfunctional groupstoyourstructures withonekeystroke. Forexample,toaddtert-butylto
theendofahydrocarbon chain:
1.Drawthechain.
2.Hoverthecursorwhereyouwantthefunctional group.
3.Press<3>(thehotkeyfortert-butyl)onthekeyboard. ‘t-Bu’isaddedtothestructure.
4.Select‘t-Bu’inthestructureandnavigatetoStructure>ExpandLabel.ChemBioDraw 14.0
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Usingthehotkeys<n>(nitrogen), <O>(oxygen),and<I>(iodine),youcanturnethylbenzene intopyridin-2-ylhypoiod-
ite.
Youcanalsolabelseveralatomsatatime.Forexample,youcanchangeneopentane (figureAbelow)intometh-
anetetraamine (figureB):
1.Createtheneopentane structure.
2.Use<SHIFT>+click toselectalltheterminalcarbonatomsandpress<n>onthekeyboard.
Note:Foracompletelistofhotkeys,see"Shortcuts andHotkeys"onpage44.
Nicknames
Thesimplestwaytoaddanatomicsymboltoastructureistotypethesymbolintoatextfield.However, youarenot
limitedtoenteringatomsone-at-a-time.Usingnicknames, youcanaddfunctional groups,chains,oranyotherstruc-
turalfeaturewithoutdrawingeachatom.
Anickname isanalphanumeric abbreviation thatrepresents asubstructure. Nicknames areusefulfordrawinglarge
structures orstructures thatrepeatedly usesimilarfeatures.
Notethatyoucanassignanickname tothestructuralfeature.YoucanalsoassignhotKeystonicknames thatyou
canlateruseasaquickwayforaddingthenickname toyourdrawing.Formoreinformation ondefiningnicknames,
see"DefiningNicknames" onpage138.
UsingNicknames
Usingnicknames, youcanaddshortnamesforfunctional groupstouseasanatomlabel,orpartofalabel.Whenan
atomislabeledwithanickname, thechemicalsignificance oftheexpanded structureisretained.ChemBioDraw 14.0
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Commonly usednicknames, suchasMe,Et,andPharestoredinyourChemDraw Itemsfolder.Youcaneditor
deletenicknames inthislist.
Youcanassignhotkeystonicknames. Forexample,thehotkey<4>labelsanatomwith“Ph”,whichrepresents a
phenylgroup.
Applying Nicknames
Youcaneithertypethenickname orselectitfromthenicknames list.Formoreinformation ondefiningnicknames,
see"DefiningNicknames" onpage138.
Touseanickname tolabelanatom:
1.Inastructure,double-clickanatomwithabondtool,orclickanatomwiththeTexttool.Anatomlabeltextfield
appears.Dooneofthefollowing:
Typeanickname label,suchas“Et”.
NavigatetoFile>Listnicknames .TheListNicknames dialogappears.
Selecttherequirednickname andclickPaste.
ClickDone.
Anexampleisshownbelow:
Toselectanickname toapplytoanatomusingahotkey:
1.Pointtoanatom.
2.Pressthehotkey<=>(equalsign).TheChooseNickname dialogappears.
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3.Selectanickname fromthelist.
Tip:Youcanmovewithinthenickname listbytypingthefirstletterofthenickname, ratherthanscrollingthrough
thelist.
4.ClickOK.
Note:Nicknames aretokensanddonotfliporientation whenappliedtotheleftsideofastructurewhenusingAuto-
maticJustification. Forexample,intheabsenceofadefinednickname, thelabel“OTHP”appearsas“PHTO”.
However, sincethenickname “THP”isdefined,thelabelappearsas“THPO”.Formoreinformation, see"Aligning
Text"onpage28.
Expanding Nicknames
Ifyourstructures containdefinednicknames, longatomlabels,orcontracted labels,ChemBioDraw canrestoreyour
structures tothefullyexpanded form.Whileexpanding astructurecontaining adefinednickname, thenickname will
bereplacedbyitsexpanded structure,asshownbelow:
ForBiopolymers, whenyouexpandthenickname, residuelabelappearsbelowtheexpanded aminoacid.For
example,assumeyouhaveachainofthreeaminoacids–glycine,isoleucine, andleucine:
Toselecttheaminoacid,double-clickthenickname, asshown:
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Toexpandatomnicknames,
1.Selecttheselectiontool.
2.Selectthelabeltoexpand,ordouble-clickthestructuretoselectalllabelsinthestructure.
3.NavigatetoStructure>Expand Label.Yourstructureisredrawninitsexpanded form.
Tocontractexpanded nicknames:
1.Inthebiopolymer structure,selecttheexpanded part.
2.NavigatetoStructure>Contract Label.Yourstructureisredrawninitscontracted form.
Note:Thisisapplicable onlytobiopolymers.
Annotations
Annotation isabriefdescription ofanobject,oracomment, aboutproperties ofanobject.Annotations areusefulin
identifying featuresandcategories ofobjectsinsearching andbrowsing. Annotations arecategorized using
keywords. Thereareseveraldefaultkeywords: Name,Description, GUID(GloballyUniqueIdentifier)Type,and
OtherInfo.Youcanalsoaddyourownkeywords. Manyoftheobjectsinthetemplatefileshaveassociated annota-
tionstohelpyouidentifytheminfiles.
Toannotateanobject:
1.Selecttheobject.
2.NavigatetoObject>Annotate.TheAnnotatedialogappears.
3.IntheKeywordlist,dooneofthefollowing:
Selectakeyword.
SelectAddNewKeyword.
4.IntheContenttextfield,enterthenotes(annotation) toapplytotheobjectordrawing.
5.ClickOK.
DeletingaKeyword
Whenyoudeleteakeyword,allnotes(annotation) forthatkeywordarealsodeleted.
1.IntheAnnotatedialog,selectthekeywordfromtheKeywordlist.
2.ClickDeleteKeyword.
3.ClickOK.
Settingpreferences
YoucanspecifyhowthecaptionsandlabelsappeareachtimeyouuseChemBioDraw. Thechangesyouspecifyare
availablethroughout theapplication. NavigatetoFile>Preferences andclicktheBuilding/Display tab.Then,
choosefromtheseoptions:
Automatic AtomLabelAlignment .Thealignment ofatomlabelsadjustsaccording tothepositionsofanybonds
attachedtotheatomlabels.Forexample,‘CH3’attheleftendofahorizontal bondchangesto‘H3C’.ChemBioDraw 14.0
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Automatically RectifyHydrogens inAtomLabels.Addsorremoveshydrogens fromatomlabelstopreserve
standardvalenceswhenyouchangeyourdrawing.Forexample,ifyouincreasethebondorderinethanetomake
ethylene,the‘CH3’changesto‘CH2’.
SettingDefaultAtomLabelStyles
Tosetthedefaultcharacterstyleforatomlabels,navigatetoFile>Document SettingsandclickAtomLabels.You
canmodifythefontstyle,baselinestyle,andwhetherterminalcarbonsandimpliedhydrogens appear.
Tosetthedefaultatomlabelstyleforadocument:
1.NavigatetoFile>Documents andSettings.
2.FromtheAtomsLabelstab,checktheShowLabelsonTerminal Carbonscheckbox.
3.ClickOK.
Tosetthedefaultatomlabelstyleforoneormorestructures:
1.Selectandright-clickthestructure(s).
2.ClickObjectSettingsinthecontextmenu.TheObjectSettingsdialogappears.
3.FromtheAtomLabelstab,checktheShowLabelsonTerminal Carbonscheckbox.
Toaddorremoveaterminalcarbonlabel,right-clicktheatomandselectordeselectShowTerminal Carbon
Labels.
Chemical Significance
Bydefault,captionsareconsidered tobechemically significant, ifpossible.Ifyoucreatealabel,forexample,
"CH3OH”, youareabletoattachbondstoit(anditismodifiedappropriately) eventhoughyoumayhaveintendeditto
bealabel,notamolecule. Moreover, it’svaluesareincludedintheAnalysiswindow.Thelabelswithincorrect
valencesaremarkedwitharedbox.
Toremovetheredbox:
1.SelectthelabelwiththeSelectiontool.
2.Right-clickanddeselectInterpretChemically inthecontextmenu.
3.Toactivatechemicalsignificance, right-clickthelabelandselectInterpretChemically .
AnalysisData
Youcanaddproperties fromtheAnalysiswindowtoacaptionand,ifAuto-updateison,thevaluesupdateasyou
modifythestructure.Formoreinformation aboutAuto-update,see"AutoUpdate"onpage147.ChemBioDraw 14.0
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Toaddanalysisdatatoacaption:
1.Right-clickthestructureandselectAnalysisfromthecontextmenu.
2.Choosetheproperties toadd.
DrawingRings
TheMainToolspalettecontainsthefollowingringtoolsthatenableyoutodrawringsizesandtypes:
Figure6.3:a)cyclopropane; b)cyclopentane; c)cycloheptane; d)cyclohexane chair(1);e)cyclopentadiene; f)cyc-
lobutane;g)cyclohexane; h)cyclooctane; i)cyclohexane chair(2);j)benzene.
Todrawaring:
1.FromtheMaintoolbar,selectaringtool.
2.Clickanddraginthedocument toorientthering.
Ifyouclickanatomorbondwitharingtoolinanexistingstructure,theringisfusedtoit.Youcanalsousehotkeysto
fuserings.Formoreinformation, see"BondHotkeys"onpage45.Youcanalsoreducethesizeoftherings.Formore
information, see"Reducing RingSize"onpage55
SpiroandSproutRings
Bydefault,clickinganatominaringusingaringtoolformsaspirolink.However, ifyouclickanatomwhilepressing
the<Alt>keyonyourkeyboard, itwillsproutthering.ChemBioDraw 14.0
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Youcanchangethisbehaviorsothatasproutbondappearsinsteadofaspiroring:
1.NavigatetoFile>Preferences .
2.FromtheBuilding/Display tab,checktheSproutRingsInsteadofSpiroWhenClickingcheckbox.
Cyclohexane ChairRings
Youcandrawcyclohexane chairringsintwoorientations: horizontal andvertical.Whenyoudrawacyclohexane chair
ringbyclicking,thechairisdrawninahorizontal orientation.
Toorientacyclohexane chairringtoaverticalorientation:
1.ClickoneoftheCyclohexane ChairRingtools.
2.Click+drag inthestructuretotheorientation youwant.
Figure6.4:a)Horizontal orientation; b)Verticalorientation.ChemBioDraw 14.0
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Aromatic Structures
Delocalized Rings
Youcandrawaresonance delocalized ringusinganyringtoolexceptforthecyclohexane chairs.
1.Clickaringtool.
2.PresstheCTRLkeyanddragorclickinthedocument window.
Resonance Structures
Youcandrawcyclopentadiene orbenzeneinmultipleversions:
Thedoublebondsinthecyclopentadiene orbenzeneringtoolscanbedrawnineitheroftwoforms.Normally, thefirst
bonddrawnisadoublebond.Thisistheorientation indicatedonthecyclopentadiene andbenzeneRingtoolpointers.
Todraw,clickinthedocument windowwitheitherthecyclopentadiene orbenzenedrawingtool.
Toshifttheorientation sothefirstbonddrawnisasinglebond,dooneofthefollowing:
<Shift>+drag fromthebeginningofthefirstsinglebondtotheendofthesinglebond.
<Shift>+click inadocument windowtodrawthebondwithafixedlength.
Chains
Youcandrawhydrocarbon chainsusingeithertheAcyclicchaintoolorSnakingchaintool.UsetheAcyclicchaintool
todrawstraighthydrocarbon chains.
1.SelecttheAcyclicchaintool.ChemBioDraw 14.0
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2.Clickanddraginthedocument windowinthedirectionyouwantthechaintogrow.Thenumberattheendofthe
chainindicateshowmanyatomsyouhavedrawn.
Changing ChainDirection
Tochangethedirectionasyoudraw,usetheSnakingchaintool,orpressthe<Control> keywithAcyclictoolselec-
ted,whiledrawinginthedirectionyouwant.
Note:Releasethemousebuttonbeforeyoureleasethe<Control> key.
Applying FixedLengths
Applyingfixedlengthsandfixedanglesenablesyoutocreatestructures withconsistent bondlengthsandangles.The
fixedlengthdimension issetintheDrawingSettingsdialog.Thefixedangledimension increments anglesby15
degrees.
FixedlengthisusedtoconstrainthelengthofthebondsdrawntothelengthyouspecifywhentheFixedLengths
command intheObjectmenuisenabled(withacheckmark).Thisalsoadjuststhepreferredbondlengthforstruc-
turesmodifiedbytheCleanUpStructure command.
WhenFixedLengthsisenabled,thepointerontheAcyclicchaincanbedraggedtomakeanyanglerelativetotheX-
axis.Ataconstantchainlength,thepositionsofthefirstbondandallsubsequent odd-numbered atomsdependonthe
directionyoudrag.Beforereleasingthemousebutton,changethispositionbydraggingintheoppositedirection.
IfFixedLengthsisdisabled,holddownthe<Control>+<ALT> keystoreversechaindirection.FixedAnglesmust
beenabledtoreversedirection.
FixedAngles
WhenFixedAnglesisenabled,theangletheAcyclicchainmakesrelativetotheX-axisisconstrained to15-degree
increments.
AddingChainstoStructures
ToaddanAcyclicchaintoanexistingstructure,clickanatominthestructure.Clickanddraginthedirectionyou
wanttodrawthechain.
Specifying ChainLength
Tospecifytheexactlengthofachainbeforeyoudrawit:
1.SelecttheAcyclicchaintool.
2.Clickanexistingatomoranemptyareainadocument window.TheAddChaindialogappears.
3.Typethenumberofcarbonatomsinthechain.
4.ClickAdd.
Toaddanotherchainofthesamelengthanywhere inadocument window,<ALT>+click whereyouwantthechainto
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Objects
Usethetoolsonthemaintoolbartoaddshapestoyourdocuments. Youcantearoffthepalettesandplacethem
whereyouwantwithinyourdrawingwindow.Youcanrotateanobjectusingitsrotationhandleandscaleordistortan
objectbyusingtheresizeordistortionhandles.
Arrows
Youcanusearrowstoshowtheconversion ofreactantstoproductsandtoindicateelectronflow.Youcancustomize
arrowsnotonlyforlengthandangle,butforarrowhead widthandshape.Youcanalsodraganarrowfromitsmiddleto
createanarcofanylength.Whenyoucreateanarc,theangleofthearrowismodified.
Whenyoumouse-overanarrowwiththeLasso,Marquee,oranArrowtoolselected,theadjustment handlesappear,
forexample:
Dragtheadjustment handlestochangethearrowlength,angle,orshape.Whenchangingtheangleofanarrow,you
arerestrictedtomultiplesof15°ifFixedAnglesisenabled.Holddownthe<Alt>keytodragtoanyangle.Youcan
alsocreateanarrowbydrawinganarbitrarysplineusingthepentools,andaddinganarrowhead.
ArrowHeads
Therearethreearrowheadshapes:solid,hollow,andangled.Tochangetheshape,right-clickanarrowandchoose
theshapefromthecontextmenu.
Arrowheadsshapesare:A)Solidarrowhead;B)Hollowhead;andC)Angledhead.
ArrowTypes
ChemBioDraw offersavarietyofarctypesandarrowtypes,suchas,crossed(no-go)arrows,equilibrium arrowsof
unequallengths,andellipticalarcs.
ArcArrows
Therearetwowaystocreateanarcarrow:
1.Clickanddragthearcadjustment handleofastraightarrow.
Figure6.5:A)Arcadjustment handle
2.SelectanarcarrowfromtheArrowspalette.
Youcancustomize arcarrowsaseasilyasstraightarrows.Someexamples are:ChemBioDraw 14.0
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a.Toundoallchangesmadetoanarrowexceptforthechangeinlength,clickthearrowwiththesamearrowtool.
b.Clickanunmodified arrow,oronethathashadonlyitslengthchanged,toreverseitsdirection.
HollowArrows
Youcanrotatehollowarrowsandchangetheirlengthandwidth.Youcanalsomodifytheangleandcreatehollowarc
arrows,justaswithregulararrows.
Youcanmodifyarrowswithacontextmenucommand. Someofthesecommands arealsofoundontheCurves
menu.Usethecontextmenutocreatearrowsforwhichtherearenotools,suchasbold-dashedordipole.ChemBioDraw 14.0
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Connecting Arrows
Youcanconnectanewarrowtoanexistingarrowateitherendoratthemidpoint.
Note:Theterms“left”and“right”inthecontextmenuarerelative,andrefertothedirectionthearrowhead ispoint-
ing.
Forexample,todrawanewarrowstartingatthemidpointofanexistingarrow:
1.SelectfromtheArrowspaletteanarrowtypeforthenewarrow.
2.Placeyourcursoroverthemidpointoftheexistingarrowandholddownthe<shift>key.  Theadjustment handle
changestoasmallhighlighted rectangleandthecursorchangestothe'+'symbol.
3.Whilepressingthe<shift>key,drawthenewarrowstartingfromtheexistingarrow’smidpoint.
Youcanalsodragexistingarrowsandconnectthem.Hereareafewexamples:ChemBioDraw 14.0
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Finally,arrowscanberotatedusingtheStructurePerspective tool,aswellastheLasso,orMarquee.Formoreinform-
ationonusingtheStructurePerspective tool,see"Structure Perspective" onpage125.Combining thesemethods
letsyoudrawanunlimitednumberofarrows.
Equilibrium Arrows
Withequilibrium arrows,changingthelengthchangesbotharrowsproportionately; changingtheshapeofthearrow-
headchangesbotharrowheads identically.
Tochangethelengthofonearrow,holddownthe<Alt>key.Twonewadjustment handlesappear.Whenadjusting
onearrowofanequilibrium arrow,thearrowcannotbeextendedbeyonditsoriginallength.
CurvedArrows
YoucancurvemostarrowsfoundontheArrowstoolbar.Afteryoupasteanarrowinyourdrawing,clickanddragthe
selectionpointinthemiddleofthearrow.
Asyoudragtheselectionpoint,theangleofthearcappears,measured indegrees.
ColoredArrows
Tocoloranarrow:
1.Inthedrawingwindow,selectthearrowtocolor.
2.SelectacolorfromtheColormenu.
Coloring BlockArrows
Forblockarrows(thosethatarenotmadeofsimplelines),youcanapplycoloredeffectsusingthefilled,faded,and
shadedoptions.
Toapplycoloreffectsonblockarrows:
1.SelectablockarrowfromtheArrowspaletteandright-clicktheblockarrow.ChemBioDraw 14.0
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2.SelectacolorfromtheColormenu.
3.Fromthecontextmenu,chooseeitherFilled,Faded,orShaded.
DrawingElements
Drawingelementsaresimpleshapes,suchas,circlesandrectangles.
1.Togroupdrawingelementswithastructure,navigatetoObject>Group.See"Grouping Objects"onpage85.
2.Tomoveanobject,selectit,andclickanddragitwithaSelectiontool.See"MovingObjects"onpage83.
CirclesandOvals
Todrawacircleoranoval:
1.SelectoneoftheCircleorOvaltools.
2.Pointwhereyouwantthecenterofthecircleoroval.
3.Dragoutwardfromthecenter.
ResizingandRotating
Youcanresizeandreshapeovalsandrectangles forbothlengthandwidth.Circleshaveonlyaradiusadjustment.
Rectangles alsohavecornerhandlesthatproportionately adjustlengthandwidth.
Figure6.6:A)rectanglecornerhandles
1.Pointtoashapewithitsdrawingtool,oraselectiontool,todisplayadjustment handles.
2.Clickanddragtomodifytheshape.
Lines
Lineslooksimilartobonds,butbehavedifferently:
Linesarenotincludedinchemicalinterpretation.
Linesthatcrossappearsolid,bondsdonot.
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1.IntheDrawingElementstoolbar,selectalinetool.
2.Clickanddraginthedrawingwindowwhereyouwanttheline.
Arcs
Youcandrawsolidordashedarcsofdifferentangles:90°,120°,180°,and270°.
Todrawanarc:
1.Dooneofthefollowing:
InChemDraw Standard, pointtoanArctoolanddraginthepalettetoselecttheangle.
InotherChemBioDraw applications, pointtotheDrawingElementstoolanddraginthetoolpalettetoselectthe
angle.
2.Dragfromlefttoright(foraconvexarc),orfromrighttoleft(foraconcavearc).
EditingArcs
Toresizeorrotateanarc:
1.PositiontheArctooloverthearc.Dragpointsappearontheendsandinthemiddle.
2.Drageitherendofthearctochangeitslength.
3.Dragthecenterpointtochangethecurvature.
4.Useaselectiontooltochangeitssizeororientation.
NavigatetoView>ShowInfoWindowtodisplaytheinfowindow.TheInfowindowindicatesthedistancebetween
theendsofthearcandtheangletheclockwise endmakeswiththeX-axis.
Whenyoudragtheresizehandle,theInfowindowindicatesthepercentage asenlargedorreduced.Whenyoudrag
theRotationhandle,theInfowindowindicatesthedegreerotated.Formoreinformation aboutInfowindow,see"The
InfoWindow"onpage84.ChemBioDraw 14.0
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Brackets
Bracketsincludesbraces{ },brackets[ ],andparentheses ( ).Bracketsarecommonly usedtoillustratepolymers. For
moreinformation onpolymers, see"Polymers" onpage243.
Singlebrackets
Youcandrawasinglebracketinanyorientation. SelectasinglebrackettoolfromtheBracketspalette.
1.Pointwhereyouwantthebrackettostart.
2.Dragfromoneendofthebrackettotheotherend.
PairedBrackets
Pairedbracketscanbeplacedonlyinaverticalorientation. Arectangleorboxdefinestheirposition.
Todrawpairedbrackets:
1.SelectapairedbrackettoolfromtheBracketspalette.
2.Pointwhereyouwantacornerofthebracket.
3.Dragdiagonally fromonecorneroftheboxtotheoppositecorner.
Daggers
Todrawadagger:
1.SelectadaggertoolfromtheBracketspalette.
2.Clickinthedrawingwindow.
Note:Toresizeadagger,selectthedaggerandclickanddragoneofitsresizehandles.
FramingObjects
Youcanencloseyourdrawingsorgroupstructures witharectangle, brackets,parentheses, orbraces.
Toencloseyourobject:
1.Selectthedrawingtoenclose.
2.NavigatetoObject>AddFrameandselectaframetype.
PenTools
Thepentoolsareusefulfordrawingfreehandcurvesandshapes.
Todrawacurve,dooneofthefollowing:
SelecttheDrawCurvetoolfromthePenToolspaletteontheMaintoolbarandclickanddragyourcursoracross
thedrawingwindow.
NavigatetoView>OtherToolbars>PenTools.SelecttheDrawCurvetool,andclickanddragyourcursor
acrossthedrawingwindow.
EditingCurves
Youcaneditacurvebyselectingitandmanipulating itwithEditCurvetool.ChemBioDraw 14.0
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Toselectanexistingcurveforediting:
1.SelecttheEditCurvetoolfromthePenToolspaletteontheMaintoolbar.
2.Pointatthecurve.Thecursorwillchangefroma“+”toanarrowwhenyouarepositioned correctly.
3.Clicktoselectthecurve.Thecurveisselectedandadjustment handlesappearalongthecurve,asshownbelow:
Thecursorappearsasahandwitha“+”signinside
.However, whenthecursorispositioned exactlyoverthe
pointsonthecurve,the'+'symboldisappears andthecursorappearsasahand.
Changing theShapeofaCurve.Usethesquarehandlesattheendofthecurvetoincreaseordecreasethelength
ofthecurve.Usetheendpoints ofthedirectionlinestochangethedirectionofthecurve.
Tochangetheshapeofacurve:
Dragthedirectionlinestocreatetheshapeyouwant.
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AddingaSegment.YoucanaddasegmenttoanexistingcurvebyselectingthecurvewithEditCurvetool,and
clickinginthedocument windowwiththeEditCurvetoolselected.Asegmentisaddedtotheendofthecurve.
Freehand Shapes
Tocreateaclosedfreehandshape,drawacurveandnavigatetoCurves>Closed.Toaddcurveproperties, select
Filled,Faded,orShadedundertheCurvemenuorintheCurvetoolbar.Curvescanalsohavearrowheads, which
letsyoucreatearbitrarily-shapedarrows.Toaddcolor,selectacolorintheColormenu.
Figure6.7:Afreehandcurvewithdifferentproperties; A)Asimplecurve;B)enclosed; C)filled;D)faded;andE)
shaded.
Selecting Objects
UsetheLassoforfreehandselections andtheMarqueetoselectrectangular regions.
Whenyouselectastructureorobject,theselectiondisplayswithacoloredframearoundit.Theframeincludes
handlesforrotating,distorting, andresizingyourselection.
TheLassoTool
UsetheLassotooltomakeafreehandselectionofirregularareas.
ToselectobjectsusingtheLassotool:
1.SelecttheLassotool.
2.Pressthemousebuttonwhilethepointerisnotoveranyobject.
3.Dragaroundpartofastructureorotherobject.
Asyoudrag,alineappearsthatdefinestheselectionarea.Bonds,structures, orotherobjectsareselectedonlyif
theyareentirelywithinthisarea.ChemBioDraw 14.0
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TheMarqueeTool
UsetheMarqueetooltoselectobjectsandstructures withinarectangular area.
1.SelecttheMarqueetool.
2.Clickanddragdiagonally overthestructures orotherobject.
Asyoudrag,arectangleappearsthatdefinestheselectionarea.Objectsareselectedonlyiftheircenter,oramajor
portionoftheobject,ortheobjectisentirelywithinselectionrectangle.
Tosetoneselectiontooltobehaveliketheother,clickeitheroneofthetoolswhilepressing<Alt>.
Totoggleaselectiontoolandthelastdrawingtoolused,press<Control>+<Alt>+<Tab> .
Selecting EntireStructures
Toselectanentirechemicalstructure,double-click abondoratominthestructureusingaselectiontool.
Ifthechemicalstructureorotherobjectispartofagroup,thegroupisselected.
Selecting ObjectsbyClicking
1.SelecttheLassoorMarqueetool.
2.Pointtoanobjectinadocument window.
Ahighlightboxappearsoverthepointedobject.
3.Clicktheobject.
Theselectedobjectsappearwithintheselectionrectangleandthecursorchangestoahand.
Note:Youcanalsoselecttheindividualobjectsinagroup.See"Grouping Objects"onpage85.
Selecting MultipleObjects
Whenyouselectmultipleobjects,eachobjectdisplaysaselectionbox.
Toaddmoreobjectstotheselection, press<shift>andselecttheotherobjects.
Toselectallobjects,navigatetoEdit>SelectAll.
Deselecting AllObjects
Todeselectallobjects,dooneofthefollowing:
Clickanemptyareaoutsidetheselectionrectangle.
Press<esc>.
Selectadifferenttool.
Selectanotherobjectwithoutholdingdownthe<shift>key.
Deselecting OneObject
Todeselectoneofseveralselectedobjects,holddownthe<shift>keyandclicktheobjectwithaselectiontool.
Note:Asshowninthefigurebelow,objectsmayappearwithinthebordersoftheselectionrectangle, butnotbe
selected.Notethatthecentralringintheexamplebelowisnotselected.ChemBioDraw 14.0
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ResizingObjects
Youcanresizeobjectsbydraggingtheresizehandleofaselectedobjectorbyscaling.
Toresizeaselectedobjectproportionately:
1.Selecttheobjectstoresize.Theresizehandleislocatedinthelowerrightcorneroftheselectionrectangle.
2.PointtotheResizehandle.Thecursorbecomesadouble-headedarrow.
3.Dragtheresizehandleuntiltheobjectisthesizeyouwant.
Inmostcases,whenyouresizeanobject,theaspectratiooftheobject(theratiooftheheighttowidth)doesnot
change.However, itispossibletodistortcertainobjectsincludingchemicalstructures, circles,boxes,andovals.
Todistortanobjectinthehorizontal orverticaldirection:
1.Selecttheobject
2.Dooneofthefollowing:
Dragthehandleonthedesiredside
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<Shift>+drag theResizehandleinthedesireddirection.The<shift>keymodifiestheresizeoperationsothat
youcandistortobjectsalongtheX-axisorY-axis.
RotatingObjects
1.Selectanobjecttorotate.Forobjectsthatcanberotated,therotationhandleappearsatthetopoftheselection
rectangle.
2.Dragtherotationhandleclockwise orcounterclockwise.
3.Torotateanatomlabelwithastructure,pressthe<control>keywhiledraggingthestructure.
Note:Ifasingleatomisunselected whenastructureisrotated,thestructurerotatesaroundtheunselected atom,
asshownintheexamplebelow:
Torotateaselectedobjectbyaspecifiedangle:
1.Dooneofthefollowing:
NavigatetoObject>Rotate.
Double-click therotationhandle.TheRotateObjectsdialogappears.
2.EnteranumberandclickeitherdegreesCWforaclockwise rotationordegreesCCWforcounterclockwise rota-
tion.
3.Torotatetheatomlabeltext,selectRotateAtomLabels.
4.ClickRotate.Objectsarerotatedaroundthecenteroftheselectionrectangle.
Torepeatthesamerotationonanyobjectinthedocument window:
1.Immediately afterrotatinganobject,selecttheotherobjectstorotate.
2.NavigatetoEdit>RepeatRotate.
MovingtheCenterofRotation
Bydefault,anobjectturnsarounditscenterwhenyourotateit.However, youcanmovethecenterofrotationsothat
theobjectrotatesaroundanatomorsomeotherlocationonthepage.
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1.Selecttheobject.Acenterofrotationindicator(‘+’)appearsinthecenteroftheobject,asshowninthefigure:
Figure6.8:A)Centerofrotation
2.Whilepressingthe<alt>key,clickanddragtheindicatortoanotherlocation.Seetheexamplebelow:
Figure6.9:B)centerofrotationmoved
3.Torotatetheobject,clickanddragtherotationhandle.
Toresetthecenterofrotationtoitsdefaultposition,deselecttheobject.
Note:Ifyoudragclosetoanatom,thecenterofrotationwillsnaptotheatomposition.
MovingObjects
1.Selectanobjecttomoveusingaselectiontool.
2.Clickanddragtheobjecttoanewlocation.
Toconstrainthemovement tothehorizontal orverticaldirection,<shift>+drag theselectedobjects.
Smallincremental movements areoftenusefulforaligningobjects.
Tomoveanobjectaincrementally:
1.Selecttheobject.
2.Pressanarrowkey.Theselectedobjectmoves1pointinthedirectionofthearrow.
Note:Tomoveinalargerincrement, holddownthe<alt>keywhilepressinganarrowkey.Theselectedobjects
moves10pointsinthedirectionofthearrow.
CopyingObjects
1.Selectoneormoreobjects.
2.<Control>+drag theobject(s)tocreateacopyandpositionit.ChemBioDraw 14.0
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Toconstrainthecopytomoveonlyverticallyorhorizontally whilepositioning it,holddownthe<shift>+<control>
keys.
TheInfoWindow
Thiswindowdisplaysthesizeandpositionofthepointerandofanythingyouhaveselected.Toshow,orhide,thewin-
dow,navigatetoView>ShowInfoWindow.
Pointer
XandYdisplaythecurrentmousecoordinates. dXanddYindicatethechangeinXandYofamovedselection.
Selection
XandYdisplaythepositionofaselection. WandHarethewidthandheight.
Other
Angleistheangleofabondorrotationofaselection. Dististhebondlengthorthedistanceaselectionhasmoved.
Whenresizinganobject,%indicatesthecurrentpercentage oftheoriginalsize.
MirrorImages
Youcanreflectstructures throughplanesperpendicular totheX-axisorY-axis.Bycopyingastructure,youcancreate
itsmirrorimagetocreatestereoisomers.
Tocreateamirrorimage:
1.Drawastructurewithdefinedstereochemistry, forexample,wedgedbonds.
2.<control>+drag thestructuretocopyit.
3.Withthecopystillselected,navigatetoObject>FlipHorizontal orFlipVertical.YoucanalsousetheFlipHori-
zontallyorFlipVerticallytoolsontheObjecttoolbar.ChemBioDraw 14.0
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DeletingObjects
Todeleteselectedobjects,dooneofthefollowing:
Pressthe<delete>key.
NavigatetoEdit>Clear.
UsetheErasertool.
JoiningStructures
Tojointwostructures sothattheyshareabond:
1.Selectabondinthefirststructure.
2.<Shift>+click toselectthebondinthesecondstructure.
3.NavigatetoObject>Join.
Tojointwostructures sothattheyshareanatom:
1.Positionthetwochemicalstructures sothattheatomsyouwanttofuseareneareachother.
2.Selectthetwoatomstobejoined.
3.NavigatetoObject>Join.
Note:Whenyoujointwodifferently coloredbondsoratomlabels,thecolorofthefrontobjectbecomesthecolorof
theresultingjoinedobject.Whenyoujointwoatomsthatarelabeled,thefrontatomlabelbecomestheatomlabel
oftheresultingatom.Formoreinformation aboutfronttobackorderingofobjects,see"PageLayout"onpage10.
Grouping Objects
Agroupisacollectionofobjectsthatactasasingleobject.Youcanselectallgroupedobjectsbydouble-clicking on
anyofthecontained objectswithaselectiontool.
Whenyougroupobjectssothattheindividualobjectsinthegroupcannotbeselected,youcreateanintegralgroup.
Whenyouselectanyobjectinanintegralgroup,theentiregroupisselected.Objectswithinanon-integralgroupcan
beselectedindividually andmanipulated whilestillremaining partofthegroup.
Youcanchangethepositionororientation ofgroupedobjects.Individualobjectswithinthegroupmaintaintheirrel-
ativepositionswhenthegroupedobjectsarerotated,aligned,ordistributed.
Atomsandbondsmakingupasinglechemicalstructurearealwaysgrouped.Ifyougrouppartofastructurewithother
objects,theresultinggroupcontainstheentirestructure.Ifyouaddatomsorbondstoagroupedstructure,thenew
atomsandbondsarepartofthegroup.
Togroupobjects:
1.Selecttheobjectsusingaselectiontool.
2.NavigatetoObject>Group.
Toselectanindividualobjectwithinagroup,movetheselectiontoolovertheobjectuntilitishighlighted, andclick
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Toselectgroupedobjects,movetheselectiontooloveranobjectinthegroupuntilitishighlighted, anddouble-click
it.
Ungrouping Objects
Toungroupobjects:
1.Selectagroup.
2.NavigatetoObject>Ungroup,orright-clickthegroupandselectGroup>Ungroup.
Tocreateagroupsothatindividualobjectscannotbeselected(integralgroup):
1.Selecttheobjects.
2.NavigatetoObject>Group.
3.Right-clickthegroupandselectGroup>Integral.
Torestoreanintegralgrouptoaregulargroup:
1.Selecttheintegralgroup.
2.Right-clickthegroupanddeselectGroup>Integral.
Note:Manyoftheshapesanddrawingswithinthetemplatedocuments areintegralgroups.However, theycanbe
ungrouped andedited.
Scalingobjects
Toscaleoneormoreobjectstoadifferentsize:
1.Selecttheobject(s).
2.Dooneofthefollowing:
GotoObject>Scale.
Double-click aresizehandle.TheScaleObjectsdialogappears.
3.Dooneofthefollowing:
ToscalebondssothattheFixedLengthbecomesthenewmedianbondlength,selectScaleselectedobjectsso
thatmedianbondisFixedLength(0.4167in).ChemBioDraw 14.0
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Toscalethebondstoanewfixedlengththatyouspecify,selectScaleselectedobjectssothatmedianbond
is,andtypethenewmedianbondlengthinthetextfield.
Toscaletheobjecttoapercentage ofthecurrentsize,selectScaleby,andspecifythepercentage inthetext
field.Avaluegreaterthan100%enlargesit;avaluelessthan100%reducesit.
4.ClickScale.
Centering Objects
Tocenteranobject(orgroupofobjects)onthepage:
1.Selecttheobject.
2.NavigatetoObject>CenteronPage.
Theselectedobjectmovessothatthecenteroftheselectionrectangleisatthecenterofthepage.
AligningObjects
Youcanalignobjectsverticallyandhorizontally alongtheircentersoredges.
Note:Objectsarealignedwiththeselectedobjectthatappearshighestonthepage.
Toaligntwoormoreobjects:
1.Selecttheobjects.
2.NavigatetoObject>Align.
Note:Ifyouselectonlypartofastructureorgroupwithaselectiontool,onlythatpartisusedforthealignment,
buttheentirestructureorgroupmoves.
Distributing Objects
Usethedistributecommand todistributeobjectshorizontally orverticallyandatanequaldistanceapart.
Todistributethreeormoreobjects:
1.Selecttheobjectstodistribute.
2.NavigatetoObject>Distribute ,andchooseVertically orHorizontally .
Figure6.10:Distributing objects
Thespacebetweentheobjectsisequalized. Theupper,lower,right,andleftpositionsofobjectsinyourselection
remainunchanged.ChemBioDraw 14.0
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CleanUpStructure
TheCleanUpStructure command isusedtoneatentheappearance ofmolecules byregularizing bondlengthsand
angles.Graphicobjects,suchasarrowsandaromaticcircles,arenotaffected.Youcanusethiscommand toredraw
structures thatyoumayhavedrawnfreehand,ortoneatenstructures thatyoumayhaveimportedfromanotherapplic-
ation.
Forcertaincompounds, theCleanUpStructure command producesastructurethatextendsbeyondtheboundsof
thepage.Toviewtheentirestructure,scalethestructureorincreasethesizeoftheprintedpage.See"Scaling
objects"onpage86and"PageSetup"onpage12.
TheCleanUpStructure featurefollowstheserules:
BondsaresettothetargetFixedLengthspecifiedinthedocument settings.Formoreinformation, see"Document
Settings"onpage38.
Aringisredrawnonlyifallofitsbondsareselected.
Multi-attachedatomlabels,variableattachment points,andmulti-centerbondscannotbecleaned.
Structures arerotatedsothatasmanybondsaspossiblearedirectedatamultipleof15degrees.
CleanUpStructurepreserves stereochemical meaningratherthanthepreciseidentityofwedged,orhashed
bonds,asshownbelow.
TouseCleanUpStructure:
1.Selectthestructure,orpartofthestructure,tocleanup.
2.NavigatetoStructure>CleanUpStructure,ortype<shift>+<ctrl>+<K> .
Note:TheCleanUpStructurecommand redrawsyourstructureiniterations. Therefore, youmayneedtoselect
thecommand morethanonce.ChemBioDraw 14.0
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Youcanalsocleanupareaction,orabiopolymer. Formoreinformation, see"CleanUpReactions" onpage130and
"CleanUpBiopolymers" onpage106
Checking Structures
Youcancheckthechemistry ofaselectedstructure,partofastructure,orcaption(inFormulastyle)withtheCheck
Structure command. Thestructureischeckedusingnormalvalencesandelements, anddefinednicknames.
Tocheckthevalencesofallselectedatomsinastructure:
1.Selectastructure,partofastructure,orcaption.
2.NavigatetoStructure>CheckStructure.
Ifastructureisincorrect,amessagewindowappears,forexample:
3.Tocontinuecheckingthestructure,clickIgnore.
4.Toignoreallsubsequent errors,clickIgnoreAll.
5.Tostopcheckingforerrors,clickStop.
Checking CopiedStructures
Toautomatically performacheckstructureanalysiseachtimeyoucopyastructurefromtheclipboard:
1.NavigatetoFile>Preferences .
2.FromtheGeneraltab,clickCheckStructure WhenCopyingtoClipboard orExporting .
Thischangeaffectsalldocuments.
Chemical Warnings
ChemBioDraw checkschemicalsyntaxasyoudraw.Ifitfindsanerrorinyourstructure,awavyredboxappears
aroundtheobject.Theboxdisplaysonthescreenonlyanddoesnotprint.
Disabling Chemical Warnings
Warningsdisplaybydefault.Todisablechemicalwarnings, navigatetoView>ShowChemical Warnings .ChemBioDraw 14.0
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Todisableerrorcheckingonaspecificobject,right-clicktheobjectanddeselectDisplayWarnings onthecontext
menu.
WhenDisplayWarningsisdisabledforanobject:
Aredboxdoesnotappeararoundtheobject.
ProblemsarereportedbytheCheckStructurecommand (Navigate toStructure>CheckStructure).
Toviewadescription oftheproblem,performoneofthefollowing:
Pointatthewarningwiththemousetodisplayatooltipthatdescribes theerror.
Right-clickthewarningandselectExplainThisWarning.
SelectthestructureandnavigatetoStructure>CheckStructure.
WarningPreferences
Toselectwhichtypesofchemicalwarningstodisplay:
1.NavigatetoFile>Preferences .
2.ClicktheWarnings tab.
3.SelectthetypesofwarningsandclickOK.
Thetypesofwarningsarelistedbelow:
Warning Description
ValenceandCharge
ErrorsAnObjectdrawnhasanimpropervalenceorcharge.Forexample,whenpositiveandneg-
ativechargeshavebeenassignedtothesameelement,chargeshavebeenassignedin
morethanoneway,orachargehasbeenassignedtoanickname, genericnickname, or
alternative groupname.
Unbalanced Par-
enthesesParentheses arenotmatchedintonestedopen-closepairs.
InvalidIsotopesGenerated forinvalidisotopes.Forexample,thiswarningisgenerated foreverylabelthat
hasanumericsuperscript immediately preceding anatomicsymbol,wherethesuper-
scriptednumberdoesnotcorrespond toarecognized isotope.Forexample,24CH3.
IsolatedBonds Anunlabeledsinglebondisnotattachedtootherbonds.
AtomsNearOther
BondsAnatomisclosetoabondbutnotattachedtoit.
Unspecified Stereo-
ChemistryAnasymmetric centeriswithoutattachedwedged,hashed,dashed,orboldbonds.
Ambiguous Ste-
reochemistryAstereocenter wheretheabsolutestereochemistry cannotbedetermined fromthestruc-
tureasdrawn.Forexample,thiswarningwouldbegenerated foracarbonatomattached
byboldbondstofourdifferentligands.ChemBioDraw 14.0
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Warning Description
Stereobond between
ChiralAtomsAstereobond connectstwostereocenters.
LinearAtomAnunlabeledatomisattachedtoexactlytwoidenticalbondsthatcreatea180degree
angle.ChemBioDraw 14.0
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BioDraw(Ultrafeatureonly)
ChemBioDraw includesavarietyoftoolsfordrawingmetabolic pathways, suchasenzymesandreceptors. Todis-
playtheBioDrawtoolbars,navigatetoView>ShowBioDrawToolbar.
Youcanalsoincludestandardshapes,suchas,circles,ellipses,andarrows,usingtheDrawingElementstoolpalette
ortheArrowstoolpalette.YoucanalsocreatecustomshapesusingtheCurvetool.
Youcanchangethecolorofanobject,changeitslineandfillproperties, androtateit.
TocreateaBioDrawobject,eitherclickordragonthepagewhereyouwantittoappear.Clickinggivesyouthedefault
sizeandshape,draggingletsyounotonlyscaletheobject,butalsodistortitbydraggingontheXandYaxes.Linear
objectselongateinthedirectiontheyaredragged.Themembrane andproteintools(DNAandhelix)addmoresub-
unitsastheyaredraggedanddisplaythesubunitcount.Youcanalsoungroupanobjectandmove,orremove,
unwanted partsandretainonlythosepartsoftheobjectthatyourequire.
Toungroupanobject:
1.Fromthecontextmenu,navigatetoGroup>Integral.
2.SelectGroup>Ungroup.Theobjectisungrouped andyoucanmoveeachobjectindependently.
BioDrawTemplates
ChemBioDraw Ultraincludesavarietyoftemplates forillustrating biologicalsystemsinfullcolorforpublication.
1.Toopenatemplate:
2.NavigatetoView>Templates .
Selectthetemplatetoolbaryouwant.SomeoftheavailableBioDrawtemplates areshownbelow.ChemBioDraw 14.0
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Advanced BioDraw
Anatomy Templates
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Animals
BioInstruments
Microorganisms
Organelles
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Formoreinformation, see"Templates" onpage136.
Customizable Objects
Thetablebelowdescribes theBioDrawobjectsintheBioDrawtoolbar,whichcanbecustomized. Whencustomizing
aBioDrawobject,youmustuseaselectiontool,orthesametoolusedtocreateit.
Tool Customization Options
Receptor width
G-protein,gamma
subunitshape
HelixProtein height,widthofthestrands,widthofthecyl-
inders,spacing
DNA height,widthofthestrands,offsetofthe
secondstrand,spacing
Membrane (line) sizeofsubunit
(Theoveralllengthremainsconstant,andthe
numberofsubunitschangesininversepro-
portiontothesize.)
Membrane (arc) length,arc,sizeofsubunit
Membrane
(ellipse)sizeofsubunit
Micelle sizeofsubunit
Plasmidmap add/adjust markersandregions
Ribosomes resize,color
tRNA resize,color
ThesetoolsintheBioDrawtoolbarcannotbecustomized:
Ionchannel G-protein,alphasubunit
Ionchannel G-protein,betasubunit
Immunoglobulin Golgibody
Endoplasmic
reticulumMitochondrion
Cloud resize,colorChemBioDraw 14.0
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Membrane Line
1.Selectthemembrane linetoolfromtheBioDrawtoolbar.
2.Clickanddragtodrawamembrane lineofthesizeyouwantorclickforthedefaultsize.
Whenorientingthemembrane, notethatyouareconstrained to15degreeincrements whenfixedanglesareapplied
(navigatetoObject>FixedAngles).Tooverridetheconstraint, press<shift>keyasyoudrag.
Toresizethemembrane units,clickanddragtheadjustment handleatthemembrane center.
Tip:Tochangethelength,selectthemembrane anddragtheleftorrighthandleoftheselectionbox.Youcan
deselectitandreadjustthesubunitsize.
Membrane Arc
Tocreateamembrane arc,clickanddraginacurveusingtheMembrane ArctoolintheBioDrawtoolbar.
Thetoolhasthreeadjustment handles:
Thehandleatthestartingpointcontrolsthelength.
Thecenterhandlecontrolsthesubunitsize.
Thehandleattheleadingedgecontrolsthearc.
HelixProteins
Tocreateahelixprotein:
1.SelecttheHelixProteintoolfromtheBioDrawtoolbar.
2.Draginthedocument window,orclicktodrawthedefaultsize.
Whenorientingtheprotein,notethatyouareconstrained to15degreeincrements whenfixedanglesareapplied(nav-
igatetoObject>FixedAngles).Tooverridetheconstraint, press<shift>keyasyoudrag.ChemBioDraw 14.0
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Thehelixproteinhasfouradjustment handles:height,widthofthestrands,widthofthecylinders, andspacing.
Figure7.1:Adjustment handlesonahelixprotein.A)heightadjustment; B)widthofstrands;C)widthofcylinder;and
D)spacingbetweencylinders.
DNAMolecules
TocreateaDNAmolecule:
1.SelecttheDNAtoolfromtheBioDrawtoolbar.
2.Dragintheworkspace,orclicktodrawthedefaultsize.
WhenorientingtheDNA,notethatiftheFixedAnglesoptionontheObjectmenuisselected,youareconstrained to
15degreeincrements. Youcanoverridethedefaultbypressing<alt>keyasyoudrag.
DNAhasfouradjustment handles:height,widthofthestrands,offsetofthesecondstrand,andspacing.
Coloring Residues
AfteryoudrawaproteinorDNAstrand,youcancoloreachresidueusinganyofthecoloringtools-shading,fading,or
filled.
1.UsingtheMarqueeorLassotool,selectaresiduetocolor.
2.SelectthedesiredcolorfromtheColormenu.
3.OntheCurvesmenu,selecteitherFilled,Shaded,orFaded.
tRNA
TocreateatRNAmolecule:
1.SelectthetRNAtoolfromtheBioDrawtoolbar.
2.Clickanddragintheworkspace untilthetRNAobjectisthedesiredsize.
OnceyoudrawthetRNAmolecule, youcanmodifyitaccordingly.ChemBioDraw 14.0
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Ribosomes
TodrawaRibosome:
1.OneithertheRibosome orBioDrawtoolbar,selectaRibosome tool.
2.Clickanddragintheworkspace untiltheRibosome objectisthedesiredsize.
Onceyoudrawtheobject,youcanmodifyitsappearance.
PlasmidMaps
Todrawaplasmidmap,youfirstenterthenumberofbasepairsyouwantyourmaptorepresent, andthenaddmark-
ers.AsimplepBIplasmidmapisshownbelow.
CreatingaPlasmidMap
1.FromtheBioDrawToolbar,selectthePlasmidMaptool.
2.Clickinthedrawingwindowwhereyouwanttheplasmidmap.TheInsertPlasmidMapdialogappears.ChemBioDraw 14.0
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3.IntheInsertPlasmidMapdialog,enterthenumberofbasepairsinthemap,andclickOK.Theplasmidmapis
drawn.
AddingRegions
Regionsrepresentthefragments intheplasmid.Youcanaddasmanyregionsyouwanttoyourmap.
Toaddregions:
1.Right-clicktheplasmidmapandselectRegionsinthecontextmenu.
2.IntheRegionsdialog,enterthebasepairsnumbersforthestartandendofthefragmentintotheirrespective fields.
Forexample,ifafragmentincludesallbasepairsfrom1to1000,type1and1000inthetextfields.
3.FortheStartandEndbasepairnumbersforthefragmenttoappearinthedrawing,selectAddMarkersAt
RegionEnds.
4.ClickAdd.
5.Toaddadditionalregions,repeatsteps2-4.
6.ClickOK.
AddingMarkers
Markersletyouannotatebasepairsintheplasmidmap.Forexample,tolabelabasepairorfragment,addamarkerto
it.
Toaddamarker:
1.Right-clicktheplasmidmapandselectMarkersinthecontextmenu.
2.IntheMarkersdialogbox,enterthenumberofthebasepairforwhichyouwanttoaddamarkerinthePosition
box.
3.IntheLabeltextbox,enterthetexttoidentifythemarker.
4.ClickAdd.
5.ClickOK.
MovingMarkers
Tomoveamarkerlabel,clickanddragthelabel.Youcanalsoeditthevalueinthelabel.
ResizingRegions
Youcanresizeregionarrowstoindicatedifferentbasepairs,orextendthemoutwardtoemphasize them.
1.Hoverovertheendoftheregion’sarrowusingaselectiontool.Thearrow’sresizehandlesappearandthecursor
changestoadouble-arrow(
).
2.Clickanddragaresizehandletoadjustthesizeofthearrow.ChemBioDraw 14.0
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Toextendanarrow,clickanddragitscenterhandleasindicatedbythecursor(
)inthefigureabove.
Enhancing theDrawing
Aplasmidmapislikeanyotherdrawing.Youcanaddcolorandaddshadetoit,changelinewidths,ormodifyitstext.ChemBioDraw 14.0
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DrawingBiopolymers
Biopolymers arecomplexmolecular assemblies thatadoptpreciseanddefinedshapesandstructures. Theirdefined
shapeandstructureareinfactkeystotheirrole.Biopolymers arechain-likemolecules madeupofrepeatingchemical
blocksandcanbeverylonginlength.Biopolymers areclassifiedinthreegroups,depending onthenatureofthe
repeatingunittheyaremadeof:
Polysaccharides aremadeofsugars
Proteinsofaminoacids
Nucleicacidsofnucleotides
ChemBioDraw providesafriendlyinterfaceallowinguserstodrawbiopolymers andcreatesequences easily.Using
theBiopolymer editor,userscandrawpolypeptides andnucleotide sequences usingpre-definedlabelsassignedto
nucleicandaminoacids.Youcanexpand,contract,orremovelabelstocompletethedrawing.
TodisplaytheBiopolymer toolbar,navigatetoView>Show Biopolymer Toolbar.TheBiopolymers toolbarappears:
TheBiopolymers toolbarincludesthefollowingoptions:
Biopolymer Editor:Enablesallthenucleicandaminoacids
SingleLetterAminoAcid:Enablesalltheaminoacids
BetaAminoAcids,L-AminoAcids,D-aminoAcids:EnablesadditionofBeta,L-,andD-aminoacids
DNASequence :Enablesthedeoxyribonucleotides thatcanbeusedtocreateaDNAmolecule
RNASequence :Enablestheribonucleotides thatcanbeusedtocreateaRNAmolecule
Todrawasequence:
1.SelectoneofthesetoolsfromtheBiopolymer toolbar:
AA1tool(Single-letteraminoacidtool).Createapolypeptide chainusingaone-letterlabeltorepresenteach
aminoacid.
Youcancreatethesequences bytypingtheIUPACcodeforthestandardaminoacids,orbypressingtheiconsonthe
toolbar.Bydefault,Lamino-acidsarecreated.Single-lettersequences aredrawnwithafixedseparation, sothat
residuesalignwithresiduesinadjacentrows.YoucancreateD-aminoacidsusingtheDaminoacidstereochemistry
option.
Single-letterD-aminoacidsaredisplayedinlowercase.Three-letterDaminoacidshavetheprefix"D-".ChemBioDraw 14.0
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Note:The<SHIFT>keyactsasatoggle.Hence,toenterD-aminoacids,press<SHIFT>whileenteringasingle-
lettersequence whileinLmode.Alternatively, toenterL-aminoacidswhileinDmode,press<SHIFT>whileenter-
ingasingle-lettersequence.
Note:Youcanenterthree-letteraminoacidsusingthe"Biopolymer Editor"onpage102,andyoucanuseeither
thekeyboardortoolbartoenterresidues.
DNAtool.CreateaDNAchainusinglabelsthatrepresenteachofthenucleicacids.
RNAtool.CreateanRNAchainusingnucleicacidlabels.
2.Clickwhereyouwanttostartthesequence. Atextboxappears.
3.Inthetextbox,enterthesingle-letterlabelfortheresidue.
Note:Foralistofresiduelabels,see"IUPACCodes"onpage111.
4.Repeatstep2foreachresidue.
5.Whenyourchainiscomplete, press<ENTER>,or<Esc>.
Bydefault,whencreatingasequence, newresiduesareinsertedafterthecurrentactiveresidue.Theinsertionpointis
indicatedbyanorangechevron.Youcanoverwriteorreplaceasequence atomusingtheresiduereplacement button.
Youcanalsoreplaceasequence atombyhoveringoveraresidueandpressingahotkey,whennoactiveresidueis
present.
Biopolymer Editor
TheBiopolymers toolbarcontainsatoolcalledBiopolymer Editor.
Usingthebiopolymer editor,youcancreateasequence byexplicitlyspecifying theresiduenameinsteadofthe
IUPACcode.Whenyouenteraletter,theauto-completion featuresuggestsamatchwithaknownresidueinthelib-
rary.Forexample,whenyouenter'a',theresidue'Ala'issuggested. Toacceptthesuggestion, press<SPACE> or
<ENTER> key.PressTABtomovethecarettotheendoftheselectedlabel.
Toenterbaminoacids,typeanickname suchasbAla.The‘b’isconverted tothebsymbol.Youcanalsocreateb
aminoacidsusingtheb-aminoacidbuttoninthebiopolymer editor.b-aminoacidsalwaysdisplayusingthree-letter
codes.Glycinedoesnothaveabetacarbon,andsothereisnobetaversion.
ToenterD-aminoacids,specify"d-"beforetheresiduename.GlycineisalsoachiralandsodoesnothaveaDver-
sion.
Note:UsetheD-aminoacidandb-aminoacidbuttonssimultaneously toproduceD-baminoacids.ChemBioDraw 14.0
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Youcanalsooverwriteandreplacethesequence atomsusingtheresiduereplacement buttoninthebiopolymer
editor.Formoreinformation, see"Replacing Residues" onpage109.
ToggleAminoAcids
ToggleAminoAcidStyleAA1<->AA3optionletsyouchangetheaminoacidrepresentation fromsingleletterto
tripleletterandviceversa.Forexample,
1.Selectthesequence.
2.Right-clickandselectTogglefromAminoAcidStyleAA1<->AA3.
Youcanalsochangetheaminoacidrepresentation ofexpanded, substituted, andprotectedaminoacids.For
example,
TheToggleAminoAcidStereoL<->Doptionletsyouchangethestereochemistry oftheaminoacidfromLtoD
andviceversa.
Totoggleaminoacids:
1.Selectthesequence.
2.Right-clickandselectToggleAminoAcidStereoL<->D.
Protecting Groups
Youcanaddprotecting groupssuchasTrtandFmoctoaminoacidscontaining additionalNH2orOHgroups(Arg,
Aad).Protected groupsarespecifiedwithinbrackets’()’.
Toaddaprotecting group:
1.Inasequence, enter‘(‘ afteracompleted residuenameasshownbelow:
2.Enterthenameoftheprotecting groupandenter‘)’attheendofthename.
Thenameoftheprotecting groupdetermines ifitwillprotecttheNH2orOHgroup.IfprefixedbyO,thenitprotectsthe
OHgroup.
Youcanexpandandcontractprotectedresiduesjustlikeanyotherresidue.ChemBioDraw 14.0
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Ifnoleavinggroupisfound,afteryouenter’)’,adialogpromptsyoutospecifytheattachment point.
Youcanexpandandcontractprotectedresiduesjustasanyotherresidues.
PastingSequences
Youcanpastesequences inFASTAformat.Sinceonlysingle-letterIUPACcodesarepresentintheFASTAformat,
youmustindicatewhetherthiscorresponds toapeptide,DNA,orRNAbiopolymer sequence. YoucanpasteALL
IUPACsymbolsforresidues,withtheexception ofthosecharacters indicatingspacesoromissions.
Topasteasequence:
1.Right-clickandnavigatetothePasteSpecialsubmenu.ChemBioDraw 14.0
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2.Selectoneofthreeoptionstopaste:
FASTAPeptide
FASTARNA
FASTADNA
Whenyouhoveryourmouseovertheresidue,adescription oftheresidueandsequence dataappears.
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PasteTextStrings
Youcanalsopastetextstringswithvalidseparators. Space,tab,anddashareconsidered asvalidseparators. The
textstringyoucopycanbegenerated withinoroutsideofChemBioDraw. Thetextstringsmustcontainvalidresidue
names/nicknames, optionallyincludingtermini.Ifnoterminiareexplicitlydefined,thendefaultterminiisassigned.
Topasteatextstring:
1.Copythetextstring(forexample,“H-Ala-Gly-Pro-NH2”)andright-clickinanemptyspace.
2.Fromthecontextmenu,selectPasteSpecial>Biopolymer .Thetextstringispastedasasequence.
Note:Thelabelsinthetextstringmustcorrespond toexplicitnicknames.
Expanding Sequences
Aftercreatingasequence, youcanexpandthewholesequence, orjustspecificlabels.
Toexpandasequence:
1.Selectoneormorelabelsinthesequence usinglassotoolormarquetool.(Holddownthe<SHIFT>keytoselect
morethanone.)
2.NavigatetoStructure>ExpandLabel.
Whenyouexpandaresidueintoitsstructure,thelabelappearsbelowthestructure.
Contracting Labels
Tocollapsethestructurebacktoitslabel(inthesequence):
1.Double-clickthelabeltoselectthestructure.
2.NavigatetoStructure>ContractLabel.
Ifyoueditthelabelpriortocontracting thestructure,thenewlabeltextisincorporated intothecontracted structure.
Forexample,if youmodifyaresidue,andchangeitsnamefromAlatoAla',oncontraction, thesequence containsthe
stringAla'.
CleanUpBiopolymers
Afteryoucontractthelabels,youcanusetheCleanUpBiopolymer command tocleanthesequence. Thiscom-
mandre-arrangesthesequence sothattheresiduesarealigned,andwrapped.Tospecifythenumberof'residuesper
line'andthenumberof'residuesperblock'inabiopolymer, selectthebiopolymer andnavigatetoObject>Object
Settings>Biopolymer Displaytab.ChemBioDraw 14.0
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Modifying Sequence Residues
Note:Whenyoumodifyaresiduestructureinyourdrawing,youmustdefineanewnickname toensurethatthe
contracted labelincludesyourchanges.
Tomodifyasequence residue.
1.Iftheresidueinthesequence iscontracted, right-clicktheresidueandselectExpandLabel.
2.Modifytheresidue.
3.UsingtheTexttool,renametheresiduelabeltoreflectanewstructure.Intheexamplebelow,the"Ser"labelhas
beenrenamedas"hSer"(forhomoserine).
Figure8.1:Twoexpanded serineresidues.Theresidueonthelefthasbeenmodifiedtocreatehomoserine.
Tocontractalabel:
1.Usingaselectiontool,right-clicktheresiduelabelandselectSelectLinkedObjects,ordouble-clickonthelabel
fortheexpanded residue,andtheassociated structureisselected.
2.NavigatetoStructure>ContractLabel.
Figure8.2:Thecontracted label.
Youmustdefineanewnickname toensurethatthecontracted labelincludesyourchanges.Forexample,youcan
defineanewnickname 'hSer',whichincludesthehydroxylgroupintheresiduedefinitionitself.
MergingSidechains withResidue
TheMergeSidechains WithResiduefeatureletsyoueditanexpanded residueandthenintegratethosechanges
intotheresiduedefinition.
Tomergeasidechain:
1.Double-clicktheresiduelabeltoselecttheresidue.ChemBioDraw 14.0
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2.Right-clickandselectBiopolymer >MergeSidechains WithResiduefromthecontextmenu.Theentireside-
chainismergedwiththeresidue.
Theresidueisselectedandyoucanedittheresiduelabel.
Removing Residues
Whenyouremovearesidue,thebondsareautomatically re-createdbetweentheadjacentlabels,andanygaps
closed.
Toremovearesidue:
1.Ifthelabelisexpanded, contractthestructurebacktoitslabel.
2.Selectthelabel,orhoveroverit.ChemBioDraw 14.0
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3.Pressthe<DELETE> key.
Replacing Residues
TheBiopolymer toolbarhastwodistinctmodesofdataentry:InsertionmodeandReplacement mode.Insertionmode
isthedefaultmode.IntheInsertionmode,anorangechevronindicatesthepositioninwhichthenextresiduewillbe
inserted.Forexample,theorangechevroninthesequence belowindicatesthatthenextresiduewillbeinsertedafter
the4thGlyresidue.
Youcanreplacearesidueinasequence usingtheReplacecurrentresiduebuttoninthebiopolymer toolbar.Inthe
replacement mode,anorangerectangleindicateswhichresidueisreplaced.Forexample,theorangerectangleinthe
sequence shownbelowindicatesthatthe3rd'G'residuewillbereplaced.
Themethodofreplacingresiduesisdemonstrated fortetraglycine sequence below:
1.Drawatetraglycine sequence.
2.SelectBioploymer EditorintheBiopolymer toolbar.
3.Inthetetraglycine sequence, clickonthe4th"Gly"residue.Anorangechevronindicatesthepositionwherethe
nextresiduewillbeinserted:
4.Select"Replacecurrentresidue"modeinthebiopolymer toolbar.The"Gly"textisselected.
5.Type"Ala"orclickthe"Ala"buttontoreplace"Gly".
Tochangetheformofaresidue:
1.Onthetetrapeptide sequence above,clickonthe2ndGlyresidue.
2.Clickandselectboththe"L-aminoacid"andthe"Beta-aminoacid".
3.Click"Cys"buttontoreplace"Gly"withbeta–Cys,asshown:
AddingResidues
Youcanaddoneormoreresiduestoanexistingsequence.
Toaddaresidue:ChemBioDraw 14.0
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1.Choosetheappropriate biopolymer tool.
2.Clickaresidueyouwantthenewresiduetobeadjacentto.Anorangechevronindicatestheinsertionpoint.
3.Typethenewresidue.Thenewlabelisaddedtotherightoftheexistingresidue.
Note:Toprepend,orinsertatthebeginningofasequence, selecttheterminusatom,selecttheaminogroup(pro-
teinsequence) or3’group(DNA/RNA sequence).
Numbering Residues
YoucandisplaytheresidueIDaboveanyresidue.
TodisplaytheresidueID:
1.Selecttheresidue.
2.Right-clickandselectShowResidueIDfromthecontextmenu.TheresidueIDappearsabovetheresidue.
Nonlinear Sequences (Multi-lineSequences)
Everysequence hasadefinedlinesizeandablocksize.Whenablocksizeisreached,anadditionalspaceisadded
tothesequence. Whenalinesizeisreached,subsequent residuesareaddedonanewline.However, youcancreate
sequence withirregularlinesbyselectinganddragging.Youcanplacearesidueonanewlinebyselectingtheresidue
inaSequence toolmode,andpressing<ALT>+<ENTER>. Subsequent residuesareplacedonanewline.
Toaddanewlineasyouareenteringthesequence, press<ALT>+<ENTER> onyourkeyboard. Subsequent
residuesareenteredonanewline,andthelinesizeissetforthatparticularsequence.
Tocreateamulti-linesequence:
1.Drawthesequence.
2.Usethesequencing tooltoselecttheresidueyouwantattheendofthefirstline(suchas‘His’intheexample
above).
3.Press<ALT>+<ENTER> onyourkeyboard.
HybridBiopolymers
Youcancreatemixedorhybridbiopolymers usingtheBiopolymer toolbarbycombining thevariousBiopolymer tools.
Hence,youcaninsertnucleicacidintoaminoacidsequences andvice-versa,andRNAandDNAcanbeused
together.ChemBioDraw 14.0
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BranchedBiopolymers
Residuelabelstypicallyhavetwoattachment points.However, youcanaddattachment pointssothatthesequence
branches. Forexample:
Whenyouaddanattachment point,youspecifytheatomintheexpanded labeltowhichthebondwillattach.
Tobondfromasequence:
1.Drawabondstartingatthelabelfromwhichtocreateabranch.TheModifyNickname dialogappears,displaying
thesequence structureyouselected.
2.IntheModifyNickname dialog,double-clicktheatominthestructureonwhichyouwanttoaddtheattachment
point.Anewattachment pointappears.
3.ClickOK.
IUPACCodes
Usethesecodestoenternucleotides oraminoacidsinyoursequence:
IUPACNuc-
leotideCodeBase IUPACAmino
AcidCodeThree
LetterCodeAminoAcid
A Adenine A Ala AlanineChemBioDraw 14.0
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C Cytosine C Cys Cysteine
G Guanine D Asp AsparticAcid
T(orU) Thymine(orUracil) E Glu GlutamicAcid
R AorG[Either
puRine]F Phe Phenylalanine
Y CorT[Either
pYrimidine]G Gly Glycine
S GorC[Threehydro-
genbond(Strong)]H His Histidine
W AorT[Twohydro-
genbonds(Weak)]I Ile Isoleucine
K GorT[Ketogroupin
base]K Lys Lysine
M AorC[AMinegroup
inbase]L Leu Leucine
B CorGorT[NotA(B
isletterafterA)]M Met Methionine
D AorGorT[NotC] N Asn Asparagine
H AorCorT[NotG] P Pro Proline
V AorCorG[NotUin
RNAcontext;notT
inDNAcontext]Q Gln Glutamine
N anybase[A/U/G/C
inRNAcontext;
A/T/G/CinDNAcon-
text]R Arg Arginine
S Ser Serine
T Thr Threonine
V Val ValineChemBioDraw 14.0
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W Trp Tryptophan
Y Tyr Tyrosine
Thetablesbelowlistthethreelettercodesfornon-specificandnon-proteinogenic aminoacids.
IUPACAmino
AcidCodeThree
Letter
CodeNon-specificAminoAcid
B Asx asparagine orasparticacid
Z Glx glutamicacidorglutamine
J Xle leucineorisoleucine
X Xaa Anyaminoacid(nonickname)
IUPACAmino
AcidCodeThree
Letter
CodeNon-proteinogenic Amino
Acid
O Pyl Pyrrolysine
U Sec Selenocysteine
Aibα-Aminoisobutyric acid
Abz 2-Aminobenzoic acid
Nle Norleucine
Cyclic,Crosslinked, andBranched Peptides
Youcancreatecyclicpeptidesbybondingtogethertheterminalresiduesinapeptidesequence. Aloopedbondindic-
atesthepeptideiscyclic.Anexampleofcyclicpeptideisshownbelow:ChemBioDraw 14.0
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Youcancreateacrosslinked peptidesuchasinsulin,usingthebiopolymer toolandbondtool.
Branched Peptides
Abranchedpeptideisformedwherearesiduehasmultiplepossibleleavinggroups.Forexample,Arghastwoamino
groupsandAsphastwocarboxylgroups.Apolymerization reactioncouldpotentially takeplaceateitherofthese
groups,oratboth.Henceprotecting groupsareoftenemployed duringthepolymerization reactionstoselectively
allowpolymerization atonlyasinglesite.
ConsiderthefollowingexampleinwhichthepeptideisbranchedattheAspresidue:
Inthefollowingexample,theresidueisbranchedattheArgresidue:
Youcancreateabranchedpeptideusingthesolidbondtooltoconnectthebranching residueinthefirstchaintothe
branching residueinthesecondchain.Iftheresidueshaveleavinggroupsthatcanbeautomatically found,thenit
branchesatthosepoints.Otherwise, theModifynickname dialogappearsandyouneedtomanuallydefinethethird
attachment point.Considerthefollowingexampleforcreatingbranchedpeptide:
1.Drawtwobiopolymer chainsasshownbelow:
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2.Usingthesolid-bondtool,dragfromthelowerchain'sGly-3totheupperchain'sArg-3.Theterminalhydrogenon
thelowerchainisremovedandthebranchedpeptideappearsas:
Iftheresiduesdoesnothaveleavinggroupsthatcanbeautomatically found,theModifynickname dialogappearsand
youneedtomanuallydefinethethirdattachment point.Considerthefollowingexample,
1.Drawtwobiopolymer chainsasshownbelow:
2.Usingthesolid-bondtool,dragfromthelowerchain'sMet-4totheupperchain'sMet-5.Sinceneitherofthese
residueshavedefinedleavinggroups,theModifyNickname dialogappearstwice,onceforeachresidue.
3.Definenewattachment points.Theresultingstructureis:
DisulfideBridges
YoucanbuilddisulfidebridgeseitherbetweenCysresidueswithinthesamestructure,orbetweenresiduesintwodif-
ferentstructures. Forexample,considertheendocrine hormoneInsulin.ChemBioDraw 14.0
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Insulinconsistsoftwochains,anAchainandaBchain,connected bydisulfidebridges.
AChain
GIVEQCCTSICSLYQLENYCN
BChain
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
YoucanbuildthesechainseitherbycopyingandpastingtheabovetextusingthePasteSpecial>FASTAPeptide
command orbyusingtheBiopolymer toolbartobuildeachchain.
Tobuildintra-sequence disulfidebridge:
1.Selectthesinglebondtool.
2.DrawabondbetweentheC(6)andC(11)residuesintheAchain,asshownbelow:
Tobuildinter-sequence disulfidebridges:
1.SelectthebondtoolanddrawabondbetweentheC(7)inAchainandC(7)inB-chain.
2.DrawanotherbondbetweentheC(20)inAchainandC(19)inBchain,asshownbelow:
LactamBridges
YoucandrawlactambridgesbetweenLys-AspandLys-Gluresidues.Theresiduesconnectviaamidebonds
betweensidechains.Youcanalsomixdisulfideandlactambridges.
Todrawalactambridge:
1.Drawasequence thatcontainsLysandeitherAsporGlu.
2.Usingsolidbondtool,drawabondfromLystotheotherresidue.Anexampleisshownbelow:
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AdvancedDrawingTechniques
Theadvanced featureshelpyousavetimeorperformfunctionsthatcannotbeaccomplished usingthebasictools.
Forexample,youcanviewyourdrawingas3Dmodelsorcreatestereoisomers attheclickofthemouse.Usingother
features,youcan:
Addbondstocharacters inatomlabels
Createbondswhoseattachment isnotexplicitlydefined
Addatomnumbers
Contractandexpandsectionsofstructures
Viewstructureperspective
Createmassfragmentation, retrosynthesis, andsynthesis drawings
Drawwithtemplates
Createandedittemplates
Labelfunctional groupswithnicknames.
Coloring Objects
Youcanselectandcolorobjects,partorallofachemicalstructure,boxes,curves,arrows,orbitals,andreaction
mechanism symbols.
Tocoloranobject:
1.Selecttheobject.
2.Dooneofthefollowing:
ClicktheColorbuttonontheStyletoolbar,andselectthecolorfromthemenuthatappears.
ChooseacolorfromtheColormenu.
Right-clickandselectthecolorfromthecontextmenu.
NavigatetoObject>ObjectSettingsandselectthecolorintheDrawingtab.ClickOKwhenfinished.
Coloring Groups
ChemBioDraw colorsgroupsdifferently fromintegralgroups.Whenyoucoloranintegralgroup,itsobjectsacquirethe
newcolorbutretaintheoriginalshading.Whenyoucoloranormalgroup,thenewcolorisappliedandtheoriginalshad-
ingisignored.ChemBioDraw 14.0
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Figure9.1:A)Themitochondrion structureinitsdefaultcolor;B)Thestructurecoloredblueasagroup;C)Thestruc-
turecoloredblueasanintegralgroup.
Thenewcolorappliestoallstructures inthegroup,eveniftheoriginalcolorsoftheobjectsinthegrouparenotthe
same.Seeexamplebelow:
Figure9.2:A)Thestructurecoloredpinkasanintegralgroup;B)Thestructurecoloredpinkasagroup.
Labels
Inadditiontorepresenting atoms,labelscanrepresentregionsofastructurethatyoudefine.Forexample,youcan
assignalabeltoanunimportant regionofamoleculeandthencontractthatregiontoreducethesizeofyourdrawing.
Youcanthenexpandthelabel,toseethewholemolecule.
CreatingLabels
Tocreateacontracted label:
1.Selecttheareaofthestructuretocontract.
2.NavigatetoStructure>ContractLabel.TheContractLabeldialogappears.
3.Typealabelforthecontracted structure.ChemBioDraw 14.0
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4.ClickOK.
Thelabelreplacestheselectedportionofthestructure.
Note:Iftheareaofthestructureyoucontractcontainserrors,anerrordialogappears.ClickIgnoretoviewother
errors.ClickIgnoreAlltoignoreallerrorsorStoptoendthecontractprocess.
Expanding Labels
Ifyourstructures containdefinednicknames, longatomlabels,orcontracted labels,ChemBioDraw canrestoreyour
structures tothefully-expanded form.
Toexpandatomlabels:
1.Selectaselectiontool.
2.Selectthelabeltoexpand,ordouble-clickthestructuretoselectalllabelsinthestructure.
3.NavigatetoStructure>ExpandLabel.YoucanalsousetheExpandLabeltoolintheStructuretoolbar.Your
structureisredrawninitsexpanded form.Belowisanexampleofexpanding labels:
Contracted:
Expanded:
Whenyouexpandalabelthatcontainsadivalentnickname, forexampleH-Ala-OH,theattachment orderdependson
theorderinwhichthebondsarecreated.
MultipleAtoms
Labelscancompriseagroupofatoms.Whenyouexpandthelabel,itexpandstocreatethestructure.
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Expanded:
AddingaLabelofMultipleAtoms
1.Usingthetexttool,clickanatominthestructurewhereyouneedtoplacethelabel.
2.Typetheformula(suchas“CH2NHCH3”).
3.Usingaselectiontool,selecttheformula.
4.Right-clicktheformulaandselectExpandLabel,ornavigatetoStructure>ExpandLabel.Youcanalsousethe
ExpandLabeltoolintheStructuretoolbar.
Figure9.3:Addingbondstoalabel
Youcandetermine theorientation oftheresultingbondbydragging.Ifyouclicktoaddabond,thereareseveralpref-
erentialorientations fortheresultingbondasoutlinedbelow.
Addingfromtheendofanatomlabelcreatesbondsthatarepreferentially horizontal.
Addingfromthemiddleofanatomlabelcreatesbondsthatarepreferentially vertical.ChemBioDraw 14.0
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AddingfromthestartofanatomlabelcreatesbondsthattrytoattainthechainanglesettingintheDrawingSet-
tingsdialog.Ifthatanglecannotbeattained,thenextbestangleisused.
Attachment Points
Youcandrawpolyhapto structures suchasferrocene((Cp)2Fe),orabbreviated notationsfordifferentpositionaliso-
mersofacompound, usingattachment points.Theprocedure issimilar,andinbothcases,thestructureretainschem-
icalsignificance. Youcangenerateallpossiblestructures fromanabbreviated combinatorial structurebyusing
ExpandGenericStructurefeature.Formoreinformation, see"ExpandGenericStructures" onpage255.
Figure9.4:Drawingapolyhapto structure
Multi-CenterAttachments
Toaddamulti-centerattachment pointtoastructure:
1.Selectallorpartofthestructure.
2.NavigatetoStructure>AddMulti-Center Attachment .Anasteriskindicatesamulti-centernode.
Todrawabondtoamulti-centerattachment point:
1.Clickthebondtool.
2.Pointtotheasteriskandeitherclickordragtocreateabond.
Theasteriskisnotvisibleonceabondisdrawntoit.However, youcanviewtheattachment pointusingabondor
selectiontool.
Tip:Iffixedlengthsisenabled,press<ALT>asyoudragthebond.
VariableAttachment Points
YoucanusetheAddVariableAttachment command todrawdifferentpositionalisomersofacompound usingan
abbreviated notationthatretainschemicalsignificance.ChemBioDraw 14.0
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Forexample,youcanexplicitlydrawthethreeisomersofdibromobenzene, asshownbelow.Alternately, youcan
expressallthreeisomersasasingleparentstructurebyusingavariableattachment asshownbelow.
Abbreviated
notationfor:
Figure9.5:Isomersofdibromobenzene
Toaddavariableattachment pointtoastructure:
1.Selectallorpartofthestructure.
2.NavigatetoStructure>AddVariableAttachment .
3.Pointtotheasteriskinthestructureanddragtodrawabond.
Note:EitherdisableortoggleFixedLengthstodrawthebondsothatitextendsfromthering.
Note:Todrawthestructurebelowyoushouldonlyselectthe5ringsatomthatdonotalreadyhaveabromine
atomboundtothem.Selectingtheentiremoleculewouldcauseavalenceproblemwiththetopmostcarbon.
Tip:Iffixedlengthsisenabled,press<ALT>asyoudragthebond.
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Note:Afteryoudrawabondfromanattachment point,theasteriskdisappears. Toviewanattachment point,pos-
itionthecursoroveritwitheitherabondtooloraselectiontool.
AtomNumbering
Youcanaddsequential numbersorletterstotheatomsinyourstructure.Youcanadd:
Numbers(1,2,3,andsoon)
Textendingwithanumber(atom1)
Greeklettersforalpha,beta,andsoon
Letters(a,b,c,andsoon)
Thedefaultindicatorisnumbers.
Tip:Tousetextinsteadofnumbers,numberanatom,andtheneditthenumber.See"Formatting AtomNumbers"
below.
Showing AtomNumbers
1.Selectoneormoreatomstonumber.
2.Whilepointingtotheselectedatomsorstructure,dooneofthefollowing:
Right-clickandselectAtom>Show Atomnumberinthecontextmenu.
Typethehotkey‘(singlequote).
Tohideatomnumbers:
1.Selecttheatomsorstructure.
2.Right-click,pointtoAtom,anddeselectShowAtomNumber.
Note:Toremoveanatomnumberindicator,clicktheindicatorwiththeErasertool.
Formatting AtomNumbers
Toedittheatomnumbertextandstyle:
1.SelecttheTexttool.
2.Selecttheatomnumberandtypethenewtext.ChemBioDraw 14.0
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Note:Whenyoutypeanewindicator,thecounterresetstothenewstyleandyoucancontinuenumbering inthat
stylewiththestandardmeans.Forexample,ifyoutypeαinatextbox,thenpointtoanotheratom,andusethe
contextmenuorhotkey,theatomislabeledβ.Switching toanotherstructureresetsthecounter.
3.Toedittheatomnumberstyle,selecttheatomnumberwiththeTexttoolandusetheTextmenu,orTextformat-
tingtoolbar,tochangethestyle.
Positioning AtomNumbers
Youcanpositioneachatomnumberanywhere arounditscorresponding atomanditsdistancefromtheatom.
Toreposition anatomnumber:
1.Right-clicktheindicatortomoveandclickthePositioncommand onthecontextmenu.ThePositionIndicators
dialogappears.
2.Clicktheappropriate positionoption,andenteravalue.
Toposition TypeaValuefor
Position
Fromtheatomorbondcentertotheindicatorcen-
terByangleorby
clock
Fromtheatomorbondcentertobottomleftof
indicatorbaselineByoffset—hori-
zontalandvertical
Atspecifiedcoordinates Absolute— hori-
zontalandvertical
Structure Perspective
Youcantiltmolecules orportionsofmolecules throughthreedimensions withtheStructurePerspective tool.
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1.SelectthestructurewitheitheraselectiontoolortheStructurePerspective tool.
2.WiththeStructurePerspective tool,clickanddragtheselectedstructure.Placethecursorinsidethemarkedrect-
angleanddraginanydirection.
Tip:Use<SHIFT>+drag tolimittherotationtotheXorYaxesonly.
Youcanalsoselectpartofacomplexmoleculeandrotateitaroundaparticularbond.
Note:Youcannotapplystructureperspective toorbitals.
ToremovetheStructurePerspective Tooleffect:
1.SelectthestructurewiththeMarqueeorLassoTool.
2.NavigatetoObject>Flatten.
Note:Flattening thestructureremovesitsz-coordinate information butdoesnotchangeitsappearance.
MassFragmentation
Massfragmentation mimicsthemolecular fragmentation inamassspectrometer. Whenyouapplythemassfrag-
mentation tooltoastructure,youcutthroughthestructure,severingitsbonds,andcreatingfragments fromtheori-
ginalstructure.This isnotapredictive tool,youmustspecifywhatbondsaretobebroken.
Tofragmentastructure,usetheMassFragmentation Tooltodragthecursoracrossoneormorebonds.Whenyou
releasethemousebutton,bondsthatyoucrossarebroken.
Bydefault,thelineyoudrawdisappears whenyoureleasethemousebutton.
Note:Todrawacurvedline,ortokeepthelinevisible,holddownthe<ALT>keywhiledrawing.
Whenthelinecrossesabond,theformulaandexactmassforthefragments oneithersideofthebondappearasifthe
bondwerehomolytically broken.Thatis,asinglebondturnsintoamonoradical oneachfragment;adoublebondturns
intoapairofdiradicals. Ifmorethanonebondiscrossed,allfragments oneachsideofthelineareconsidered
together.Iftheonlybondcrossedisaringbond,asingleformula/mass pairdisplays.ChemBioDraw 14.0
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Youcanreposition theformulaandmassdisplays,ordeletethem.
Synthesis andRetrosynthesis
ChemBioDraw includestwotoolstohelpyoudrawsynthesis reactions. TheSynthesis tooldrawsasynthesis reac-
tionbasedonaproductstructurethatyouspecify.Alternatively, theRetrosynthesis tooldrawsthereactionwiththe
productontheleftandanarrowpointingtothereactants. Thesetoolsareinthefragmentation toolspaletteofthemain
toolspalette.
Todemonstrate thesefeatures,weusetheBeyerMethodforquinolines, startingwiththestructurebelow.
Youcancreateeithertypeofreactionusingtheappropriate toolanddraggingthroughbondsindicatedbythedotted
line.Forexample,usetheRetrosynthesis tooltocreatethisreaction:
Figure9.6:QuinolineRetrosynthesis
Quinlinesynthesis
DrawingReactions
Todemonstrate howtodrawreactions, wewillusethisexample:ChemBioDraw 14.0
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DrawinganArrow
Startingwith2-propanone (see"Tutorial1:DrawingaStructure" onpage298),drawthereactionarrow:
1.OntheArrowstoolbar,clickthethirdarrowfromtheleftinthetoprow,asshownbelow:
2.Inthedocument window,clickanddragthemousehorizontally totherightofthe2-propanone structure.Thearrow
appears.
3.SelecttheTexttool.
4.Clickabovethearrow.Atextboxappears.
5.TypeOHandpress<ESC>.Re-alignthetextboxasnecessary usingaselectiontool.
Note:IfShowChemical Warnings isturnedon(thedefault),aredboxwillappeararoundtheOHlabelwhenyou
changetoolsoropenanothertextboxindicatinganerror.Ignorethisfornow.
AddachargesymbolusingtheChemicalSymbolstoolpalette:
1.IntheMainTooltoolbar,clicktheChemicalSymboltool.
2.Holdingthemousebuttondown,selectthecircledCircleMinussymbol.
3.PointtothecenteroftheOHlabel.MovethecursorslightlyrightorlefttoselecttheO.
4.Withtheoxygenatomselected,dragthechargesymbolaroundtheatomtothedesiredposition.
ObjectsthatyouaddfromtheChemicalSymbolspaletteareassociated chemically withthestructuretheyarenear.
Notethattheredvalenceerrorwarningdisappears whenyouaddtheminuscharge.
DrawingtheProduct
Wenowcreate4-hydroxy-4-methyl-2-pentanone usingacopyofthe2-propanone structure.Youcancreatethe
productfromscratch,oryoucancopyanexistingstructure.ChemBioDraw 14.0
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Tocopyastructure:
1.Selectthe2-propanone structureanditscaption.
2.Pressandholdthe<CTRL>key.
Thehandpointerwithaplussignindicatesthatyouareintheduplication modeofaselectiontool.
3.Dragtheselectionrectangletotherightandreleasethemousebutton.
Note:Tokeepthecopyalignedwiththeoriginal,pressthe<SHIFT>keywhiledragging.
Modifytheduplicatestructure:
1.SelecttheSolidBondtool.
2.Clickthefarrightbondofthecopiedstructure(Figurebelow).
3.Pointtoaterminalcarbon.
4.Clickthecarbonatomuntilthreebondsappear,allowingapausebetweeneachclick.
Note:Ifyouclicktoofast,theclickisinterpreted eitherasadouble-click,whichopensatextboxoratriple-click,
whichduplicates yourlastatomlabel.
5.Pointtoaterminalcarbonatom.
6.TypeOH.
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Replacetheproductcaption:
1.SelectthecaptionwiththeTexttoolandtype4-hydroxy-4-methyl-2-pentanone ,pressthe<ENTER> keyand
type1mole.
2.UsingtheTexttool,add2Moletothecaptionforthereactant.
CleanUpReactions
Afteryoudrawareaction,youcancleanthereactionusingtheCleanUpReactioncommand undertheStructure
menu.WhenyouapplytheCleanUpReactioncommand, thespacingbetweenthereactioncomponents ismod-
ified,thecomponents areevenlydistributed, plussignsareinsertedwherevernecessary, andthelengthofthearrow
isadjusted.
Tocleanupareaction:
1.Selectthereaction.
2.NavigatetoStructure>Clean UpReaction.
Ifthereactionistoowideforthedocument, thereactioniswrappedtofillmultiplelines,asshownintheexample
below:
Figure9.7:ThereactionbeforeapplyingtheCleanUpReactioncommandChemBioDraw 14.0
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Figure9.8:ThereactionafterapplyingtheCleanUpReactioncommand
Note:TheCleanUpReactionisavailableonlyforsingle-stepreactions.
Note:TheCleanUpReactioncommand isavailableonlyforreactionswithstraightarrows.Incaseofarrows
withcurvatures theCleanUpReactioncommand isdisabled.
TheReaction Interpreter
TheReactionInterpreter parsesreactionsasdrawn,andbreaksthereactionintothefollowingdistinctcomponents:
ReactionScheme
ReactionStep
Reactants
Products
Conditions
Youcansavetheinterpretation todiskbysavingthefileasCDXML.Thisstoreddataisoftenimportantifreactions
aretobestoredindatabases.
Thereactioninterpreter color-codesthereactants, products,catalysts, andannotations inareactionwhenyouhover
overthemwithShowReaction Interpretation selected.Thishelpsindetermining whetherthereactionisbeingcor-
rectlyperceived, andletsyouadjustthereactiontocorrecttheinterpretation.
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Tointerpretthereaction:
1.NavigatetoView>ShowReaction Interpretation .
2.Hoveryourcursoroverthereactionarrow.
Forareactiontobeinterpreted:
Eachreactantandproductmustcontainatleastoneatom.
Eachreactantandproductmustbedescribed usingasinglelabel.
Multiplereactantsandproductsshouldbelinkedbya“+”sign.
Reactionconditions mustresidecompletely withintheleftandrightboundaries ofthereactionarrow.
Thereactioncannotincludeacurvedarrow.
Thereactioniscoloredasfollows:
Reactions arered.
Productsaremagenta.
Everything abovethereactionarrowiscyan.
Everything belowthereactionarrowisblue.
ElectronandRadicalPushing
Acommonpracticewhenillustrating organicreactionmechanisms istouseelectronpushingarrowstodisplaythe
transferofelectrons. ChemBioDraw providestheElectronPushingandRadicalPushingtoolsforillustrating electron
transfer.Electrontransferscanbedrawnbetweenatoms,bonds,andorbitals.
Todisplaythetransferofanelectronpair:
1.SelecttheElectronPushingTool
fromtheChemicalSymbolstoolbar.
2.Clickanddragthemousefromthesourceobjecttothetargetobjectandreleasethemouse.Afull-headarrow
appearssignifyingtheelectronpairtransfer,suchas:
Figure9.9:Exampleofelectronpushing
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1.SelecttheRadicalPushingToolfromtheChemicalSymbolstoolbar.
2.Clickanddragthemousefromthesourceobjecttothetargetobjectandreleasethemouse.Ahalf-headarrowsig-
nifyingonlyoneelectrontransferappears,suchas:
Figure9.10:Exampleofradicalpushing
Youcandeletetheelectrontransferarrowbyeitherselectingorhoveringoverthearrowandpressingthe<DELETE>
key.YoucanmodifytheelectrontransferarrowshapebyusingeithertheArrowtool,ortheElectronPushingTool.
Whenyouhoverovertheelectronorradicalpushingarrows,theassociated objectsarehighlighted inadditiontothe
arrows.
Stoichiometry Grid
UsetheStoichiometry Gridtocalculatestoichiometric dataforareaction.Thegridfillsinasyoumodifyareaction
drawing,andallcalculations aredoneautomatically.
Tocreateastoichiometry grid:
1.Drawareaction,oropenafilecontaining areaction.
2.NavigatetoView>Show Reaction Interpretation .TurningonShowReaction Interpretation ensuresthereac-
tionisproperlyinterpreted byChemDraw. Whenyouhoveroverthereaction,forexample:
Reactants inred
Productsinmagenta
Anythingaboveandbelowthereactionarrowincyanandblue
3.SelectthereactionandnavigatetoStructure>AnalyzeStoichiometry .Thegrid,withseveraldatafieldsfilled
withdefaultvalues,appearsunderthereaction.ChemBioDraw 14.0
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Note:Ifacatalystorconditionlabelisabovethereactionarrow,right-clickthelabelanddeselect Interpret Chem-
icallyinthecontextmenubeforecreatingthegrid.
Toenterdatainthegrid:
1.Setthelimitingcompound. Ifthedefaultsettingisincorrect,right-clickthewordNointhelimitingrow,andselect
SetLimitingfromthecontextmenu.
2.SelecttheTexttool,andclickwheretoenterthedata.Entervaluesforallreactants, asapplicable. Ifyouareusing
unitsotherthanthedefaults,typeintheunitsalongwiththevalues(nospacerequired).
Value Comments
Limiting? Indicatesthelimitingreactant.Onlyonereactantmaybespecifiedaslimiting.
SampleMassMassofreactant.Defaultunits:g.
%Weight Reactantpurity.Defaultsto100%.
Volume Defaultunits:ml.Requireseitheramolarityoradensitytobeentered.ChemBioDraw 14.0
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Value Comments
Molarity Defaultunits:M
Density Defaultunits:g/ml
Afteryouentertheminimumamountofinformation thevaluesarecalculated.
Thevaluesareautomatically recalculated whenyouenteranewvalue,editinput,ormodifythereaction.Toeditinput,
clicktheinputandenterthenewvalue.Forexample,considerthefollowingtable:
IfyoueditthevalueintheReactantMolesfieldforthereactantinthetableto30.00mol,therestofthetableis
updated.
Note:Enteredvaluesareinbold-face;calculated valuesareinnormalfont.
Youcanshoworhiderowsorcolumnsinthegrid.Tohidearow,right-clicktherowandselectHideRowfromthe
contextmenu.ChemBioDraw 14.0
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Tohideacolumn,right-clickthecolumnandselectHideColumnfromthecontextmenu.
Todisplayhiddenrowsorcolumns,selectShowAllfromthecontextmenu.Tochangethecolorofthetext,select
Colorfromthecontextmenu.
Templates
ChemBioDraw includesalibraryoftemplates.Youcanuseatemplateasastartingpointforanewdrawingortoadd
toanexistingdrawing.Apaletteisasetoftemplates.
Thetemplates youdefinearenotlimitedtoatomsandbonds.Templates canalsocontaincaptions,colors,boxes,
arcs,orbitals,arrows,reactionmechanism symbols,andcurves.Youcanpastepicturesfromotherapplications into
atemplatepane.Youcandownloadtemplates fromthePerkinElmer Informatics websiteandusethem.Formore
information onavailabletemplates anduserdownload- abletemplates, seeChemBioDraw templatefiles,and
BioDrawtemplates.
Toopenatemplate,dooneofthefollowing:
SelectatemplatetoolbarfromtheMaintoolbar.
NavigatetoView>Templates andselectatemplatetoolbarfromthelist.
Toaddtoadrawingusingatemplate:
1.Selecttherequiredtemplatefromthetemplatetoolbar.
2.Inthedocument window,clickanddragthemouseuntilthetemplateisorientedthewayyouneed.
Tip:Tomodifythetemplatesize,pressthe<ALT>keywhiledrawingit.
Youcanalsousethetemplates toaddstructuralfeaturestoexistingdrawings.
Toaddstructuralfeaturestoexistingdrawings:
1.Selecttherequiredtemplatefromthetemplatetoolbar.
2.Clickanatomorbondintheexistingdrawingtoaddthetemplatestructure.ChemBioDraw 14.0
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Customizing Templates
Youcanmodifyatemplatepalettetocreateyourownpalette.Whenyoucreateapalette,asetofemptytemplate
panesappearabovethedocument window.Afteryousaveyourpalette,itcontainsthetemplates youhavedrawn.
YoucanthenselectyourpalettefromthepalettelistintheTemplates tool.Youcanalsostoretemplates asgroups,or
evenintegralgroups,sothattheyaretreatedasanindividualentitywithinthedocuments intowhichtheyaredropped.
Tocreateatemplatepalette:
1.NavigatetoFile>OpenTemplates >NewTemplates .
2.Clickatemplatepane.
3.Inthedocument window,drawanewstructure.
4.Clickanothertemplatepaneanddrawanotherstructureasdesired.
5.Afteryoudrawallthetemplates youwant,gotoFile>Save.
Note:SaveyourpaletteintheChemDraw ItemsfoldertoensureitappearsintheMaintoolbar.
6.Inanydrawing,selecttheTemplatetoolontheMaintoolbartouseyoupalette.
Modifying aTemplate
1.NavigatetoFile>OpenTemplates andchooseapalette.
2.Inthepalette,clickatemplatepane.Thetemplateappearsinthedocument window.
3.Inthedocument window,editthetemplate.
4.Savethetemplate.
Toaddordeleteapaletteroworcolumninapalette:
1.Inthepalette,clickacellintheroworcolumn.
2.Selecttheappropriate optionintheEditmenu.
AddingaTemplate
Toaddatemplate,clickinanemptytemplatepaneanddrawthetemplateinthedocument window.Navigateto
File>Save.
Annotating aTemplate
1.NavigatetoFile>OpenTemplates andchooseapalette.
2.Right-clickonanemptyspaceinatemplatepane,andselectAnnotate.TheAnnotatedialogappears.ChemBioDraw 14.0
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3.SpecifyanewnameforthetemplateintheContenttextbox.
4.ClickOK.
5.ClickSave.Theannotation appearsasatooltip,whenyoupointtotheannotated template.
DeletingaTemplate
1.Selectthetemplatepaneforthetemplatetodelete.
2.Inthedocument window,selecttheentiredrawing.
3.NavigatetoEdit>Clear.
4.NavigatetoFile>Save.
Orienting Templates
Tomaketemplates youcreatesimpletouse,orientthetemplatestructuresothatyoucanmodifythebondsyouuse
mostoften.
ResizingTemplate Panes
ToresizetheTemplatepanesintheTemplatepanel,dragthelowerrightcorneroftheTemplatepanel.Ifnecessary,
firstclickanddragtheresizehandle.
DefiningNicknames
Anickname isanalphanumeric abbreviation thatrepresents asubstructure1.Nicknames areusefulfordrawinglarge
structures, orstructures thatrepeatedly usesimilarfeatures.Contracted labelsaresimilartonicknames, buttheyare
forone-timeuseonly,inthecurrentdocument.
ChemBioDraw includesalibraryofnicknames ofcommonfunctional groupsandmonomers. Forexample,ifyoutyp-
icallydrawproteinstructures, youmayconsiderusingaminoacidnicknames inyourdrawingsratherthandrawing
eachaminoacid.
Thesubstructure thatanickname represents connectstotherestofthestructureusingoneormoreattachment
points.Attachment pointsmustbesinglebonds.Forsubstructures withtwoormoreattachment points,theattach-
mentpointnumbering sequence determines theorderinwhichotherpartsofthestructureareattached.Forexample,
1Asubstructure canbeanypartofadrawnstructure.ChemBioDraw 14.0
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ifyouexpandthestructureH-Leu-OH,thehydrogenisbondedtothefirstattachment pointinleucineandthehydroxyl
grouptothesecond.
Formoreinformation, see"UsingNicknames" onpage62.
Todefineanewnickname:
(Intheexamplebelow,ab-alaninestructureisused.)
1.Drawtheb-alaninestructure.
2.DrawabondtotheNH2group.
3.DeletethelabelontheOHgroup.
4.UsingtheAttachment Pointtool,addanattachment totheN-terminus.
5.Addanattachment totheC-terminus.
6.Selectthestructure,andnavigatetoStructure>Define Nickname .
7.Typeashortnameforthenickname.
Tip:Toavoidpossibleconflictswithelements, specifynameswithmorethantwocharacters.
8.ClickOK.
Note:Theattachment pointorderisdetermined bytheorderinwhichyouaddtheattachment pointstothestruc-
ture.
Youcanalsodefinenicknames fromastructurecontaining asingleradical.Attachment pointsareaddedatthesiteof
theradical.ChemBioDraw 14.0
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Nicknames canalsobedefinedbycarvingasubstructure outofastructure.
Nicknames andAtomLabels
Ifyouuseanickname thatisthesameasanelementname,amessageindicatesthattheelementisreplacedwith
thenickname. Forexample,usingAcforanacetylgroupreplacestheelementActinium.TheCheckStructurecom-
mandrecognizes thelabelasanacetylgroupratherthanActinium.
Thenicknames listprovidestheseNickname/Element conflicts:
Symbol Nickname Element
Ac Acetyl Actinium
Am Amyl Americium
Np para-Nitrophenyl Neptunium
Pr Propyl Praeseodymium
Note:IfyouusethePeriodicTabledialogtoinsertatomsintostructures, theelementswillpreferentially bedepos-
ited.SelectingAcfromthePeriodicTableandclickingonanatomwillplaceActiniumratherthanAcetyl.
Toremovetheoverriding nicknames, navigatetoFile>ListNicknames anddeletetheoverriding nickname definition.
DeletingNicknames
Todeleteanickname fromthenickname library:
1.NavigatetoFile>ListNicknames .
2.Selectthenickname andclickDelete.
Troubleshooting Nicknames
IftheDefineNicknames command isdisabled,checkforthefollowing:
Aconnection pointthatisnotpresent
Morethantwoconnection pointsthataredefined
Aconnection pointthatisnotasinglebond
InFigureabelow,theentirefunctional groupwasselected.Becausethereisnoatomthatindicatesaconnection
point,youcannotdefineanickname. Whenasulfonamide groupisattachedtoanunselected bond,youcandefinea
nickname.
InFigureb,thereismorethanoneattachment pointonasingleatominanickname.ChemBioDraw 14.0
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Incorrect Correct
a
b
ChemScript
ChemScript isthecheminformatics SoftwareDevelopment Kit(SDK).Itcontainstheprogramming algorithms com-
monthroughout PerkinElmer Informatics products.Withenoughknowledge writingsoftwarecode,youcanapply
ChemScript tocreateyourownscriptstousewithChemBioOffice applications.
ChemBioDraw Ultraalsoincludesalibraryofsamplescriptsforyoutouse.NavigatetoFile>ChemScripts and
selectanoption.
Torunascriptonthecurrentdrawing:
1.NavigatetoFile>RunChemScript .
2.IntheOpendialog,selectthescriptandclickOpen.
3.(Optional) Torunthescriptagain,navigatetoFile>Re-runPreviously SelectedChemScript .
ChemScript Integration
Note:ChemScript isanadvanced featureintendedforuserswithsomeprogramming experience.
ChemScript letsyouaddcustomfunctionstoChemBioDraw. Customscriptscanbelaunchedfromtheapplication,
andtheresultsofthescriptarereturnedtoanewChemBioDraw document. Scriptsmustbewrittenusingeither
PYTHON or.NET.Youusecustomscriptsto:ChemBioDraw 14.0
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ApplycustomdrawingrulesusingChemScript
Launchexternalapplications fromChemBioDraw
Automate workflowfromChemBioDraw
TheinputdataforthescriptconsistsofCDXMLdatafromthecurrentlyactivedocument inChemDraw. Ifyouselecta
portionofthedocument, onlytheselectedpartofthedocument isusedasinputtothescript.
Youcanapplyscriptstochemicalstructures andreactions.
YoucanplacescriptsintheScriptsdirectoryforeasyusage.TheScriptsdirectoryisinthesamedirectoryasthe
ChemDraw itemsdirectory.
Tolaunchascript,dooneofthefollowing:
NavigatetoFile>ChemScripts ,andselectascriptfromtheScriptsdirectory.
NavigatetoFile>RunChemScript ,andselectascriptfromadirectoryotherthantheScriptsdirectory.
YoucanalsousethesamplescriptsavailableinChemDraw underFile>ChemScripts .Oneexampleisgivenbelow:
1.Drawaminimumofthreestructures inthedocument window.
2.NavigatetoFile>ChemScripts >LayoutMolecules inaCircle.Anewdocument windowappearswiththestruc-
turesarrangedinacircle.ChemBioDraw 14.0
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Struct=Name (UltraFeature)
ChemBioDraw includestwofeaturesforgenerating structures andchemicalnames—Name>Struct and
Struct>Name .Collectively, thesefeaturesarecalledStruct=Name .
Struct>Name generates thenamesofchemicalstructures usingtheCahn-Ingold-Prelogrulesforstereochemistry.
Usingthisoption,youcangeneratethenameofstructures youhavedrawn.
Name>Struct letsyouconvertchemicalnamesintotheircorresponding chemicalstructures. Itisdesignedtointerpret
chemicalnamesastheyareusedbychemists. Inotherwords,itrecognizes theshorthand andslangofeveryday
usage,inadditiontorecognizing mostoftheofficialIUPAC,IUBMB,andCASrulesandrecommendations.
Struct>Name
Struct>Name caninterpretavarietyofchemicalstructures. Thismeansthatyoucandrawastructureand
Struct>Name willprovideitsname.Italsoupdatesthenamewhenyoumodifythestructure.
UsingStruct>Name
Togeneratethenameofyourstructure:
1.Selectthestructure.
2.NavigatetoStructure>ConvertStructure toName.Thenameappearsunderthestructure.
Supported Structures
However, Struct>Name willinterpret:
Stereochemistry
Principal GroupinRingsandChains
CarboxylicAcids S,Se,andTeAcids
Peroxyacids S,Se,andTeEsters
Amidederivativesofacids S,Se,andTeAcidHalides
Carbonicacids S,Se,andTeAmides
Nitricacids Sulfidesandchalcogenanalogs
AcidHalides Sulfoxidesandchalcogenanalogs
CarboxylicEsters Heteroatomic acids(P,B,As)
Salts Heteroatomic esters
Anhydrides Heteroatomic acidhalides
Hydrazides Aldehydesandchalcogenanalogs
Imides Ketonesandchalcogenanalogs
Amides Alcoholsandchalcogenanalogs
Hydrazines Hydroperoxides
Nitriles Peroxides
AminesandIminesChemBioDraw 14.0
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Non-RingedStructures
Isolatingandnamingthefunctional groups
Identifying thebasechainofthemolecule
Identifying andbuildingsubstituents
Nomenclature ofgroupscitedonlybyprefixes
Heteroacyclic compounds
Namingofsubstituent groups
Locants
Namegeneration (alphabetization, punctuation, etc.)
RingedStructures
Struct>Name supportsthethesetypesofringedstructures:
Carbomonocyclic structures
Heteromonocyclic structures
Fusedpolycyclic structures:
Fusedpolycyclic trivially-namedstructures
Ringfusionsofmultiplerings
Ringfusionsoftwomultipleringsystems
Ringfusionsofmorethantworingsystems
Bridgedmonocyclic structures
Spiroringsystems
Someoftheseringstructures aredefinedbelow.
RingAssemblies
Aringassembly hastwoormoreidenticalcyclicsystemsjoinedtogetherbysingleordoublebonds.Allthecyclicsys-
temsareeitherasinglering,fusedsystem,alicyclicvonBaeyersystem,spirosystem,phanesystem,orfullerene.ChemBioDraw 14.0
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Figure10.1:Anexampleofaringassembly structure:1,1':2',1''-terphenyl.
FusedRingSystems
Struct>Name supportsfusedringsystemsoftwoormorerings,suchasthestructurebelow.
Figure10.2:cyclopenta [ij]pentaleno[2,1,6-cde]azuleneisafusedringsystem.
BridgedFusedRingSystems
ChemBioDraw supportsbipodal(bothbivalentandpolyvalent) simpleacyclic(chained)homogeneous (atomsofonly
oneelement)independent bridgedfusedringsystems.Forexample:
Figure10.3:Thebridgedfusedringsystem9,10-epidioxyanthracene.ChemBioDraw 14.0
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Polymers
Polymerstructures cannotbeexpressed bySMILES.However, Struct>Name supportsmanyhomopolymers, copoly-
mers,andalternating polymers. Forexample:
Figure10.4:polyaziridine compound withsulfamicacid(1:1)
OtherCompounds
Phosphorous andArseniccompounds
Si,Ge,Sn,andPbcompounds
Boroncompounds
Organometallic compounds
Struct>Name generates nameswithproperCIPstereochemistry descriptors.
Struct>Name providesdirectsupportforstoichoimetry specifiedasbracketproperties, includingfractionalstoi-
chiometry. Also,themannerinwhichthestoichiometry of0.5("hemi")and1.5("sesqui") ishandledisimproved. For
example:
Figure10.5:2-(aminooxy) aceticacidhemihydrochloride
Struct>Name followsIUPACrulesascloselyaspossiblewhengenerating chemicalnames.However, whilehandling
indicatedhydrogens, itconformstoCASnomenclature recommendations. Forexample,thecarbonatombetween
twooxygenatomsin1,3-dioxolecanneverformdoublebondsasitstwoneighbors (oxygenatoms)havenofree
valences. WhilepreferredIUPAC(PIN)nameforthatstructureis2H-1,3-dioxole,Struct>Name generates thename
1,3-dioxole.ThenameproducedbyStruct>Name conformstoCASnomenclature recommendations inthisregard.
Unsupported Structures
Thisfeaturehasafewlimitations forinterpreting somestructures suchas:
Sulfonesandchalcogen analogsChemBioDraw 14.0
Chapter10:Struct=Name (UltraFeature) 146of315

Isotopically modifiedcompounds
Radicals,ions,andradicalions
AutoUpdate
Youcanincludechemicalproperties, includingthechemicalnameandanalysis,inacaption,andthecaptioncontent
willupdateautomatically whenyoumodifythestructure.Formoreinformation onaddingchemicalproperties tocap-
tions,see"AnalysisData"onpage66.
Totoggletheauto-updatefeature:
1.Pointtothecaption.
2.Right-clickandselectAuto-update.Acheckmarkappearsnexttothecommand whenitisselected.Successive
clickstogglethecommand onandoff.
Whenauto-updateison(default)thelabelupdateseachtimeyoumodifythestructure.
Note:Forlargestructures, thenewlabelmaynotappearforafewseconds.Youdonothavetowaitforthenew
labeltoappearbeforecontinuing tomodifyyourstructure.
Name>Struct
YoucantypeachemicalnameandName>Struct willdrawthestructure.
Althoughsometradenamesaresupported, Name>Struct isnotintendedtointerprettradeorcommonnames.Achem-
icaldatabase, suchasChemBioFinder.com, ismoreappropriate forobtainingthesestructures.
Note:Usethewords‘alpha’and‘beta’whenenteringformsofaminoacids.Forexample,‘alphaalanine’and‘beta
alanine’arevalidname>struct chemicalnames.
Note:Name>Struct canalsointerpretmanyGermannames.
Converting NamestoStructures
Toenterthenameandconvertittoitsstructure:
1.NavigatetoStructure>ConvertNametoStructure.
TheInsertStructuredialogboxappears.
2.Typethename(example: 2-bromobenzoic acid)orpastethecopiednamefromtheclipboard.
Tip:Youcanpastethenameusingkeyboardcommands: <CTRL>+<V> .
3.Toplacethenamebelowthestructure,selectPastenamebelowstructure.
4.ClickOK.
Converting Clipboard Names
Topasteanameontheclipboardasastructure:ChemBioDraw 14.0
Chapter10:Struct=Name (UltraFeature) 147of315

1.Clickinthedocument window.
2.NavigatetoEdit>PasteSpecial>NameasStructure.Thestructureappearsinyourdocument.
Converting Captions
Youcanconvertacaptiontoastructure.
1.Selectthecaption.
2.NavigatetoStructure>ConvertNametoStructure.
Supported Structures
Struct>Name cannamecompounds inclassesofstructures:
Principal GroupsinRingsandChains
AcidHalides
Amidederivatives ofacids
Alcoholsandchalcogen analogs
Anhydrides
Aldehydes andchalcogen analogs
Carbonicacids
Amides
Imides
AminesandImines
Nitricacids
Carboxylic Acids
Peroxyacids
Carboxylic Esters
Salts
Heteroatomic acidhalides
Sulfidesandchalcogen analogs
Heteroatomic acids(P,B,As)
Sulfoxides andchalcogen analogs
Heteroatomic esters
Peroxides
Hydrazides
S,SeandTeAmides
Hydrazines
S,Se,andTeAcidHalides
Hydroperoxides
S,Se,andTeAcids
Ketonesandchalcogen analogs
S,Se,andTeEsters
Nitriles
RingedStructures
Bridgedmonocyclic structures
Heteromonocyclic structures
Carbomonocyclic structures
Ringfusionsofonlytworings
Fusedpolycyclic trivially-namedstructures
Ringfusionsoftwomultipleringsystems
OtherCompounds
Boroncompounds
Si,Ge,Sn,andPbcompounds
Organometallic compounds
Phosphorous andArseniccompounds
Name>Struct recognizes mostorganicandinorganicnomenclature. However, sometypesarenotsupported:
Coordination complexes
Polyboranes
Polymers
Somehighly-bridgedringsystems,includingfullerenes andporphyrins/porphines
Somestereochemistry designators: +,-,+/-,+-,D,l,dl,endo,exo,syn,anti,r,t,cChemBioDraw 14.0
Chapter10:Struct=Name (UltraFeature) 148of315

Chemistry Features
Structure Analysis
Youcandisplaythechemicalformula,exactmass,molecular weight,m/z,andelemental analysisfortheentiredoc-
ument,astructure,orapartofastructureusingtheAnalysiswindow.
Valuesforselectedobjectsinthedocument windowareshown.Ifnostructureisselectedinyourdocument, values
fortheentiredocument areshown.
Youcanhavethiswindowopenasyoudrawinthedocument. Itshowsthecurrentvaluesasyoudraw,seeexample
below:
TheDecimalssettingappliestoExactMass,Molecular Weight,andm/zonly.ThevaluesdisplayedintheAnalysis
windowincludes:
Formula.Themolecular formulashowingtheexactnumberofatomsofeachelementinthemoleculeandcharges,
radicals,andisotopes.
ExactMass.Theexactmolecular massofthestructure,whereatomicmassesofeachatomarebasedonthemost
commonisotopefortheelement.
Molecular Weight.Theaveragemolecular massofthestructure,whereatomicmassesarebasedonthenatural
abundance ofallisotopesoftheelement.
m/z.Mass/charge. Theweightsofthemostcommonisotopesandagraphicalrepresentation oftheisotopicabund-
anceisshown.
Themolecular weightaccountsfortheisotopesforeachatomandtheirnaturalabundance. Wherethereismorethan
oneabundantisotope,thisfeaturecomputes multiplemolecular weights.Lowabundance combinations (whether
becausetheisotopeisinlowabundance orbecauseitincludesmanymoderate-abundance contributions) arenot
takenintoaccount.
Elemental Analysis.Thepercentbyweightofeachelementinthestructure.
Toopentheanalysiswindow:
1.Selecttheentirestructure,orpartofthestructure.Ifnothingisselected,theanalysiswindowdisplaysvalueforthe
entirestructure.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 149of315

2.NavigatetoView>Show AnalysisWindow.Theanalysiswindowsdisplaysvaluesforthepartsofthedrawing
youselect,ortheentiredrawingifnothingisselected.
3.(Optional) SelectPastetoaddtheanalysisinformation toyourdrawing.Theinformation appearsasacaptionthat
youcanedit.
Figure11.1:Structural analysis
Theinformation updatesasyoueditthestructure.Youcanshoworhidetheinformation:
1.Usinganytool,right-clickthecaption.
2.PointtoAnalysis,andselectordeselecttheitemtoshow/hide.
ChemBioFinder hotlink
PerkinElmer Informatics maintains avastdatabaseofcompounds andtheirproperties. ChemBioDraw providesalive
Internetconnection toadatabase, thatincludes:
Linkstoavailabledataresources suchasthePerkinElmer Informatics ChemIndex.
LinkstoChemSpider database.
Namesandsynonyms.
Chemicalidentifiers suchasCASRegistryNumbersandChemACX IDs.
TheHotLinkinformation andthedataitselfarecontinually updated.
TheHotLinkdisplaysinformation forthestructureinthedocument window.
ToopentheChemBioFinder HotLink:
1.Selectastructure.
2.GotoView>ShowChemBioFinder HotLinkWindow.
Note:ToaccessChemSpider database, clickonthevalueofeitherInchiKeyorStdInchiKeyintheProperties
tableintheChemBioFinder Hotlinkwindow.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 150of315

Stereochemistry
ChemBioDraw calculates theabsolutestereochemistry according totheCahn-Ingold-Prelog(CIP)priorityrules.For
moreinformation, see"Cahn-Ingold-Prelog"onpage284.
Onlytetrahedral anddouble-bondstereochemistry aresupported, andonlynon-racemicstereochemistry isinter-
preted.Stereochemical indicators foraromaticbondsarenotdisplayed.
ChemBioDraw usesthisnotation:
(R),(S)
Standardtetrahedral stereochemistry
(r),(s)
Tetrahedral stereochemistry determined byotherstereochemical centers.Forexample:cis-decalinandmyo-inositol
(E),(Z)
Standarddouble-bondstereochemistry
Stereochemistry Indicators
ChemBioDraw updatesstereochemistry indicators asyouchangeyourdrawing.
Toincludestereochemistry indicators inyourdrawing:
1.Selectthestructure.
2.Right-clickandselectObjectSettingsfromthecontextmenu.
3.FromtheDrawingtab,underAtomIndicators andBondIndicators, selectShowStereochemistry .
Thestereo-centersaremarked,asshowninthisexample:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 151of315

HidingIndicators
1.Selecttheindicatoryouwanttohide.
2.Right-clickandselectHideIndicatorfromthecontextmenu.
Formatting Indicators
Tochangethefontstyle:
1.Selecttheindicatoryouwanttomanipulate.
2.Right-clickandselecttheStylefromthecontextmenu.
Applying Parenthesis
Toapplyparentheses tostereochemistry indicators:
1.NavigatetoFile>Preferences .
2.FromthePreferences dialog,undertheBuilding/Display tab,selectIncludeParentheses WhenShowing Ste-
reochemistry .
Removing Indicators
Toremoveanindicator,clickonitusingtheErasertool.
Positioning Indicators
Youcanpositionaqueryindicatorbyeitherdraggingitorenteringanumericvalueforthenewlocation.
Toindicateanexactlocation:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 152of315

1.Selecttheindicatoryouwanttore-position.
2.Right-clickandchoosePositionfromthecontextmenu.ThePositionIndicatordialogappears.
3.Clicktheappropriate option,andtypeavalue,asdescribed inthetablebelow:
ToPosition TypeaValueforthePositionby
Fromtheatomorbondcenter
toindicatorcenterAngle,indegrees
or
Clock,inclocktime
Fromtheatomorbondcenter
tobottomleftofindicator
baselineOffset,horizontal, andvertical
Atspecifiedcoordinates Absolute,horizontal, andvertical
Relativestereochemistry
Youcanspecifyrelationships betweengroupsofstereocenters withinamolecule.
Thisnotationenablesyoutodescribestereochemical properties andindividualstereocenters ratherthantheentire
molecule. Asaresult,youcanillustrateproperties ofseveralenantiomers usingonlyafew(orjustone)structures.
Thenotationisillustrated below:
Toaddstereochemical notationtoastructure,gotoStructure>Enhanced Stereochemistry .
Thepowerofthisnotationbecomesclearwhenyoudrawcomplexenantiomers. Forexample,beta-cypermethrin isa
mixtureoffourdistinctstereoisomers consisting oftwoenantiomeric pairs.However, drawingthisrequiresonlyone
structure:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 153of315

Figure11.2:beta-Cypermethrin
Twostereo-centershavethe&1designation becauseoftheirfixedrelativeconfiguration: whenoneis(R)theother
mustbe(S).Asaresult,theyformagroup.Thethirdstereocenter variesindependently andisdesignated &2.Group
numbersareincremented automatically. Toseeallthebeta-cypermethrin stereoisomers, gotoFile>Open
Samples>b-Cypermethrin .
Toindicatestereochemistry foragroup:
1.SelectallatomsinthegroupusingSHIFT+click.
2.GotoStructure>Enhanced Stereochemistry andselectastereochemistry marker.
See"Relativestereochemistry" onpage153forinformation onshowingandhidingindicators.
Youcansaveenhanced stereochemistry notationinanyoftheseformats:CDX,CDXML,MOLV3000,RXNV3000,
SKC,TGF.
WhensavingtoSKCorTGFformat,theindicators areconverted intocorresponding DataSGroups.Whenever you
openSKCorTGFfilescontaining suchDataSGroups,theyareconverted intotrueEnhanced Stereochemistry val-
ues.
Chemical Annotations
ChemBioDraw providesthefollowingtoolsandtoolpalettesthatenableyoutoaddchemicalannotations toyourdoc-
uments:
Orbitaltoolspalette.Draworbitals
Chemical SymbolToolspalette.Drawcharges,radicals,andothersymbols
Orbitals
Youdraworbitalssothatthenodeappearsfirst.Thenyoucanchangethebackground color,shading,andsolidcolor
usingtheColormenu.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 154of315

DisplaytheInfowindowtoviewtheorbital’slengthandanglerelativetotheX-axiswhileyoudrawit.Toconstrainthe
lengthandangleofanorbital,navigatetoObject>FixedLengthsorFixedAngles.
Note:Orbitalsarenotnormallyapartofthestructuretheyaredrawnnearandarenotselectedwhenyou
double-click abond,atom,oratomlabelwithaselectiontool.Togrouptheorbitalswiththestructure,navigateto
Object>Group.See"Grouping Objects"onpage85.
S-orbitals
Thes-orbitalisshownbelow:
Todrawansorbital:
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthes-orbitaltoolfromthepalette.
2.Clickanatominthedrawingwheretheorbitalwillbecentered.
SigmaOrbitals
Thesigma-orbitalisshownbelow:
Todrawaσ-orbital:
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselecttheσ-orbitaltoolfromthepalette.
2.Clickanatominthedrawingwheretheorbitalwillbecentered.
SingleLobeOrbitals
Todrawasinglelobeorbital:
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthesinglelobeorbitaltoolfromthepalette.
2.Clickanatomwherethenarrowendoftheorbitalwillbeattached.
P-orbitals
Thep-orbitalisshownbelow:
Todrawaporbital:
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthep-orbitaltoolfromthepalette.
2.Clickanatomwherethenodeoftheorbitalwillbeattached.
HybridOrbitals
Thehybridorbitalisshownbelow:
Todrawahybridorbital(‘sp3’):
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthehybrid-orbitaltoolfromthepalette.
2.clickanatomwherethenodeoftheorbitalwillbeattached.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 155of315

D-orbitals
Thed-orbitalisshownbelow:
Todrawadorbital(‘dxy’):
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthed-orbitaltoolfromthepalette.
2.Clickanatomwherethenodeoftheorbitalwillbeattached.
Todrawadz2-orbital:
1.HolddownthemousebuttonovertheOrbitaltoolanddragtoselectthedz2-orbitaltoolfromthepalette.
2.Clickanatomwherethenodeoftheorbitalwillbeattached.
Chemical Symbols
Youcanmoveanyattachedchemicalsymbol(otherthanH-dotandH-dash)anydistancefromitsrelatedatom.The
availablechemicalsymbolsare:
Figure11.3:Chemical Symbols:A)CirclePlus;B)Plus;C)Radicalcation;D)Lonepair;E)ElectronPushing;F)H-
dot;G)Attachment point;H)Polymerbeadattachment point;I)Attachment point;J)Attachment point;K)H-dash;L)
RadicalPushing;M)Radical;N)Radicalanion;O)Minus;P)Circleminus.
Youcanplaceunattached symbolsanywhere withinyourdocument andresizethem.
H–dotandH–dash
TorepresentahydrogenatomthatiscomingoutoftheplanetowardyoualongtheZaxis,usetheH–dotsymbol.
Torepresentahydrogenatomthatisdirectedbackwards intotheplaneawayfromyoualongtheZaxis,usetheH–
dashsymbol.ToinsertH–dotsandH–dashes,clickanatom.
LonePair/Diradical
UsethelonepairsymboltoindicatealonepairofelectronscommoninLewisstructures.
Tousethelonepairsymbol:
1.HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthelonepairfromthepalette.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 156of315

2.Clickanddragtheatomtowhereyouwantthelonepair.Thelonepairisoffsetfromtheatomatafixedposition.
ElectronandRadicalPushing
ChemBioDraw providestheElectronPushingandRadicalPushingtoolsforillustrating electrontransfer.Electron
transferscanbedrawnbetweenatoms,bonds,andorbitals.Formoreinformation, see"ElectronandRadicalPush-
ing"onpage132.
Radical
Usetheradicalsymboltoindicateasinglenon-bondedelectron.
Tousetheradicalsymbol:
1.HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselecttheradicalfromthepalette.
2.Clickanddragtheatomtowhereyouwanttheradicalsymbol.
Note:Thelonepairsymbolisinterpreted asadiradicalwhenitisplacednexttoanunlabeledcarbonatom.
RadicalCationandRadicalAnion
Usethechargeradicalsymbolstorepresentradicalsthatarecharged.
Tousethechargeradicalsymbols:
1.HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthesymbolfromthepalette.
2.Clickanddragtheatomtowhereyouwantthesymbol.
3.Clickanatomtoaddaradicalcationorradicalanionsymbolinahorizontal orientation.
ChargeSymbols
Todrawachargeandassociate itwithastructure:
1.HolddownthemousebuttonovertheChemicalSymbolstoolanddragtoselectthechargesymbolfromthe
palette.
2.Clickanddragtheatomtowhichyouwantthechargetocorrespond.
Thenumberofhydrogenatomsincreases ordecreases asappropriate fortheadditionofthecharge.
Attachment Points
Indicating anattachment pointisusefulinpolymer-boundcombinatorial synthesis, proteinchemistry, andothersitu-
ations.TheChemicalSymbolstoolbarincludesattachment pointdrawingtoolsthatindicateapointofattachment
whilemaintaining chemicalmeaning.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 157of315

Thebeadtoolsareintendedtoindicateattachment toaresin.Anyofthesetoolsmaybeusedforvariableattach-
mentsinqueries(see"Attachment Points"onpage122);but,onlythediamondtoolshowsranknumbers.Thismeans
that,asyouadddiamondsymbolstoastructure,thepointswillhavesequential numbers.
Note:Youcanresizeapolymerbeadbyselectingitwithamarquetool,anddraggingtheresizedraghandles.
RotatingaSymbol
Youcanrotatetheradicalanion,cation,andlonepairsymbolsaroundthesameendfromwhichtheywereoriginally
drawn.Forexample,theradicalcationsymbolisrotatedandresizedfromthecharge.TheInfowindowshowsthe
anglethatoneoftheendsofasymbolmakeswiththeX–axisasyourotate.
Torotateachemicalsymbol:
1.Selectthechemical symbol.
2.Dragtherotationhandleonthechemicalsymbol.See"RotatingObjects"onpage82.
Chemical Properties
ChemicalPropertyPrediction isafeaturesupported byChemBioOffice. Itenablesyoutocalculatevaluesforawide
rangeofmethodologies; forexample,topological descriptors suchastheWeinerindexandBalabanindex,ther-
modynamic descriptors suchassolubility,meltingandboilingpoints,andpartitioncoefficients suchasCLogP,prop-
ertiesrelatedtothethree-dimensional shapeandvolumeofachemicalsuchastheConnollysurfaceareaand
volume.Intotal,youcancalculatemorethan100chemicalproperties foragivenstructure.
Foralistofproperties availableinaspecificapplication, clicktherespective linkbelow,orvisitthePerkinElmer
Informatics website.
"PropertyPredictions inChemBioDraw" onpage158
"PropertyPredictions inChem3D" onpage163
"PropertyPredictions inChemDraw/Excel" onpage162
"ChemBioFinder Properties" onpage164
Property Predictions inChemBioDraw
Youcanenterpredictedvaluesforthephysicalandthermodynamic properties ofachemicalstructureofupto100
atoms.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 158of315

Theproperties arecalculated usingthemostreliablemethodsforthegivenstructure.Log P,andCMRvaluesbased
onliteraturevaluesratherthanacalculation areincludedinthereportfile.Thereportisproducedasatextfileandthe
information initcanbecutandpastedtootherdocuments likeaworddocument.
Alistofalltheproperties calculated isasfollows:
B H P
BoilingPoint HeatofFormation pKa
C Henry’sLawConstant T
CriticalPressure L tPSA
CriticalTemperature LogP
CriticalVolume LogS
CLogP/CMR M
G Meltingpoint
GibbsFreeEnergy MR
AboutMolecular Networks
*MOSES.pKa, MOSES.logS andMOSES.logP forpredicting aciddissociation constants, aqueoussolubilityand
octanol/water distribution coefficients ofchemicalcompounds arecomputational calculator modulesbasedonMolecu-
larNetworks' cheminformatics platformMOSES.MOSESisdeveloped, maintained andownedbyMolecular Net-
worksGmbH,Erlangen,Germany. Forfurtherinformation pleasevisitwww.molecular- networks.com/moses .All
rightsreserved.Molecular Networks GmbH,Erlangen,Germany(www.molecular- networks.com ).
Limitations
Onlythefollowingatomtypesandhybridization statesareparameterized:
Csp3Csp2
CaromaticCsp
Nsp3Nsp2
NamideNaromatic
NspOsp3
Osp2 Psp3
Ssp3
Ssp2 SsulfoxideSsulfone
F Cl Br IChemBioDraw 14.0
Chapter11:ChemistryFeatures 159of315

Boiling Point
TheboilingpointisreportedinKelvin.
Asolutionboilsataslightlyhighertemperature thanthepuresolvent.Thechangeinboilingpointiscalculated using
theformula:
WhereKbisthemolalboilingpointconstant,mistheconcentration ofthesoluteexpressed asmolality,andΔTbis
thechangeintemperature.
Critical Pressure
Reportedinbars,thisistheleastappliedpressurerequiredatthecriticaltemperature toliquefyagas.
Critical Temperature
ReportedinKelvin,thisisthetemperature abovewhichagascannotbeliquefied,regardless ofthepressureapplied.
Critical Volume
Reportedincm3/mol,thisisthevolumeoccupiedbyonemoleofasubstance atthecriticaltemperature andpres-
sure.
CLogP/CMR
UseCLogPtocalculaten-octanol/water partitioncoefficient (logPow).LogPvaluesbasedonliteratureratherthancal-
culationsareincludedinthereportfile.
UseCMRtocalculateMolarRefractivity. MRvaluesbasedonliteratureratherthancalculations areincludedinthe
reportfile.
Note:CLogPandCMRvaluesappearonlyinChemBioDraw UltraandChemDraw Ultra.
GibbsFreeEnergy
Gibbsfreeenergyisdefinedas:
Whichissameas:
ChemBioDraw 14.0
Chapter11:ChemistryFeatures 160of315

Where:
Uistheinternalenergy(SIunit:Joule)
pispressure(SIunit:Pascal)
Visvolume(SIunit:m3)
Tisthetemperature (SIunit:Kelvin)
Sistheentropy(SIunit:jouleperKelvin)
Histheenthalpy(SIunit:Joule)
Note:HandSarethermodynamic valuesfoundatstandardtemperature andpressure.
HeatofFormation
ReportedinKJ/mole,theheatofformationistheincreaseinenthalpyresultingfromtheformationofonemoleofasub-
stancefromitsconstituent elementsatconstantpressure.
Henry’s LawConstant
Aunitlessvalue,Henry'sLawConstantcanbeexpressed as:
Where‘p’isthepartialpressureofthesoluteinthegasabovethesolution,‘c’istheconcentration ofthesoluteand
‘kH,pc’isaconstantwiththedimensions ofpressuredividedbyconcentration. Theconstant,knownastheHenry's
lawconstant,dependsonthesolute,solvent,andtemperature.
LogP
Thepartitioncoefficient isaratioofconcentrations ofun-ionizedcompound betweentwosolutions. Tomeasurethe
partitioncoefficient ofionizablesolutes,thepHoftheaqueousphaseisadjustedsothatthepredominant formofthe
compound isun-ionized.Thelogarithmoftheratiooftheconcentrations oftheun-ionizedsoluteinthesolventsis
calledLogP.
Normally, oneofthesolventschoseniswater;thesecondishydrophobic, suchasoctanol.
TheformulatocalculateLogPis:
LogS
LogSdetermines thesolubilityofasubstance, measured inmol/liter.
Theaqueoussolubilityofacompound isknowntosignificantly affectabsorption anddistribution characteristics of
thatcompound.ChemBioDraw 14.0
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Note:LogScalculations areavailableonlyinMicrosoftWindowsversionofChemBioDraw.
Melting point
Isthetemperature atwhichasolidbecomesaliquidatstandardatmospheric pressure.Atthemeltingpoint,thesolid
andliquidphaseexistinequilibrium. Theformulatocalculatemeltingpointis:
Where‘T’isthetemperature atthemeltingpoint,‘ΔS’isthechangeinentropyofmelting,and‘ΔH’isthechangein
enthalpyofmelting.
MR
TheMolarRefractivity isestimated byCrippen'sfragmentation andViswanadhan's fragmentation method.Additional
empiricalLogPdataappearsforselectedsubstances inthereportfile.
pKa
pKaisthenegativelogoftheaciddissociation constantKa.Itdescribes thetendencyofcompounds orionstodis-
sociateinsolution.Itiscalculated usingtheformula:
EmpiricalpKadataappearsforselectedsubstances inthereportfile.
Note:pKacalculations areavailableonlyinMicrosoftWindowsversionofChemBioDraw.
tPSA
Calculation ofpolarsurfaceareabasedonfragmentcontributions.
Property Predictions inChemDraw/Excel
TheProperties featureinChemDraw/Excel letsyouviewthevaluesofdifferentproperties foragivenstructure.Each
propertyiscalculated usingthe“bestavailable”method.Alistofproperties availableinChemDraw/Excel islistedin
thetablebelow.Formoreinformation ontheseproperties, seeChemDraw/Excel onlinehelp,orvisitthePerkinElmer
Informatics website.
Theproperties availableinclude:
B F MeltingPoint ShapeAttribute
BalabanIndex FormalCharge MolarRefractivity ShapeCoefficient
BoilingPoint FreezingPoint MolecularFormula SumOfDegrees
C G MolecularWeight SumofValenceChemBioDraw 14.0
Chapter11:ChemistryFeatures 162of315

Degrees
ClusterCount GibbsFreeEnergy N T
CriticalPressure HNumberofRotatable
BondsTotalConnectivity
CriticalTemperature HeatofFormation OTopologicalDia-
meter
CriticalVolume Henry'sLawConstantOvality TopologicalIndex
ConnollyAccessibleArea I PTotalValenceCon-
nectivity
ConnollyMolecularSurface
AreaIdealGasThermal
CapacityPrincipalMomentsof
Inertia(X,Y,Z)V
ConnollySolventAccess-
ibleSurfaceAreaL PolarSurfaceArea VaporPressure
ConnollySolvent-Excluded
VolumeLogP R W
E M Radius WaterSolubility
ExactMass Mass S WienerIndex
Property Predictions inChem3D
Chem3Dletsyoubuild,analyze,andcomputeproperties veryeasily.Inadditiontoanalyzingstructures tocalculate
massandformula,predicting numerous physicalproperties, youcanalsoperformcalculations formolecular topology.
Alistofproperties availableinChem3Dislistedinthetablebelow.Formoreinformation ontheseproperties, see
Chem3DonlinehelporvisitthePerkinElmer Informatics website.
B G MolWeight SpinDensity
BalabanIndex GibbsFreeEnergy MolecularMass SumOfDegrees
BoilingPoint H MolecularSurfacesSumofValence
Degrees
CHarmonicZeroPoint
EnergyMolecularTopological
IndexT
CPHeatCapacity MolecularVolumeThermodynamic
Energy
CvHeatofFormation MullikenChargesTopologicalDia-
meter
ClusterCount Henry’sLawConstantMullikenPopulations TotalConnectivityChemBioDraw 14.0
Chapter11:ChemistryFeatures 163of315

ConnollyAccessibleAreaHyperPolarizability m/z TotalEnergy
ConnollyMolecularAreaHyperfineCoupling
ConstantsNTotalValenceCon-
nectivity
ConnollySolventExcluded
VolumeI NumRotatableBonds V
CriticalPressureIdealGasThermal
CapacityO VaporPressure
CriticalTemperature InternalEnergy Ovality W
CriticalVolume IonizationPotential P WaterSolubility
D K PartitionCoefficient WienerIndex
Dipole KineticEnergy pKa Z
E L PolarSurfaceArea Zero-PointEnergy
ElectronDensity LogP Polarizability
Electrostatic Potential LogS PotentialEnergy
ElementalAnalysis LowdinCharges PrincipalMoment
Enthalpy LowdinPopulations R
Entropy M Radius
ExactMass Mass RMSForce
F MeltingPoint S
FormalCharge MolFormula SCFEnergy
Frequencies MolFormulaHTMLShapeAttribute
MolRefractivity ShapeCoefficient
ChemBioFinder Properties
Theproperties listedbelowcanbecalculated inChemBioFinder UltraforChemBioOffice. Formoreinformation on
theseproperties andhowtocalculatethem,seetheChemBioFinder onlinehelp.
B H P
BalabanIndex HeatofFormation PartitionCoefficient
BoilingPoint Henry’sLawConstant pKa
C I PolarSurfaceArea
ChemicalName IdealGasThermalCapacity PrincipalMoment
ClusterCount L R
CriticalPressure LogP Radius
CriticalTemperature LogS SChemBioDraw 14.0
Chapter11:ChemistryFeatures 164of315

CriticalVolume M ShapeAttribute
ConnollyAccessibleArea Mass ShapeCoefficient
ConnollyMolecularArea MeltingPoint SumofDegrees
ConnollySolventExcludedVolume MolFormula SumofValenceDegrees
E MolFormulaHTML T
ElementalAnalysis MolRefractivity TopologicalDiameter
ExactMass MolWeight TotalConnectivity
F MolecularTopologicalIndex TotalValenceConnectivity
FormalCharge m/z V
G N VaporPressure
GibbsFreeEnergy NumRotatableBonds W
O WaterSolubility
Ovality WienerIndex
ViewingChemical Properties
Toviewchemicalproperties:
1.Selectthestructurewhoseproperties youwanttoview.
2.NavigatetoView>ShowChemical Properties Window.TheChemicalProperties windowappears.
3.Topastethebasicproperties intoyourdocument, clickPaste.
4.Tocreateareportandviewresultsforotherfragmentation methods,clickReport.
3DViewing
Asyoucreateyourdrawing,youcanviewitinthree-dimensions. TwofeaturesinChemBioDraw letyouviewstruc-
turesinthreedimensions.
Note:ChemBio3D mustbeinstalledonyourcomputertopreviewstructures inthreedimensions.
3DModel
Usea3Dmodeltopastea3Dversionofthestructureintoyourdrawing.
1.Selectthestructure.
2.NavigatetoEdit>Get3DModel.The3Dstructureappearsinthedocument window.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 165of315

ToviewthemodelinChemBio3D, double-clickonit.
Note:3Dobjectsinsertedinthiswaycannotbetransferred betweenplatforms. Formoreinformation, see"File
Formats"onpage273.
Note:Youcancopyamodelusing"CopyasCDX"fromChemBio3D andpasteintoChemBioDraw. Theresultis
aChemDraw structurewith3Dcoordinates, anditispossibletorotatethisstructurein3Dusingthestructureper-
spectivetool.
ChemBio3D PreviewOptions
Thepreviewwindowdisplaysstructures youselectin3D,anddisplaysallstructures ifnoneareselected.ChemBio
3DPreviewworksonlyforchemicalstructures.
Toview,navigatetoView>ShowChemBio3D HotlinkWindow.Forexample:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 166of315

Withthepreviewwindowopen,youcanchangethestructure’s appearance, ineitherthedocument window,orthepre-
viewwindow.
IntheDocument Window
Withthepreviewwindowopen,youcanstillchangeyourdrawinginthedocument window.Thepreviewwindow
updatestoreflectthechanges.
InChemBio3D Preview
Thepreviewwindowoffersseveraloptionstoviewstructures.
Figure11.4:A)LaunchChem3D; B)Displaymode;C)Select;D)Translate; E)Rotate;F)Zoom;G)Spin;H)Rock.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 167of315

LaunchChem3D.ThestructurewillappearinChemBio3D asamodelthatyoucanedit.
DisplayMode.Choosedisplayoptionsforthemodel:wireframe,stick,ball&stick,cylindrical bonds,andspace
filling.
Select.Selectthestructureorpartsofit.
Translate.Movethestructure.
Rotate.Rotatethestructureinthreedimensions (theimagerotatesonlyintheChemBio3D Preview).
Zoom.Enlargeorreducetheapparentsizeofthestructure.
Spin.Rotatethestructurehorizontally inonedirection.
Rock.Rotatethestructurehorizontally backandforth.
Returning totheDocument Window
ToexittheChemBio3D Preview,closethepreviewwindow.
Toeditthe3Dmodel:
1.Double-clickthe3Dstructure.ChemBio3D opens.
2.EditthestructureandcloseChemBio3D.
TheeditedstructureappearsintheChemBioDraw document window.
TLC
TheTLC (ThinLayerChromatography) Toolletsyoudepictthinlayerchromatography plates.Thetoolcreatesarect-
angularplatewithanoriginline,solventfront,andoneormorelanes.Thelanescanbepopulated withspotsofdif-
ferentRf,size,shape,orcolor.
TocreateaTLCplate:
1.SelecttheTLCtoolfromtheChromatography toolbar.
2.Draginanydirectionfromthepointoforigin.Thewidthoftheplatedetermines thenumberoflanes.
Youcanmodifytheplateasfollows:
Ifyouwantto Then
Changetheheightorwidthoftheplate. Dragaborderorcorner.
Movetheoriginorsolventfront. Clickanddragtheoriginorsolventfrontline.
Showorhidetheorigin,solventfront,borders,or
sideticks.Right-clickintheplateandselecttheappropriate
action.
UsetheTransparent optiontooverlaytheTLCplateon
ascannedplate.
Changetheorderoflanes. Dragtheoriginticktothenewlocation.
Add,delete,orduplicatealane. 1.PositionthecursoronthelanetodeleteorduplicateChemBioDraw 14.0
Chapter11:ChemistryFeatures 168of315

Ifyouwantto Then
(orbetweenlanestoadd).
2.Right-clickintheplate.
3.Selecttheappropriate action.
4.(Optional) Todeletealane,clickonitwiththeEraser
tool.
Moveaspot. Dragthespot.TheRfdisplaysasyoudrag.
Duplicateaspot. <CTRL>+drag thespottoadifferentlane.
Deleteaspot. ClickthespotwiththeErasertool.Ifyoueraseallspots
inalane,thelaneisdeleted.
DisplayorsettheRfforaspot;addacustom
spot..1.Right-clickonaspot.
2.PointtoTLCSpots,andtaketheappropriate action.
3.TodisplayRfforallspots,right-clickintheplate
andselectShowRffromtheTLCSpotssubmenu.
Changethestyleorcolorofaspot. 1.Right-clickaspot..
2.Choosethestyleorcolor.
Note:Keepingallstylesunchecked createsahollow
spot.
3.Tochangethestyleforallspots,right-clickinthe
plateandchoosethestylefromtheTLCSpotssub-
menu.
Enlargeor“smear”aspot. <Shift>+drag thespot.Whenyoupositionthecursor
onaspotandpress<Shift>,thecursorassumesoneof
threeshapes,depending onhowitispositioned:
Crossarrows,usedtoenlargeaspot
Horizontal arrow,usedtowidenaspot
Verticalarrow,usedtoelongateaspotorcreatea
crescent
RfDisplay
Right-clickaspotandselectShowRftoindicatethespot’sretentionvalue.Bydefault,thevalueofRfissettotwo
decimalplaces.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 169of315

MovingtheTag
EitherclickanddragthetagusingaselectiontoolorRight-clickthetagandchoosePosition. Editthevaluesin
thePositionIndicators box.
EditingtheRfValue
SelectthetagwiththeTexttoolandeditthevalue.
IfyouchangetheRfthespotwillmovetothenewpositionindicated.
IfyouedittheRftohavedifferentprecision, thatprecisionwillbepreserved.
ResizingSpots
Youcanresizespotsbyholdingdownthe<Shift>keywhilepointingatanedgeofthespot.Dragtheleftorrightsides
ofthespottoadjustthewidthonly.Dragfromthetoptoadjusttheheight.Dragfromthebottomtoadjustthetail.Drag
fromanyoftheotherfourcornerstoscaleallthreevalues.
Customizing Spots
TheTLCtoolcancreatethemostcommonspotshapes.Othertypesofspots,suchassmears,canbereproduced as
customspots.TheSetCustomSpotcommand letsyouinsertagraphicfileforaspot.Typically, thesefileswould
beproducedbyscanningaTLCplateandsavingthespotsinalibraryofspotshapes.
Gelelectrophoresis tool
GelElectrophoresis toolisavailableintheChromatography toolbarandfunctionsmuchliketheTLCtool.Itconsists
ofaplatecontaining severallaneswithoneormorebands.Thebandscanberesizedandmovedalongthelane.For
example,considerthefigurebelow:
Youcanperformthefollowingactiononaplate:
Option Action
Showscale. Ascalebarappearsontherightoftheplate.Bydefault,theunitis
displayedinkDa.HoweveryoucanchangeittoLog(Mass),ChemBioDraw 14.0
Chapter11:ChemistryFeatures 170of315

Option Action
Mass,ordistancefromthe“Units”submenu. ForLog(Mass)and
Massthehighestvalueisonthetop.Fordistancethehighest
value'1'isatthebottom.
ShowLane
Labels.Alabelappearsforeverylane.Youcanrenameandrotateitto
anydesiredangle.Whenoneofthelabelsisrotated,alltheother
labelsarealsorotatedbythesameangle.
SetRange… Adialogboxprompting forthenewrangeappears.Theexpected
valuesenteredinthisdialogarealways“kDa”.Thedefaultvalue
forrangeis10to10,00,000 (Mass),1to6(Log),and0to1
(Distance). Whenyouchangetherange,thebandsthatfalloutof
rangearehidden.
AddBands… Adialogboxprompting forthemassofthenewbandstobecre-
atedintheselectedlaneappears.Spaceisusedasaseparator.
Onlynumbersareallowed.Youcanalsoaddbandsbyhovering
overtheplatelanewiththeALTkeypressed.Thecursor
changesto'+',andclickingontheplatewilldepositanewband.
AddLane Addsanewlane.
DuplicateLaneAddsaduplicatelane.CTRL+dragging aselectedlane
alsoduplicatesalane.
DeleteLaneDeletesalane.
Alloftheitemsinaparticularlanecanbemodifiedsimultaneously, byhoveringoverthelaneandselectingthe
requiredcontextmenuoption.Forexample,youcandisplayalltheitemsinalaneinaspecificcolor,orhavethemdis-
playspecificstyles.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 171of315

Youcanperformthefollowingactiononaband:
Option Action
Showsize. Thecurrentvalueofthebandappearsaboveit.Thevalueis
alwaysshownontopoftheband,andisalwaysboundtoit.
Ifyoudragittoanotherposition,atetherappearsbetween
thebandandthetext.
YoucanmovethemarkerlabelbypressingtheALTkey.
SetSize. Adialogboxprompting forthenewmass(size)oftheband
appears.Thebandwillbeautomatically movedaccording to
itsnewvalue.Youcanlocatethebandsthatfalloutofrange
andarehidden.
Style Specifythestylefortheselectedband.Therearefourpos-
siblestyleoptionsavailable-Filled,Notfilled,dashed-bold,
anddoubled-filledbands.Thestylescanalsobecombined.
SetCustom
BandAdialogboxprompting youtoselectagraphicfiletobedis-
playedastheselectedbandappears.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 172of315

Option Action
DuplicateBandToduplicateaband,selectabandandCTRL+drag.
RemoveCus-
tomBandThecustombandsettingisremovedfortheselec-
tedbandandthebandappearsinitsdefaultstyle.
DeleteBand Deletesabandfromthelane.Youcanalsodeletethebands
inalanebyhoveringoverthemandpressingDelete.
Note:Youcanhaveemptylanes.
ChemNMR (UltraFeature)
UsingChemNMR, youcanestimateanddisplayprotonandCarbon-13chemicalshiftsforaselectedmolecule.
AswithChemBioDraw, youcanalsouseChemBio3D topredictNMR.ChemBio3D includesseveralinterfaces to
computational chemistry packages whichpredictNMR.Somepackages predictIRspectraandotherspectraaswell.
Formoreinformation onChemBio3D packages, whichhaveNMRpredictions, andtheiravailableparameters, seethe
Chem&Bio3DUserGuide.
SettingParameters ValuesinChemNMR
UsetheChemNMR optioninPreferences dialogtosettheparameter valuesinChemNMR. Seetheexamplebelow:
Solvent
Thesolventisnotuser-definableinChemNMR, exceptbyaddingnewcustomshiftcorrection data.Mostspectrain
thedefaultChemNMR databasearerunindeuterated chloroform, butthedatabaseisintendedtobesolvent-free.In
ChemBioDraw, youcanseteitherdeuterated chloroform, ordeuterated dimethylsulfoxideassolventfromthePrefer-
encesdialog.Spectralshiftswhichdependonthesolventaregenerallyindicatedas"rough"predictions.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 173of315

Spectrometer Frequency
ChemNMR's defaultforestimating protonNMRisaspectrometer frequency of300MHz.Tochangethedefaultfre-
quency,eithersetthenewfrequency usingthePreferences dialog,orholdthe<Alt>keywhileselectingPredict1H-
NMRShifts,andenterafrequency inMHzandrunthespectrum. Thenewfrequency willapplyuntilyouresetit,
includingafterclosingChemBioDraw. Thespectrometer frequency parameter onlyappliestoprotonNMR.
Forfurtherinformation, see:
"NMRShifts"onpage174(HowtorunNMRpredictions inChemDraw)
"Assigning Structures toSpectra"onpage175(Re-linkingatomstopeaks)
"ViewingSpectralAssignments" onpage175(Peaksassociated withatoms)
"Removing SpectralAssignments" onpage175(Dissociating peaksfromatoms)
"CustomShiftCorrection Data"onpage176(Addingnewspectruminformation)
"ChemNMR Limitations" onpage179(Elements andstandarddeviations)
"NMRReferences" onpage179(Sourcecitations)
NMRShifts
ChemNMR estimates chemicalshiftsforallhydrogenorcarbonatomsforwhichadditivityrulesareavailable.Fol-
lowingahierarchical list,itfirstidentifieskeysubstructures ofamolecule. Asubstructure providesthebasevaluefor
theestimated shift.Forexample,benzenewouldbethekeysubstructure oftrinitrotoluene.
Whenasubstructure isaringsystemnotavailableinthedata,ChemNMR approximates itsbaseshiftusingembed-
dedringsand,ifnecessary, willdisassemble theringintoacyclicsubstructures.
ChemNMR viewsremaining partsofthemoleculeassubstituents ofasubstructure. Eachsubstituent addsto,orsub-
tractsfrom,thebaseshiftofthesubstructure towhichitisattached.Additivityrulesdetermine theincrement ofeach
contribution. Ifanincrement forasubstituent cannotbedetermined, ChemNMR usesembedded substituents— smal-
lerstructuralunitswiththesameneighboring atoms.Or,itwilluseincrements ofidentical,orembedded substituents,
ofacorresponding substructure byassuming thattheeffectsofthesubstituents areofthesamemagnitude.
ChemNMR providesadetailedprotocoloftheestimation processapplied.Itgivessubstructures asnames,com-
poundclassesinmostcases,substituents intheformofalinearcode,respectively.
Italsoimplements modelsforethylenes (cis/trans) andcyclohexanes (equatorial/axial)
Toview1Hor13CNMRinformation:
1.Selectastructure.
2.NavigatetoStructure>Predict1H-NMRShiftsorPredict13C-NMRShifts.
ChemNMR redrawsthemoleculewiththeestimated shiftsanddisplaystheinformation andlinespectruminanew
window.
Modifying NMRFrequency
YoucanchangethedefaultNMRfrequency of300MhzinChemDraw ProtonNMRpredictions.
Tochangethefrequency:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 174of315

1.NavigatetoFile>Preferences .ThePreferences dialogappears.
2.SelectChemNMR option.
3.Specifythenewfrequency intheFrequency textbox.
4.ClickOK.
5.NavigatetoStructure>Predict1H-NMRShifts..ThepredictedNMRspectrumappears.
Assigning Structures toSpectra
ChemBioDraw Ultraletsyouassignstructures tospectra.Youcanthendisplaythestructureassociated withaspe-
cificpeakbyplacingthepointeronthatpeak.
Toassignstructures tospectra:
1.Openaspectralfile.
2.Drawthestructure(orstructures) toassigntothespectrum.
3.Selectspecificatomsandbondsinthestructure.
4.<Shift>+click thepeak,orpeaks,towhichyouwantthestructureassigned.
Theselectionrectanglesurrounds theselectedobjects.
5.NavigatetoStructure>MakeSpectrum-Structure Assignment .
Theselectedatomsandbondsinthestructureareassociated withtheselectedspectralpeaks.
ViewingSpectralAssignments
Toviewspectralassignments:
1.ClicktheLassoorMarqueetool.
2.Placethepointeroverapeak.Theassignedatomsorbondsarehighlighted.
Removing SpectralAssignments
Toremovespectrumtostructureassignments:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 175of315

1.ClicktheLassoorMarqueetool.
2.Selecttheobjectsfromwhichtoremovetheassignment.
3.NavigatetoStructure>ClearSpectrum-Structure .
CustomShiftCorrection Data
Youcanaddyourownshiftcorrection dataforprotonprediction tosupplement theexistingdatathattheChemNMR
algorithmuses.YouprovideyourdatainanSDfileandusethefiletoupdatetheChemBioDraw ChemNMR database.
Usingathird-partytool,suchasACDLabssoftwareorMnovaLite,youcanenhanceyourprediction results,thereby
supporting youranalysisprocess.WithMnovaLite,youcanassignyourspectrainMnovaNMRandsavethose
assignments toanSDfile.AddthemtoChemNMR database. Withenoughaddeddata,theprediction results
improve.(Consultyourapplication’s UserGuideforinstructions).
NMRDataFormat
Thecorrection datathatyouaddtoyourSDFfilemustbeinthisformat:
><SHIFT>
<atom_id>,<shift_ value>,<ignored>
Forexample:
><SHIFT1>
2,9.61,0.0
><SHIFT2>
3,8.92,0.0
Thecorrection dataforeachmoleculemustappearafterthemolecule’s structuraldata.Forexample,ifyourSDFfile
includesbenzene,theNMRdatamustimmediately followthebenzenestructuraldata.
Updating theChemNMR Database
OnceyouhaveanSDFfilethatcontainsthesupplementary, followthesestepstoupdatetheChemNMR database:
1.ExitChemBioDraw.
2.LocatetheChemBioDraw ChemNMR directory.
3.OpenaDOSprompt:
InWindows8,navigatetoStart>RunandentercmdintheRunwindow.ClickOK.
InWindows7,gotoStartandentercmdinthesearchfield.Pressthe<Enter>key.
4.AttheDOSprompt,navigatetotheChemNMR directoryinstep2.
5.Enterthecommand:
MakeChemNMRUserDB.exe <inputfile><resource directory> <outputdirectory>
where
<inputfile>isthefullpathandfilenameoftheSDFfilethatcontainsthecorrection data.
<resource directory> and<outputdirectory> arethefullpathtotheChemNMR directory.
6.RestartChemBioDraw.
Restoring DefaultNMRData
TostopusingyourowndataandrestoreChemBioDraw toitsoriginalsettings:ChemBioDraw 14.0
Chapter11:ChemistryFeatures 176of315

1.ExitChemBioDraw.
2.LocatetheChemNMR directory.
3.DeletethefilesUshiftdb5H1.txt andUsimilvecx.h1 .
4.RestartChemBioDraw.
ExampleSupplementary Data
Theexamplebelowrepresents anSDFfilethatincludessupplementary NMRdatafortwostructures. Thesup-
plementary datafollowsthestructuredataandisshadedgrayforclarity.
ACD/Labs07190711112D
14140000000015V2000
5.7578-1.99920.0000C000000000000
5.7578-3.32670.0000C000000000000
4.6062-1.32750.0000C000000000000
4.6062-3.98250.0000N000000000000
3.4547-1.99920.0000C000000000000
3.4547-3.32670.0000C000000000000
6.9094-1.32750.0000N030000000000
8.0609-1.99920.0000O050000000000
6.9094-0.00000.0000O000000000000
2.3031-1.32750.0000C000000000000
2.3031-0.00000.0000C000000000000
1.1516-1.99920.0000C000000000000
1.1516-3.32670.0000O000000000000
0.0000-1.32750.0000O000000000000
1210000
1320000
1710000
2420000
3510000
4610000
5620000
51010000
7810000
7920000
101110000ChemBioDraw 14.0
Chapter11:ChemistryFeatures 177of315

101210000
121320000
121410000
MZZC15
MZZC26
MZZC34
MZZC41
MZZC53
MZZC62
MCHG2718-1
MZZC79
MZZC813
MZZC910
MZZC107
MZZC118
MZZC1211
MZZC1312
MEND
><ID>
1
><solvent>d6- DMSO><SHIFT1>2,9.61,0.0> <SHIFT2>3,8.92,0.0>
<SHIFT3>6,9.01,0.0> <SHIFT4>10,3.11,0.0> <SHIFT5>11,1.16,0.0>
<SHIFTS>5$$$$  TH><solvent>d6- DMSO><SHIFT1>2,9.6,0.0>
<SHIFT2>3,8.91,0.0> <SHIFT3>6,9.11,0.0> <SHIFT4>10,2.75,0.0>
<SHIFT5>11,1.17,0.0> <SHIFT6>12,2.41,0.0> <SHIFTS>6$$$$
ACD/Labs07190711112D 15150000000016V20007.1683-1.95210.0000C0000
000000007.1683-3.24840.0000C0000000000006.0438-1.29620.0000C
0000000000006.0438-3.88870.0000N0000000000004.9194-1.9521
0.0000C0000000000004.9194-3.24840.0000C0000000000008.2927-
1.29620.0000N0300000000009.4171-1.95210.0000O050000000000
8.2927-0.00000.0000O0000000000003.7950-1.29620.0000C00000000
00003.7950-0.00000.0000C0000000000002.2489-2.17080.0000C0000
000000001.1401-1.51490.0000C0000000000000.0000-2.15520.0000O
0000000000001.1401-0.21860.0000O0000000000001210000132
000017100002420000351000046100005620000510100007
810000792000010111000010121000012131000013142000013
1510000MZZC15MZZC26MZZC34MZZC41MZZC53MZZC62MCHG2718-
1MZZC79MZZC814MZZC910MZZC107MZZC118MZZC1211MZZC1312MZZC
1413MEND><ID>2
><solvent>d6- DMSO><SHIFT1>2,9.6,0.0> <SHIFT2>3,8.91,0.0>ChemBioDraw 14.0
Chapter11:ChemistryFeatures 178of315

<SHIFT3>6,9.11,0.0> <SHIFT4>10,2.75,0.0> <SHIFT5>11,1.17,0.0>
<SHIFT6>12,2.41,0.0> <SHIFTS>6$$$$
ChemNMR Limitations
Theprogramhandlesthefollowingelementsandisotopes:
H,D,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Ga,
Ge,As,Se,Br,Kr,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd,
Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,At,Rn,Fr,Ra,Ac,
Th,Pa,U,Nep,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr.
Functional groupsareexpanded automatically.
Inthecaseof1HNMR,itestimates shiftsofabout90%ofallCHx-groupswithastandarddeviationof0.2.-0.3
ppm.Theuseofpolarsolventsmaystronglyincreasethesedeviations. Itdoesnotestimateshiftsofhydrogen
atomsbondedtoheteroatoms becausetheyaresignificantly affectedbysolvents,concentration, impurities, and
stericeffects.
Incaseof13CNMR,itestimates over95%oftheshiftswithameandeviationof-0.29ppmandstandarddeviation
of2.8ppm.
NMRReferences
SourcesforChemBioDraw NMRdataincludethefollowingpublications:
Fürst,A.;Pretsch,E.Anal.Chim.Acta1990,229,17.
Pretsch,E.;Fürst,A.;Badertscher M.;Bürgin,R.;Munk,M.E.J.Chem.Inf.Comp.Sci.1992,32,291-295.
BürginSchaller,R.;Pretsch,E.Anal.Chim.Acta1994,290,295.
BürginSchaller,R.;Arnold,C.;Pretsch,E.Anal.Chim.Acta1995,312,95-105.
BürginSchaller,R.;Munk,M.E.;Pretsch,E.J. Chem.Inf.Comput.Sci.1996,36,239-243.ChemBioDraw 14.0
Chapter11:ChemistryFeatures 179of315

ChemDraw/Excel andCombiChem
ChemDraw/Excel isanadd-inforMicrosoftExcelforWindows. Youcanaddchemicalstructures andotherdatafrom
ChemBioDraw oraChemBioFinder databasetoanExcelworksheet. Afterward, youcancalculateanyofavastarray
ofstructuralproperties orexaminesearchresultsfromanSDfile.IthasthesamesearchfeaturesasChemFinder.
Whenyouinstalltheadd-in,aChemOffice menuisaddedtotheExcelmenuandatoolbarappears.
SettingUpChemDraw/Excel
WhenyouinstallChemDraw orChemBioDraw, ChemDraw/Excel isalsoinstalled.TheChemDraw/Excel add-in
addsanewtabtoExcel2007,Excel2010,Excel2013ribboninterface.
IftheChemDraw/Excel add-inisdisabled,toenableit:
1.GotoFile>Options>Add- ins.
2.SelectChemDraw forExcelandclickGo.
3.FromAdd-InswindowmakesureChemDraw forExcelandChemDrawExcel 14 functions arechecked.
4.ClickOK.
ChemDraw/Excel add-inmayalsobedisabledbysomeotherthird-partyproductbyprogrammatically changing
registryvalues.Inthiscase,youcanenableitbyresettingthevalueof"LoadBehavior" at:HKEY_LOCAL_
MACHINE\SOFTWARE\Microsoft\Office\Excel\Addins\ChemDrawExcelAddIn14.ExcelAddIn andHKEY_LOCAL_
MACHINE\SOFTWARE\Wow6432Node\Microsoft\Office\Excel\Addins\ChemDrawExcelAddIn14.ExcelAddIn ( for
64-bitsystemrunning32-bitMicrosoftOffice).Resetthevalueof‘LoadBehavior’ to3from0andre-launchExcel.
TouseChemDraw/Excel, openaChemOffice worksheet. GotoChemOffice14 >NewChemOffice Worksheet .
Whenaworksheet isactive,ChemDraw/Excel appearsinthetitlebar.
ToconvertanormalExcelworksheet intoaChemDraw/Excel worksheet, gotoChemOffice14 >ConvertWork-
sheet.“ChemDraw forExcel”appearsintheExceltitlebar.
OlderChemDraw/Excel workbooks maybeincompatible withthelatestadd-in.Therefore, youmayneedtoupgrade
them.Toupgrade,gotoChemOffice14 >UpgradeWorkbook .
Importing tables
ChemDraw/Excel letsyouimportfrom:
MDLSDFiles.Importsallrecordsinthefile.Bydefault,thenameofthestructureisitschemicalformula.However,
youcanchangethenamebyusingNameMolecule command. MDLSDFilesaresupported onlyinChemBioDraw
UltraandChemDraw Proonly.
ChemBioFinder Databases (CFW,CFX).Importsallfieldsstoredinthemainform.ChemBioDraw 14.0
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Note:ToimportCFWfilesintoExcel,savethemwiththe“allowCAL/OLE Automation access”securitysetting
checked.See“SettingSecurityOptions”intheChemBioFinder userguidefordetails.
Note:Structures savedasChemFinder XMLfilescanbeimportedintoExcelusingtheadd-in.
Whenyouimportatable,structuredataaretransformed intostructuredrawingsinthefirstcolumn,andallotherfields
areimportedinseparatecolumns.
Toimportatable:
1.InExcel,selectthecellwhereyouwanttheimporttostart.Theupper-leftcorneroftheimportisatthiscell.Datais
filleddownandtotheright.
2.GotoChemOffice14 >Import/Export >ImportTable.TheImportTabledialogboxappears.
3.TypeorselectthefilenametoimportandclickOpen.Allrecordsareaddedtoyourworksheet.
Note:Aprogressdialogdisplaystheimportprogress.Youcancanceltheimportprocessatanytimebyclicking
Cancel.OnclickingCancel,youwillbepromptedeitherkeeptherecordswhichwereimported,orcancelthe
importprocessorcontinuewithimporting.
Note:YoucanonlyimportatableintoanewChemOffice worksheet.
Importing hitlists
YoucansearchrecordsinChemBioFinder andimportthehitliststructures withdataintoExcelusingtheImport
ChemFinder Listcommand.
Toimportahitlist:
1.GotoChemOffice14 >Import/Export >ImportChemFinder List.
2.IfyouarepromptedtostartChemBioFinder, clickYes.
3.Inthemessagebox,clickYestoimportthehitlist.TherecordsareimportedintoExcel.
Exporting tables
ChemDraw/Excel letsyouexporttablestoMDLSDFilesformat.Thefirstcolumnoftheareayouselecttoexport
musthavetheword“Structure” initstopcell.Structures outsidethefirstcolumnarediscarded.
Toexportdata:
1.Selectthecellstoexport,includingthecellthatcontainstheword“Structure”.
Note:Youcanexportselectedrowsandcolumnsfromastructuretable.Ensurethatthecellselectioniscontinuous.
Seeexamples below.ChemBioDraw 14.0
Chapter12:ChemDraw/Excel andCombiChem 181of315

2.GotoChemOffice14 >Import/Export >ExportTable.
3.IntheSaveTableTodialogbox,typethefilenameandclickSave.Thestatusbardisplaystheprogress.
Synchronizing Tables
Youcansynchronize atableinyourworksheet withaChemBioFinder database, forexample,a.CFXfile.Onsyn-
chronizing aChemDraw/table withaChemBioFinder table,fields(andtheirdata)intheChemBioFinder tablethatare
notintheMSExceltableareaddedtotheMS Excel table.
Note:ChangesyoumakeinMSExceldonotaffectthetableinChemBioFinder.
Tosynchronize atable:
1.Selectthetable.
2.GotoChemOffice14>Sync TablewithChemFinder DB.
3.SelecttheChemBioFinder tableandclickOpen.
4.Selectthefieldstobeusedformatchingaworksheet rowwiththedatabaserecordandclickOK.
5.Selectthefieldstobeupdated.Toselectmultiplefields,press<Ctrl>+clickeachfield.Selectingfieldsmarked
‘New’willaddacolumntoyourworksheet.
6.ClickOK.ChemBioDraw 14.0
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Addingstructures
Youcanaddchemicalstructures toaworksheet fromanyfileformatthatChemBioDraw supports.ChemDraw/Excel
assignsthechemicalformulaasstructurenamewhichcanbechangedbyusingtheNameMolecule command.
Thesimplestwaytoinsertanewstructureinacellisbydouble-clickingacell.
1.CreateaChemOffice worksheet.
2.Double-clickinacell.ChemDraw/Excel displaysadialogaskingyouifyouwanttoaddastructuretothecell.
3.ClickYes.ChemBioDraw opens.
4.DrawastructureandgotoFile>Close orpress<Ctrl>+<W> toreturntoChemDraw/Excel. Structureappearson
theworksheet.
Note:Double-clickingastructure(orcellcontaining astructure)onaworksheet willstartstructureeditingin
ChemBioDraw.
Addingastructure fromafile
1.InExcel,selectthecellintowhichyouwanttoaddthestructure.
2.GotoChemOffice14 >Molecule>Load.TheChooseMolecule ToLoaddialogboxappears.
3.TypeorselectthefilenameofthestructureandclickOpen.
Thefollowingformatsaresupported:
ChemBioDraw (*.cdx) MDLRxn(*.rxn)
ChemBioDraw XML(*.cdxml) MDLGraphic(*.tgf)
ChemDraw3.5(*.chm) ConnectionTable(*.ct)
ChemBio3DXML(*.c3xml) MSIMolfile(*.msm)
MDLMolfile(*.mol) SMD4.2(*.smd)
MDLSketch(*.skc)
SMILESstrings
YoucaninsertSMILESstringsintocellsandconvertthemtostructures.
1.TypeorpastetheSMILESstringsintooneormorecells.
2.Selectthecellstoconvert.
3.GotoChemOffice14 >Convert>SMILEStoMolecule.Alternatively, youcanusethecontextmenucommand to
convertSMILEStomolecule. IfthecelldoesnotcontainavalidSMILESstring,awarningindicatingthatthenum-
berofSMILESstringsthatcannotbeconverted appears.
Inchistrings
YoucaninsertInchistringsintocellsandconvertthemtostructures.
1.TypeorpastetheInchistringsintooneormorecells.
2.Selectthecellstoconvert.ChemBioDraw 14.0
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3.GotoChemOffice14 >Convert>InchitoMolecule.IfthecelldoesnotcontainavalidInchistring,anerrormes-
sageappears.
Addingstructures byname
Youcantypeorpastechemicalnamesintocellsandconvertthenamestostructures.
1.Enterthenamesintocells.
2.Selectthecellstoconvert.
Tip:Youcanalsoconvertnamesgenerated fromExcelformulas.
3.SelectChemOffice14 >Convert>NameToMolecule.IfthecellcontainsanamethatName=Struct supports,the
structureappearswiththegivennameasthenameofthecell.
Savingstructures
Youcansaveachemicalstructuretoaseparatefile.
1.Intheworksheet, selectthecellcontaining thestructure.
2.GotoChemOffice14 >Molecule>Save.TheSavetoFiledialogboxappears.
3.SelectanexistingfileorenteranewfilenameandclickSave.
Thefollowingformatsaresupported:
ChemBioDraw (*.cdx) ConnectionTable(*.ct)
ChemBioDraw XML(*.cdxml) MSIMolfile(*.msm)
ChemDraw3.5(*.chm) SMD4.2(*.smd)
ChemBio3DXML(*.c3xml) Metafile(*.wmf)
MDLMolfile(*.mol) GIF(*.gif)
MDLSketch(*.skc) TIFF(*.tif)
MDLRxn(*.rxn) PNG(*.png)
MDLGraphic(*.tgf) Bitmap(*.bmp)
PostScript(*.eps)
Searching
Youcansearchforstructures basedonthecriteriaandsearchfunctionyouuse.ChemDraw/Excel offersthreebasic
searchfunctions:
Normalsearch
Similaritysearch
R-Groupanalysis
Openingadatabase
Beforesearching, youmustopenastructuredatabase.ChemBioDraw 14.0
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1.InExcel,gotoChemOffice14 >NewChemOffice Worksheet .
2.GotoChemOffice14 >Import/Export >ImportTableorImportChemFinder listandselectthefiletoimport.
Normalsearches
Useanormalsearchtofindfullstructures andsubstructures thatmatchtheoneyoudefineinthesearchdialogbox.
1.Selectacellcontaining thelabelStructure.
2.GotoChemOffice14 >Search>Normal.TheChemDraw forExceldialogboxappears.
3.SelecttheSearchTab.
4.Clickintheemptywindowanddrawthestructureforwhichyouwanttosearch.
5.SelecttheNormaltabatthebottomofthedialogbox.
6.ForSearchType,selecteitherFullStructure orSubStructure .
7.ForFilterType,selecttoeitherincludeorexcludehits.
8.Enteraformulaquery.
9.ClickSearch.ThehitlistisdisplayedinacolumnnamedMatch.Itemsmatchingthesearchcriteriaarelabeledas
TRUE.
Similarity searches
Performasimilaritysearchtofindstructures withfeaturescorresponding toastructureofyourchoosing. Formore
information aboutsimilaritysearching, seetheChemFinder User’sGuide.
Tosearchforsimilarity:
1.Selectacellcontaining thelabelStructure.
2.GotoChemOffice14 >Search>Similarity .TheChemDraw forExceldialogboxappears.
3.SelecttheSearchTab.
4.Clickintheemptywindowanddrawthestructureforwhichyouwanttosearch.
5.SelecttheSimilarity tab.
6.ForSearchType,selecteitherFullStructure orSubStructure.
7.SelecttheSortResultsorder.
8.SelecttheSimilarity Percentvalue.
9.ClickSearch.ThehitlistisdisplayedinacolumnnamedSimilarity. Itemsmatchingthesearchcriteriaarelabeled
asTRUE.
R-Groupanalysis
AnR-groupanalysisreturnsallmolecules inthequerydatabasethatincludeatemplatestructurethatyouprovide.For
example,assumeyouwanttofindallmolecules thatincludetolueneinitsstructure,suchasp-cresoloro-xylene
(assuming yourdatabaseincludesthesemolecules). Simplydrawtolueneasyourtemplateandtheanalysiswill
returnallmolecules thatcontainatleastonetoluenestructure.ChemBioDraw 14.0
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Toillustrate,assumethatyouhaveasmalldatabasecomprising offourmolecules: o-,m-,andp-cresol,andbro-
mobenzene. FurtherassumeyouwanttorunanR-groupanalysisonthisdatabasetofindallmolecules thatcontain
tolueneinitsstructure.Youwillfindthattheresultsincludethreemainparts:
Thelistofmolecules thatcontainthetoluenetemplate.Inthisexample,theresultsincludeo-,m-,andp-cresol.Bro-
mobenzene isnotincludedbecauseitdoesnotcontainthetemplate.
Thetoluenetemplatewithallvariations ofR-groupattachments thatwerefoundinthedatabase. Inthisexample,
theattachments arerepresented byfunctional groups.ThesearethelocationsoftheR-groupsfoundintheanalysis
results;thehydroxylgroupsforo-,m-,andp-cresol.
Thefunctional groupfoundateachRnpositionforeachsearchresult.Foragivenreturnedmolecule, lookacross
itsrowtoviewthefunctional groupateachR-groupposition.Inthisexample,thesearchresultsconsistofahydro-
genandhydroxylgroupforR1,R2,andR3.
WorkingwithStructures
ChemDraw/Excel letsyourenamestructures andusetheclipboardtocut,copy,andpastestructures.
Renaming Structures
Excelrecognizes certaincharacters asformulas.Topreventthesystemfrominterpreting achemicalstructurename
asanExcelformula,youcanrenamethestructure.
Torenameastructure:
1.Selectthestructure.
2.GotoChemOffice14 >Molecule>Name.Ifmultiplecellsareselected,gotoChemOffice14 >Molecule>NameAll
Selected.TheNameMolecule dialogboxappears.ChemBioDraw 14.0
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Note:YoucanremoveastructurenamebyclickingClear.IfyouselectUseDefault,thenameofthestructurewillbe
replacedbythedefaultnamei.e.Chemical Formula.
3.TypethenameandclickOK.
UsingtheClipboard
Youcancut,copy,andpastestructures usingtheclipboard. TheCopyAscommand inChemDraw/Excel letsyou
copyastructureasInChI,InChIkey, orSMILESstring.
Tocutastructurefromacell:
1.Selectthestructure.
2.GotoChemOffice14 >Molecule>Cut.Thestructureisplacedontheclipboard. WhenyouselectPaste,thestruc-
turewillberemovedfromthecellandpastedinthespecifiedcell.
Tocopyastructurefromacell:
1.Selectthestructure.
2.GotoChemOffice14 >Molecule>Copy.
Thestructureremainsinthecellandacopyisplacedontheclipboard.
TocopyastructureasInChI,InChIkey, orSMILES:
1.Selectthestructure.
2.GotoChemOffice14 >Molecule>CopyAsandselectfromtheseoptions:
InChI
InChIKey
SMILES
Thestructureremainsinthecellandacopyinthedesiredstringformatisplacedontheclipboard.
Topasteastructureinacell:
1.Selectthecellwhereyouwanttopastethestructure.
2.GotoChemOffice14 >Molecule>Paste.Thestructureispastedfromtheclipboard.ChemBioDraw 14.0
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Displaying Structures
Youcandisplayorhidestructures inyourspreadsheet. Youcanalsoadjustthesizeofcellstodisplaytheirentirecon-
tents.
Toshoworhidestructures:
1.Selectthestructures.
2.SelectChemOffice14 >Structure>ShoworHide.
AligningStructures
Astructuremaybetoobigforitscellorbeimproperly positioned.
Toalignstructures, selectthecellthatcontainsthestructureandgotoChemOffice14 >Structure>Align.Thecells
adjusttodisplaytheircontents.
ResizingStructures
1.Selectthecell(s)whosestructure(s)youwanttoresize.
2.GotoChemOffice14 >Structure>Resize .Resizehandlesappearontheselectedstructures.
3.Click-dragtheresizehandlestoresizeastructure.Anychangesyoumaketoapictureisproportionately reflected
intheotherstructures.
4.Toendresizing,clickacellandthestructures aredeselected.
Bydefault,thestructure’s resizepropertyissetto‘MoveandResizewithcells’toavoidbunchedupstructures.
Tochangetheresizepropertyortoallowstructureovelapping (Excel2007):
1.Selectthecellswhosestructures youwanttoresize.
2.GotoChemOffice14 >Structure>Resize .Resizehandlesappearontheselectedstructures.
3.Right-clickandselectSizeandProperties fromthecontextmenu.
4.ClickontheProperties tab.
5.SelectDon’tmoveorsizewithcells.
6.ClickClose.
ChemDraw/Excel Functions
ChemDraw/Excel suppliesalibraryoffunctionsthatreturnchemicalproperties ofstructures inaChemDraw/Excel
worksheet.
ToinsertaChemDraw/Excel functionintoyourworksheet:
1.Selectthetargetcell.
2.GotoChemOffice14 >ChemBioDraw Functions (Options>ChemBioDraw Functions inExcel2010).The
ChemDraw forExceldialogboxappears.
3.Double-clickthefunctionyouwanttoinsertfromthelistavailableintheFunctions tab.AFunctions Argument dia-
logboxappears.
4.Selectthestructure.ChemBioDraw 14.0
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5.ClickOK.
Eachpropertyiscalculated usingthe“bestavailable”method.Ifthecellreferenceargumentdoesnotpointtoavalid
structurecell,#N/Aappearsinthecell.
AllChemDraw/Excel functionsaredescribed below.
Chemical name
Displayssystematic namesforchemicalstructures withsupportfortheCahn-Ingold-Prelogrulesforste-
reochemistry.
Function
CFW_CHEMICAL_ NAME(cellref)
Example
Incell:=CFW_CHEMICAL_ NAME(A2)
Result:1-(2,3-dihydro-1H-inden-2-yl)propan-2-one
Note:SomePerkinElmer Informatics productpackages andlevelsallowunlimitedstructure-to-namecon-
versions,whileothersimposeadailylimit.
Chemical composition
Whenthisfunctioniscalledwithjustacellreference, itdisplaystheelemental percentbyweightforallelementsin
thestructure.Whenthisfunctioniscalledwithacellreferenceandanatomicsymbol,itdisplaysthefractionby
weightofthegivenelementinthestructure.
Functions
CHEM_COMPOSITION (cellref)
CHEM_COMPOSITION (cellref,atomicsymbol)
Examples
Incell:=CHEM_COMPOSITION (A2)
Result:C,82.72;H,8.10;O,9.18
Incell:=CHEM_COMPOSITION (A2,"C")
Result:0.827188133
Chemical formula
Displaysthechemicalformulaforthestructure(s)inthecell.
Functions
CHEM_FORMULA(cellref)
CHEMPROPSTD_ MOL_FORMULA(cellref)
Examples
Incell:=CHEM_FORMULA(A2)
Result:C12H14O
Incell:=CHEMPROPSTD_ MOL_FORMULA(A2)ChemBioDraw 14.0
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Result:C12H14O
Molecular weight
Displaystheaveragemolecular massofthestructure,whereatomicmassesarebasedontheweightedaverageofall
isotopemassesfortheelement.
Units
atomicmassunits
Functions
CHEM_MOLWEIGHT (cellref)
CHEMPROPSTD_ MOL_WEIGHT(cellref)
CHEMPROPSTD_ MASS(cellref)
Examples
Incell:=CHEM_MOLWEIGHT (A2)
Result:174.23896
Incell:=CHEMPROPSTD_ MOL_WEIGHT(A2)
Result:174.238960
Incell:=CHEMPROPSTD_ MASS(A2)
Result:174.238960
Exactmass
Displaystheexactmolecular massofthemolecule, whereatomicmassesofeachatomarebasedonthemostcom-
monisotopefortheelement.
Units
g/mole
Function
CHEMPROPSTD_ EXACT_MASS(cellref)
Example
Incell:=CHEMPROPSTD_ EXACT_MASS(A2)
Result:174.104465
Numberofatoms
Whenthisfunctioniscalledwithjustacellreference, itdisplaysthetotalnumberofatomsinthestructure.Whenthis
functioniscalledwithacellreferenceandanatomicsymbol,itdisplaysthenumberofatomsofthegivenelementin
thestructure.
Functions
CHEM_NUM_ATOMS(cellref)
CHEM_NUM_ATOMS(cellref,atomicsymbol)ChemBioDraw 14.0
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Examples
Incell:=CHEM_NUM_ATOMS(A2)
Result:27
Incell:=CHEM_NUM_ATOMS(A2,"C")
Result:12
Numberofhydrogen- bondacceptors
Displaysthenumberofhydrogen-bondacceptors basedontopology.
Function
CHEM_NUM_HBACCEPTORS (cellref)
Example
Incell:=CHEM_NUM_HBACCEPTORS (A2)
Result:1
Numberofhydrogen- bonddonors
Displaysthenumberofhydrogen-bonddonorsbasedontopology.
Function
CHEM_NUM_HBDONORS (cellref)
Example
Incell:=CHEM_NUM_HBDONORS (A2)
Result:0
SMILESstring
DisplaystheSMILESstringforthestructure.
Function
CHEM_SMILES(cellref)
Example
Incell:=CHEM_SMILES(A2)
Result:O=C(C)CC(C1)Cc2c1cccc2
Formalcharge
Displaysthenetchargeonthemolecule.
Function
CHEMPROPSTD_ FORMAL_CHARGE(cellref)
Example
Incell:=CHEMPROPSTD_ FORMAL_CHARGE(A2
Result:-1ChemBioDraw 14.0
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Doescellhaveastructure drawing?
ReturnsTRUEifthecellhasaChemOffice/Excel structuredrawingorreactiondrawings, returnsFALSEotherwise.
Function
ISSTRUCTURE (cellref)
Example
Incell:=ISSTRUCTURE (A2)
Result:False
Doescellhavereactiondrawing?
ReturnsTRUEifthecellcontainsadrawingofareaction.
Function
ISREACTION (cellref)
Example
Incell:=ISREACTION (A2
Result:True
Boilingpoint
Theboilingpointforthemoleculeat1atm.
Units
Kelvin
Function
CHEMPROPPRO_ BOILING_ POINT(cellref)
Example
Incell:=CHEMPROPPRO_ BOILING_ POINT(A2)
Result:540.059
Melting/freezing point
Themelting/freezing pointforthestructureat1atm.
Units
Kelvin
Function
CHEMPROPPRO_ MELTING_ POINT(cellref)
Example
Incell:=CHEMPROPPRO_ MELTING_ POINT(A2)
Result:331.31ChemBioDraw 14.0
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Vaporpressure
Thevaporpressureforthestructureat25°C.
Units
Pa
Function
CHEMPROPPRO_ VAPOR_PRESSURE (cellref)
Example
Incell:=CHEMPROPPRO_ VAPOR_PRESSURE (A2)
Result:47.57999897
Criticalpressure
Theminimumpressurethatmustbeappliedtoliquefythestructureatthecriticaltemperature.
Units
bar
Function
CHEMPROPPRO_ CRITICAL_ PRESSURE (cellref)
Example
Incell:=CHEMPROPPRO_ CRITICAL_ PRESSURE (A2)
Result:49.804
Criticaltemperature
Thetemperature abovewhichthegasformofthestructurecannotbeliquefied,nomattertheappliedpressure.
Units
Kelvin
Function
CHEMPROPPRO_ CRITICAL_ TEMPERATURE (cellref)
Examples
Incell:=CHEMPROPPRO_ CRITICAL_ TEMPERATURE (A2)
Result:615.351
Criticalvolume
Thevolumeoccupiedatthecompound's criticaltemperature andpressure.
Units
cm3/mole
Function
CHEMPROPPRO_ CRITICAL_ VOLUME(cellref)ChemBioDraw 14.0
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Example
Incell:=CHEMPROPPRO_ CRITICAL_ VOLUME(A2)
Result:562.5
Gibbsfreeenergy
TheGibbsfreeenergyforthestructureat298.15Kand1atm.
Units
kJ/mole
Function
CHEMPROPPRO_ GIBBS_FREE_ENERGY(cellref)
Example
Incell:=CHEMPROPPRO_ GIBBS_FREE_ENERGY(A2)
Result:84.77
Heatofformation
Theheatofformationforthestructureat298.15Kand1atm.
Units
kcals/mole
Function
CHEMPROPPRO_ HEAT_OF_FORMATION (cellref)
Examples
Incell:=CHEMPROPPRO_ HEAT_OF_FORMATION (A2)
Result:-105.73
Idealgasthermalcapacity
Theconstantpressure(1atm)molarheatcapacityat298.15Kforanidealgascompound.
Units
J/[moleK]
Function
CHEMPROPPRO_ IDEAL_GAS_THERMAL_ CAPACITY (cellref)
Example
Incell:=CHEMPROPPRO_ IDEAL_GAS_THERMAL_ CAPACITY (A2)
Result:201.036
LogP
Thelogarithmofthepartitioncoefficient forn-octanol/water.ChemBioDraw 14.0
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Functions
CHEMPROPPRO_ LOGP(cellref)
CLOGP_DRIVER_PARTITION_ COEFFICIENT (cellref)
Examples
Incell:=CHEMPROPPRO_ LOGP(A2)
Result:2.233
Incell:=CLOGP_DRIVER_PARTITION_ COEFFICIENT (A2)
Result:2.243
Molarrefractivity
Themolarrefractionindex.
Units
cm3/mole
Functions
CHEMPROPPRO_ MOL_REFRACTIVITY (cellref)
CLOGP_DRIVER_MOL_REFRACTIVITY (cellref)
Examples
Incell:=CHEMPROPPRO_ MOL_REFRACTIVITY (A2)
Result:53.305
Incell:=CLOGP_DRIVER_MOL_REFRACTIVITY (A2)
Result:5.3297
Watersolubility
Prediction ofthewatersolubilityofthestructureat25°C.
Units
mg/L
Function
CHEMPROPPRO_ WATER_SOLUBILITY (cellref)
Example
Incell:=CHEMPROPPRO_ WATER_SOLUBILITY (A2)
Result:0
Connolly solventaccessible surfacearea
Thelocusofthecenterofasphericalprobe(representing thesolvent)asitisrolledoverthemolecular model.
Units
Angstroms2ChemBioDraw 14.0
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Function
CHEMPROPSTD_ CONNOLLY_ ACCESSIBLE_ AREA(cellref)
Example
Incell:=CHEMPROPSTD_ CONNOLLY_ ACCESSIBLE_ AREA(A2)
Result:428.557
Note:Thedefaultproberadiususedinthecalculations is1.4angstroms.
Connolly molecular surfacearea
Thecontactsurfacecreatedwhenasphericalprobe(representing thesolvent)isrolledoverthemolecular model.
Units
Angstroms2
Function
CHEMPROPSTD_ CONNOLLY_ MOLECULAR_ AREA(cellref)
Example
Incell:=CHEMPROPSTD_ CONNOLLY_ MOLECULAR_ AREA(A2)
Result:212.294
Note:Thedefaultproberadiususedinthecalculations is1.4angstroms.
Note:Thesurfaceareacalculation isperformed withMichaelConnolly's programforcomputing molecular surface
areasandvolume(M.L.Connolly.TheMolecular SurfacePackage.J.Mol.Graphics 1993,11).
Connolly solvent-excluded volume
Thevolumecontained withinthecontactmolecular surface.
Units
Angstroms3
Function
CHEMPROPSTD_ CONNOLLY_ SOLVENT_ EXCLUDED_ VOLUME(cellref)
Example
Incell:=CHEMPROPSTD_ CONNOLLY_ SOLVENT_ EXCLUDED_ VOLUME(A2)
Result:170.277
Note:Thevolumecalculation isperformed withMichaelConnolly's programforcomputing molecular surface
areasandvolume(M.L.Connolly.TheMolecular SurfacePackage.J.Mol.Graphics 1993,11).
Ovality
Theratioofthemolecular surfaceareatotheminimumsurfacearea.Theminimumsurfaceareaisthesurfaceareaof
aspherehavingavalueequaltothesolvent-excludedvolumeofthemolecule. Computed fromtheConnollyMolecular
SurfaceAreaandSolvent-ExcludedVolumeproperties.ChemBioDraw 14.0
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Function
CHEMPROPSTD_ OVALITY(cellref)
Example
Incell:=CHEMPROPSTD_ OVALITY(A2)
Result:1.428947
Principal moments ofInertia(X,Y,Z)
ThemomentsofinertiawhentheCartesian coordinate axesaretheprincipalaxesofthemolecule.
Units
grams/mole angstroms2
Function
CHEMPROPSTD_ PRINCIPAL_ MOMENT(cellref)
Example
Incell:=CHEMPROPSTD_ PRINCIPAL_ MOMENT(A2)
Result:249.5461409.2791658.824
Balabanindex
Function
MOLECULAR_ TOPOLOGY_ BALABAN_ INDEX(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ BALABAN_ INDEX(A2)
Result:29909
Clustercount
Function
MOLECULAR_ TOPOLOGY_ CLUSTER_ COUNT(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ CLUSTER_ COUNT(A2)
Result:13
Topological index
Function
MOLECULAR_ TOPOLOGY_ MOLECULAR_ TOPOLOGICAL_ INDEX(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ MOLECULAR_ TOPOLOGICAL_ INDEX(A2)
Result:1998ChemBioDraw 14.0
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Numberofrotatable bonds
Function
MOLECULAR_ TOPOLOGY_ NUM_ROTATABLE_ BONDS(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ NUM_ROTATABLE_ BONDS(A2)
Result:2
Polarsurfacearea
Function
MOLECULAR_ TOPOLOGY_ POLAR_SURFACE_ AREA(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ POLAR_SURFACE_ AREA(A2)
Result:17.07
Radius
Function
MOLECULAR_ TOPOLOGY_ RADIUS(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ RADIUS(A2)
Result:4
Shapeattribute
Function
MOLECULAR_ TOPOLOGY_ SHAPE_ATTRIBUTE (cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ SHAPE_ATTRIBUTE (A2)
Result:11.076923
Shapecoefficient
Function
MOLECULAR_ TOPOLOGY_ SHAPE_COEFFICIENT (cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ SHAPE_COEFFICIENT (A2)
Result:0ChemBioDraw 14.0
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Sumofdegrees
Function
MOLECULAR_ TOPOLOGY_ SUM_OF_DEGREES(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ SUM_OF_DEGREES(A2)
Result:28
Sumofvalencedegrees
Function
MOLECULAR_ TOPOLOGY_ SUM_OF_VALENCE_ DEGREES(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ SUM_OF_VALENCE_ DEGREES(A2)
Result:40
Topological diameter
Function
MOLECULAR_ TOPOLOGY_ TOPOLOGICAL_ DIAMETER (cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ TOPOLOGICAL_ DIAMETER (A2)
Result:7
Totalconnectivity
Function
MOLECULAR_ TOPOLOGY_ TOTAL_CONNECTIVITY (cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ TOTAL_CONNECTIVITY (A2)
Result:0.009821
Totalvalenceconnectivity
Function
MOLECULAR_ TOPOLOGY_ TOTAL_VALENCE_ CONNECTIVITY (cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ TOTAL_VALENCE_ CONNECTIVITY (A2)
Result:0.001157ChemBioDraw 14.0
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Wienerindex
Function
MOLECULAR_ TOPOLOGY_ WIENER_INDEX(cellref)
Example
Incell:=MOLECULAR_ TOPOLOGY_ WIENER_INDEX(A2)
Result:249
MOLECULAR_ NETWORKS_ LOGP
Thepartitioncoefficient isaratioofconcentrations ofun-ionizedcompound betweentwosolutions. Thelogarithmof
theratiooftheconcentrations oftheun-ionizedsoluteinthesolventsiscalledLogP.
Function
MOLECULAR_ NETWORKS_ LOGP(cellref)
Example
Incell:=MOLECULAR_ NETWORKS_ LOGP(A4)
Result:3.019
MOLECULAR_ NETWORKS_ LOGS
MOLECULAR_ NETWORKS_ LogSdetermines thesolubilityofasubstance, measured inmol/liter.
Function
MOLECULAR_ NETWORKS_ LOGS(cellref)
Example
Incell:=MOLECULAR_ NETWORKS_ LOGS(A4)
Result:-2.029
MOLECULAR_ NETWORKS_ PKa
MOLECULAR_ NETWORKS_ PKaisthenegativelogoftheaciddissociation constantKa.Itdescribes thetendency
ofcompounds orionstodissociate insolution.
Function
MOLECULAR_ NETWORKS_ PKa(cellref)
Example
Incell:=MOLECULAR_ NETWORKS_ PKa(A4)
Result:14.834000
Predicting druglikeness
UsingChemDraw/Excel functions, youcancreatecalculators todetermine thedruglikneness ofastructure.Youcan
calculatevaluesfor:theLipinskiruleoffive,Ghose,andCongreve ruleofthree:ChemBioDraw 14.0
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1.TheLipinskiruleoffive.
2.TheGhosemodifications
3.TheCongreve Rule-of-Three.
Lipinskiruleoffive
TheLipinskiruleusesfivecriteriatodetermine whetherasubstance isdruglike.Thesubstance musthave:
FiveorfewerH-bonddonors.
TenorfewerH-bondacceptors.
Amolecular weightunder500daltons.
LogPlowerthan5.
Fewerthantwoviolationsoftheabovefourrules.
Todetermine whetherthesubstance meetstheLipinskirulerequirement:
1.Calculatethevalueofeachofthesefunctions:
CHEM.NUM.HBDONORS ()
CHEM.NUM.HBACCEPTORS ()
CHEM.MOLWEIGHT ()
CHEMPROPPRO.LOGP ()
2.Verifythatthevaluereturnedbythefunctionsmeetsthelipinskirulecriteria.Forexample,ifthe
CHEM.MOLWEIGHT ()returnsavalue<500,itsatisfieslipinsky’sthirdcriteria.
3.Calculatethenumberofcriteriasatisfied.Ifthenumberofviolationsislessthantwo,theLipinskyruleissatisfied.
Ghosemodifications
TheGhosemodifications usethesecriterias:
Atomcountbetween20and70.
Molarrefractivity between40and130.
Amolecular weightbetween160and480daltons.
LogPintherange-0.4to+5.6.
Fewerthantwoviolationsoftheabovefourrules.
Todetermine whetherthesubstance meetstheGhosemodification requirement:
1.Calculatethevalueofeachofthesefunctions:
CHEM.NUM.ATOMS ()
CHEMPROPPRO.MOL.REFRACTIVITY ()
CHEM.MOLWEIGHT ()
CHEMPROPPRO.LOGP ()ChemBioDraw 14.0
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2.VerifythatthevaluereturnedbythefunctionsmeetstheGhosemodification criteria.Forexample,ifthevalue
returnedbythefunctionCHEMPROPPRO.LOGP ()forthatstructureiswithintherange-0.4to+5.6,itsatisfies
Ghosemodification’s fourthcriteria.
3.Calculatethenumberofcriteriasatisfied.Ifthenumberofviolationsislessthantwo,thentheGhosemodifications
requirement issatisfied.
Congreve ruleofthree
The"Congreve RuleofThree"usesthesecriterias:
ThreeorfewerH-bonddonors.
ThreeorfewerH-bondacceptors.
Amolecular weightunder300daltons.
LogPlowerthan3.
Fewerthantwoviolationsoftheabovefourrules.
Todetermine ifthesubstance meetstheCongreve Rule-of-Threerequirement:
1.Calculatethevalueofeachofthesefunctions:
CHEM.NUM.HBDONORS ()
CHEM.NUM.HBACCEPTORS ()
CHEM.MOLWEIGHT ()
CHEMPROPPRO.LOGP ()
2.VerifythatthevaluereturnedbythefunctionsmeetstheCongreve Rule-of-Threecriteria.Forexample,iftheifthe
functionCHEMPROPPRO.LOGP ()returnsavalueforthestructurethatis<3,itsatisfiesCongreve Rule-of-
Three’sfourthcriteria.
3.Calculatethenumberofcriteriasatisfied.Ifthenumberofviolationsislessthantwo,thentheCongreve Rule-of-
Threeissatisfied.
Chemical Properties
Chemicalpropertyprediction isanimportantfeaturethatChemBioOffice applications support.Itenablesyoutocal-
culatevaluesforawiderangeofmethodologies; forexample,topological descriptors suchastheWeinerindexand
Balabanindex,thermodynamic descriptors suchassolubility,meltingandboilingpoints,andpartitioncoefficients
suchasCLogP,properties relatedtothethree-dimensional shapeandvolumeofachemicalsuchastheConnollysur-
faceareaandvolume.Intotalyoucancalculatemorethan100chemicalproperties foragivenstructure.
Foralistofproperties availableinanyspecificapplications, clicktherespective linkbelow.Formoreinformation on
theproperties availableinanyspecificapplications, seetherespective onlinehelpavailableorvisitthePerkinElmer
Informatics Website.
"Propertypredictions inChemDraw/Excel" onpage203.
"PropertyPredictions inChemBioDraw" onpage158.
"PropertyPredictions inChem3D" onpage163.ChemBioDraw 14.0
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Property predictions inChemDraw/Excel
ChemDraw/Excel includesavarietyoffunctionsforreportingproperties foragivenstructure.Eachpropertyiscal-
culatedusingthe“bestavailable”method.
Toviewtheproperties foragivenstructure:
1.Selectthestructurecell.
2.Right-clickthecellandselectStructure>Properties fromthecontext-menu.The Properties dialogboxdisplaying
variousproperties anditsvaluesappears.
Theproperties include:
B FMOLECULAR_ NETWORKS_
LOGPS
Balabanindex FormalchargeMOLECULAR_ NETWORKS_
LOGSShapeattribute
Boilingpoint Freezingpoint MOLECULAR_ NETWORKS_ PKaShapecoefficient
C G Molecularformula SumOfdegrees
Clustercount Gibbsfreeenergy Molecularweight Sumofvalencedegrees
Connollyaccessiblearea H N T
ConnollymolecularsurfaceareaHeatofformation Numrotatablebonds Topologicaldiameter
Connollysolventaccessiblesur-
faceareaHenry’sLawconstant O Totalconnectivity
ConnollysolventexcludedvolumeI OvalityTotalValenceCon-
nectivity
Criticalpressure Idealgasthermalcapacity P V
Criticaltemperature M Polarsurfacearea Vaporpressure
Criticalvolume Mass PrincipalmomentOfinertia W
E Meltingpoint R Watersolubility
Exactmass Molarrefractivity Radius Wienerindex
Aboutmolecular networks
*MOSES.pKa, MOSES.logS andMOSES.logP forpredicting aciddissociation constants, aqueoues solubilityand
octanol/water distribution coefficients ofchemicalcompounds arecomputational calculator modulesbasedon
Molecular Networks' chemoinformatics platformMOSES.MOSESisdeveloped, maintained andownedbyMolecular
Networks GmbH,Erlangen,Germany. Forfurtherinformation pleasevisitwww.molecular- networks.com/moses .All
rightsreserved.Molecular Networks GmbH,Erlangen,Germany(www.molecular- networks.com ).
BalabanindexChemBioDraw 14.0
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Where:
qisthenumberofedgesinthemolecular graph.
=(q-n+1)isthecyclomatic numberofmolecular graph.
nisthenumberofatomsinthemolecular graph.
Siisthesumofallentriesintheithrow(orcolumn)ofthetopological distancematrixofthemolecule. Thedistance
matrixstorestheshortestpathbetweenallpairsofatoms.
Boiling point
TheboilingpointisreportinKelvin.
Asolutionboilsataslightlyhighertemperature thanthepuresolvent.Thechangeinboilingpointiscalculated using
theformula:
WhereKbisthemolalboilingpointconstant,mistheconcentration ofthesoluteexpressed asmolality,andΔTbisthe
changeintemperature.
Cluster count
Isthenumberofpathsofagivenlengthinthedistancematrix.
Connolly accessible area
Thisisthelocusofthecenterofasphericalprobe(representing thesolvent)asitisrolledoverthemolecular model.
Connolly molecular surface area
Thecontactsurfacecreatedwhenasphericalprobe(representing thesolvent)isrolledoverthemolecular model.
UnitsAngstroms2.
Connolly solvent accessible surface area
Thelocusofthecenterofasphericalprobe(representing thesolvent)asitisrolledoverthemolecular model.Units
Angstroms2.
Connolly solvent excluded volume
Thisisthevolumeofspaceboundedbythesolventaccessible molecular surface.ChemBioDraw 14.0
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Critical pressure
Reportedinbars,thisistheleastappliedpressurerequiredatthecriticaltemperature toliquefyagas.
Critical temperature
ReportedinKelvin,thisisthetemperature abovewhichagascannotbeliquefied,regardless ofthepressureapplied.
Critical volume
Reportedincm3/mol,thisisthevolumeoccupiedbyonemoleofasubstance atthecriticaltemperature andpres-
sure.
Exactmass
Thisisthesumofthemassesoftheindividualisotopesinthemolecule. Forexample,theexactmassofwatercon-
tainingtwohydrogen-1(1H)andoneoxygen-16(16O)is1.0078+1.0078+15.9994=18.0106.Theexactmassof
heavywater,containing twohydrogen-2(deuterium or2H)andoneoxygen-16(16O)is2.014+2.014+15.9994=
20.027.
Formal charge
Thisisthechargeassignedtoanatominamolecule, assuming thatelectronsinachemicalbondaresharedequally
betweenatoms,regardless ofrelativeelectronegativity.
Theformalchargeofanyatominamoleculecanbecalculated usingtheformula:
FC=V-N-B/2
Where‘V’isthenumberofvalenceelectronsoftheatominisolation(atomingroundstate);‘N’isthenumberofnon-
bondingelectronsonthisatominthemolecule; and‘B’isthetotalnumberofelectronssharedincovalentbondswith
otheratomsinthemolecule.
Freezing point
Thefreezingpointforthestructureat1atm.UnitsKelvin.
Gibbsfreeenergy
ReportedinKJ/mole,Gibbsfreeenergyisdefinedas:
whichissameas:
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Where:
Uistheinternalenergy(SIunit:Joule)
pispressure(SIunit:Pascal)
Visvolume(SIunit:m3)
Tisthetemperature (SIunit:Kelvin)
Sistheentropy(SIunit:jouleperKelvin)
Histheenthalpy(SIunit:Joule)
Note:HandSarethermodynamic valuesfoundatstandardtemperature andpressure..
Heatofformation
ReportedinKJ/mole,theheatofformationistheincreaseinenthalpyresultingfromtheformationofonemoleofasub-
stancefromitsconstituent elementsatconstantpressure.
Henry’s Lawconstant
Aunitlessvalue,Henry'sLawConstantcanbeexpressed as:
Where‘p’isthepartialpressureofthesoluteinthegasabovethesolution,‘c’istheconcentration ofthesoluteand
‘kH,pc’isaconstantwiththedimensions ofpressuredividedbyconcentration. Theconstant,knownastheHenry's
lawconstant,dependsonthesolute,solvent,andtemperature.
Idealgasthermal capacity
Thethermalcapacityatconstantvolumeofanidealgasis:
Where:
cVisaconstantdependent ontemperature
Uistheinternalenergy
Tistheabsolutetemperature
Visthevolume
nistheamountofsubstance ofthegas
Risthegasconstant(8.314J·K−1mol- 1inSIunits)ChemBioDraw 14.0
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Nisthenumberofgasparticles
kBistheBoltzmann constant(1.381×10−23J·K−1 inSIunits)
Thethermalcapacityatconstantpressureofanidealgasis:
Where‘H’istheenthalpyofthegas,calculated as:H=U+pV.
MOLECULAR_ NETWORKS_ LOGP
Thepartitioncoefficient isaratioofconcentrations ofun-ionizedcompound betweentwosolutions. Tomeasurethe
partitioncoefficient ofionizablesolutes,thepHoftheaqueousphaseisadjustedsothatthepredominant formofthe
compound isun-ionized.Thelogarithmoftheratiooftheconcentrations oftheun-ionizedsoluteinthesolventsis
calledLogP.
Normally, oneofthesolventschoseniswater;thesecondishydrophobic, suchasoctanol.
MOLECULAR_ NETWORKS_ LOGS
MOLECULAR_ NETWORKS_ LogSdetermines thesolubilityofasubstance, measured inmol/liter.Theaqueoussol-
ubilityofacompound isknowntosignificantly affectabsorption anddistribution characteristics ofthatcompound.
MOLECULAR_ NETWORKS_ PKa
MOLECULAR_ NETWORKS_ PKaisthenegativelogoftheaciddissociation constantKa.Itdescribes thetendency
ofcompounds orionstodissociate insolution.
Mass
Thisisthemassofonemoleculeofasubstance, relativetotheunifiedatomicmassunitu(equalto1/12themassof
oneatomof12C).Alsocalledmolecular mass.
Melting point
Isthetemperature atwhichasolidbecomesaliquidatstandardatmospheric pressure.Atthemeltingpoint,thesolid
andliquidphaseexistinequilibrium. Theformulatocalculatemeltingpointis:
Where‘T’isthetemperature atthemeltingpoint,‘ΔS’isthechangeinentropyofmelting,and‘ΔH’isthechangein
enthalpyofmelting.ChemBioDraw 14.0
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Molarrefractivity
Isameasureofthetotalpolarizability ofonemoleofasubstance. Itisdependent onthetemperature, indexofrefrac-
tion,andpressure.
Themolarrefractivity, ‘A’isexpressed as:
Where‘NA’istheAvogadroconstantandαisthemeanpolarizability.
Molecular formula
Thisisthemolecular formulaofthecompound.
Molecular weight
Thisisthesumoftheatomicweightsofallatomsinamolecule.
Numrotatable bonds
Isthenumberofrotatablebondsinamolecule. Arotatablebondisdefinedasanacyclicbonddrawnasasinglebond
(amideC-Nbonds,O=C–N,arerotatable)wheretheatomoneachendhasatleastoneothernon-hydrogensub-
stituent.Thistopological parameter isameasureofmolecular flexibility.Unsaturated bonds,andsinglebondscon-
nectedtohydrogens orterminalatoms,singlebondsofamides,sulphonamides, andthoseconnecting twohindered
aromaticrings(havingatleastthreeorthosubstituents) areconsidered non-rotatable.
Ovality
Thisreferstoameasureofhowtheshapeofamoleculeapproaches asphere(atoneextreme)oracigarshape(atthe
other).Ovalityisdescribed byaratioofvolumetoarea:
Where‘A’isarea,‘V’isVolume,and‘O’isOvality.
Theovalityofaheliumatomis1.0andHC24H(12triplebonds)is~1.7(equivalent to1.7).
Polarsurface area
ThePolarSurfaceArea(PSA)isdefinedasthesurfacesumoverallpolaratoms
Principal moment Ofinertia
Thisreferstotheprincipalmomentsofinertiaabouttheprincipalaxesofamolecule. Themomentsofinertiaarecom-
putedforaseriesofstraightlinesthroughthecenterofmassusingtheformula:ChemBioDraw 14.0
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Distances areestablished alongeachlineproportional tothereciprocal ofthesquarerootofIoneithersideofthe
centerofmass.Thelocusofthesedistances formsanellipsoidal surface.Theprincipalmomentsareassociated
withtheprincipalaxesoftheellipsoid.
Ifallthreemomentsareequal,themoleculeisconsidered tobeasymmetrical top.Ifnomomentsareequal,the
moleculeisconsidered tobeanasymmetrical top.
Radius
Theeccentricity ofanatomisthelargestvalueinitsrow(orcolumn)ofthedistancematrix,andrepresents howfar
awayfromthemolecular centeritresides.
Thediameter(D)isthemaximum suchvalueforallatoms,andisheldbythemostoutlyingatom(s).Examples: Dia-
meterofmethane=0;ethane=1;propane=2;n-butane=3.
TheradiusRistheminimumsuchvalue,andisheldbythemostcentralatom(s).Examples: Radiusofmethane=0;
ethane=1;propane=1;n-butane=2.
Shape attribute
Theshapeattribute(kappa)measures thebranching ofamolecule, andisscaledsoastofallbetweentheminimum
andmaximum valuespossibleforthegivenorder.Thefirst-ordershapeattributecountsthenumberofone-bond
paths.Thesecond-orderattributecountsthenumberoftwo-bondpaths,andsoon.Thefirstthreeorders(1..3)are
available.
Shape coefficient
Theshapecoefficient, Iisgivenby:
Wherethediameter(D)isthemaximum suchvalueforallatoms,andisheldbythemostoutlyingatom(s).Theradius
(R)istheminimumsuchvalue,andisheldbythemostcentralatom(s).
Examples valuesforD:methane=0;ethane=1;propane=2;n-butane=3.
ExamplevaluesforR:Radius:methane=0;ethane=1;propane=1;n-butane=2.
SumOfdegrees
Isthesumofdegreesofeveryatom.Anatom’sdegreeisthenumberofnonhydrogen atomstowhichitisbonded.
Sumofvalence degrees
Isthesumofdegreesofeveryatom.Anatom’svalencedegreeisequaltothesumofitsadjacentbonds'orders,
includinghydrogens.ChemBioDraw 14.0
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Topological diameter
Isthelongestdimension ofamolecule.
Totalconnectivity
Istheconnectivity considered overalltheheteroatoms.
TotalValence Connectivity
Isthevalenceconnectivity considered overalltheheteroatoms.
Vaporpressure
Isthepressureexertedbyavaporinequilibrium withitssolidorliquidphase.Vaporpressuremeasures thecon-
centration ofsolventmolecules inthegasphase.
Vaporpressurecanbecalculated usingRaoult’slaw.Theformulatocalculatevaporpressureis:
Where‘p’isvaporpressure,‘i’isacomponent index,and‘χ’isamolefraction.
Water solubility
Isthemaximum amountofasubstance thatcanbedissolvedinwateratequilibrium atagiventemperature andpres-
sure.Watersolubilityismeasured inmg/L.
Wiener index
Providesmeasureofbranching definedas:
WhereDijaretheoff-diagonalelementsofthedistancematrix.
GeneralPreferences
FromtheGeneralPreferences dialog,youcancustomize ChemDraw forExcelforyourspecificworkneeds.
Tocustomize ChemDraw forExcel:
1.NavigatetoChemOffice >Options>Preference .TheGeneralPreferences dialogappears.ChemBioDraw 14.0
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2.Customize theoptionsfoundintheGeneralPreferences dialogbasedonyourworkneeds.Theoptionsdis-
playunderthreecategories: Molecules & Structures, Import/Export, andMisc:
Molecules & Structures:
lDoubleClickToAddMolecule:Launches ChemDraw whenyoudouble-clickacell.
lAskBeforeAddingMolecule:Promptsamessagewhenyoudouble-clickacelltoaddamolecule.
lUseFilename inLoadMolecule:Displaysfilenameinsteadofchemicalformulabelowthemoleculeafter
loadingthemolecule.
lAlignStructure:Specifieshowthestructureisalignedinacell.Youcanchoosetoreducethecolumnwidth,
rowheight,orboth.
Import/Export:
lImportTable:Specifieswhethertooverwritethetableortoappendrecordstotheexistingtable.
lAutomatically generatestructures whileimporting atable:Generates structurepicturesforeachrecord
whileimportingatableusingtheImportTablecommand. Disablingthisoptioncanspeeduptheimportpro-
cess.Onlystructureandtabledataareimportedandnopicturesaregenerated. Selectthestructurecellsand
useShowPicturetodisplaythepictures.
lAskIfRecordImportCountExceeds:Promptsamessagewhenthetablebeingimportedcontainsmore
recordsthanthecountnumberspecified.
lSDFExportVersion:SpecifiestheStructureDataFile(SDF)versionexportedbyChemDraw forExcel.SDF
FilescaneitherbeV2000orV3000.ThedefaultvalueisV2000,whichlimitsthenumberofatomsandbondsin
amolecule: V2000filesallowupto1000ofeach.V3000isasupersetofV2000,andoffersanenhanced ste-
reochemistry specification. UnlikeV2000,theV3000formatdoesnotlimitthenumberofatomsandbondsina
molecule.ChemBioDraw 14.0
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Misc:
lAskBeforeClearingCells:PromptsamessagewhenyouattempttodeletethecellcontentinaChemOffice
worksheet byeitherpressing<Delete>or<Backspace> keys.
lCopyStructure toMS Word As: Letsyouselecttheformatthatyouwanttousetocopyyourstructuretoan
MS Worddocument, forexample,BitmaporOLEObject.
lSearchResults:Bydefault,thesearchresultappearsinthesameworksheet onwhichthesearchisper-
formed.TheDisplayinanewworksheet optioncreatesanewworksheet withthename"SearchResults X"
(whereXis1,2.3…)anddisplaysthesearchresultsinthisnewworksheet, withoutchanginganythingintheori-
ginalworksheet.
lDefaultStyleSheet:Specifiesthestylesheetalwaysappliedtothestructures whenstructures areadded
usingImportTable,LoadMolecule, orbyAddMoleculecommands. Toapplyastyletoparticularmolecules,
navigatetoChemOffice >Molecule >Style.ThedefaultstylesheetisNewDocument.cds.
CombiChem
UsingCombiChem, youcanbuildvirtualcombinatorial librariesofstructurally relatedmolecules. Youcanthenscreen
yourlibrariesforvariousproperties todetermine whichcompounds youwanttosynthesize.
CombiChem isapluginforMicrosoftExcelandisincludedwithChemDraw/Excel. IfyouarefamiliarwithExcel,you
willfindCombiChem simpletouse.However, ifyouneedhelp,seetheExcelUser’sGuide.
GettingStarted
WhenyouinstallChemBioFinder orChemBioOffice, theCombiChem add-inisalsoinstalled.CombiChem requires
MicrosoftExcel2003orlater.
Assistance withCombichem
Combichem providesHelpintheExcelworksheets. GotoChemOffice14 >CombiChem >Help.
Bydefault,eachworksheet youcreatealsoincludesbriefinstructions tohelpguideyou.Ifyoudonotseetheinstruc-
tions:
1.GotoChemOffice14 >CombiChem >Preferences.
2.SelectAddInstructions toEverySheet.
3.ClickOK.
Theinstructions appearonnewworksheets thatyoucreate.
Creatingcombinatorial libraries
Tocreateacombinatorial library,youfirstneedagenericreaction.Thisreactionresembles therealreactionyouwill
useinthelabtosynthesize compounds. Thegenericreactioncontainsoneormorequerystructures thatrepresentthe
reactantsandproductsintherealreaction.Anexampleofagenericreactionisshownbelow:ChemBioDraw 14.0
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Youusethegenericreactiontosearchyourchemicaldatabaseforcompounds thatmatchthereactantquerystruc-
tures.Onceallthematchingcompounds arefound,CombiChem generates alistofreactionsfromthecompounds
thatwerefoundinthequery.
Thegenericreactionyoucreatemustmeetthesecriteria:
Allgenericatomsinthereactant(s)mustberepresented byR-groups.
Solvents,catalysts, andother“real-world”elementsmustnotbeincludedinthegenericreaction.
Multi-stepgenericreactionsaresupported.
Enteringagenericreaction
Toenterthegenericreaction,youmustfirstcreateareactionworksheet:
GotoChemOffice14 >CombiChem >NewReaction.Anewworksheet, named“Reactions” appearsinyourwork-
book.
Youthenaddthegenericreactiontothereactionworksheet byeitherimportingitordrawingitinChemBioDraw.
Toimportthereaction:
1.Placeyourcursorinthecellthatcontainsthetext“Reaction -Double-clicktoedit.”
2.EitherclicktheLoadMolecule iconontheChemOffice toolbarorgotoChemOffice14 >Molecule>Load.
3.BrowsetothefilethatcontainsthegenericreactionandclickOpen.ThereactionappearsintheReactions work-
sheet.
TodrawthereactioninChemBioDraw:
1.Double-clickthecellthatcontainsthetext“Reaction -Double-clicktoedit.”.
2.Whenaskedwhethertoaddanewmolecule, clickYes.ChemBioDraw launches.ChemBioDraw 14.0
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3.InChemBioDraw, drawthegenericreaction.
4.InChemBioDraw, gotoFile>Exit.YouwillbereturnedtoExcelandthereactionwillappearintheworksheet.
Tip:Todisplayorhidethereaction,clicktheShowPictureorHidePictureicon.
Note:Donotaddmorethanonereactiontoareactiontemplate.
Creatingreactantworksheets
Thegenericreactioncontainsatleastonegenericreactant(areactantthathasoneormoreR-groupattachments).
AfteryouenterthegenericreactioninExcel,youcreateaworksheet foreachgenericreactant.CombiChem usesthe
reactantworksheet (s)tosearchyourdatabaseforstructures thatmaybeusedinsynthesis. Inmulti-stepreactions,
CombiChem searchesforreactantsinthefirststep;butignoresintermediate reactants.
Tocreatereactantworksheets:
1.SelecttheReactions worksheet tab.
2.GotoChemOffice14 >CombiChem >Reactants >MakeReactantWorksheets .Anewworksheet isaddedfor
eachgenericreactant.
CombiChem createsaworksheet foreachgenericreactant(typically, eitheroneortworeactantworksheets forthe
reactionyouentered).
Searching forreactants
Reactantworksheets areemptywhenCombiChem createsthem.Topopulateeachworksheet withstructures from
yourdatabase, youmusteitherimportthedatabaseasanSDfileoruseChemBioFinder tosearchforrecords.
TosearchforreactantsinanSDfile:
1.SelectaReactantworksheet tab.
2.GotoChemOffice14 >CombiChem >Reactants >SearchforReactants .Adialogboxappears.
3.SelectSearchDirectlytoimportanSDfiletosearch.
Note:SDfileshavetheextension .sdf.
4.EnterthefilepathintheDatabase fieldorclickBrowsetolocatethefile.
5.ClickOK.Recordsinthefilethatmatchthegenericreactionarereturned.
TosearchforreactantsusingChemBioFinder:
1.GotoChemOffice14 >CombiChem >Reactants >SearchforReactants .
2.Inthedialogbox,selectSearchinChemFinder .
3.IntheDatabase field,enterthepathtotheChemBioFinder formtobeusedtosearchtheChemBioFinder data-
base.
Note:ChemBioFinder formfileshavetheextension .cfxor.cfw.
4.ClickOK.ChemBioFinder launches.ChemBioDraw 14.0
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Afterlaunching, ChemBioFinder usestheformyouenteredtosearchitscorresponding databaseforrecordsthat
matchthegenericreactant.YoucanbrowsethesearchresultsinChemBioFinder beforeimportingthemintothe
Excelreactantworksheet.
Tip:Toomitarecordfromthesearchresults,navigatetotherecordinChemBioFinder andgotoRecord>Omit
fromListintheChemBioFinder mainmenu.
5.InExcel,gotoChemOffice14 >CombiChem >Reactants >ImportChemBioFinder Hitlist.
Alternatively, youcancopyandpastethequerystructureintoChemBioFinder toperformasearch.
1.InExcel,selectthecellthatcontainsthegenericreactant.
2.ClicktheCopyMoleculeiconontheChemOffice toolbar.
3.InChemBioFinder, openthedatabasetosearch.
4.Pastethegenericreactantstructureintoaqueryformandrunthesearch.
5.Inthereactantworksheet inExcel,gotoChemOffice14 >CombiChem >Reactants >ImportChemBioFinder
Hitlisttoimportthesearchresults.Thesearchresultsappearinthereactantworksheet (s).
Tip:UsetheShowPicture/Hide Picturecommands totogglethedisplay.
Recreating reactantworksheets
Youcaneditthegenericreactionatanytime.However, youmustthendeleteandrecreateeachreactantworksheet.
Torecreateareactantworksheet:
1.Right-clickthereactantworksheet tabandselectDelete.
2.Whenprompted, confirmthatyouwanttodeletetheworksheet.
3.GotoChemOffice14 >CombiChem >Reactants >MakeReactantWorksheets .
4.GotoChemOffice14 >CombiChem >Reactants >SearchforReactants .(Formoreinformation, see"Searching
forreactants" onpage214.)
Ifyoutrytocreatenewreactantworksheets inaworkbook thatalreadycontainsreactantworksheets, youwillbe
askedwhetheryouwanttodeletetheexistingworksheets. Whenprompted, chooseoneoftheseoptions:
ClickYestoreplacetheexistingworksheet (s).Theexistingworksheet ispermanently deleted.
ClickNo.Nonewworksheet iscreatedandthecurrentworksheet (s)arekept.
Topreservetheexistingworksheets gotoFile>SaveAsandsavetheworkbook. Then,followthestepsaboveto
recreatethereactantworksheet (s).Whenpromptedtodeleteeachexistingworksheet, clickYes.Newreactantwork-
sheetswillbecreatedandthepreviousworkbook willbeavailableasasavedfile.
Creatinganexperiment
Anexperiment isalibraryofproductstructures thatiscreatedwhenthereactantsearchresultsareappliedtothegen-
ericreaction.Youcancreateorenumerate multipleexperiments perworkbook.ChemBioDraw 14.0
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Forexample,youcantakeallthereactantsyouimportedandenumerate anexperiment containing allpossiblecom-
binationsofreactants. Aftercalculating properties ontheseproducts,youmightdecidethat10%oftheseproductsare
worthsynthesizing inthelab.Youcouldthencreateanexperiment withjustthoseproductsthatthecalculations show
tobepromising.
The‘Use(Y/N)’columninareactantlistdetermines whethertheassociated reactantinthelistwillbeused(‘Y’)inthe
experiment ornot(‘N’).Bydefault,Y,appears.
Note:OnlytheStructureandUse(Y/N)columnsarenecessary. OthercolumnsmayalsobeincludedbutCom-
biChemignoresthem.Youcandeletethemifyouwant.
Tocreateanewexperiment:
1.Ineachreactantlist,selectthereactantstousebytypingYintheir“Use(Y/N)”column.TypeNforthosereactants
youdonotwishtouse.
Note:Cellswithout“n”or“N”defaultto“Y”.
2.GotoChemOffice14 >CombiChem >Experiments >Neworusethefloatingexperiments form(CombiOption-
s>Experiment>New ).Adialogboxappearsaskingwhetheryouwanttocreatetheexperiment withtheselected
numberofreactants.
Note:Enumeration ofaproductlibrarymaytakealongtime,especially iftherearemanyreactantsoryouare
usingaslowerprocessor.
CombiChem/Excel savesyourenumeration toaChemFinder databasefile.
3.Whenprompted, savetheexperiments file.
Note:Whentheenumeration isdone,CombiChem/Excel importsyourdatatoaworksheet.
Experiment worksheets
Afteryoucreatetheexperiment, severalsheetsareaddedtoyourworkbook:
Experiment Reactantsheets.Containlistsofthereactantsusedintheexperiment. ThereisoneExperiment React-
antsheetforeachreactant.ThesesheetsarenamedExperiment n-Reactant mwherenisthedesignates aspe-
cificexperiment (incaseyoucreatemorethanone)andmisthereactantfortheexperiment.
Experiment Productsheet.Containsthegenericreactionandtheenumerated productsintheexperiment basedon
thereactantsyoumarked‘Y’inthereactantworksheet (s).Bydefault,onlytheproductsarelisted.Tolistthecomplete
enumerated reactions:
1.GotoChemOffice14 >CombiChem >Preferences .
2.IntheCombiPreferences dialogbox,selectShowFullReaction foreachproduct.
3.Selectareactantworksheet.
4.GotoChemOffice14 >CombiChem >Experiments >New.Anewexperiment isaddedwiththefullreactions
appearing intheproductworksheet.ChemBioDraw 14.0
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Note:Whenever youcreateanewexperiment, existingexperiment worksheets areretained.Ifyouwanttodelete
them,right-clickeachexperiment tabandselectDeleteorusetheexperiments floatingform(CombiOption-
s>Experiment>Delete ).
GotoCombiOptions>Experiment>Toggle tohide/unhide alltheexperiment worksheets intheworkbook.
Configuring plates
Afteryoucreateanexperiment, youcanassignyourproductstoproductwellsandyourexperiment reactantstoreact-
antblockplates.Thisisusefulifyouaregoingtousearoboticsynthesizer. Youcanconfigureplatesofupto50rows
and50columns.
Tosetupassignments:
1.OpeneitheranExperiment ReactantorExperiment Productworksheet.
2.GotoChemOffice14 >CombiChem >Plates>Configure Plates.
TheConfigure Platesdialogboxappears.
3.IntheConfiguration of:drop-downlist,selecteitherProductPlatesorReactantBlockPlates.
4.Enterthenumberofrowsandcolumnstoassigntotheplate.
Thenumbered buttonsrepresentwellsintheplateyouchose.
5.Designate whichwellsyouwanttouseascontrols,synthesized compounds, andleftempty.Clickawellto
changeitsdesignation.
6.Whenyouarefinished,clickApply.
Assigning plates
Thenextstepistoassignplatestoeachreactantandproduct.
Toassignthereactantsorproductstoplates:
1.SelectanExperiment- Reactantworksheet.
2.GotoChemOffice14 >CombiChem >Plates>AssigntoWells.
3.Selectaproductworksheet.ChemBioDraw 14.0
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4.GotoChemOffice14 >CombiChem >Plates>AssigntoWells.
Threecolumnsareaddedtothereactantorproductworksheet: WellPlate,WellRow,andWellColumn.
Tochangespecificplateassignments, editthevaluesontheworksheet.
Toremoveallplatewellassignments:
1.Selecttheworksheet whereyouwanttoremoveassignments.
2.GotoChemOffice14 >CombiChem >Plates>Removewellassignments .
Browsing plates
Afterassigningreactantsorproductstowells,youcanviewwhichonehasbeenassignedtoeachwell.
1.Selecteitherareactantorproductworksheet.
2.GotoChemOffice14 >CombiChem >Plates>BrowsePlates.ThePlateBrowserdialogboxappears.
3.InthePlatescrolllist,selectorentertheplatenumbertoview.
4.Inthedialogbox,selectthewelltoview.Theworksheet scrollstothereactantorproductassignedtothewellyou
select.
Viewingrelatedstructures
Afterenumerating anexperiment, youmayviewwhichreactantswentintoaproductorwhichproductsarosefroma
givenreactant.ChemBioDraw 14.0
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Toviewtherelatedstructures:
1.SelectarowonanExperiment ReactantorExperiment Productsheet.
2.GotoChemOffice14 >CombiChem >Highlight RelatedRecords.
TherelatedrecordsontheExperiment ReactantandExperiment Productsheetaredisplayedincolor.
3.(Optional) Toremovethehighlighting fromallrows,gotoChemOffice14 >CombiChem >Highlight>Unhighlight
All.
Settingpreferences
Combichem providesseveraloptionsforyoutochoosehowandwhethercertaininformation appearsoneachwork-
sheet.GotoChemOffice14 >CombiChem >Preferences andselectfromtheseoptions:
Bydefault,row1ofeachCombichem worksheet containsinstructions. Select/deselect thisoptiontodisplayor
removethemfromeachnewsheetyoucreate.
Bydefault,thereactionarrowandproductsappearoneachExperiment worksheet. Selectthisoptiontodisplaythe
fullreactiononeachnewExperiment sheet.
Assignrowsandcolumnsinplates.ChooseLefttoRighttoassignwellnumbersbyrow(1-1,1-2,1-3,etc.).Choose
ToptoBottomtoassignwellnumbersbycolumn(1-1,2-1,3-1,etc.).
Assignnumericoralphabetic labelstoplatecolumns.
Assignnumericoralphabetic labelstoplaterows.ChemBioDraw 14.0
Chapter12:ChemDraw/Excel andCombiChem 219of315

ChemScript
ChemScript isthecheminformatics SoftwareDevelopment Kit(SDK).Itcontainstheprogramming algorithms that
arecommonthroughout PerkinElmer products.Asasoftwaredeveloper, youcanapplyChemScript tocreateyour
ownscriptstousewithChemBioOffice applications.
AllexamplescriptfilesintheChemScript libraryareavailableinPythonandC#/.NET. Ifyouarefamiliarwitheitherof
theselanguages, youwillfindthesescriptseasytounderstand. However, ifyouarenewtoeitherPythonorC#/.NET,
wesuggestthatyourefertotheWebsitesandbookslistedattheendofthischapter.
AlthoughChemScript isavailableinPythonandC#/.NET, wewillusePythoninthisguidetoexplainChemScript.
Pythonisanon-proprietary andwidelyusedprogramming language.
WhyuseChemScript?
ChemScript addsconsiderable versatility tohowyoumanageyourchemicaldata.UsingChemScript, youcan
modify,view,andtransferyourdatafromoneplacetoanotherusingyourowncustomrules.1
Herearejustafewcommonuses:
Saltsplitting andstripping
Identifyandremovesaltfragments fromadrawnstructureandregisterthepurecompound.
Canonical codes
Generatecanonicalcodesforasetofstructures andusethecodestofindduplicates inyourdata.
Fileformat conversion
Convertstructureorreactionfilesfromoneformattoanother.
Generate properties
ExecuteStruct=Name orgeneratephysicalpropertyfeaturesfoundinChemBioDraw.
Common scaffold orientation
Enforcestandardorientations ofstructures basedontheestablished orientation ofacommonsubstructure.
2DStructure Diagram Generation (SDG) andCleanup
Generatenew2Dstructures fromconnection tableswithoutcoordinates andcleanupexisting2Dstructureusingthe
ChemBioDraw algorithms.
1ChemScript letsyouconvertupto10,000datarecordsperday.Forgreatercapacity,youwillneedChemScript Ultra.Forinform-
ation,contactPerkinElmer.ChemBioDraw 14.0
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HowChemScript works
Themostfundamental useforChemScript istoreaddatafromonesource,modifythedatausingascript,andwrite
themodifieddatatoanotherlocation.Youcanretrievedatafromorwritetoalmostanydatabase, file(s),orapplic-
ation.
Figure13.1:AChemScript scriptcanretrievedatafromonesource,modifythedata,andwriteittoanotherlocation.
Howthedataismodifiedisdetermined entirelybythescript.Thescriptcandeletedata,calculateoraddnewdata,or
editexistingdata.Thedatacanbeeithertext,structures, orboth.
SinceChemScript scriptsarelikeanyotherPythonscriptsor.NETprogram,youcanexecutethescriptsusingeither
theWindowscommand lineoranydevelopment environment.
GettingStarted
Bydefault,ChemScript andPython3.2areinstalledonyourlocalcomputerwhenyouinstallChemBioOffice. After
theinstallation, wesuggestthatyoufollowthesimpleexercises inthissectiontofamiliarize yourselfwith
ChemScript.
ForeditingChemScript files,werecommend thatyouuseoneofthemanyprogramming toolsthatareavailable.One
ofthesetools,IDLE,isincludedwiththePythoninstallation. TolearnmoreaboutIDLE,seetheonlineHelpinthe
IDLEmainmenu.
StartingIDLE
FromtheStartmenu,gotoAllPrograms >Python3.2>IDLE(PythonGUI).AfterPythonstarts,aPythonshell
opensinIDLEandtheheaderindicatesaversionofPython(Ex.3.2),andaversionofIDLE(Ex.1.2).Apromptwill
alsoappear:“>>>”
LoadingtheChemScript Library
Atthecommand prompt,typethelinebelowandpress<Enter>:
importChemScript14 *ChemBioDraw 14.0
Chapter13:ChemScript 221of315

Note:Thecommand iscase-sensitive.
A“Welcome toCSChemScript” messageappears,followedbyacommand prompt.
ChemScript Help
Youcanreadadescription ofanyChemScript classwithinIDLE.Forexample,enterthelinebelowtoreturnHelpfor
theChemScript Atomclass.
help(Atom)
Thehelpwillbeginwithamessagesuchas:
“HelponclassAtominmoduleChemScript14:”
EnterSMILESData
YoucanalsotesttoverifythatChemScript isworkingcorrectly.OnecommonuseforChemScript istoapplyfunc-
tionstoSMILESstrings.Forexample,youcanassignaSMILESstringtoavariable.Typethefollowinglineandpress
<Enter>:
myMol=Mol.LoadData ('C1CCCCC1C')
Thismessageappears:
Openmolecule successfully: chemical/x- smiles
Reporting aChemical Name
Youcannowusethevariabletoreportthechemicalname.Forexample,atthecommand prompttypethelinebelow
andpressEnter:
myMol.chemicalName ()
Thelinemethylcyclohexane isreturned.
Counting Atoms
Tocounttheatomsinthestring,typethefollowinglineandpress<Enter>:
myMol.CountAtoms ()
Thecommand returnstheatomcountforthestructuredefinedwiththechemical/x- smilesformatfor'C1CCCCC1C',
whichis7.
ExitingIDLE
Toexit,typethislineandpress<Enter>:
exit()
Confirmanypromptstocompletetheexitcommand. PythonIDLEexits.
GettingStartedGuide
ChemScript includesaGettingStartedguidetohelpyoubegindeveloping andusingyourownscripts.Toopenthe
guide,gotoStart>AllPrograms >ChemBioOffice2014 >ChemScript 14.0>GettingStarted.
Thedocument includesnotesontheChemScript objectsandfunctionality, Python,andanoverviewofexamples
installed.
EditingScripts
UsingIDLEoranotherdevelopment environment, youcaneithereditthescriptsprovidedwithChemBioOffice orcre-
ateyourown.Regardless ofhowyoudevelopascript,itmustincludethesecommands:ChemBioDraw 14.0
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fromsysimport*
fromosimport*
fromos.path import*
fromChemScript14 import*
Thefirstcommand importsthepythonsystem.Thesecondandthirdcommands importtheoperatingsystemmod-
ules.Thelastcommand importsalltheChemScript functions. Afteryouincludethesecommand lines,howyou
developtherestofyourscriptisentirelyuptoyou.
Introducing theChemScript API
ChemScript includesaChemScript APIreferenceguide.YoucanfindtheguideatStart>All
Programs >ChemBioOffice 2014>ChemScript 14.0>APIReference. Itprovideslinksandinformation forthe
ChemScript classes.
TheChemScript objectmodelcomprises twofundamental levelsoffunctionality, described below.
ChemScript Classes
Atthetoplevel,theAPIconsistsoffourclasses:
Atom
Chemicalelement,charge,bondstoneighboring atoms,drawingcoordinates, 3Dcoordinates (ifavailable), ste-
reochemistry, etc.
Bond
Bondedatoms,bondorder,etc.
Molecule (Mol)
Achemicalconnection table,whichcanrepresentoneormoremolecular fragments. ThisclassalsoincludesfileI/O
capabilities andotheradvanced chemistry functionality suchasstereochemistry.
Reaction (Rxn)
Achemicalreactionwithoneormoresteps.
Functions andAlgorithms
Thesecondary levelconsistsofthecoresetofhigh-levelfeaturesthatyoucanmodifytomeetyourspecificbusiness
needs.Someexamples aredescribed below.
Template Based Normalization
Enforcestandardrepresentations offunctional groupstructures inchemicaldata.
Template Based Product Generation
Automatic generation ofproductsfromasetofreactantsandagenerically definedreaction.Forexample,reactions
likethosebetweenaminesandcarboxylates.ChemBioDraw 14.0
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Substructure Identification andMapping
Atom-by-atomcomparison ofamoleculewithasubstructure. Positivematchingprovidesanatom-by-atommapofthe
substructure atomstothoseinthemolecule.
SaltStripping
Removesaltsfromareactionbasedonapre-definedlistofsaltfragments.
Structure Orientation
Enforcestandardorientation ofstructures basedontheestablished orientation ofacommonscaffold.
2DStructure Generation andCleanup
UseChemBioDraw- basedalgorithms togeneratestructurefromscratchoraftermodifying chemicaldatausingapro-
gram.
Canonical Codes
Generateuniqueidentifying codesfromachemicalstructure.
FileFormat Conversion
ReadandwritefiledatausingallPerkinElmer supported fileformats(CDX,CDXML,MOL,CHM,SKC,SMILES,
etc.).
Chemical NameandStructure Conversion1
UsetheChemBioDraw Struct=Name featuretogeneratestructures fromchemicalnamesandnamesfromtheirstruc-
tures.
Molecular Mechanics
Optimizemolecular structures usingtheMM2force-field.
TheChemScript APIonline
PerkinElmer alsoprovidesthedocumentation oftheAPIonline.YoucanfindtheAPIatsdk.cambridgesoft.com.
Tutorials
Weprovideseveralsamplescriptstoillustratehowyoucandevelopyourowncustomcodetomeetyourbusiness
needs.ManyofthescriptsweuseareintheChemScript samplesdirectory.Bydefault,thisdirectoryiswhere
ChemBioOffice 2014auxillaryfilesareinstalled:
OnWindows7and8:
C:\ProgramData\CambridgeSoft\ChemOffice2014\ChemScript\Examples\
1Premium functionality thatmaybelicensedfromPerkinElmer.ChemBioDraw 14.0
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Forthesakeofbrevity,wewon’trepeatthescriptsinthismanualortrytoteachPython.However, webrieflydescribe
whatyoucandowiththecodeexamples sothatyoucanmodifyandexpanduponthemforyourownuse.Asyouread
thetutorials,youareencouraged toviewthecodeinIDLEandedititasdesiredtoseehoweachexampleworks.For
moreonIDLE,see"GettingStarted"onpage221.
Example1:Automated Structure Cleanup
Thissamplescriptcleansupthestructures inmultipleChemBioDraw filesallatthesametime.Itusesthesame
cleanupfunctionthatisinChemBioDraw. ThescriptisinthedirectoryExample.001/script.py .Thescriptreads
theCDXstructurefilesfromasourcedirectory,appliesthecleanupfeaturetoeachstructure,andwritethemodified
filestoanoutputdirectory.Theoriginalfilesremainunchanged.
Figure13.1:Thestructurecleanupscriptreadsastructurefile(left)andcreatesanew,cleanedupstructurefile(right).
ThisexampleusestheCDXMLformat.Otherformats,suchasMDLMOL,mayalsobeapplied.Youcanalsoforce
ChemScript tousespecificfileformatsforreadingandwritingdata.
Example2:CreateanSDfile
Thisexampleillustrates howyoucancreateanSDfilefromexistingCDXMLfiles.Youcanfindthescriptat
Example.002/script.py .WebeginwithalistofCDXMLfilesthateachcontainachemicalstructure.Thelistof
filesishard-codedintotheChemScript script.Whenexecuted, thescriptusestheSDFileWriter methodtocreate
anSDfilethatincludesallthestructures.
Example3:CreatealistofCDXMLfiles
Thisexampleillustrates howtoreadanSDfileandwritealistofCDXMLfiles.Youcanfindthesourcefileat
Example.003/script.py .
Example4:FilteranSDfile
ThisexampleusestheatomByAtomSearch methodtodemonstrate asimpleapplication ofthe"atom-by-atom"sub-
structuresearchinChemScript. TheprogramreadsanSDfileandfiltersstructures intooneoftwooutputSDfiles,
structures thatcontainaphenylgroupandstructures thatdon’t.Italsoillustrates howyoucanreadchemicaldata
formattedasaSMILESstring.SeeExample.004/script.py .
Example5:Computing Canonical Codes
Thisexamplescriptcheckswhetheranystructures appearinbothoftwoSDfilesbasedonthestructures’ canonical
codes.TheoutputisanewSDfilewiththeduplicatestructures excluded. SeeExample.005/script.py .ChemBioDraw 14.0
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Thisexamplefirstcomputes thecanonicalcodeforeachstructure.Sincethecanonicalcodedoesnotvarywithdif-
ferentrepresentations ofthesamechemicalstructure,youcanuseittodetermine whethertwostructures arechem-
icallyequivalent.
Thisexamplealsointroduces thePythonDictionary, whichisanassociative array.Thedictionary mapsakeytoa
value.Thedictionary isusedtodetermine whetheracanonicalcodehasbeenpreviously encountered.
ThisexampleusesanalternateloopingconstructtoreadanSDfile.
Canonicalcodesshouldneverbepermanently storedbecausetheirrepresentation can
changeamongdifferentversionsofChemScript.
Example6:Structure Overlay
Thisscriptintroduces theChemScript structureoverlayfeature.Itusesascaffoldstructurefiletosuperimpose two
chemically similarstructures. Thescriptfirstexamines thestructures inanSDfilethatcontainacommonscaffold
substructure. Itthenalignsthesestructures sothattheyhavethesameorientation withrespecttothescaffold.See
Example.006/script.py .
Note:Theoverlayfunctionality canalsobeusedtoalignthreedimensional structures.
Example7:Reaction Transformation
Thisexampledemonstrates reactiontransformation. Thismeansthatyoucandrawareactionthatdefinesatrans-
formationofamoleculeandthenapplythattransformation toasetofstructurefiles.
Allthefilesnecessary forthistutorialareintheExample.007 directory.Thetransform1.cdxml fileprovidesthe
reactionthatdefinesthetransformation. Theinput.sdffilecontainsallthestructures thatwillbetransformed.
Figure13.2:Thetransformfiledefineshowthetransformation isappliedtothesourcestructures.
Thescriptsearchestheinputfileforstructures thatcontainanitrogroup,shownasareactantinthetransformation
file.Ifastructureisfound,thescripttransforms thenitrogrouptotheformshownintheproductandcopiestheentire
structuretoanewfile.Thefigurebelowshowsoneexample.
ChemBioDraw 14.0
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Figure13.3:A)beforethetransformation isapplied;B)aftertransformation.
Structures thatdon’tmeetthesearchcriteriaareignored.
Example8:Simplesaltstripping
TheprogramreadsanSDFile,identifiesandremovessaltcomponents (ifanyarepresent),andoutputstwoSDfiles.
Theoutputstructurefilecontainstheoriginalstructures withoutthesaltcomponent, andtheoutputsaltfilecontains
thesaltcomponents thatwerestripped,alongwithareferencetotheoriginalstructure.See
Example.008/script.py .
Note:ThisexampleusesadefaultsetofsaltsthatPerkinElmer provides.However, youcanalsodefineacus-
tomizedsalttablethatenablesyoutodesignate whichchemicals areconsidered salts.
UsefulReferences
Therearenumerous resources availableforlearningPythonandC#/.NET. JustafewofthemanybooksandWeb
sitesarelistedbelow.
Books
Python
Beginning Python:FromNovicetoProfessional byMagnusLieHetland.
DiveintoPythonbyMarkPilgrim.
LearningPythonbyMarkLutz&DavidAscher.Thisisabeginner/intermediate learningmanualandreference.
PythoninaNutshellbyAlexMartelli.Thisbookisabriefintroduction andgoodreferencetoPython.
C#/.NET
C#inaNutshellbyPeterDrayton,BenAlbahari,andTedNeward.
ProC#with.NET3.0byAndrewTroelsen.
C#Essentials byBenAlbahari,PeterDrayton,andBradMerrill.
C#3.0Cookbook byJayHilyardandStephenTeilhet.
WebSites
Python
Youcanfindmoreinformation onPythonat:http://www.python.org. ThisistheofficialPythonprogramming language
site.
.NET
Forinformation on.NET,see
http://msdn.microsoft.comChemBioDraw 14.0
Chapter13:ChemScript 227of315

QueryStructures
Aqueryisasearchforinformation thatisstoredinadatabase. IfyouhaveeversearchedtheInternetusingaWeb
browser,thenyouhaveperformed asimplequery.
Aquerystructureisaparameter youusetosearchachemicaldatabase(thedatabasemustincludestructures forthe
querytobeuseful).Thequerystructurecanincludebondandatomproperties thatyouspecifytonarroworbroaden
thelistofsearchresults.Belowaretwoquerystructureexamples:
Figure14.1:Twoexamplestructurequeries.A)Theresultsincludeanyconnected atomatthelocationspecifiedby
‘R’;B)Theresultsincludeeitherasingleordoublebondatthelocationspecifiedby‘S/D’.
Toperformaquery,youfirstdrawthequerystructureinChemBioDraw. Youthenenterthestructureinadatabase
application suchasChemBioFinder. Theapplication searchesoneormoredatabases thatyouspecifyandreturnsthe
queryresults.
SearchLimitations
Severalfactorsdetermine thesearchresultsthatarereturned.Togettheresultsyouexpect,youmustfirstensure
thatthestructureyoudrawaccurately represents thequeryyouwanttoperform.Forexample,ifyourquerystructure
requiresthatnocarbonatomsinanaromaticstructurecanbepartofanyring,youarelikelytoreturnnoresultsoran
error,depending onthequerysystemused.
Thesearchapplication youusecanalsoaffectyourquery.Iftheapplication doesnotaccurately interpretyourquery
structure,orthestructures inthedatabase, youcouldreceiveinaccurate results.
GenericLabels
Agenericlabelrepresents anonspecific attachment. Itcanbeeitheranunspecified atom,functional group,orstruc-
turalfeature.Whenyouperformaquery,thequerylooksforstructures basedonthetypeofgenericlabelyouuseand
whereitisinthequerystructure.Recordsthatmatchthequerystructurearereturnedinthesearchresults.
Forexample,thequerystructurebelowusestheletter‘Q’toindicatethatanonhydrogen, noncarbon atommust
appearatthespecifiedlocation.ChemBioDraw 14.0
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Youcanuseothergenericlabelstoindicateothertypesofquerycriteria.ThegenericlabelsthatChemBioOfficesup-
portsarelistedbelow(allarerecognized aschemically significant).
A:Represents anynonhydrogen.
M:Represents ametal.
Q:Represents anatomthatisneitherhydrogennorcarbon.
X:Represents anyhalide.
R:Unrestricted; represents oneormoreconnected atomsofanykind.
Toaddagenericlabeltoastructure,dooneofthefollowing:
1.Double-clicktheatomtoopenatextbox,andtypeinthenickname.
2.Right-clicktheatom,pointtoInsertGenericLabelonthecontextmenu,andclickthelabelyouwishtoinserton
thesub-menu.
GenericNickname Hotkeys
Youcanassignhotkeystogenericnicknames, justlikeothernicknames. Forinformation onassigningahotkeytoa
nickname, see"Customizing Hotkeys"onpage33.
DefiningGenericNicknames
Thegenericnicknames recognized aschemically meaningful arelistedintheGenericNicknames fileinthe
ChemDraw Itemsfolder.
Toeditthegenericnickname files,opentheGenericNicknames fileinatexteditorandmakeyourchanges.Follow
examples inthefileforthecorrectformat.
Note:Ifyoucheckastructurethathasagenericnickname, amessagedisplaysbecausethestructurecontains
variablesubstituents. Ifyouignorethismessage, thegenericnicknames areignored,andthechemicalformula,
mass,etc.,arereportedasiftheatomlabelcontaining thegenericnickname werenotselected.
Reaxys
Reaxysisaweb-basedchemicalsearchenginedesignedforsyntheticandmedicalchemists. TheReaxysdatabase
includeschemicalproperties, structures, reactionsandexperimental data.UsingChemDraw forReaxys®with
ChemDraw, youcandrawquerystructures tosearchtheReaxysdatabase.ChemBioDraw 14.0
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Note:FortheWindowsversion,youneedboththeReaxysStructureEditorplug-inandeithertheChemDraw
application orplugininstalledonyoursystem.
InadditiontoA,M,Q,X,andR,Reaxysrecognizes severalothergenericatoms.
ToaddaReaxysgenericlabeltoastructure:
Right-clickanatom,pointtoInsertGenericLabelonthecontextmenu,pointtoReaxysandclickthelabelinthe
sub-menuyouwishtoinsert.
Thetablebelowliststhelabelsandtheirmeaning.
Labels Meaning
AHAnyorH
MHMetalorH
QHAny,exceptCarbonorH
XHHalogenorH
GUnspecified
GHUnspecifiedorH
G*Unspecified, ringclosureallowed
GH*Unspecified, ringclosureallowedorH
ACYAcyclic
ACHAcyclicorH
ABCCarbacyclic
ABHCarbacyclicorH
AYLAlkynyl
AYHAlkynylorH
ALKAlkyl
ALHAlkylorH
AELAlkenyl
AEHAlkenylorH
AHCHeteroacyclic
AHHHeteroacyclicorH
AOXAlkoxy
AOHAlkoxyorHChemBioDraw 14.0
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Labels Meaning
CYCCyclic
CYHCyclicorH
CBCCarbocyclic
CBHCarbocyclicorH
ARYAryl
ARHArylorH
CALCycloalkyl
CAHCycloalkylorH
CELCycloalkenyl
CEHCycloalkenyl orH
CHCHeterocyclic
CHHHeterocyclic orH
HARHeteroaryl
HAHHeteroarylorH
CXXNocarbon
CXHNocarbonorH
AtomProperties
Atomproperties determine thestructuralfeaturesallowedatthesiteofanatom.Forexample,youcanspecifythata
carbonatommustbepartofaring,haveatleasttwoattachments, havenoattachments, orperhapsbeaspecificiso-
tope.
Assigning AtomProperties
Toassignproperties toselectedatomsinastructure:
1.Selectoneormoreatoms.
2.ToopentheAtomProperties dialog,dooneofthefollowing:
Right-click,selectAtomProperties .
NavigatetoStructure>AtomProperties .
Pressthehotkey“/”.
3.IntheAtomProperties dialog,selecttheproperties toassociate withtheselectedatom(s).
4.ClickOK.ChemBioDraw 14.0
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QueryIndicators
Queryindicators displaytheatomproperties youassigntoastructure,asshownbelow.Ifmorethanonepropertyis
assigned, anindicatorforeachpropertyappearsadjacenttotheatom.
Figure14.2:Thisstructureillustrates severalpossibleatomproperties thatcanbeassigned.
Thelistbelowdescribes eachindicator:
*—Substituents: FreeSites(Followed bythenumberoffreesites)
U—Substituents: Upto(Followed bythemaximum numberofsubstituents)
X—Substituents: Exactly(Followed bythenumberofsubstituents)
H—ImplicitHydrogens. See"ImplicitHydrogens "onpage235.
R—RingBondCount
S—Unsaturation
C—ReactionChange
T—ReactionStereo
L—Translation
(none)—AbnormalValence
ViewingIndicators foranAtomorBond
Exceptforthesubstituents queryproperties, thecharacters indicatethatagivenpropertyisapplied,butnotthevalue
ofthatproperty.
Tofindthevalueofaquerypropertysetting:
1.Selecttheatom.
2.Dooneofthefollowing:
Selecttheatom,right-click,pointtoanatom,andpointtotheappropriate property.
NavigatetoStructure>Properties andviewthesettingsontheAtomProperties tab.
Todisplayqueryindicators foranatomorbond:
1.Right-clicktheatomorbond.
2.ChooseShowQueryIndicatoronthecontextmenu.
Displaying Indicators foraStructure
Todisplayqueryindicators forastructure:ChemBioDraw 14.0
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1.Selectthestructure.
2.Right-clickandnavigatetoAtom>orBond>ShowQueryIndicator onthecontextmenu.
Positioning QueryIndicators
Youcanpositionaqueryindicatorbyeitherdraggingitorenteringanumericvalueforthenewlocation.
1.Right-clicktheindicatorandchoosePosition.ThePositionIndicatordialogappears.
2.Clicktheappropriate Positionoption,andtypeavalue:
ToPosition Typeavaluefor
Fromtheatomorbondcenterto
indicatorcenterAngle,degreesorclock,o’clock
Fromtheatomorbondcenterto
bottomleftofindicatorbaselineOffset,horizontal, andvertical
Atspecifiedcoordinates Absolute,horizontal, andvertical
HidingaQueryIndicators
Tohideanindicator:
1.Right-clicktheindicator.
2.ChooseHideIndicatoronthecontextmenu.
Removing AtomProperties
Toremoveallproperties fromanatom:
1.Selecttheatom.
2.NavigatetoStructure>AtomProperties .
3.ClickUseDefaults.
Toremovespecificproperties fromanatom,dooneofthefollowing:
Right-clicktheatom.Inthecontextmenu,selectAtomProperties andchoosetheproperties toremove.
NavigatetoStructure>AtomProperties andclicktheatomproperties toremove.
Withqueryindicators shown,clickthequeryindicators usingtheErasertool.
AtomProperty Options
Theproperties youcanassigntoatomsaredescribed below.
Substituents
Asubstituent isdefinedasanon-hydrogenatomconnected byabondofanyorder.Thesubstituents properties spe-
cifythenumberofsubstituents thatmaybebondedtotheselectedatoms.ChemBioDraw 14.0
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Forexample,inthefigurebelow,thecarbonylcarbon(B)hasasubstituents countoftwo,thealphacarbon(A)andthe
aldehydeoxygen.(hydrogen atomsarenotcounted).Thealdehydeoxygenhasonlyonesubstituent.
Thesubstituent countatompropertyletsyouspecifythenumberofbondstoanatominthetargetstructure.This
includesbondsalreadydrawninthequerystructure.
Thesubstituent optionsare:
Unspecified .Default.Thetargetbasedetermines thesearch.Somedatabases findcompounds withanysub-
stitutionatthisatom;otherdatabases (includingDARC)findonlycompounds withsubstitution exactlyasdrawn.
FreeSites.Findscompounds inwhichtheselectedatomsmaycontainarangeofsubstituents uptothenumberspe-
cifiedplusthenumberofbondsasdrawn.Avalueofzerofindsasubstituent countasdrawn.Youcanalsousethe
FreeSitessymbolintheQuerytoolbartoapplyfreesites.Inboththefreesite,orinexactsubstitution, youdefinethe
maximum numberofsubstituents anatomcanhave.Thenumberyouuseintheinexactcountmustincludethesub-
stitution(s)showninthequerystructure,whereas,thefreesitecountdoesnot.
Upto.Findscompounds inwhichtheselectedatomsmaycontainarangeofsubstituents uptothenumberspe-
cified.
Exactly.Findscompounds inwhichtheselectedatomscontaintheexactnumberofsubstituents asspecified, upto
15substituents.
Note:Youcanspecifyasubstituent countofupto‘4’usingthe‘Substituents ’optionfromthecontextmenu.To
specifyasubstituent countofupto‘15’,select‘AtomProperties ’optionfromthecontextmenu.Clickingwiththe
freesitetoolselectedincrements thesubstituent countupto‘9’whereas<Alt>+click decrements thecount.
Forexample:
Query Finds Doesnotfind
Freesite
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Query Finds Doesnotfind
Upto
Exact
ImplicitHydrogens
Animplicithydrogenisahydrogenatominwhichit,oritsbond,isimplied,butisnotvisible.Anexplicithydrogenand
itsbondarevisible.
Figure14.3:A)Examples ofimplicithydrogens; B)Anexplicithydrogen.
Theimplicithydrogens propertyspecifieswhetheradditional, implicithydrogenatomsmaybeattachedtotheselec-
tedatoms.Ifimplicithydrogenatomsarenotallowed,allvalencestothatatommustbefilledbybondstonon-hydro-
genatoms.
Allowed.Default.Findscompounds regardless ofwhetherhydrogenatomsareattachedtotheselectedatoms.
Notallowed.Findscompounds withnoadditionalhydrogenatomsattachedtotheselectedatoms.
RingBondCount
TheRingBondCountspecifiesthenumberofbondsattachedtoanatomthatarepartofringsofanysize.Forsimple
cases,thisalsospecifiesthemaximum numberofringsinwhichanatomcanreside.ChemBioDraw 14.0
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Any.Default.Findscompounds inwhichtheselectedatomscanbeamemberofanytypeofring,oramemberofno
ringatall.
Noringbonds.Findscompounds inwhichtheselectedatomsareacyclic.
Asdrawn.Findscompounds inwhichtheselectedatomsresideinthesametypeandnumberofringsasdrawn.
Simplering.Findscompounds inwhichtheselectedatomsisamemberofonlyonering(theatomhastworing
bonds).
Fusion.Findscompounds inwhichtheselectedatomsliesatringfusions(theatomhasthreeringbonds).
Spiroorhigher.Findscompounds inwhichtheselectedatomsisamemberofaspiroorhigherlinkage(theatom
hasfourormoreringbonds).
Unsaturation
TheUnsaturation propertyspecifieswhetheramultiplebondisattachedtotheselectedatoms.
Unspecified .Default.Findscompounds regardless ofwhetheramultiplebondisattachedtotheatom.
Mustbeabsent.Findscompounds thatdonothaveamultiplebondattachedtotheselectedatoms.
Mustbepresent.Findscompounds thathaveatleastonemultiplebond(double,tripleoraromatic)attachedtothe
selectedatoms.
Reaction Change
TheReactionChangepropertyspecifieswhetherachangeoccursatselectedatomsafterareaction.Thispropertyis
meaningful onlywhensearching adatabasethatcontainschemicalreactions. InChemBioFinder, onlytheproduct
atomischecked.Thestereodesignation isignoredonreactants.
Maybeanything.Default.Findsallreactionsregardless ofanychangetoselectedatomsafterareaction.
Mustbeasspecified.Findsallreactionsthatarechangedattheselectedatomsexactlyasspecifiedbythereaction
centerpropertyintheAtomProperties dialog.
Reaction Stereo
TheReactionStereopropertyspecifiesthattheselectedatomsarestereocenters inareaction.Thispropertyismean-
ingfulwhenonlysearching adatabasecontaining chemicalreactions.
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Figure14.4:Thereactionstereoindicator(circled).
Any.Default.Findsallcompounds regardless ofthestereochemistry attheselectedatoms.
Inversion.Findscompounds inwhichtheselectedatomshaveaninvertedstereoconfiguration afterareaction.
Retention .Findscompounds whoseselectedatomshaveanunchanged stereoconfiguration afterareaction.
FreeSites
Usingfreesites,youcanspecifythemaximum numberofsubstituents aresultcanhave.However, italsorequires
thatthebondsintheresultsappearexactlyastheyappearinthequerystructure.ChemDraw usesthefollowingnota-
tionsforfree-sites:
*0(Zerofreesites)
*1(Onefreesites)
*2(Twofreesites)
*3-*15(Threethroughfifteenfreesites)
Forexample,assumeyouwanttousethequerystructurebelowtosearchforasmanyastwosubstitutions onthe
vinylcarbonatomwhilemaintaining thebondpattern.Yourquerystructurewouldlooksomething likethis:
Someoftheresultscaninclude:
Figure14.1:(E)-3-(4-aminophenyl) acrylicacidChemBioDraw 14.0
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Figure14.2:4-(cyclohexylidenemethyl) aniline
Figure14.3:(E)-3-(4-aminophenyl) -2-phenylacrylic acid
Toincreasethenumberoffreesites:
1.Todisplaythequerytools,navigatetoView>OtherToolbars>QueryToolsorclicktheQueryToolsicononthe
MainToolpalette.
2.ClicktheFreeSitetoolontheQuerytoolspalette.
3.Clicktheatomtowhichyouwanttoapplyfreesites.
4.Continuetoclicktheatomtoincreasethefreesitenumber.
Toreducethenumberoffreesites,press<Alt>keywhileclickingtheatom.
YoucanalsochangethefreesitesusingtheAtomProperties dialogortheshortcutmenu.See"AtomProperties" on
page231.
Translation
TheTranslation propertyspecifieswhatisrequiredtomatchinthestructurequeryandpossibledatabasehitsina
MarkushDARCquery.
Equal.Default.Matchesspecifictospecificorgenerictogenericterms.
Broad.Translates specificqueryatomstocorresponding superatoms inthedatabase.ChemBioDraw 14.0
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Narrow.Translates querysuperatoms tocorresponding specificatomsorgroupsinthedatabase.
Any.Translates genericorspecifictermstoanyterm.
Formoreinformation, seetheMarkushDARCUserManual.
IsotopicAbundance
TheIsotopicAbundance propertyletsyoudistinguish differentisotopiccompounds— forexamplebetweenmono-and
hexa-deuterobenzene— byspecifying anuclideatanylocation.
Note:Theisotopicabundance propertyisavailableinChemBioDraw Ultra,ChemDraw Ultra,andChemDraw Pro
only.
Unspecified .Default
Any.ForChemFinder, thesameasdefault.Includedforcompatibility withothersystemswherethedefaultmaybe
different.
Natural.Indicatesanisotopically unmodified nuclide.
Enriched.Indicatesamixtureofisotopically substituted andisotopically unmodified nuclides.
Deficient.Indicatesadepletedlabel,thatis,thenuclideispresentinlessthanthenaturalratio.
Nonnatural .Indicatesanisotopically substituted nuclide,thatis,essentially allthemolecules ofthecompound have
onlytheindicatednuclide.
Abnormal Valence
TheAbnormalValencepropertyspecifieswhetherselectedatomscanhaveavalenceotherthannormal.“Normal”
valencesforeachelementaredefinedintheIsotopesTablefileintheChemBioDraw Itemsfolder.
Note:TheAbnormalValenceatompropertydoesnotprovideavisualindicator.
Notallowed.Default.Findscompounds wheretheselectedatomshaveonlynormalvalences. IftheCheckStruc-
tureWhenCopyingtoClipboardorExportingpreference isturnedon,anerrormessagewarnsofabnor-
malvalences.
Allowed.Findscompounds withthespecificvalencedrawn.
Note:IfAbnormalValenceisallowed,anyInvalidValencemessages forthoseatomsareignoredbytheCheck
Structurecommand.
BondProperties
Anindicatorappearsnexttoabondforeachpropertyyouassign.
Assigning BondProperties
Todefinebondproperties:
1.Selectoneormorebondsinastructure.
2.Dooneofthefollowing:
Right-clicktoopenacontextmenu,pointtoBond,pointtothepropertyyouwant,andchoosethedesired
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NavigatetoStructure>BondProperties .OntheBondProperties tab,selecttheproperties fromthedrop-
downlistandclickOK.
Pointtobondandpressthehotkey“/”.TheBondProperties dialogappears.
3.IntheBondProperties dialog,selecttheproperties toassociate withtheselectedatoms.ClickOK.
Formoreinformation, see"QueryIndicators" onpage232.
Theindicators are:
Indicator BondQueryProperty
Any "BondTypes"onpage241:Any
S/D "BondTypes"onpage241:SingleorDouble
D/A "BondTypes"onpage241:DoubleorAromatic
S/A "BondTypes"onpage241:SingleorAromatic
Rng "Topology" onpage241:Thebondmustbepartofa
ring.
Chn "Topology" onpage241:Thebondmustbepartofa
chainandnotpartofaring.
R/C "Topology" onpage241:Thebondmaybepartofa
ringorchain.
Rxn "Reaction Center"onpage241:Thebondmustbe
partofareactioncenter.
ViewingBondProperties
Thedescriptor fortheReactionCenterquerypropertyindicatesthepropertyisapplied,butnotthevalueoftheprop-
erty.
Tofindthevalueofaquerybondpropertysetting:
1.Selectthebond.
2.Dooneofthefollowing:
Right-clicktoopenacontextmenu,pointtoBondProperties ,andselecttoaproperty.
NavigatetoStructure>BondProperties .
Removing BondProperties
Toremoveallqueryproperties fromoneormorebonds:
1.Selectthebonds.
2.NavigatetoStructure>BondProperties .ChemBioDraw 14.0
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3.ClickUseDefaults.
Toremovespecificbondproperties:
1.Selectthebond.
2.Dooneofthefollowing:
Right-clicktoopenacontextmenu,pointtotheappropriate property,andclickthepropertytoremove.
NavigatetoStructure>BondProperties andclickthebondpropertytoremove.
BondProperty Options
Theproperties youcanassigntobondsaredescribed below.
BondTypes
Thispropertyspecifiesthebondtypeoftheselectedbonds.
TheDefaultbondtypecorresponds tothecurrenttypeofthebond(single,double,andsoon.)asdrawn.
Single(all)andDative.Findscompounds withthebondtypeyouselectfortheselectedbonds.
DoubleorDoubleBold.Findscompounds whoseselectedbondsaredouble.
DoubleEither.Findscompounds whoseselectedbondsaredoublebondsandhaveeithercis/transstereochemical
configuration.
Aromatic.Findscompounds whoseselectedbondsarearomatic.
Tautomeric .Findscompounds whoseselectedbondsaretautomeric.
Triple.Findscompounds whoseselectedbondsaretriple.
Quadruple .Findscompounds whoseselectedbondsarequadruple.
Any.Findsanycompound, regardless ofthebondtypeoftheselectedbonds.
S/D.Findscompounds whoseselectedbondsaresingleordouble.
D/A.Findscompounds whoseselectedbondsaredoubleoraromatic.
S/A.Findscompounds whoseselectedbondsaresingleoraromatic.
Note:Notallbondtypesaresupported inallfileformats.Whenanunsupported bondtypeissavedtoagivenfile
format,itisconverted totheclosestequivalent thatissupported.
Topology
TheTopologypropertyspecifiestheringenvironment oftheselectedbonds.
Unspecified .Default.Findscompounds regardless oftopology.
Ring.Findscompounds wheretheselectedbondsarepartofaring.
Chain.Findscompounds wheretheselectedbondsarepartofachain(butnotpartofaring).
RingorChain.Findscompounds wheretheselectedbondsarepartofeitheraringorachain.
Reaction Center
TheReactionCenterpropertyspecifieshowtheselectedbondsareaffectedinareaction.Thispropertyismeaningful
onlywhensearching adatabasecontaining chemicalreactions.
Unspecified .Default.Findscompounds regardless ofwhethertheselectedbondsareaffectedbythereaction.ChemBioDraw 14.0
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Center.Findscompounds wheretheselectedbondsareaffectedbyareaction,butthetypeofchangeisunspecified.
Make/Break .Findscompounds wheretheselectedbondsareeitherbrokenorcreatedinareaction.
Change.Findscompounds wherethebondorderoftheselectedbondschangesinareaction.
Make&Change.Findscompounds wheretheselectedbondsareformed,broken,orundergoachangeinbond
order.
NotCenter.Findscompounds wheretheselectedbondsarenotpartofthereactioncenter.
NotModified.Findscompounds wheretheselectedbond’sordersdonotchange,butmay(ormaynot)bepartofthe
reactioncenter.
Unmapped .Findsallcompounds.
ElementLists
Anelementlistisalistofatomsallowedataspecifiedlocation.Forexample,thequerystructurebelowallowsbro-
mobenzene, Iodobenzene, orchlorobenzene tobereturned.Anexampleofanelementlistis:
Figure14.4:Anelementlistasanatomlabel
Theelementsinthelistmustbeseparated bycommas.Aspaceaftereachcommaandbracketsareoptional.
Note:Anelementlistmaycontainonlyatomicsymbols,plusD(deuterium) andT(tritium).
Tocreateanelementlist:
1.Openanatomlabeltextbox.
2.Typeanopenbracket("[")followedbyalistofelementsseparated bycommas(“Cl,Br,I”),followedbyaclose
bracket("]"),forexample:[Cl,Br,I].
3.Closethetextbox.
Thefigurebelowshowsaquerystructurecreatedtofindcompounds matchingthefollowingcriteria:ChemBioDraw 14.0
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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. Thebracketproperties letsyouspecifythecontextandorientation oftherepeatingunits.
Forexample:
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Toenclosestructures withbrackets:
1.TodisplaytheBrackettoolbar,navigatetoView>OtherToolbars>Bracket.
2.OntheBrackettoolbar,selectoneofthedoublebrackettools.
3.Todrawthebrackets,clickanddragacrossthestructuretoenclose.
Thisgivesdefaultvalueforcomponent order,multiplegrouprepeatcount,orsinglerepeatingunitlabel.
SettingBracketProperties
TosettheBracketProperties:
1.Selectabracket.
2.NavigatetoStructure>BracketProperties .TheBracketProperties dialogappears.
TheFlipTypeoptionappearsonlyforladderpolymers. See"FlipType"onpage248.
Youcancustomize thetextthatappearstothebottomrightofthebracketforthesebrackettypes:
Component (c#)—thecomponent ordermustbeanon-negativeinteger,andisdisplayedastheletter“c”followed
byaninteger(or“c”aloneifanorderofzeroisspecified).
MultipleGroup(#)—therepeatcountmustbeapositiveinteger.
SRU(n)—theSRUlabelcanbeanytext.
Youcanalsoeditthetextforthesebracketusagetypesinthedocument usingtheTexttool.Youcannoteditthetext
displayedforotherbracketusagetypes.
BracketUsage
PolymerRepresentations areeitherstructure-based orsource-based.Thetypeofbracketyouusedependsonthe
typeofrepresentation.
Structure- basedPolymers
Structure-basedrepresentations encloseonlypartofastructurewithinbrackets.Oneormorebondscrosseachofthe
enclosingbrackets.Thecrossingbonds“matchup”,makingthepolymerstructuremoreexplicit.
Yourepresentastructure-basedpolymerbyenclosingaportionofastructureinbracketswithabrackettypeofSRU
(n).IUPACrecommends thesubscript“n”todenotestructure-basedrepresentations ofunknownsize,butyoucan
editthetextusingthetexttool.
Astructure-basedrepresentation ofpoly(vinyl chloride) isshownbelow:
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Youcanalsousethebracketusagetypes“Crosslink  (xl)”,“Graft(grf)”,and“Modification (mod)”torepresenttypesof
repeatingunitsinastructure-basedrepresentation.
Source-basedPolymers
Source-basedpolymerrepresentations encloseadiscretechemicalsubstance inbrackets.Themodeofpoly-
merization maybeobviousfromcontextorbeunknown. Source-basedrepresentations areusefulwhendescribing
processes wherethestartingmaterialsareknown,buttheexactstructureofthereactionproductisnot.
Youcancreateasource-basedrepresentation byenclosingastructurein“Monomer (mon)”brackets.
Asource-basedrepresentation ofpoly(vinylchloride)isshownbelow:
Youcanuse“Mer(mer)”bracketsforcomponents ofacopolymer wherethoseindividualcomponents areknownnot
torepeatthemselves ortheyalternatewithothercomponents. Forexample:
Copolymers representsubstances withmorethanonerepeatingunit.Ingeneral,youcanusebrackettype“Com-
ponent(co)”.Youcanalsouse“Copolymer, alternating (alt)”,“Copolymer, random(ran)”,and“Copolymer, block(blk)”
torepresentdifferentcopolymer typesinasource-basedrepresentation.
Thebrackettype,“Mixture,unordered (mix)”maybeusedtorepresentacollectionofsubstances thatmayallbe
present,butnotnecessarily inknownamounts.Brackettype“Component (c)”indicateseachmixtureelement,as
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Figure14.6:Bracketsusedtoindicatemixtures
Brackettype“Mixture,ordered(f)”isprimarilyusedtodescribemanufacturing processes, wherecomponent orderis
critical.Aswithunordered mixtures,individualelementsofanorderedmixtureshouldbesurrounded bybracketswith
abracketusageof“Component (c)”.However, components oforderedmixturesmustbenumbered toshowtheir
order.Youcandothisbyeditingthe“c”labelwiththetexttooltoincludeanumber(“c1”,“c2”,andsoon.)
MultipleGroups
Youusethebrackettype,“MultipleGroup(#)”toindicatethattheencloseditemsarerepeatedaknownnumberof
times.Multiplegroupbracketsmayencloseentirestructures, orpartofthestructures. Someexamples are:
Figure14.7:Bracketstoindicatemultiplegroups
Becausemultiplegroupbracketsrepresentaspecificrepeatcount,youcandisplaythemolecular weights(and
relateddata)fortheenclosedstructures intheAnalysiswindow.ChemBioDraw 14.0
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RepeatPattern
Forsimplelinearpolymers, therepeatingunitsmayconnecthead-to-tailorhead-to-head(ortheirrepeatpatternmight
beamixtureorunknown). Youcanalsoassignthispropertytobrackets.
Thehead-to-tail typeisthedefaultrepeatpattern,asshownbelow:
Figure14.8:Head-to-tailrepeatpattern.AandBrepresentthepolymersshown.Crepresents amixtureofAandB.
Removing BracketUsageLabels
Toremovethebracketusagelabels,dooneofthefollowing:
Hoveronthelabelandpress<delete>.
UsetheErasertooltodeletethelabel.
Note:Settingthebracketusagetypeto'Unspecified' removesanyspecificbracketusageassignment.
LinkNodes
Youcanspecifyavariable-lengthchain,orring,byindicatingthatoneoftheatomscanrepeatanumberoftimes
usinglinknodes.
Linknodesmusthaveexactlytwoconnecting bonds.
Theatomlabelmustmeettheseconditions:
Itmustconsistofagenericname,ornomorethanoneelementsymbol.
Thelastpartofthelabelmustbeintheform:numberhyphennumber,withthenumbersandhyphensubscripted.
Parentheses orbracescanbeusedinsteadofbrackets.
Note:ChemBioFinder supportsonlybrackets,’[ ]’,forlinknodes.Parentheses orbracescannotbeusedforlink
nodesinChemBioFinder.
Bracketscanbeomitted,ifnotrequiredforclarity,forexamplewithO1-3ChemBioDraw 14.0
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Tocreatealinknode:
1.Openanatomlabeltextbox.
2.Typethelinknodeinthisformat:
[CH2]3-7
FlipType
Forladderpolymers(polymers withtwoconnecting bondsoneachside)theconnection ordermaybeundefined. You
canassigntheFlipTypepropertytodefineit.Thispropertyisonlyforbracketswithexactlytwocrossingbonds.
Becauseofitsprevalence, theNoFliptypedoesnotreceivespecialannotation. Theexamplebelowillustrates aflip
typeinladderpolymers.
Alternative Groups
Youcancreateasearchquerythatcontainsvariablefunctional groupsorsubstructures. Insteadofsubmitting mul-
tiplequeriesonstructures thatshareacommonsubstructure, youcansubmitasinglequerywiththeparentstructure.
Theparentstructurecanhaveattachment pointstoalistofalternative groupsthatyoudefine.ChemBioDraw 14.0
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DefiningAlternative Groups
Youcancreatealternative groupdefinitions (R,G,andsoon.)thatrepresentasetofsubstituents, eachofwhichis
usedinthequery.
Todefinealternative groups:
1.NavigatetoView>OtherToolbars>QueryToolstoopentheQuerytoolbar.
2.ClicktheAlternative Groupquerytoolanddragwiththetooltocreateanarealargeenoughtodrawthealternative
groups.
3.Typeatitle,suchasR1,intheAlternative GroupTitlebox,anddrawthesubstructure fragments intheAlternative
Groupbox.
Tip:Youcandrawtheboxafterwardtoenclosethelistofalternative groups.
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Figure14.9:Defininganalternative group
Specifywherethefragments shouldbondtotheparentstructureonthealternative grouplabelbydefiningattachment
Points.
1.Dooneofthefollowing:
Selectthediamond-shapedAttachment PointtoolontheChemicalSymbolspalette(View>Other
Toolbars>Chemical Symbols),andclickasubstructure fragmentwhereyouwanttoplacetheattachment point.
Pointtoasubstructure fragmentwhereyouwanttoplacetheattachment pointandpressthehotkey“.”(period).
Anattachment pointsymbolappears.
2.Repeatforallfragments.
Figure14.10:Addingattachment points.Anattachment pointsymbolhasbeenappliedtothenitrogenatom.
Whenyoucreateastructurethatcontainsanalternative group,anattachment pointsymbolappearsnexttothelabel.
Theattachment pointnumbermatchesthatfoundinthedefinition.
Figure14.11:StructurewithR-grouptable
Thenumberdisplayedintheattachment pointsymbolistheattachment rankorder.Seetheexamplein"Multiple
Attachment Points"onpage251.ChemBioDraw 14.0
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MultipleAttachment Points
YoucanuseR-groupsthatcontainmorethanoneattachment point,forexample:
ForthistypeofR-group,youmustindicatetheattachment pointorderinyourtable.Ifyouhavewell-definedmultiple
attachment pointsonyourstructurefragments, youcansearchforspecificmaterials. Thistypeofsearchisusefulfor
findingsimilarstructures thatconform.
Forexample,assumeyouwanttofindcompounds infigureAbelow,butnotcompounds infigureB.
Figure14.12:Multipleattachment points
Byspecifying theattachment pointorder,youcanexcludetheunwanted compounds.
Tospecifytheattachment pointsorder:
1.Drawthestructureshownbelow
2.Createanalternative groupboxlabeled“R1”.ChemBioDraw 14.0
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3.Drawthestructurefragments andlabelthemwithattachment points.
Whenthealternative groupdefinitioniscomplete, theattachment pointsymbolsappearintheparentcompound.
Figure14.13:R-groupswithmulti-attachment points
Bynumbering yourattachment points,youspecifythatthemethylgroupmustbeadjacenttotheaminegroup.The
conformations thatarenotofinterestareexcluded.
Attachment PointNumbering
Numbered attachment pointsletyouspecifyhowthestructurefragments connecttoyourparentstructure.
Tosettheorderoftheattachment points,usetheAttachment Pointtooltoclicktheendsofthebondsintheorderyou
want.
Tochangeattachment pointorder:
Clicktheattachment pointswiththeAttachment Pointtool.
HidingRankIndicators
Youcanhidetheattachment rankindicators ifrequired.Forexample,inpublication- qualitydrawingsthenumbering of
attachment pointsisimplicitandthenumbered attachment rankindicators aresuperfluous.
Tohidetheattachment rankindicators andremovethenumbersfromtheattachment points:
1.NavigatetoFile>Preferences .
2.InthePreferences dialog,clickBuilding/Display .
3.DeselectShowAttachment RankIndicators .
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Thefigurebelowshowsanalternative groupdefinitionandaparentstructurewiththeattachment rankindicators hid-
den.
Figure14.14:Hiddenattachment indicators
R-groupreactionqueries
Youcansearchandstorereactions. Inareaction,oneorseveralcompounds (reactants) aretransformed intoother
compounds (products). Individualreactants(orproducts)areseparated fromeachotherwithplussigns.Thereact-
antsareseparated fromtheproductswithanarrow.
Youcanalsosearchforchemicalreactionscontaining r-groups.Anexampleofachemicalreactioncontaining r-
groupsisshownbelow:
Searching forreactants
Searching forreactantsisusefulifyouhaveaknownstartingmaterialandyouareinterested inlearningmoreabout
whatsubstances itcanproduce.Areactantsqueryisverysimilartoareactionsearch,exceptthatthereisnothingto
therightofthearrow.Forexample,considerthequery:
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Figure14.15:Sampler-groupreactantquery
Alikelyhitfortheabovequeryisshownbelow:
Searching forproducts
Ifyouknowthedesiredendproductbutnothowtogetthere,youcandoaproductsquery.Aproductsqueryissimilar
toareactionsearch,exceptthatthereisnothingtotheleftofthearrow.Forexample,considerthequery:
Figure14.16:Sampler-groupproductquery
Anonymous Alternative Groups
Anonymous alternative groupsareacrossbetweenanelementlistandanalternative group.Elementlistscomprise
singleelements, butanonymous alternative groupscancontainanystructurethatcanberepresented bytext,suchas
nicknames andgenericnicknames. Anonymous alternative groupsareshortcutnotationsforregularalternative
groups,eliminating theneedtospecifyaname,suchas“R1”.
Youcanconciselydefineyoursearchqueryusinganonymous alternative groups.Bylabelinganatompositionasa
listofsubstructures youspecifythatoneofthesesubstructures mustmatchinthestructureforwhichyouaresearch-
ing.Commasmustseparatetheitemsintheanonymous alternative group.Aspaceaftereachcommaandthebrack-
etsareoptional.Examples ofanonymous alternative groupsareshownbelow.
Figure14.17:Anonymous alternative groups.
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1.Openanatomlabeltextbox.
2.Typeanopenbracket“[”followedbyalistofelements, fragments, nicknames, orgenericnicknames separated by
commas,followedbyaclosebracket“]”.
ExpandGenericStructures
Youcangeneratemultiplestructures fromanabbreviated combinatorial structurewiththeExpandGenericStructure
tool.Thetoolislimitedto500generated structures. Forlargecombinatorial expansions, useCombiChem forExcel.
Fourkindsofabbreviated combinatorial definitions maybeused:
Definition Example
Alternative Groupsand
R-tables
Anonymous Alternative Groups
Element
Lists
Variable
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Definition Example
Definitions areexpanded intomultiplecompletemolecules. Ifmorethanonesiteispresentintheselection, theexpan-
sionincludesallpermutations ofsubstitutions. Expansions aregenerated inanewdocument.
Toexpandagenericstructure:
1.Selectoneormoregenericstructures toexpand.
Note:Foralternative group/R-tables,youmustselectthealternative grouplabelandthetablemustbeselected.If
thelabelisselectedbutnotthetable,thelabelwillnotchangeintheexpansion, andwillappearasalabelinallgen-
eratedstructures.
2.NavigatetoStructure>ExpandGenericStructure.
Thestructures aregenerated inanewdocument.
R-LogicQueries
AfteryouhaveyourgenericstructureandasetofR-groups,youcanusethemtorunqueriesagainstastructuredata-
base.ThisiscalledanR-Logicquery.
WhenyourunanR-Logicquery,yousearchforstructures thatallhavethegenericstructureandacombination ofyour
R-groups.Thecombinations arebasedonaBooleanexpression thatyoudefine.ToprepareanR-Logicsearch,nav-
igatetoStructure>R-LogicQuerytoopentheR-LogicQuerydialog.
Todefineaquery,selectoneormoreR-groupsinyourstructureandhowmanytimesitmustoccur.Youcanindicate
thatifthefirstR-groupconditionismet,anotherR-groupmustalsobefoundbeforethestructureisreturnedasares-
ult.Forexample,considerthisquerystructure:ChemBioDraw 14.0
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ThisstructureindicatesthatbothR1sitesmustconsistofeitherafluorineorchlorineatomandthattheR2sitemust
beeitherabromineoriodineatom.
Assumeyouwanttofindallstructures inyourdatabasethathaveeitheraForClatomatbothR1locationsandeither
BrorIatR2:
1.NavigatetoStructure>R-LogicQuery.
2.IntheR-Groupdropdownlist,selectR1.
3.ForOccurrence range,select2.Thisindicatesthattwoinstances ofanR1groupmustoccurinastructureforitto
bereturnedasaresult.
4.ForIfR(i),selectR2.ThisindicatesthattheR2locationmustconsistofeitherBrorI.
5.ClickAdd.
6.ClickOK.
RestH
SelectRestHintheR-LogicQuerydialogtoindicatethatifyouhavetwopossibleR-grouplocations, andonlyoneis
filled,theothermustbeahydrogentoreturnapositiveresult.
Atom-to-AtomMapping
Youcancreatecorrespondences betweenatomsindifferentstructures forsearching areactiondatabase. Thereac-
tionsmappedcanbesingleormulti-step.Adrawingthatincludesatom-to-atommappingcanbeaddedtoadatabase
orbeusedtosearch.
Youcanassignatommappingintwoways:
Automatic mapping(navigatetoStructure>MapReaction Atoms).
Manualmapping,usingtheReactionAtom-Atom Maptoolonthemaintoolspalette.
Usingeithermethod,ChemBioDraw assignsareactioncenterforthereactantsandproducts.ChemBioDraw 14.0
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Whenareactionmapisestablished, youcanpointtoanatominonestructurewiththeReactionAtom-Atom Maptool
tohighlightthemappedatomintheotherstructure.
Displaying andPrinting
Todisplayreactionmappingsymbolsonscreenandinprint:
1.NavigatetoFile>Preferences .
2.InthePreferences dialog,clicktheBuilding/Display tab.
3.SelectAlwaysDisplayandPrintReaction Mapping.
4.ClickOK.
DeselectAlwaysDisplayandPrintAtomMappingtoshowthesymbolsonlywhenyouselecttheReactionAtom-
AtomMaptool.Thesymbolsdonotprint.
Automatic Mapping
Tocreateareactionmap:
1.Selectthereaction.
Tip:Double-clickthearrowwithaselectiontooltoselectthereaction.
2.NavigatetoStructure>MapReaction Atoms.
ThesymbolRxnappearsnexttothebondsinthereactantandproductthataremodifiedbythereaction.Formore
information abouttheReactionCenterbondproperty,see"BondProperties" onpage239.
Figure14.18:Automatic reactionmapping
ManualMapping
Whenmanualatom-to-atommappingisrequired,youcanusetheReactionAtom-AtomMaptool.Thismightbeneces-
sarywhentheautomatic mappingisappliedtocomplicated reactions, butgivesincorrectresults.InthesecasesyouChemBioDraw 14.0
Chapter14:QueryStructures 258of315

canmanuallyreadjustthereactionmapping.
ThefigurebelowshowstheinitialmappingbeingamendedbyusingtheReactionAtom-AtomMaptool.
Figure14.19:Automatic mappingtobeamended
WhenyoumanuallymapreactionswiththeReactionAtom-AtomMaptool,youcansuppressautomatic re-mapping
ofatomsotherthanyourtargetatom.
Tosuppressautomatic remapping:
1.NavigatetoFile>Preferences .
2.OntheGeneraltab,de-selectAutomatic Reaction Mapping.
3.ClickOK.
TousetheReactionAtom-AtomMaptooltosupplement theautomatic mapping:
1.ClicktheReactionAtom-AtomMaptoolontheQuerytoolbar.
2.Pointtotheatominthereactantwhosemappingyouwanttoestablish. Forexample,inthefollowingdrawingyou
wouldpointtotheacycliccarbonadjacenttotheetheroxygen.
3.Dragfromthereactantatomtothecorresponding productatom.
Theremaining atomsaremappedbasedonthemanualmapping.ChemBioDraw 14.0
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Figure14.20:Finalizedmapping
Youcansetorchangethemappingforotheratomsinthereaction.
ClearingReaction Mapping
Toclearreactionmapping:
1.Selectthestructures whosemappingyouwanttoclear.
2.NavigatetoStructure>ClearReaction Map.
ClickinganddraggingfromanyatomtoanemptyspaceintheChemDraw windowusingtheReactionAtom-Atom
Maptoolwillclearthemappingfromthatatom.
Exporting Reaction Mapping
Reactionmappingandreactioncenterperception information arestoredinthe*.cdxfileformat.Youcanopenthefile
inChemBioDraw fortransfertootherapplications thatreadatommapping,suchasChemBioFinder. Youcanalso
copymappedreactionstothesesameapplications usingtheClipboard.
Stereochemical Symbols
Therearethreetypesofflagsthatindicatestereochemistry:
Racemic.Aracemicmixture.
Absolute.Apureenantiomer ofknownconfiguration.
Relative.Apureenantiomer ofunknownconfiguration.
Thedefaultatomlabelsizeforthedocument determines fontandsizeforstereochemical flags.
Todrawastereochemical flag:ChemBioDraw 14.0
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1.TodisplaytheQuerytools,navigatetoView>OtherToolbars>QueryTools,orclicktheQueryToolsicononthe
MainToolpalette.
2.OntheQuerytoolspalette,clickthetoolfortheflagyouwanttouse.
3.Clicknexttothestructuretowhichyouwanttoassigntheflag.
3DProperties
3Dqueriesareusefulinpharmacophore searching whenlookingfora3Drelationship amongatomsandbonds,(for
exampleinaseriesofpotentialreceptorligands).Tocreatea3Dquery,youaddgeometries (lines,planes,andsoon)
andconstraints (specified asranges)toaquerystructure.Forexample,youcanspecifythattwoatomsmustbe
between4and5Åapart,orthattwoplanesmustbeseparated by80-100degrees.
Toassign3Dproperties toastructure:
1.Selectthestructureorsubstructure.
Note:Becausesome3Dproperties specifyanorder,useSHIFT+Click toselectthemintheorderyouwant.
2.NavigatetoStructure>Add3DPropertyandselectanoptionfromthetablebelow.
Note:Inthetable,pointsmaybeatoms,centroids, orpoints.Linesmaybelinesornormals.
Angle.Definesanangleconstraint betweenthreepoints(inorder).Indicatedasarange.
Dihedral.Definesadihedral(torsional) angleconstraint amongfourpoints(inorder),betweentwolines,ortwo
planes.Indicatedasarange.
Distance.Definesadistanceconstraint betweentwopoints,apointandaline,orapointandaplane.Indicatedasa
range,inangstroms.
Line.Definesthebest-fitlinefortheselectedpoints.
Plane.Definesthebest-fitplanefortheselectedpoints,orforapointandaline.
Exclusion Sphere.Definesanexclusionspherearoundapoint.Ifmorethanonepointisselected,theexclusion
sphereisaroundthefirstselectedpoint,andthesubsequent pointsareallowedwithintheexclusionspherewhenthe
queryisevaluated. Indicatedasarange,inangstroms, beginningat0.
Normal.Definesthenormalfromadefinedplaneinthedirectionofapoint.
Point.Definesapointpositioned ataspecifieddistancefromafirstpointinthedirectionofasecondpoint(inorder),
orinthedirectionofthenormal.
Centroid.Definesapointpositioned attheaveragepositionofallotherpointsselected.
Note:
Allconstraint valuescanbeeditedwiththetexttool.Onlyexclusionspheresshowthechange.
Whenyoucreateapoint,adialogappearswhereyouspecifythedistancefromthefirstselectedpointtothecal-
culatedpoint.ThedistancemaybeanabsolutevalueinÅorapercentage ofthedistancebetweentheselected
points.ChemBioDraw 14.0
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Negativevaluesindicatethatthecalculated pointisfurtherfromthesecondpointthanthefirstpointis,rather
thanbetweenthem.
Geometry andconstraint objectsupdatewhenyouchangethestructure;theycannotbemovedindependently.
TheymaybeusedwithCDX,MOL,SKC,andTGFfiles(fullread-writecompatibility); theyarenotcompatible
withotherformats.
Theycan,however,besavedinprint-onlyformatssuchasTIFF.
ExportCompatibility
Becausequeryproperties areusefulonlyinachemicaldatabase, youmusttransferyourstructures from
ChemBioDraw intoyoursearchsystem.Notallfileformatssupportthesamequeryproperties andnotallchemical
databases supportthesamefileformats.Consultthedocumentation foryourdatabaseforwhichfileformatsaresup-
ported.
Thefollowingtableliststhequeryproperties thatChemBioDraw writestoSKC,TGF,andClipboardfileformats.The
CDXformatretainsallqueryproperties.
.
Exported QueryProperties ISIS™MolRxn
AtomProperties
Substituents
Unspecified XXX
FreeSites bbb
Upto aaa
Exactly XcXcXc
ImplicitHydrogens
Notallowed XXX
Allowed XXX
RingBondCount
Any XXX
Noringbonds XXX
Asdrawn XXX
Simplering XXX
Fusion XXXChemBioDraw 14.0
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Exported QueryProperties ISIS™MolRxn
Spiroorhigher XXX
Unsaturation
Unspecified XXX
Mustbeabsent
Mustbepresent XXX
ReactionChange
Maybeanything X X
Mustbeasspecified X X
ReactionStereo
Any X X
Inversion X X
Retention X X
Translation
Equal
Broad
Any
Narrow
AbnormalValence
NotAllowed XXX
Allowed XXX
BondProperties
BondType
Single XXX
Dashed XdX
Hashed dddChemBioDraw 14.0
Chapter14:QueryStructures 263of315

Exported QueryProperties ISIS™MolRxn
WedgedHashed XXX
Bold Xee
Wedged XXX
Wavy XXX
HollowWedged eee
Dative fff
Double XgXX
DoubleEither XXX
DoubleBold hhh
Aromatic XXX
Tautomeric iii
Triple XXX
Quadruple lll
Any XXX
S/D XXX
D/A XXX
S/A XXX
Topology
Unspecified XXX
Ring XXX
Chain XXX
ReactionCenter
Unspecified X X
Center X X
Make/Break X XChemBioDraw 14.0
Chapter14:QueryStructures 264of315

Exported QueryProperties ISIS™MolRxn
Change X X
Make&Change X X
NotCenter X X
OtherQueryAttributes
GenericNicknames XjXjXj
ElementLists XkoXkoXko
ElementNotLists XkXkXk
Alternative Groups XXm
Anonymous Alternative
Groupsnn
LinkNodes ppp
Bracketproperties XXX
Atom-Atommapping X X
VariableAttachment Pos-
itions
3Dqueryproperties
a—Converted totheappropriate numberofexactsubstituents.
b—Freesitescountsofzerotranslated to“Substitution asdrawn”;allotherfreesitesvalueswrittenassubstitution
countsequaltothetotalcurrentvalence,plusthefreesitesvalue.
c—Substituent countsofgreaterthan5aretranslated to“6ormore”.
d—Converted towedgedhashed.
e—Converted towedged.
f—Converted toasingle,withapositivechargeappliedtothatatomatthebaseofthedativebondandanegative
chargeappliedtotheatomatthepointofthedativebond.
g—Interpreted byISIS™asunspecified cis/transstereochemistry.
h—Converted todouble.
i—Converted toaromatic.
j—OnlyM,X,Q,A;otherswrittenasaliases.
k—Truncated tothefirst5elements.
l—Converted tosingle.
m—AnRGfilewillbecreatedautomatically.ChemBioDraw 14.0
Chapter14:QueryStructures 265of315

n—Converted tonon-anonymous alternative groups.
o—Listsofgreaterthan5elementsconverted toalternative groups.
p—Thelowendoftherepeatrangeisalwaystreatedas1.ChemBioDraw 14.0
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SharingInformation
Manyofthesystemcommands youcommonly usetotransfercontentfromoneplacetoanothercanalsobeusedin
ChemBioDraw:
Copy/paste
Importandexportcontentfiles
Whenyouusetheclipboard, theobjectsyoucopycanbeedited.
TheClipboard
Youcanusetheclipboardtotransferpart,orall,information withinanactivedocument windowbetweenapplications
onthesamecomputeroronanetwork.Usethestandardcopy-and-pasteorcut-and-pastetoolstotransferinformation
toanyapplication thatsupportsthesetools.Theinformation istransferred asadrawingobject.Double-clicktheobject
toedititinChemBioDraw .
YoucanalsousetheCopyAstooltotranslateaselectedstructuretoaSMILES,SLN,orInChI™string.
IftheClipboardcontainsstructures andyoupasteintoanotherChemBioDraw document, thepastedinformation is
scaledtothesettingsinthenewdocument. Formoreinformation, see"Autoscaling" onpage270.
TextLineNotation
Usetextlinenotation1toexpandalineoftextintothestructurethatitrepresents. Severalsoftwarepackages use
SMILESstringstoenterandstorechemicalstructureinformation.
IfyouselectareactionandusetheCopyAsSMILEScommand, aSMIRKSstringiscopiedtotheclipboard. Ifyou
usethePasteSpecialSMILEScommand whenaSMIRKSstringisontheclipboard, areactionispastedintoyour
document.
CreatingSMILESStrings
TocreatetheSMILESstringforastructure:
1.Selectthestructure.
2.NavigatetoEdit>CopyAs>SMILES.
TheSMILESstringistransferred totheClipboard.
TodisplaytheSMILESstring,pastethestringinadocument window.
WhentheSMILESstringisontheClipboard, youcantransferittoanotherapplication thatcaninterpretSMILES
strings.
IfyoucopymorethanonestructurefromChemBioDraw totheClipboard, theSMILESstringareseparated bya
period.
1ASMILES stringisalineoftextthatrepresents thestructure ofamolecule. ASMIRKS stringdescribes chemicalreac-
tionsintext.ChemBioDraw 14.0
Chapter15:SharingInformation 267of315

SMILESsupportsanalternatenotationforaromaticstructures usinglowercase letters.ChemBioDraw generates this
typeofSMILESstringforanystructuredrawnwithexplicitaromaticbonds.
PastingSMILES
TopasteaSMILESstringasastructure:
1.SelecttheSMILESstringinthesourcefileandpressCTRL+C.
2.FromChemBioDraw, navigatetoEdit>PasteSpecial>SMILES.
CreatingSLNStrings
YoucancopyastructuretotheClipboardasanSLNstringforexporttootherapplications.
TocopyastructureasanSLNstring:
1.Selectastructure.
2.NavigatetoEdit>CopyAs>SLN.
TheStructureiscopiedtotheclipboardasanSLNString.
CreatingInChI™Strings
ChemBioDraw supportsIUPACInternational ChemicalIdentifier(InChI™) l.
Tocopystructures asInChI™stringstootherdocuments:
1.Selectthestructure.
2.NavigatetoEdit>CopyAs>InChI.
Youcancopyonlylegitimate InChI™structures. IfyouattempttocopyastructurethattheInChIprotocoldoesnot
support,awarninginformsyouthatthestructureisnotsupported.
CreatingInChIKey Strings
ChemBioDraw supportsStandardInchIKey, availableinInChI1.02.AnInChIKeystringisacondensed digitalrep-
resentation ofanInChIstring.AllInChiKeystringsarethesamelengthwhereasInChIstringsarenot.ThisstandardChemBioDraw 14.0
Chapter15:SharingInformation 268of315

makesInChIKeystringsusefulforWebsearching anddatabaseindexing.
TocopyastructureasanInChIKeystringtootherdocuments:
1.Selectthestructure.
2.NavigatetoEdit>CopyAs>InChIKey.
Formoreinformation onInChI™andInChIKey, seewww.iupac.org/inchi/ .
CreatingCDXMLorMOLText
TocreatetheCDXML text orMOLtextforastructure:
1.SelectthestructureyouwanttocreatetheCDXML or MOLtextfor.
2.NavigatetoEdit>CopyAs>CDXMLTextorMOLText.
TheCDXML text orMOLtextistransferred totheclipboard.
PastingCDXML or MOLText
TopasteanddisplaytheCDXMLtextorMOLtextfromtheclipboardtothedocument window:
3.NavigatetoEdit>PasteSpecial>CDXMLTextorMOLText.
ScrapandClippingFiles
Youcanusescrapfilestocopypartsofadrawingtootherapplications aftersavingthefileinChemBioDraw.ChemBioDraw 14.0
Chapter15:SharingInformation 269of315

Tocreateascraporclippingfile:
1.Selectanobjectinadocument.
2.Dragtheselectionoutofthedocument windowontothedesktop.Thefileappearsonthedesktop.
Toviewthefilecontents,double-clickitsicon.Tousecontentsinadocument, dragthefileintoanopenwindowofan
application thatsupportsdrag-and-drop.
Transferring Objects
Thissectionexplainsbehaviors ofcertainfeaturesinChemBioDraw whenyoutransferobjectsusingtheclipboard, or
draganddropfromonedocument toanother.
Autoscaling .Objectsthatyoutransferarescaledtomatchthesettingsofthedestination document.
Bonds.Whenyoucopyormoveastructuretoanotherdocument, thestructureadoptsthenewdocument’s fixed-
lengthvalue,butretainsitsscalingfactor.
Forexample,assumethefixedlengthissetto1.0cminasourcedocument. Abenzeneringisresizedto200%.The
bondlengthisthen2.0cm.Inthedestination document, assumethefixedLengthsetto1.7cm.Whenthebenzene
ringispastedintothedestination document, thebondsarescaledbyafactorto200%toafinalbondlengthof3.4cm.
AtomLabels.Atomlabelsarescaledthesamewayasbonds.Forexample,inthesourcedocument, assumethe
atomlabelfontsizeissetto16points.Oneortwoatomlabelsinthesourcedocument areresizedto8points,aratio
of8:16orascalefactorof0.5.Assumethatthedestination document hasanatomlabelfontsizesetto14points.If
youpastetheatomlabelintothedestination document, thefontsizeisscaledbyafactorof0.5togiveafinalatom
labelfontsizeof7points.
Captions.ChemBioDraw autoscales captionsusingtheratioofthefixedlengthinthedestination document tothe
fixedlengthinthesourcedocument timesthecaptionfontsize.Thefontsizeofthecaptioncanbeanysizeandisnot
relatedtothesettingintheSettingsdialog.Thisensuresthatcaptionsarealwaysinproportion tothebondswith
whichtheyarepasted.
Forexample,ifthesourcedocument hasafixedlengthof1.0cmandthedestination document hasafixedlengthof
2.0cm,andthecaptionyouarepastingis12points,thentheresultingcaptionsizeafterautoscaling is(2.0cm/1.0
cm)x12points=24points.
Non-bondObjectsandColor.Thedocument settingsdonotaffectallobjects.Objectssuchasarrowsandboxes,
arescaledtomaintainthesameproportions tobondsthatwereinthesourcedocument.
Exceptfortheforeground andbackground color,thecolorspresentintheselectiontobepastedareaddedtothedes-
tinationdocument’s Colorpaletteiftheyarenotalready(upto20totalcolors).Thebackground colorinthedestination
document remains,andallobjectscoloredusingtheforeground colorarechangedtomatchtheforeground colorinthe
destination document.
PastingtoanEmptyDocument .IfyoupasteaChemBioDraw drawingintoanemptydocument thathasdifferent
settings,theChangeSettingsdialogappears.
Tochangethesettingsinthedestination document tomatchthesettingsinthesourcedocument, clickChangeSet-
tings.ChemBioDraw 14.0
Chapter15:SharingInformation 270of315

Allofthesettingsinthedestination document arechangedtomatchthoseofthesourcedocument. Allofthecolorsin
theColorpaletteofthedestination document arechangedtothosespecifiedinthesourcedocument.
Toscaletheobjectsfromthesourcedocument tothesettingsinthedestination document, clickDon’tChangeSet-
tings.
Thesettingsfromthesourcedocument arescaledtothoseinthedestination document usingtheratiosgivenabove.
Note:Ifthesourcedocument wascreatedinaChemDraw versionearlierthan3.0,thenameofthedocument
appearsas“Unknown” inthedialogbox.
Embedding Objects
ChemBioDraw supportstheObjectLinkingandEmbedding (OLE)protocolonWindows. Thisletsyoueditstructures
thatarepastedinothertypesofdocuments. ChemBioDraw isanOLEserver,whichmeansitcancreateOLEobjects
thatyoucancopyandpasteintootherOLEclientapplications.
WhenyoutransferdrawingfromChemBioDraw toanotherdocument typethatsupportsOLE,youcanopenandedit
thedrawingwithinthenewapplication.
Forexample,toeditadrawinginsertedintoMicrosoftWord2003orlater,dooneofthefollowing:
InMicrosoftWord,selectthedrawingandnavigatetoEdit>CS ChemDraw DrawingObject.
Double-clickthedrawing.
TheChemBioDraw toolsandmenusreplacethoseofWord.Usethetoolstoeditthedrawing.
Whenyoufinishmakingchanges,clickinanotherareaoftheWorddocument. TheWordtoolsandmenusare
restored.
Exporting
YoucanexportChemBioDraw drawingsinvariousfileformatsandopentheminotherapplications. Conversely,
ChemBioDraw recognizes avarietyoffileformatsandcanopendocuments fromotherapplications.
Toexportafile:
1.NavigatetoFile>SaveAs.
2.IntheSaveAsdialog,dothefollowing:
a.Typeanameforthefileandalocationtosaveitto.ClickGoToChemDraw ItemstolocatetheChemDraw
Itemsfolder.
b.Selectafileformat.
c.ClickOK.
Somefileformatsdonotsupportatomlabelsthatcontainnicknames orstructuralfragments. Whenyousaveinthese
formats,ChemBioDraw expandsallatomlabelsandsavesthefileusingtheexpanded form.
Theseformatsdonotsupportnicknames orstructuralfragments:
Connection Table
MSIMolFile
SMDChemBioDraw 14.0
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Note:SomeversionsofChemBioDraw donotsupportalltheformatslisted.
Someformatscanbesavedwithdifferentoptions.Ifaformathasnosaveoptions,Optionsisgrayedout.Thesetext-
basedformatscanusetheTextOptions:
ChemDraw XML
CML
Connection Table
ISIS/TGF
ISIS/Reactions
MDLMolFile
AccelrysMolFile
SMD
Otherformatoptionsarenotedinformatdescriptions.
Importing
Youcanimportgraphicsordocuments fromotherapplications intoChemBioDraw.
Objects
InsertedobjectsareOLEfilesandcanberesizedandrotatedbutnotflipped.Youalsocanedititinitsnativeapplic-
ationfromwithinthedrawingwindow.
Files
Filesthatyouinsertbecomepartofthedrawing.YoucaneditafileonlyifitisinaChemBioDraw format.
Toinsertafile:
1.NavigatetoEdit>InsertFile.
2.IntheOpendialog,selectthefiletypefromthedrop-downlist.
3.SelectthefileandclickOpen.Thefileisembedded inthedrawing.
Toinsertanobject:
1.NavigatetoEdit>InsertObject.
2.IntheInsertObjectdialog,clickCreatefromFile.
3.BrowsetotheobjectfileandclickOK.
Note:YouwillgetanerrormessageifyouchooseafiletypethatChemBioDraw doesnotsupport(suchasTXT).
Tocreateanobject:
1.NavigatetoEdit>InsertObject.
2.ClickCreateNew.
3.SelecttheObjectType.ChemBioDraw 14.0
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4.ClickOK.
ISIS™Compatibility
ChemBioDraw Ultra,andChemDraw ProsupportISIS/Sketch includingR-Logicandleavinggroups.
Attached Data
Usingfieldnames,youcanattachtexttoobjectssuchasatomsandbonds.Thefeatureiscompatible withthe“Data
SGroup”inMDLformats,andisconverted toDataSGroupswhensavedinMDLformatsifafieldnameisspecified
anditisattachedtoacollectionofatomsandbonds,orsinglesetofbrackets.
Whenattachedtoacollectionofatomsandbondsandasetofbrackets,afieldnameisconverted totwodifferent
DataSGroups.
Toattachdatatoanobject:
1.Selecttheobject.
2.NavigatetoObject>AttachData.
TheAttachDatadialogboxappears.
3.EnterthefieldnameandclickOK.
4.Enterthedatainthetextboxundertheobject.
Note:YoucannoteditfieldnamesinChemBioDraw. WhileChemBioDraw allowsanyfieldnamelength,MDL
formatshavetheirownrestrictions. Likewise,ChemBioDraw allowsdatatobeattachedtoanyobject.Whensav-
ingtoMDLformats,dataislostunlesstheobjectmeetstheconditions notedabove.
Modifying Attached Data
Twoadditionalcommands appearonthecontextmenuwhenyouselectattacheddata.
SelectLinkedObjects:Changestheselectiontoincludealloftheobjectsassociated withthedata.
Position:Letsyoupositionthedatarelativetotheassociated structure.
Note:Positioning information islostwhenever yousavetoMDLformats.
Graphics ExportBorderPreference
Youcanspecifythebordersizewhenexportingpictures.Thispreference affectstheoutputofallgraphicalformats,
suchas:WMF,PICT,EPS,TIFF,GIF,BMP,andPNG.Itappliestotheclipboardandsavedfiles.Thedefaultvalue
is2points(0.278in;0.071cm).
FileFormats
ThefileformatsavailableinChemBioDraw are:
Format Windows
ChemDraw (CDX) YESChemBioDraw 14.0
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Format Windows
ChemDraw XML(CDXML) YES
ChemDraw (CHM) YES
ChemDraw StyleSheets(CDS) YES
Connection Table(CT) YES
ChemicalMarkupLanguage (CML) YES
Bitmap(BMP) YES
TIFFfile(TIF) YES
GraphicImageFormat(GIF) YES
ISIS(SKC,TGF,RXN) YES
JCAMP(JDX,DX) YES
JPEG(JPG,JPEG) YES
MDLSDfile(SDF) YES
MDLMolFile(MOL) YES
MSIChemNote (MSM) YES
PNGImage(PNG) YES
StandardMolecular Data4.2(SMD) YES
GalacticSpectra(SPC) YES
WindowsMetafile
(WMF)YES
EnhancedMetafile (EMF) YES
ChemDraw Templates CTP) YES
ChemDraw Templates Stylesheets(CTS)YES
PDF NO
MDLMolfileV3000 YES
ReactionMolfileV3000(RXN) YESChemBioDraw 14.0
Chapter15:SharingInformation 274of315

Format Windows
PICT
PICTScaled4x NO
Encapsulated PostScript YES
ScalableVectorGraphics YES
ChemBioDraw supportsimportingandexportingthefileformatslistedbelow.Toexportinoneoftheseformats,use
theSaveAs…option.Notallformatsaresupported inallChemBioDraw products.Referto"Importing" onpage272.
Format ImportExport
ChemDraw (CDX) YESYES
ChemDraw XML(CDXML) YESYES
ChemDraw 3.5(CHM) YESYES
ChemDraw 2.0andChemDraw 2.1(CHM) YESNO
ChemDraw Template(CTP) YESYES
ChemDraw TemplateStyleSheet(CTS) YESYES
ChemDraw StyleSheets(CDS) YESYES
Connection Table(CT) YESYES
ChemicalMarkupLanguage (CML) YESYES
Bitmap(BMP) YESYES
PostScript (EPS) NOYES
GraphicImageFormat(GIF) YESYES
ISIS(SKC,TGF,RXN) YESYES
JCAMP(JDX,DX) YESNO
JPEG(JPG,JPEG) YESYES
MDLMolFile(MOL) YESYES
MDLRGFile(MOL) YESYES
MDLV3000MolFile(MOL) YESYESChemBioDraw 14.0
Chapter15:SharingInformation 275of315

Format ImportExport
MSIChemNote (MSM) YESYES
PortableNetworkGraphics(PNG) YESYES
StandardMolecular Data(SMD) YESYES
StructureDatafile(SDF) YESYES
GalacticSpectra(SPC) YESNO
WindowsMetafile
(EMF,WMF)YESYES
ScalableVectorGraphics(SVG) NOYES
PortableDocument Format(PDF) YESYES
TaggedImageFile(TIF,TIFF) YESYES
Transferring AcrossPlatforms
YoucancanopencdxfilesineitherChemBioDraw forMacintosh, orWindows. Whenyoutransferfilesacrossplat-
forms,fontsarenottransferred. Ifafontinthetransferred document isnotavailable,ChemBioDraw substitutes fonts
forthosethatareavailableonthenewplatform.ChemBioDraw 14.0
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Chemical Interpretation
ChemBioDraw convertslines,characters, andothersymbolsintochemically meaningful figuresasyouwork.This
occursinthebackground, butyoucanalsochoosetoviewthischemicaldata.ChemBioDraw usesthedatawhen
exportingtofileformatsthatsupportonlyasubsetofthenotationsthatChemBioDraw does.
Thissectiondescribes howChemBioDraw interpretsdrawings.
Database Conventions
Mostdatabases requirenotonlythatyoudrawastructureinawaythatmakessense,butthatyoudrawitintheway
thatthedatabaseexpectsit.Considerferrocene, whichisrepresented inatleastfourdifferentwaysinmajordata-
bases:
Figure16.1:Representations offerroceneChemBioDraw 14.0
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Asuccessful searchinonedatabasemightnotproduceresultsinanother.Whenindoubt,consultthedocumentation
fortheconventions yourdatabaseuses.
BondConventions
Thefollowingtabledescribes thechemicalconventions ChemBioDraw recognizes.
Bond Description
Singlebond,unspecified stereo-chemistry.
Singlebond,“down”stereochemistry (intotheplaneofthepaper,awayfromtheviewer),from
thefirstdrawnatomtotheseconddrawnatom.
Singlebond,“up”stereochemistry (outoftheplaneofthepaper,towardtheviewer),fromthe
firstdrawnatomtotheseconddrawnatom.
Singlebond,mixtureof“up”and“down”stereochemistries insomeunspecified proportion.
Dativebond.Oftenusedtoindicatepolarbonds,suchastheN-ObondinpyridineN-oxide.
Doublebond,withcis/transstereochemistry asdrawn.
Doublebond,withcis/transstereochemistry unknown.
Tautomeric bond,eithersingleordoubleaccording torulesoftautomerism.
Aromaticbond,partofadelocalized resonance system.
Triplebond.
Quadruple Bond.
Asinglebondnearaclosedcircleisrecognized asaromatic:ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 278of315

AtomLabels
Asimpleatomlabelmaycontainanyofthefollowing:
Asingleelement.
Anelementandsomenumberofhydrogenatoms.
Anickname.
Repeating unitswithinparentheses.
Aseriesofanycombination oftheabove.
ChemBioDraw analyzesatomlabelsfromlefttoright,applyingstandardvalencerulestodetermine whichatomsare
bondedtogether.Theexception iswithanatomlabelinAutomatic alignment ontheleftsideofacompound. Thistype
ofatomlabelisdisplayedinreverse(H3COinsteadOCH3)andisparsedfromrighttoleft.Standardvalencesforeach
atomaredefinedintheIsotopesTable.
Bydefinition, a“simple”atomlabelhasallbondsattachedtothefirst(orlast)character. Amulti-attachedatomlabel
hasbondsconnected tomorethanonecharacter, orhasallofitsbondsattachedtoacharacterinthemiddleofthe
atomlabel.Multi-attachedatomlabelsarealwaysparsedfrombeginningtoend,butthebeginningmightbeonthe
rightiftheatomlabelwasinAutomatic styleandontheleftsideoftheoriginalstructure:ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 279of315

Amulti-attachedlabelthatisparsedfromlefttoright.
Amulti-attachedlabelthatisparsedfromrighttoleft.
Abondattachedtotheopenparenthesis ofarepeating
groupistreatedasifbondedtothefirstofthosegroups.
Abondattachedtothecloseparenthesis orrepeatcountof
arepeatinggroupistreatedasifbondedtothelastofthose
groups.
Multiplefragments withinasinglelabelcanbespecified:
Implicitly, usingstandardvalencerules.
Explicitly, usingaspace,period(unsuperscripted orunsub-
scripted),bullet,orcombination.
Anunsuperscripted, unsubscripted integeratthestartofafrag-
mentisrecognized asastoichiometric multiplierandistreatedas
iftheappropriate numberoffragments weredrawnexplicitly.
Chemically Significant Text
Often,itissimplertowriteachemicalformulalikeMeOHorH2Othantodrawanatoms-and-bondsstructure.
ChemBioDraw interpretsanyunambiguous structuralformula.Forexample,CH3COCH2CH3isrecognized asChemBioDraw 14.0
Chapter16:ChemicalInterpretation 280of315

methylethylketoneandMeOHisrecognized asmethanol. Ontheotherhand,C6H6mightmeanbenzene,oranother
isomer.Generally, empiricalformulas(C2H6andH2SO4)arenotrecognized, butstructuralformulas(CH3CH3and
HOSO2OH)are.
Molecular weightandelemental analysesofempiricalstructures arepossible,buttheExpandLabelcommand does
notworkwiththem.Empiricalstructures arediscarded whentheyaretransferred tootherapplications thatrequire
unambiguous structures.
Chemically- significant textmustbeentirelyinformulaor,forisotopesandcharges,superscript style.ChemBioDraw
doesnotrecognize achemicalformulaembedded withinalargerblockoftext.
Ifyoudrawabond,addanatomlabel,andthendeletethebond,you
haveachemically meaningful textblockwhosefont,size,andstyle
matchotheratomlabels.
IfyoucreateacaptionwiththetexttoolandsetittoFormulastyle,
youhaveachemically meaningful textblockwhosefont,size,and
stylematchothercaptions.
Charges
Youcancreatechargesaspartofaatomlabelorwiththeappropriate symbolfromtheChemicalSymbolstoolbar.
Chargesarealwaysassignedtoaspecificelementintheatomlabel,whoseacceptable valencesbecomethoseof
thesimilarisoelectronic neutralelement
.
Achargefollowinganelementisassignedtothatelement.
Achargethatdoesnotfollowanelementisassignedtothenextelement.
Chargesthatfollowamonovalent elementwitharepeatcountare
assignedtotheelementbeforethatelement.
Chargesthatfollowotherrepeatingunitsaredistributed amongthoseChemBioDraw 14.0
Chapter16:ChemicalInterpretation 281of315

units.
Chargesmaybesuperscripted.
Multiplechargesarerecognized appropriately.
Chargesmayhaverepeatcountsaslongasboththechargeandthe
repeatcountaresuperscripted.
A“floating”chargeplacedwiththeChemicalSymbolsToolisassignedto
thenearestatom.IfnoatomiswithinthedistancesetastheFixedLength,
thechargeisignoredandnotassignedtoanyatom.
A“floating”chargeplacedwithinadelocalized systemisrecognized bythe
AnalyzeStructurefunction,butisdiscarded whensavedtoformatsthat
requireallchargestobeassociated withspecificatoms.
IsotopesandElements
Bydefault,allisotopesarerecognized inthefullTableoftheElements. ThisdataisprovidedbyCRCPress,Inc.Iso-
topesaredefinedintheIsotopesTablefile.Youcaneditthisfileinanytexteditortoaddnewisotopes.
Asuper-scriptednumberbeforetheelementsymbolindicatesisotopenum-
bers.
Isotopescanbeincludedanywhere thatregularelementscan.
Deuterium andTritiumappearasone-lettersymbols.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 282of315

Radicals
Radicalsareindicatedwiththeappropriate symbolfromtheChemicalSymbolspalette.Aswithcharges,theyare
assignedtothenearestatom.Radicalsalwaysoccupyonefreevalence,inadditiontoanychargeeffects.Two
examples are:
Note:Thelonepairsymbolisinterpreted asadiradicalwhenitisplacednexttoanunlabeledcarbonatom.
H-Dot/H-Dash
H-DotandH-DashsymbolsfromtheChemicalSymbolspaletteindicatethestereochemistry ofasinglehydrogen
atom.Thesesymbolsaremostcommoninfusedsystems,suchasbelow:
Complexes
Compounds withelectronpairscanactasLewisbases,bondingwithLewisacidsthatareelectron-deficient.Similar
behaviorcanbeseenbetweenlonepairsandmetals.
Thebestrepresentation ofthesetypesofinteraction iswithadativebondfromtheelectron-pairdonortotheacceptor.
Usingaplainbondinsteadofthedativebond,willcauseavalenceerror.Thedativebondmoreaccurately represents
theelectrondonation.
Complexes mayalsoberepresented withexplicitlonepairsandwithoutanybonds.
Ifyouuseasimplebondtoindicateacomplex,youmaywanttosetAbnormalValencetoAllowedintheAtomProp-
ertiesdialog.
Multi-centerAttachments
Multi-centerattachments aremeaningful onlywhencreatedusingStructure>AddMulti-CenterAttachment .Multi-
centerattachments createapseudo-atomthatisdisregarded duringchemicalcalculations butstillletsyoucreateChemBioDraw 14.0
Chapter16:ChemicalInterpretation 283of315

diagramsthatlookmeaningful toanexperienced chemist.Afewexamples areshownbelow:
η3orπ-Allylcomplex:
Ferrocene, aπ-Arylcomplex:
Cp2TiCl2,anotherπ-Arylcomplex:
η-C5H5Mn(CO):
Cahn-Ingold-Prelog
Absolutestereochemistry iscalculated fortetrahedral atomsanddoublebondsaccording totheCahn-Ingold-Prelog
(CIP)priorityrules.
TheCIPrulesaredesignedtoorderligandsbytheirpriorityanddetermine adescriptor basedontheorientation ofthe
orderedligandsinspace.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 284of315

Aligandisanentityattachedtoastereocenter. Forexample,atetrahedral carbonhasfourligandscorresponding toits
foursubstituents. Whenatetrahedral carbonisinaring,itstillhasfourligands:thetwoligandsoutsidethering,athird
consisting ofthering“unpeeled” clockwise, andafourthconsisting ofthering“unpeeled” counterclockwise.
Fiverulesusedtodetermine thepriorityofligandsaresummarized belowinsimplifiedform.Formoredetailedinform-
ation,seethereferences.
Rule1.Higheratomicnumberprecedeslower
Rule2.Higheratomicmassprecedeslower
Rule3.cisprecedestrans
Rule4.Likepairsofdescriptors precedeunlikepairs
Rule5.RprecedesS
ChemBioDraw checksdifferences upto15atomsdistantfromthestereocenter.
Stereochemical Indicators
Aftertheligandsareranked,anindicatorisassignedasshowninthefollowingtable.
Stereocenter Indicator
Doublebond Zifthehighestrankingligandofeachpairareonthesamesideofthebond;otherwise E.
Tetrahedral atom Whenthelowest-rankingligandislocatedbehindthecentralatom:
Rwhenremaining 3ligandsarearrangedclockwise indescending order
Swhenremaining 3ligandsarearrangedcounterclockwise indescending order
rorsisusedforpseudoasymmetric atoms
Stereochemical Flags
Whilethechiralityofaspecificstereocenter canbeindicatedwiththeappropriate wedged,hashed,orplainbond,
sometimes itisusefultoindicatetherelativestereochemistry ofamoleculeasawhole,considering therelationship
betweenallstereo-centers.Stereochemical flagsapplytotheneareststructure;ifnostructureiswithinthedistance
specifiedbytheFixedLengthvalue,thestereochemical flagisnotassignedtoanystructure.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 285of315

Figure16.2:TheAbsoluteflagindicatestheexactstereoisomer asdrawn.
Figure16.3:Therelativeflagindicatestheexactstereoisomer asdrawn,oritsenantiomer.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 286of315

Figure16.4:Theracemicflagindicatesamixtureoftheexactstereoisomer asdrawnanditsenantiomer.
PolymerRepresentations
Polymersarerepresented bybracketsusedtoencloserepeatedstructures orstructuralfragments. Bracketproperties
specifytheorientation andcontextoftherepeatingunits.Foranexplanation ofthebracketproperties, see"Setting
BracketProperties" onpage244.
Note:ThepolymerdrawingfeatureisavailableonlyinChemBioDraw Ultra,andChemDraw Pro.
References
“GraphicRepresentations (Chemical Formulae) ofMacromolecules (Recommendations 1994)”PureAppl.Chem.,66,
2469-2482(1994).
“Source-BasedNomenclature forCopolymers (Recommendations 1985)”PureAppl.Chem.,57,1427-1440(1985).
Alsoavailableat:http://www.iupac.org/publications/books/pbook/PurpleBook- C7.pdf.
“BasicDefinitions ofTermsRelatingtoPolymers(1974)”PureAppl.Chem.,40,479-491(1974)Alsoavailableat:
http://www.iupac.org/reports/1996/6812jenkins/index.html .
AlsoseetheGuidefortheauthorsofpapersandreportsinpolymerscienceandtechnology fromIUPAC.
AnalysisMessages
Whenastructurecannotbefullyanalyzed, twogeneraltypesofmessages aredisplayed:
Statusmessages thatreportaproblemthatmaynotaffectthefinalanalysis
Criticalmessages thatmayaffectthefinalanalysis
Message Description
Therearetoomanybondstothis
unlabeledCarbon.Displayed foreveryunlabeledatomwithmorethanfourfilledvalences.
Filledvalencesincludesumofbondorders,charge,radicals,andfreesites.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 287of315

Message Description
Aromaticbondscount1.5each,roundeddownunlessitistheonlybondto
theatom.Chargeissignedandincludeschargeimpliedbydativebonds.
TheSubstituents querypropertytreatsfreesites,uptoandexactlythe
sameway:anatomwithtwoexplicitbondsand“Substituents: UpTo3”or
“Substituents: Exactly3”or“Substituents: FreeSites1”hasthreefilled
valences.
Anatominthislabelhasaninvalid
valence.Displayed incaseswhereaplacecannotbefoundtoplaceabondorabond
cannotbefoundtoplaceanatom.Validvalencesforeachelementarelis-
tedintheIsotopesTablefile.
ChemDraw can’tinterpretthis
label.Displayed whentextisfoundthatcannotbeidentifiedasanelement,nick-
name,genericnickname, oralternative groupname.
Parentheses don’tmatch. Displayed whenparentheses cannotbematchedintonestedopen-close
pairs.
Thislabelhasconflicting orunas-
signablecharges.Displayed whenaplusandminuschargehavebeenassignedtothesame
element,chargeshavebeenassignedinmorethanoneway,oracharge
hasbeenassignedtoanickname, genericnickname, orAlternative Group
name.
Formulacannotbecomputed for
queries.Displayed foreverylabelthatcontainsagenericnickname, anelementlist
oranalternative group.Thisisastatusmessageonly;analysiscontinues
asiftheproblematic labelwerenotselected.
TextnotinFormulastylewon’tbe
interpreted.Displayed forthefirstcaptionthatisnotanatomlabelorAlternative Group
name,andwhichcontainsanytextnotinFormula,Subscript, orSuper-
scriptstyle.Thisisastatusmessageonly,andappearsonlyonceregard-
lessofhowmanycaptionsareintheselection.
Thisnamedalternative groupcon-
tainsnoattachment point.Displayed foranystructurewithinanAlternative GroupBoxwherethestruc-
turelacksanattachment point.Thisisastatusmessageonly.
Thisnamedalternative groupcon-
tainsfragments withinconsistent
valences.Displayed foranyAlternative GroupBoxwhosecontained structures have
varyingnumbersofattachment points.Sinceallstructures withinanAltern-
ativeGroupBoxaretobeusedinterchangeably, theymusthavethesame
numberofattachments. Thisisastatusmessageonly.
Thisnamedalternative groupcon-
tainsnofragment.Displayed foranyAlternative GroupBoxthatisempty.Thisisastatusmes-
sageonly.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 288of315

Message Description
Partofamoleculeisoutsideofthe
alternative groupdefinition.Displayed foranyAlternative GroupBoxwhosebordercrossespartofa
structure.Thisisastatusmessageonly.
Thisisolatedbondisprobablynot
intendedtohavechemicalsig-
nificance.Displayed forunlabeledsinglebondsunattached tootherbonds.Allbonds
areinterpreted chemically, usuallyasC2H6,andmaycauseunexpected
resultsifintendedasagraphicallineonly.Thisisastatusmessageonly.
Theatomisveryclosetoanother
atomorbond.Displayed foranyatomthatisnearlytouchinganotheratomorbondbutnot
boundtoit.Ifabondreallywasintended,theanalysisofthestructurepro-
ducesincorrectresults.Thisisastatusmessageonly.
Thestereocenter hasnoste-
reobondsspecified.Displayed foranyasymmetric centerwithoutattachedwedged,hashed,
dashed,orboldbonds.Thisisastatusmessageonly,andappearsonly
whenShowStereochemistry istunedonandthereisatleastoneother
wedged,hashed,dashed,orboldbondinthestructure.
Thereisavalenceandchargeerror
somewhere inthisaromaticsys-
tem.Displayed foranyodd-membered ringdrawnasadelocalized system(with
acircleinthemiddle),wherethereisnocorresponding associated charge.
Forexample,adelocalized representation ofcyclopentadiene mustinclude
eitheranegativechargeoramulticenter attachment.
Thestereocenter hasconflicting or
ambiguous stereobonds specified.Displayed foranystereocenter (tetrahedral atom,asymmetric doublebond,
etc.)wheretheabsolutestereochemistry cannotbedetermined fromthe
structureasdrawn.Forexample,thismessagewouldbeshownforacar-
bonatomattachedbyboldbondstofourdifferentligands.Thismessageis
displayedonlywhenShowStereochemistry isalsoturnedon.
Thislabelhasanunrecognized iso-
topicmass.Displayed foreverylabelthathasanumericsuperscript immediately pre-
cedinganatomicsymbol,wherethesuperscripted numberdoesnotcor-
respondtoarecognized isotope.Forexample,24CH3.ChemBioDraw 14.0
Chapter16:ChemicalInterpretation 289of315

PropertyCalculations
Youcancalculatepredictedvaluesofselectedphysicalandthermodynamic properties forstructures ofupto200
heavyatoms.Thissectiondescribes howthevaluesaredetermined.
LogP
Threefragmentation methodsareusedtopredictthelogPvalues:
MethodOne:Basedon94atomiccontributions evaluated from830molecules byleastsquaresanalysis.This
methodworkswithastandarddeviationof0.47logPunitsandcanhandlemolecules containing hydrogen, oxygen,
nitrogen,sulfur,andhalogens.
MethodTwo:Anextension ofmethodonebutisbasedon120atomiccontributions evaluated from893molecules
byleastsquaresanalysis.Inadditiontotheatomsintroduced formethodone,itcanhandlemolecules thatcontain
phosphorus andseleniumatoms.Thismethodworkswithastandarddeviationof0.50logPunits.
MethodThree:Basedon222atomiccontributions calculated from1868molecules byleastsquaresanalysis.This
methodallowsacalculation oflogPwithastandarddeviationof0.43logPunitsandcanhandlemolecules con-
taininghydrogen, oxygen,nitrogen,sulfur,halogens, andphosphorus atoms.Ifthismethodisappliedtomolecules
withinternalhydrogenbonds,thestandarddeviationis0.83LogPunits.
Henry’sLaw
TwomethodsareusedtopredictHenry’sLawconstant:
MethodOne:Anapproachbasedonthebondcontribution method,thismethoduses59bondcontribution values
and15correction factors.Thecontributions werecalculated byleastsquaresanalysisusingadatasetof345chem-
icals.Thismethodestimates withameanerrorof0.30unitsandastandarddeviationof0.45units,andcanhandle
molecules containing carbon,hydrogen, oxygen,nitrogen,sulfur,phosphorus and,halogens.
MethodTwo:Henry’sLawconstantisestimated fromanequationfoundusinglinearregression. Multifunctional
compounds wereomittedfromthisstudy.Thismethodshouldnotbeusedforcompounds wheredistantpolarinter-
actionispresent.
MolarRefractivity
Twofragmentation methodsareusedtoestimatethemolarrefractivity value:
MethodOne:Includes93atomiccontributions evaluated from504molecules byusingaconstrained leastsquares
technique. Thismethodworkswithastandarddeviation1.27cm3/molandcanhandlemolecules containing hydro-
gen,oxygen,nitrogen,sulfur,andhalogens.
MethodTwo:Isanextension ofmethodonethatincludes120atomiccontributions evaluated from538molecules
byusingaconstrained leastsquaresanalysistechnique. Inadditiontotheatomsintroduced formethodone,this
methodcanhandlemolecules withphosphorus andseleniumatoms.Thismethodworkswithastandarddeviation
of0.77cm3/mol.ChemBioDraw 14.0
Chapter17:PropertyCalculations 290of315

pKa,CLogP,andCMR
Specificalgorithms forcalculating LogPandmolarrefractivity fromfragment-basedmethodsdeveloped bythe
MedicinalChemistry ProjectandBioByte.Formoreinformation, seehttp://www.biobyte.com/blqsar/index.html .
LogPandCLogPestimatetheOctanol/Water PartitionCoefficient, butusedifferentmethods.
CLogPandCMRarecalculated aspartoftheChemicalProperties window.SeveralothersourcesexistforLogP
data,however:
TheChemBioDraw ReportWindowforLogPPrediction :TheChemicalProperties windowshowsaveraged
LogPandMRvalues.Viathe"Report"button,youcanseetheoriginalvaluesfromeachapplicable estimation
method.Theestimation methodsareCrippen'sfragmentation, Viswanadhan's fragmentation, andBroto's
method.
TheChemBioDraw ReportWindowforLogPEmpirical Data:Forselectedsubstances, theChemicalProp-
ertieswindow'sReportbuttonincludesasection"DatafromDatabase," whichincludesmeasured valuesofthe
partitioncoefficient andpKavalues,atspecifiedpHlevels,withsourcecitations.
TheChemBioDraw ChemBioFinder HotlinkWindow:Severalavailabledatabases includeLogPandpKa
information, including:
–ChemSpider (fromInChIlink)predictsseveralvariations ofLogPandLogD
–ChemINDEX (PhysicalProperties section,Environment ScienceCenterdatabase) includesempiricalpKaand
LogPdata
ChemDraw/Excel
TheChemDraw add-inmoduleinMicrosoftExcelpredicts:
LogP(functionCHEMPROPPRO_ LOGP)
CLogP(functionCLOGP_DRIVER_ PARTITION_ COEFFICIENT)
MR(functionCHEMPROPPRO_ MOL_REFRACTIVITY)
CMR(functionCLOGP_DRIVER_ MOL_REFRACTIVITY)
ChemBioFinder/ChemBioViz
ThePropertyPopulatorpredicts:
LogP(serverChemPropPro, propertyLogP)
CLogP(serverCLogPdriver,propertyPartition_Coefficient)
MR(serverChemPropPro, propertyMolRefractivity)
CMR(serverCLogPdriver,propertyMolRefractivity)
ChemBio3D
ThePropertyPickerpredicts:
LogP(ChemPropPro LogP)
CLogP(CLogPdriverPartitionCoefficient)
MR(ChemPropPro MolRefractivity)
CMR(CLogPdriverMolRefractivity)ChemBioDraw 14.0
Chapter17:PropertyCalculations 291of315

TheChemBio3D MOPACInterface
Calculates thepKaofthemostacidichydrogenatomattachedtoanoxygen.Formoreinformation, see
http://www.openmopac.net/pKa_ table.html.
Formoreinformation, "ChemDraw/Excel Functions" onpage188,"LogP"onpage290,"PropertyCalculations" on
page290,and"pKa,CLogP,andCMR"onpage291.
Topological PolarSurfaceArea
Thepolarsurfaceareaofamolecule(measured insquareangstroms) canbeusedtopredictofpharmaceutical trans-
portproperties inthebody.ChemBioDraw implements amoreinnovative algorithm. Historically, thispropertyhas
beencalculated usingtime-consuming 3Dtechniques. However, arecentpaperprovidedaremarkably accurateway
ofpredicting itrapidly.
OtherProperties
NormalBoilingPointandMeltingPoint
Estimated inKusingtwomethods:
MethodOne:Joback'sfragmentation method
MethodTwo:Joback'sfragmentation methodasmodifiedbyStein.Allboilingpointsareestimated forapressure
of1 atm.
Miscellaneous Properties
HeatofFormation, GibbsFreeEnergy,IdealGasThermalCapacity, FreezingPoint,CriticalTemperature, Critical
Pressure, andCriticalVolumeareestimated usingJoback’sfragmentation method.ChemBioDraw 14.0
Chapter17:PropertyCalculations 292of315

ChemBioDraw WebResources
ThePerkinElmer Informatics Websiteisavaluablesourceofhelpfulinformation. Youcan:
Registeryoursoftware.
Searchforchemicalinformation bynameorACXnumber;or,insertastructureintoaworksheet.
Gettechnicalsupport,documentation, softwaredownloads, andmore.
YoucannavigatetothesitedirectlyfromChemBioDraw byselectingtheappropriate optionintheSearchmenu.
Registering Online
ToactivateanyChemBioOffice application, registerwiththePerkinElmer Informatics Websitetoreceivearegis-
trationcode.Uponfillingoutaregistration form,youwillreceivearegistration codebye-mail(thisdoesnotapplyto
sitelicenses).
IfyourserialnumberisinvalidoryoudonothaveanInternetconnection, contactPerkinElmer Informatics Supportto
receivearegistration code.
YoumayuseyourChemBioOffice 2014applications alimitednumberoftimeswhilewaitingfortheregistration pro-
cesstofinish.Afteryoureachthelimit,youmustregisterthesoftware.
Inadditiontoregistering yoursoftware,youcanrequestliterature,orregisterforlimitedfreeaccesstoChemBioFinder –
.com,ChemACX.com, andthee-maileditionofChemBioNews. Toregisteronline,navigatetoSearch>Register
Online.Theuserregistration Webpageopensinyourbrowser.
User’sGuide
TheSearchmenualsoletsyoufindcurrentandpreviousversionsofthedocumentation. Toaccessthedoc-
umentation page,navigatetoSearch>BrowsePerkinElmer Documentation .
TheDesktop>>SupportDocumentation Webpageappears.SelecttheManualslink.
Note:IfyoudonothaveaPerkinElmer Informatics useraccount,youwillfirstbedirectedtoasign-uppage.
Technical Support
TheSearchmenulinkBrowsePerkinElmer Technical SupportopenstheTechnical SupportWebpage.Hereyou
canfinddesktopsupportresources, includingthePerkinElmer Informatics Knowledge Base,productdownloads,
FAQ,anddocumentation.
1.NavigatetoSearch>BrowsePerkinElmer Technical Support.TheTechnical SupportWebpageopens.
2.ClickDesktopSupport.
Suppliers onChemACX.com
ChemACX (Available Chemicals Exchange) providesadatabaseofcommercially availablechemicals. Thedatabase
containscatalogsfromresearchandindustrialchemicalvendors.
TolinktotheChemACX.com recordofsuppliersforcompounds thatyoudraw:ChemBioDraw 14.0
Chapter18:ChemBioDraw WebResources 293of315

1.InChemBioDraw, selectastructureyouhavedrawn.
2.NavigatetoSearch>FindSuppliers onChemACX.com .TheChemACX.com pageopenswithinformation
abouttheselectedstructure.
Formoreinformation onusingtheChemACX Website,seetheChemOffice Enterprise Workgroup &Databases
Guide.
ACXStructures andNumbers
ChemBioDraw searchesACXandreturnsinformation aboutrelatedstructures andnumbers.Youcanplacethe
returnedinformation inyourdocument.
ACXStructures
TherearetwowaystofindACXstructures, byACXnumberorbyname.
TofindastructurebyACXnumber:
1.NavigatetoSearch>FindStructure fromACXNumber.TheFindStructurefromACXNumberdialogappears.
2.TypetheACXregistrynumberinthedialog.
3.ClickOK.Thestructureappearsinyourdocument.
Tofindastructurebyname:
1.NavigatetoSearch>FindStructure fromNameatChemACX.com .TheFindStructurefromNamedialog
appears.
2.Typeeitherachemicalnameortradenameinthedialog.
3.ClickOK.Thestructureappearsinyourdocument.
ACXNumbers
ToFindanACXnumberforastructure:
1.Selectthestructure.
2.NavigatetoSearch>FindACXNumbers fromStructure.TheACXnumberappearsintheFindACXNumbers
fromStructuredialog.
ChemBio3D ActiveXControl
TheChemBio3D ActiveXControlpageprovidesChem3DPlugin/ActiveX documentation forendusersaswellas
administrators (webdevelopers) whowanttoincorporate thecontrolswithintheWebpages.
SciStore.com
SciStoreofferslifesciencedesktopsoftware,enterprise solutions, chemicaldatabases, andconsulting servicesto
biotechnology, pharmaceutical, andchemicalindustries. TovisitSciStore,navigatetoSearch>BrowseSciStore.-
com,orvisitSciStoreatwww.scistore.com .ChemBioDraw 14.0
Chapter18:ChemBioDraw WebResources 294of315

PerkinElmer Informatics
ToopenthePerkinElmer Informatics Homepage,navigatetoSearch>BrowsePerkinElmer.com .Checkthe
PerkinElmer Informatics Websitefornewproductinformation. YoucanalsovisitChemNews.Com, andotherpages
throughPerkinElmer Informatics Homepage.
UsingtheChemOffice SDK
TheChemOffice SoftwareDeveloper’s Kit(SDK)letsyoucustomize yourapplications.
TobrowsetheChemOffice SDK,navigatetoSearch>BrowseChemOffice SDK.
TheChemOffice SDKpagecontainsdocumentation, samplecode,andotherresources fortheApplication Pro-
gramming Interfaces (APIs).
Querying SciFinder®withChemBioDraw (UltraFeature)
SciFinder®isaresearchdiscovery application createdbyCAS(Chemical AbstractServices)thatprovidesintegrated
accesstotheworld'smostcomprehensive andauthoritative sourceofreferences, substances, andreactionsinchem-
istryandrelatedsciences.
ChemBioDraw providesaninterfacetosearchSciFinder®withqueriescreatedonthedesktop.SendaChemBioDraw
structureorreactionquerytoSciFinder®usingoneofthefollowingmethods:
ClicktheSciFinder®icononthemainhorizontal toolbarundermenubar.
NavigatetoSearch>SearchSciFinder .
Note:TheSciFinder®iconandSearchmenuitemwillbegrayedoutunlessthestructure(s)beingqueriedisselec-
ted.
TheSearchSciFinderdialogwindowopens.Ifyouhaveselectedastructure,ormultiplestructures, youwillseethe
followingwindow:ChemBioDraw 14.0
Chapter18:ChemBioDraw WebResources 295of315

Youcannowchoosewhetheryouareinterested inasubstructure searchoranexactsearchofthesubstances data-
base,or,ifyouwanttosearchthereactiondatabase, whetherselectedstructure(s)isareactantoraproduct.Allreac-
tionsearchesaresubstructure searches.
Ifyouhaveselectedanentirereactionsequence, thefollowingwindowwillopentoconfirmyourreactionsearch.
PressOKandSciFinder®willbelaunchedtoretrievetheresultsofyoursearchanddisplaytheminabrowserwin-
dow.
IfyousubmitasecondorlatersearchtoSciFinder®,youwillseeanintermediate screenwarningthatyoualready
haveaSciFinder®answerset.Toproceedwiththelatestsearch,clickOK.
Note:Forasearchtoproceed,youmust:
Beconnected totheInternetChemBioDraw 14.0
Chapter18:ChemBioDraw WebResources 296of315

HaveavalidSciFinder®individualsubscription toaccessthedatabase.
Note:Ifyoursubscription isthroughauniversity andutilizesaproxyservertoconnectyoutoSciFinder®,you
mustclicktheProxySettingsbutton(Windows), orthearrownexttotheProxyserverindicatorline(Mac)and
entertheproxyserverURLfortheaccountyouareusing.Thiswillonlybenecessary forthefirstsearchyourun.
IfyouarenotloggedinordonothaveavalidSciFinder®subscription, youwillberedirected tothemainSciFinder®
page.Thereyoucaneitherloginorfindinformation abouthowtosubscribe. Someoftheadvanced structurequery
creationcapabilities ofChemBioDraw cannotbefullyinterpreted bySciFinder®.Whenyourquerycontainsspe-
cifications thatSciFinder®cannothandle,itwilltrytosimplifyandinterpretthemtothebestofitsability,andwill
displayawarningmessage. Theinterpreted searchstructurewillbedisplayedintheSciFinder®sketcherforfurther
manipulation asneededbeforestartingthesearch.Iftheresultsobtainedarenotappropriate, pleasecontactCus-
tomerSupportatCAS,orPerkinElmer, andtheywilltrytoaddresstheissueand/orproposeanalternatequerythat
mightachievetheresultsyouseek.
Someadditionalinformation aboutsearching:
Ifyouselectamoleculewithinareaction,youcanstillspecifyasearchofthesubstances database, ratherthana
searchofthereactiondatabase.
Youcanselectaportionofamoleculeasyoursearchentity.Itwillbetreatedjustlikeanentiremoleculeforexact
orsubstructure searching. Iftheselectionconsistsofmorethanonefragment,thesewillbetreatedasindependent
moieties,allofwhichmustbecontained withintheCAS record inorderforittoberegistered asahit.
Multi-stepreactionsormultiplereactions, inasinglesearch,arenotsupported. Eachstepinthereactionsequence
mustbesearchedseparately.ChemBioDraw 14.0
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Tutorials
Thetutorialsillustratefundamental drawingtechniques. Eachtutorialintroduces newtechniques, orvariations oftech-
niquesfromprevioustutorials.We,therefore,suggestthatyoufollowthetutorialsinorder.
Beforeyoubegin,review"Conventions usedinthisGuide"onpage1tofamiliarize yourselfwiththeterminology.
ChemBioDraw checksforcorrectchemicalsyntaxasyoudraw.Ifthereisanerror,aredboxappearsaroundtheerro-
neousobject(theredboxdoesnotprint).Todisabletheredboxonaspecificobject,right-clicktheobjectand
deselectDisplayWarnings onthecontextmenu.
Tutorial1:DrawingaStructure
Inthistutorial,weexplainhowtodrawthisstructure:
Ifyouwantthewantthebondanglesandlengthstobefixed,navigatetoObject>FixedLengthsandFixedAngles.
Thisensuresthatbondlengthsandbondanglesareconsistent throughout thestructure.
Note:Thefixedlengthdimension issetintheDrawingtaboftheDocument Settingsdialog.Thefixedangledimen-
sionincrements anglesby15degrees.
Tocreatebonds:
1.NavigatetoView>ShowMainToolbar.
2.OntheMaintoolbar,selecttheSolidBondtool.
3.Clickinthedocument window.Abondappears.
4.Toaddasecondbond,clicktheright-endofthebondyoujustcreated.
Thetwobondsforma120-degreeangle.
Note:Thechainanglesettingdetermines theanglebetweenthetwobonds.Tochangethechainangle,see"Draw-
ingSettings"onpage24.
5.Tocreateatertiarycarbon,clickthesameplace,asshowninstep4above.
Changing BondOrder
Tocreatethedoublebond,eitherhoveroverthecenterofthebondandtype"2"orclickonthebond.ChemBioDraw 14.0
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AddingAtomLabels
1.UsingtheTexttool,clicktheendofthedouble-bondshownbelow.Atextboxappearsattheendofthebond.
2.Typeanuppercase Ointhetextbox.
3.Pressthe<Esc>keyonyourkeyboardtoclosethetextbox,orchoosinganothertool.
4.Analternative ishoverovertheatomattheendofthedoublebondandhitthe"o"key.ThisisutilizingtheHotkey
functionality ofChemDraw (seeChapter5Shortcuts andHotkeys).
AddingCaptions
Tonamethemolecule:
1.UsingtheTexttool,clickbelowandtotheleftofthestructure.Atextboxappears.
2.Inthetextbox,type“2-propanone”.
3.Pressthe<Esc>keyonyourkeyboardtoclosethetextbox,orchooseanothertool.
Tutorial2:Drawingrings
Inthistutorialyouuseringstocreatethisstructure:
Tocreatetheringsystem:
1.UsingtheBenzenetool,SHIFT-clickinanemptyareaofthedocument.
Note:HolddowntheSHIFTkeytochangeresonance structures whenusingthecyclopentadiene orbenzenetools.
2.Pointtothecenterofthelowerrightbondinthebenzenering.
3.Clicktofuseanotherring.ChemBioDraw 14.0
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4.Inthefinalstructure,thereisonlyonedoublebondinthesecondring.Tocorrectthecurrentstructure,hoverthe
mouseoveroneofthedoublebondsinthesecondringandtype‘1’.Dothesamefortheotherdoublebond.
Figure19.1:Tochangethebondorder,type‘1’.
5.Tocreatethedoublebondinthesecondring,eitherhoverthemouseoverthebondandtype‘2’orclickit.
6.Usingthebondtool,clickthecarbonatomscircledinthefigurebelow.Threenewbondswillappear.
7.Hoveryourmouseoveroneofthebondshownbelowandtype‘2’.Dothesamefortheotherbond.ChemBioDraw 14.0
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8.Hoverthemouseovertheright-mostterminalcarbonandtypetheletter‘o’tocreatetheketonefunctional group.
9.Toconnecttheleftterminalcarbons,selectthesolidbondtoolandclick-dragabondfromonecarbontotheother.
Thestructureiscomplete.
Tutorial3:Fischerprojections
Thistutorialdemonstrates howtocreateaFischerprojection ofglucose:ChemBioDraw 14.0
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Figure19.2:Fischerprojections
Todrawthefirstbond:
1.ClicktheSolidBondtool.
2.Pointinthedocument window.Dragdownward todrawthefirstbond.
3.Pointtotheloweratom,anddragdownward againtodrawthesecondbond.
TheredwavyboxappearsbecauseShowChemicalWarningsisselected.Wewillkeepitselectedfornow.
4.Repeatstep3therearefivebonds.
Figure19.3:DrawingthebackboneChemBioDraw 14.0
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Note:Whenyoudragthepointeralongthelengthofthebonds,thepointeralternates betweenanarrowanda
cross.Thearrowindicatesyouarepointingoverthecenterofabond,andthecrossindicatesyouarepointingto
anatom.
Addhorizontal bondstothesecondatominthestringofbondsyoucreated:
1.Toaddahorizontal bond,pointtotheuppermost ChemicalWarningboxandclickit.
Notethattheredwavyboxdisappears whenyouaddabond.
2.Clickagaintoaddahorizontal bondintheoppositedirection.
3.Repeatsteps1and2witheachChemicalWarningboxuntilallhorizontal bondsareadded.
Figure19.4:Addinghorizontal bondstothebackbone
Addlabelstothefirstandlastcarbonatoms:
1.SelecttheTexttool.
2.Clicktheuppermost carbonatomtocreateatextbox,andtypeCHO.
3.Clickthelower-mostcarbonatom,andtypeCH2OH.
Figure19.5:Addingatomlabels
Addtherepeatinglabelsforthehydrogens andhydroxylgroups:
1.ClicktheatomshowninAbelowandtypetheletterH.ChemBioDraw 14.0
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2.Double-clickeachoftheotheratomslabeledashydrogeninB.
Figure19.6:Addingrepeatingatomlabels
Tip:Doubleclickanatomwiththetexttooltorepeatthelastlabel.
3.Clickoneoftheremaining atomsandtypeO.
4.Double-clicktheremaining atomstorepeatthelabel.
Figure19.7:Completing thedrawing
Viewthebasicproperties ofthestructureandpastetheinformation intoyourdocument:
1.Clickaselectiontooltoselectthelaststructuredrawn.Ifthestructureisnotselected,double-clickthestructure.
2.GotoView>ShowAnalysisWindow.
3.IntheAnalysiswindow,clickPaste.Theanalysisinformation appearsasacaptionbelowthestructure.
Tutorial4:Perspective Drawings
Inthistutorial,weexplainhowtocreateaperspective drawingbycreatingamodelofα–D–glucoseasaHaworthpro-
jection.
Createanewdocument usingthedefaultstyle:ChemBioDraw 14.0
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GotoFile>OpenStyleSheets>NewDocument .
Note:Ifyouarefollowingthetutorialsinorder,ChemBioDraw willremember yourlastdrawingusedtheACSstyle
sheetandopenitasthedefault.This stepresetsthedefaulttoNewDocument.
Drawaring:
1.ClicktheCyclohexane Ringtool.
2.Clickinanemptyareaofadocument window.Acyclohexane ringappears.
Rotatethering:
1.GotoEdit>SelectAll(ortypeCTRL+A).
2.GotoObject>Rotate(ortypeCTRL+R)
3.IntheRotateObjectsdialogbox,enter30degreesforanangleandclickRotate.Thecyclohexane ringrotates.
Changecyclohexane totetrahydropyran:
1.Clickoutsidethestructuretodeselectit.
2.Pointtotheatominthefigurebelow,andtypethelettero.
Resizehorizontally:
1.GotoEdit>SelectAll(ortypeCTRL+A).
2.Usingaselectiontool,click-dragtherightsidehandletohorizontally resizethering.Releasethemousebutton
whentheringisstretchedabout200%.ChemBioDraw 14.0
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Enlargethering:
1.GotoEdit>SelectAll(ortypeCTRL+A).
2.Click-dragtheringcorneradjustment handletoincreasethesizeoftheringto150%.Adialogboxappears,asking
youwhetheryouwanttoscalethedrawingandtextsettings.
3.ClickNo.
Addverticalbonds:
1.ClicktheSolidBondtool.
2.Pointtotheatomshowninthefigurebelowanddragupwardtocreateabond.
3.Pointtothesameatom,anddragdownward tocreateanotherbond.
4.Repeatthisprocedure fourmoretimes,addingthepairsofverticalbondsshownbelow:
CreateOHlabels:
Youcanusetherepeatingbondlabeltechnique inTutorial4,orusehotkeys.FortheHotkeymethod,justpointand
typetheletter"o".TheTexttoolmethodisrepeatedhere,withaslightvariation.
1.SelecttheSolidBondtool,pointtotheatomshowninthefigurebelow,anddouble-clicktoopenatextbox.
2.TypeOH.ChemBioDraw 14.0
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Figure19.8:AddingtheOHlabels
3.Movethepointertotheotheratomsasshown,andtriple-clicktorepeattheatomlabel.
Tip:Ifthedrawingistoosmalltoplacethelabels,gotoView>Magnifytoenlargeit.
AddtheCH2OHlabel:
1.Triple-clicktheupperatomofC5.
2.PressENTERtoopentheatomlabeltextbox.TypeCH2beforetheOH.
Changethetypeofthefrontbonds:
1.ClicktheBoldBondtool.ChemBioDraw 14.0
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2.Clickthebondshowninthefigure.
3.Thecursorchangestoaboldarrowasyoupointtothebond.
4.ClicktheWedgebondtool.
5.Clickeachringbondadjacenttotheboldbond.
Foreachbond,pointslightlyoffcenterinthedirectionthatyouwantthewideendofthewedgetobeorientedand
click.
Tip:Ifyoumovethepointertoofar,thehighlightboxdisappears. Ifplacingthepointerisdifficult,gotoView>Mag-
nify.
Note:Ifthewedgeispointedinthewrongdirection,clickthebondagaintoflipitsorientation.
Thefinalstructureis:
Tutorial5:Newman projections
Thistutorialdemonstrates howtodrawaNewmanprojection ofethane:ChemBioDraw 14.0
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Drawethane:
1.ClicktheSolidBondtool.
2.Inthedocument window,click-dragdownward tocreatethefirstbond.
3.Clicktheatomatthebottomofthebondtoaddasecondbond.
4.Clickthebottomatomagaintoaddathirdbond.
5.Hoverthemouseovertheendofeachbond(withoutclicking)andtypeHtoaddthehydrogenatoms.
Duplicatethestructure:
1.Clickaselectiontool.Thelaststructureyoudrewisselected.
2.Tocreateaduplicate, holddowntheCTRLkeywhiledraggingtheselectionrectangleupwardtotherightoftheori-
ginal.
Theselectionboxdisappears whileyouaredragging.
Addabondbetweentheduplicated structures:
1.ClicktheSolidBondtool.
2.Clickanddragfromthetertiarycarbonatomofthelowerfragmenttotheothertertiarycarbon.
Note:Whenconnecting existingatoms,theFixedLengthandFixedAnglescommands areignored.
Whenyoureleasethemousebutton,theethanestructureiscomplete. Now,createitsNewmanprojection.ChemBioDraw 14.0
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DrawingtheNewmanprojection
Inthisstep,youdrawthehollowcirclethatisparticulartoNewmanprojections.
1.ClicktheOrbitaltool,andselectthes(Open)orbital.
2.Pointtotheleftcentercarbonandclick-dragoutward.
Thesizeoftheorbitalisconstrained justasbondsare.Theconstraint isbasedonapercentage oftheFixedLength
settingintheDrawingtaboftheDocument settingsdialogbox.
Note:Orbitalsarenotautomatically groupedwiththestructure.Togrouptheorbitalwiththeexistingstructureso
youcanmovethemtogether,gotoObject>Group.
1.ClicktheMarqueetool.Theorbitalisselected.Clickanemptyspacetodeselectit.
2.Pointabovethestructureanddragaroundtheupperfragmenttoselectthethreebonds.Donotselectthebondcon-
nectingthetwofragments.
Rotatetheselection:
1.Double-clicktherotationhandletoopentheRotateObjectsdialogbox.
2.Type180intheAngletextboxandclickRotate.
Withtherotatedbondsstillselected,changethestructurelayeringsothattheselectionisinfront.
3.GotoObject>BringtoFront(thereisnovisiblechangewhenyoudothis).
MovethefrontpartofthestructuretocreateaNewmanprojection:
1.PointwithintheSelectionRectangle sothepointerchangestoahand.
2.Dragtheselectionuntilthetertiarycarboniscenteredwithintheorbital:ChemBioDraw 14.0
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Note:Ifchemicalwarningsareturnedon,aredwarningboxappearswhenyouoverlaythestructure,becausethe
carbonatomsoverlaytheC-Cbond.Toturnoffthechemicalwarning,deselectChemicalWarningsintheView
menu.Todisablethistypeofwarning,gotoPreferences anddeselect AtomsNearOtherBondsintheWarn-
ingstab.
3.ReleasethemousebuttonandclickoutsidetheSelectionRectangle todeselectthestructure.
Tutorial6:Stereochemistry
Thistutorialdemonstrates stereochemistry markersandtheFlipcommand.
First,wedrawthisstructure:
Todrawthestructure:
1.ClicktheSolidBondtool.
2.Inthedocument window,clickanddragdownward tocreatethefirstbond.
3.Pointattheloweratomandclicktoaddasecondbond.
4.Continuepointingatthesameatomandclickagaintoaddathirdbond.ChemBioDraw 14.0
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5.Pointtotheatomshownbelowandclicktwicetocreatetwobonds.
6.Pointingtothebondshownbelow,right-click,andselectDouble>Plain fromthecontextmenu.
7.ClicktheWedgedBondtool,pointtotheatombelow,andthenclick.
Addingatomlabels
1.WiththeTexttoolselected,clicktheatomshownbelow,andthentype'NH2'inthetextboxthatappears.
2.WiththeTexttoolselected,clicktheatomshownbelow,andthentype'O'inthetextboxthatappears.ChemBioDraw 14.0
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3.WiththeTexttoolselected,clicktheatomshownbelow,andthentype'OH'inthetextboxthatappears.
Displaying stereochemical markers
Wenowdisplaythestereochemical markers,(R)and(S)forthetwoisomers.
Toaddthemarkers:
1.SelecttheentirestructurewiththeLassoorMarqueetool.
2.GotoObject>ShowStereochemistry .TheSmarkerappears.
3.SelectthestructureandgotoObject>FlipHorizontal .TheRmarkerappears.
4.Withthestructureselected,gotoObject>Rotate180°Vertical.Youcanalsousetheobjecttoolbartorotatethe
structure.ChemBioDraw 14.0
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TheWedgedbondbecomeshashedandthe(R)stereochemistry ispreserved.
Tutorial7:Templates
ChemBioDraw comeswithanextensive templatelibraryofpre-drawnstructures andimages.Youcanuseatemplate
toeitherstartanewdrawingortomodifyonethatalreadyexists.
Inthistutorial,weusethephenanthrene templatetocreateperoxydibenzene. Thetemplateandfinaldrawingare
shownbelow:
Toaddthetemplateforphenanthrene:
1.GotoFile>OpenStyleSheets>NewDocument .
2.IntheMaintoolbar,selectthetemplatetool.Thelistoftemplatepalettesappears.
3.IntheAromatics palette,selectthephenanthrene template.
4.Clickinthedocument window.Phenanthrene appears.
Nowyoumustremovetwobondsfromthecenterringofthestructureandaddtwooxygenatoms.
Tomodifyphenanthrene:
1.IntheMaintoolbar,selecttheErasertool.ChemBioDraw 14.0
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2.Clickthebottombondinthecenterring.
3.Clickthedoublebondatthetopofthering.Itisnowasinglebond.
4.IntheMaintoolbar,selecttheTexttool.
5.Selectoneofthecarbonatomsinthehydrocarbon chain(whatwasthemiddlering).
6.TypeOtochangeittoanoxygenatom.
7.Selecttheothercarbonatomandchangeittoanoxygen.Peroxydibenzene isnowshown.ChemBioDraw 14.0
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