Usethecharactermaptoaddsymbolstoyourdocumentinvariousfontstyles.Toshoworhidethemap,navigateto
View>ShowCharacterMapWindow.Thecharactermapisshownbelow.
Thecharactermapisactiveonlywhenatextfieldisopenforediting.Withatextboxopen,mouseoverthecharacter
maptoviewalargerversionofthecharactersinthetoprightcornerofthewindow.Clickanycharacterinthetableto
enteritinthetextfield.Theselectedfont(showninthecharactermapwindow)isappliedtothatcharacteronly.It
doesnotchangetheactivefontinthetextfield.
Theeightmost-recentlyusedcharactersappearatthetopofthewindow.Acharactermayappearmorethanoncein
thissectioniftheversionsusedifferentfonts.ClicktheBackbuttontotoggleamongallthedisplayedcharacters.
Hotkeys
Hotkeysarekeysonyourkeyboardthatarelinkedtospecificatomlabels.UseChemBioDrawhotkeystoquickly
labelatomsandapplyatomproperties.TheHotkeys.xmlfileintheChemDrawItemsfoldercontainsthehotkeys
providedwithChemBioDraw.Youcanaddorchangehotkeysbyeditingthisfileinatexteditor.
UsingHotkeys
Usinghotkeys,youcanaddfunctionalgroupstoyourstructureswithonekeystroke.Forexample,toaddtert-butylto
theendofahydrocarbonchain:
1. Drawthechain.
2. Hoverthecursorwhereyouwantthefunctionalgroup.
3. Press<3>(thehotkeyfortert-butyl)onthekeyboard.‘t-Bu’isaddedtothestructure.
4. Select‘t-Bu’inthestructureandnavigatetoStructure>ExpandLabel.
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Usingthehotkeys<n>(nitrogen),<O>(oxygen),and<I>(iodine),youcanturnethylbenzeneintopyridin-2-ylhypoiod-
ite.
Youcanalsolabelseveralatomsatatime.Forexample,youcanchangeneopentane(figureAbelow)intometh-
anetetraamine(figureB):
1. Createtheneopentanestructure.
2. Use<SHIFT>+clicktoselectalltheterminalcarbonatomsandpress<n>onthekeyboard.
Note:Foracompletelistofhotkeys,see"ShortcutsandHotkeys"onpage44.
Nicknames
Thesimplestwaytoaddanatomicsymboltoastructureistotypethesymbolintoatextfield.However,youarenot
limitedtoenteringatomsone-at-a-time.Usingnicknames,youcanaddfunctionalgroups,chains,oranyotherstruc-
turalfeaturewithoutdrawingeachatom.
Anicknameisanalphanumericabbreviationthatrepresentsasubstructure.Nicknamesareusefulfordrawinglarge
structuresorstructuresthatrepeatedlyusesimilarfeatures.
Notethatyoucanassignanicknametothestructuralfeature.YoucanalsoassignhotKeystonicknamesthatyou
canlateruseasaquickwayforaddingthenicknametoyourdrawing.Formoreinformationondefiningnicknames,
see"DefiningNicknames"onpage138.
UsingNicknames
Usingnicknames,youcanaddshortnamesforfunctionalgroupstouseasanatomlabel,orpartofalabel.Whenan
atomislabeledwithanickname,thechemicalsignificanceoftheexpandedstructureisretained.
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Commonlyusednicknames,suchasMe,Et,andPharestoredinyourChemDrawItemsfolder.Youcaneditor
deletenicknamesinthislist.
Youcanassignhotkeystonicknames.Forexample,thehotkey<4>labelsanatomwith“Ph”,whichrepresentsa
phenylgroup.
ApplyingNicknames
Youcaneithertypethenicknameorselectitfromthenicknameslist.Formoreinformationondefiningnicknames,
see"DefiningNicknames"onpage138.
Touseanicknametolabelanatom:
1. Inastructure,double-clickanatomwithabondtool,orclickanatomwiththeTexttool.Anatomlabeltextfield
appears.Dooneofthefollowing:
Typeanicknamelabel,suchas“Et”.
NavigatetoFile>Listnicknames.TheListNicknamesdialogappears.
SelecttherequirednicknameandclickPaste.
ClickDone.
Anexampleisshownbelow:
Toselectanicknametoapplytoanatomusingahotkey:
1. Pointtoanatom.
2. Pressthehotkey<=>(equalsign).TheChooseNicknamedialogappears.
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3. Selectanicknamefromthelist.
Tip:Youcanmovewithinthenicknamelistbytypingthefirstletterofthenickname,ratherthanscrollingthrough
thelist.
4. ClickOK.
Note:NicknamesaretokensanddonotfliporientationwhenappliedtotheleftsideofastructurewhenusingAuto-
maticJustification.Forexample,intheabsenceofadefinednickname,thelabel“OTHP”appearsas“PHTO”.
However,sincethenickname“THP”isdefined,thelabelappearsas“THPO”.Formoreinformation,see"Aligning
Text"onpage28.
ExpandingNicknames
Ifyourstructurescontaindefinednicknames,longatomlabels,orcontractedlabels,ChemBioDrawcanrestoreyour
structurestothefullyexpandedform.Whileexpandingastructurecontainingadefinednickname,thenicknamewill
bereplacedbyitsexpandedstructure,asshownbelow:
ForBiopolymers,whenyouexpandthenickname,residuelabelappearsbelowtheexpandedaminoacid.For
example,assumeyouhaveachainofthreeaminoacids–glycine,isoleucine,andleucine:
Toselecttheaminoacid,double-clickthenickname,asshown:
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Toexpandatomnicknames,
1. Selecttheselectiontool.
2. Selectthelabeltoexpand,ordouble-clickthestructuretoselectalllabelsinthestructure.
3. NavigatetoStructure>ExpandLabel.Yourstructureisredrawninitsexpandedform.
Tocontractexpandednicknames:
1. Inthebiopolymerstructure,selecttheexpandedpart.
2. NavigatetoStructure>ContractLabel.Yourstructureisredrawninitscontractedform.
Note:Thisisapplicableonlytobiopolymers.
Annotations
Annotationisabriefdescriptionofanobject,oracomment,aboutpropertiesofanobject.Annotationsareusefulin
identifyingfeaturesandcategoriesofobjectsinsearchingandbrowsing.Annotationsarecategorizedusing
keywords.Thereareseveraldefaultkeywords:Name,Description,GUID(GloballyUniqueIdentifier)Type,and
OtherInfo.Youcanalsoaddyourownkeywords.Manyoftheobjectsinthetemplatefileshaveassociatedannota-
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
availablethroughouttheapplication.NavigatetoFile>PreferencesandclicktheBuilding/Displaytab.Then,
choosefromtheseoptions:
AutomaticAtomLabelAlignment.Thealignmentofatomlabelsadjustsaccordingtothepositionsofanybonds
attachedtotheatomlabels.Forexample,‘CH
3
’attheleftendofahorizontalbondchangesto‘H
3
C’.
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AutomaticallyRectifyHydrogensinAtomLabels.Addsorremoveshydrogensfromatomlabelstopreserve
standardvalenceswhenyouchangeyourdrawing.Forexample,ifyouincreasethebondorderinethanetomake
ethylene,the‘CH
3
’changesto‘CH
2
’.
SettingDefaultAtomLabelStyles
Tosetthedefaultcharacterstyleforatomlabels,navigatetoFile>DocumentSettingsandclickAtomLabels.You
canmodifythefontstyle,baselinestyle,andwhetherterminalcarbonsandimpliedhydrogensappear.
Tosetthedefaultatomlabelstyleforadocument:
1. NavigatetoFile>DocumentsandSettings.
2. FromtheAtomsLabelstab,checktheShowLabelsonTerminalCarbonscheckbox.
3. ClickOK.
Tosetthedefaultatomlabelstyleforoneormorestructures:
1. Selectandright-clickthestructure(s).
2. ClickObjectSettingsinthecontextmenu.TheObjectSettingsdialogappears.
3. FromtheAtomLabelstab,checktheShowLabelsonTerminalCarbonscheckbox.
Toaddorremoveaterminalcarbonlabel,right-clicktheatomandselectordeselectShowTerminalCarbon
Labels.
ChemicalSignificance
Bydefault,captionsareconsideredtobechemicallysignificant,ifpossible.Ifyoucreatealabel,forexample,
"CH3OH”,youareabletoattachbondstoit(anditismodifiedappropriately)eventhoughyoumayhaveintendeditto
bealabel,notamolecule.Moreover,it’svaluesareincludedintheAnalysiswindow.Thelabelswithincorrect
valencesaremarkedwitharedbox.
Toremovetheredbox:
1. SelectthelabelwiththeSelectiontool.
2. Right-clickanddeselectInterpretChemicallyinthecontextmenu.
3. Toactivatechemicalsignificance,right-clickthelabelandselectInterpretChemically.
AnalysisData
YoucanaddpropertiesfromtheAnalysiswindowtoacaptionand,ifAuto-updateison,thevaluesupdateasyou
modifythestructure.FormoreinformationaboutAuto-update,see"AutoUpdate"onpage147.
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Toaddanalysisdatatoacaption:
1. Right-clickthestructureandselectAnalysisfromthecontextmenu.
2. Choosethepropertiestoadd.
DrawingRings
TheMainToolspalettecontainsthefollowingringtoolsthatenableyoutodrawringsizesandtypes:
Figure6.3:a)cyclopropane;b)cyclopentane;c)cycloheptane;d)cyclohexanechair(1);e)cyclopentadiene;f)cyc-
lobutane;g)cyclohexane;h)cyclooctane;i)cyclohexanechair(2);j)benzene.
Todrawaring:
1. FromtheMaintoolbar,selectaringtool.
2. Clickanddraginthedocumenttoorientthering.
Ifyouclickanatomorbondwitharingtoolinanexistingstructure,theringisfusedtoit.Youcanalsousehotkeysto
fuserings.Formoreinformation,see"BondHotkeys"onpage45.Youcanalsoreducethesizeoftherings.Formore
information,see"ReducingRingSize"onpage55
SpiroandSproutRings
Bydefault,clickinganatominaringusingaringtoolformsaspirolink.However,ifyouclickanatomwhilepressing
the<Alt>keyonyourkeyboard,itwillsproutthering.
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Youcanchangethisbehaviorsothatasproutbondappearsinsteadofaspiroring:
1. NavigatetoFile>Preferences.
2. FromtheBuilding/Displaytab,checktheSproutRingsInsteadofSpiroWhenClickingcheckbox.
CyclohexaneChairRings
Youcandrawcyclohexanechairringsintwoorientations:horizontalandvertical.Whenyoudrawacyclohexanechair
ringbyclicking,thechairisdrawninahorizontalorientation.
Toorientacyclohexanechairringtoaverticalorientation:
1. ClickoneoftheCyclohexaneChairRingtools.
2. Click+draginthestructuretotheorientationyouwant.
Figure6.4:a)Horizontalorientation;b)Verticalorientation.
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AromaticStructures
DelocalizedRings
Youcandrawaresonancedelocalizedringusinganyringtoolexceptforthecyclohexanechairs.
1. Clickaringtool.
2. PresstheCTRLkeyanddragorclickinthedocumentwindow.
ResonanceStructures
Youcandrawcyclopentadieneorbenzeneinmultipleversions:
Thedoublebondsinthecyclopentadieneorbenzeneringtoolscanbedrawnineitheroftwoforms.Normally,thefirst
bonddrawnisadoublebond.ThisistheorientationindicatedonthecyclopentadieneandbenzeneRingtoolpointers.
Todraw,clickinthedocumentwindowwitheitherthecyclopentadieneorbenzenedrawingtool.
Toshifttheorientationsothefirstbonddrawnisasinglebond,dooneofthefollowing:
<Shift>+dragfromthebeginningofthefirstsinglebondtotheendofthesinglebond.
<Shift>+clickinadocumentwindowtodrawthebondwithafixedlength.
Chains
YoucandrawhydrocarbonchainsusingeithertheAcyclicchaintoolorSnakingchaintool.UsetheAcyclicchaintool
todrawstraighthydrocarbonchains.
1. SelecttheAcyclicchaintool.
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2. Clickanddraginthedocumentwindowinthedirectionyouwantthechaintogrow.Thenumberattheendofthe
chainindicateshowmanyatomsyouhavedrawn.
ChangingChainDirection
Tochangethedirectionasyoudraw,usetheSnakingchaintool,orpressthe<Control>key withAcyclictoolselec-
ted,whiledrawinginthedirectionyouwant.
Note:Releasethemousebuttonbeforeyoureleasethe<Control>key.
ApplyingFixedLengths
Applyingfixedlengthsandfixedanglesenablesyoutocreatestructureswithconsistentbondlengthsandangles.The
fixedlengthdimensionissetintheDrawingSettingsdialog.Thefixedangledimensionincrementsanglesby15
degrees.
FixedlengthisusedtoconstrainthelengthofthebondsdrawntothelengthyouspecifywhentheFixedLengths
commandintheObjectmenuisenabled(withacheckmark).Thisalsoadjuststhepreferredbondlengthforstruc-
turesmodifiedbytheCleanUpStructurecommand.
WhenFixedLengthsisenabled,thepointerontheAcyclicchaincanbedraggedtomakeanyanglerelativetotheX-
axis.Ataconstantchainlength,thepositionsofthefirstbondandallsubsequentodd-numberedatomsdependonthe
directionyoudrag.Beforereleasingthemousebutton,changethispositionbydraggingintheoppositedirection.
IfFixedLengthsisdisabled,holddownthe<Control>+<ALT> keystoreversechaindirection.FixedAnglesmust
beenabledtoreversedirection.
FixedAngles
WhenFixedAnglesisenabled,theangletheAcyclicchainmakesrelativetotheX-axisisconstrainedto15-degree
increments.
AddingChainstoStructures
ToaddanAcyclicchaintoanexistingstructure,clickanatominthestructure.Clickanddraginthedirectionyou
wanttodrawthechain.
SpecifyingChainLength
Tospecifytheexactlengthofachainbeforeyoudrawit:
1. SelecttheAcyclicchaintool.
2. Clickanexistingatomoranemptyareainadocumentwindow.TheAddChaindialogappears.
3. Typethenumberofcarbonatomsinthechain.
4. ClickAdd.
Toaddanotherchainofthesamelengthanywhereinadocumentwindow,<ALT>+clickwhereyouwantthechainto
begin.
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