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Figure9.8:ThereactionafterapplyingtheCleanUpReactioncommand
Note:TheCleanUpReactionisavailableonlyforsingle-stepreactions.
Note:TheCleanUpReactioncommandisavailableonlyforreactionswithstraightarrows.Incaseofarrows
withcurvaturestheCleanUpReactioncommandisdisabled.
TheReactionInterpreter
TheReactionInterpreterparsesreactionsasdrawn,andbreaksthereactionintothefollowingdistinctcomponents:
ReactionScheme
ReactionStep
Reactants
Products
Conditions
YoucansavetheinterpretationtodiskbysavingthefileasCDXML.Thisstoreddataisoftenimportantifreactions
aretobestoredindatabases.
Thereactioninterpretercolor-codesthereactants,products,catalysts,andannotationsinareactionwhenyouhover
overthemwithShowReactionInterpretationselected.Thishelpsindeterminingwhetherthereactionisbeingcor-
rectlyperceived,andletsyouadjustthereactiontocorrecttheinterpretation.
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Tointerpretthereaction:
1. NavigatetoView>ShowReactionInterpretation.
2. Hoveryourcursoroverthereactionarrow.
Forareactiontobeinterpreted:
Eachreactantandproductmustcontainatleastoneatom.
Eachreactantandproductmustbedescribedusingasinglelabel.
Multiplereactantsandproductsshouldbelinkedbya“+”sign.
Reactionconditionsmustresidecompletelywithintheleftandrightboundariesofthereactionarrow.
Thereactioncannotincludeacurvedarrow.
Thereactioniscoloredasfollows:
Reactionsarered.
Productsaremagenta.
Everythingabovethereactionarrowiscyan.
Everythingbelowthereactionarrowisblue.
ElectronandRadicalPushing
Acommonpracticewhenillustratingorganicreactionmechanismsistouseelectronpushingarrowstodisplaythe
transferofelectrons.ChemBioDrawprovidestheElectronPushingandRadicalPushingtoolsforillustratingelectron
transfer.Electrontransferscanbedrawnbetweenatoms,bonds,andorbitals.
Todisplaythetransferofanelectronpair:
1. SelecttheElectronPushingTool
fromtheChemicalSymbolstoolbar.
2. Clickanddragthemousefromthesourceobjecttothetargetobjectandreleasethemouse.Afull-headarrow
appearssignifyingtheelectronpairtransfer,suchas:
Figure9.9:Exampleofelectronpushing
Todisplaythetransferofoneelectron:
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1. SelecttheRadicalPushingToolfromtheChemicalSymbolstoolbar.
2. Clickanddragthemousefromthesourceobjecttothetargetobjectandreleasethemouse.Ahalf-headarrowsig-
nifyingonlyoneelectrontransferappears,suchas:
Figure9.10:Exampleofradicalpushing
Youcandeletetheelectrontransferarrowbyeitherselectingorhoveringoverthearrowandpressingthe<DELETE>
key.YoucanmodifytheelectrontransferarrowshapebyusingeithertheArrowtool,ortheElectronPushingTool.
Whenyouhoverovertheelectronorradicalpushingarrows,theassociatedobjectsarehighlightedinadditiontothe
arrows.
StoichiometryGrid
UsetheStoichiometryGridtocalculatestoichiometricdataforareaction.Thegridfillsinasyoumodifyareaction
drawing,andallcalculationsaredoneautomatically.
Tocreateastoichiometrygrid:
1. Drawareaction,oropenafilecontainingareaction.
2. NavigatetoView>ShowReactionInterpretation.TurningonShowReactionInterpretationensuresthereac-
tionisproperlyinterpretedbyChemDraw.Whenyouhoveroverthereaction,forexample:
Reactantsinred
Productsinmagenta
Anythingaboveandbelowthereactionarrowincyanandblue
3. SelectthereactionandnavigatetoStructure>AnalyzeStoichiometry.Thegrid,withseveraldatafieldsfilled
withdefaultvalues,appearsunderthereaction.
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Note:Ifacatalystorconditionlabelisabovethereactionarrow,right-clickthelabelanddeselectInterpretChem-
icallyinthecontextmenubeforecreatingthegrid.
Toenterdatainthegrid:
1. Setthelimitingcompound.Ifthedefaultsettingisincorrect,right-clickthewordNointhelimitingrow,andselect
SetLimitingfromthecontextmenu.
2. SelecttheTexttool,andclickwheretoenterthedata.Entervaluesforallreactants,asapplicable.Ifyouareusing
unitsotherthanthedefaults,typeintheunitsalongwiththevalues(nospacerequired).
Value
Comments
Limiting?
Indicatesthelimitingreactant.Onlyonereactantmaybespecifiedaslimiting.
SampleMass
Massofreactant.Defaultunits:g.
%Weight
Reactantpurity.Defaultsto100%.
Volume
Defaultunits:ml.Requireseitheramolarityoradensitytobeentered.
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Value
Comments
Molarity
Defaultunits:M
Density
Defaultunits:g/ml
Afteryouentertheminimumamountofinformationthevaluesarecalculated.
Thevaluesareautomaticallyrecalculatedwhenyouenteranewvalue,editinput,ormodifythereaction.Toeditinput,
clicktheinputandenterthenewvalue.Forexample,considerthefollowingtable:
IfyoueditthevalueintheReactantMolesfieldforthereactantinthetableto30.00mol,therestofthetableis
updated.
Note:Enteredvaluesareinbold-face;calculatedvaluesareinnormalfont.
Youcanshoworhiderowsorcolumnsinthegrid.Tohidearow,right-clicktherowandselectHideRowfromthe
contextmenu.
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Tohideacolumn,right-clickthecolumnandselectHideColumnfromthecontextmenu.
Todisplayhiddenrowsorcolumns,selectShowAllfromthecontextmenu.Tochangethecolorofthetext,select
Colorfromthecontextmenu.
Templates
ChemBioDrawincludesalibraryoftemplates.Youcanuseatemplateasastartingpointforanewdrawingortoadd
toanexistingdrawing.Apaletteisasetoftemplates.
Thetemplatesyoudefinearenotlimitedtoatomsandbonds.Templatescanalsocontaincaptions,colors,boxes,
arcs,orbitals,arrows,reactionmechanismsymbols,andcurves.Youcanpastepicturesfromotherapplicationsinto
atemplatepane.YoucandownloadtemplatesfromthePerkinElmerInformaticswebsiteandusethem.Formore
informationonavailabletemplatesanduserdownload-abletemplates,seeChemBioDraw
template
files
,and
BioDraw
templates
.
Toopenatemplate,dooneofthefollowing:
SelectatemplatetoolbarfromtheMaintoolbar.
NavigatetoView>Templatesandselectatemplatetoolbarfromthelist.
Toaddtoadrawingusingatemplate:
1. Selecttherequiredtemplatefromthetemplatetoolbar.
2. Inthedocumentwindow,clickanddragthemouseuntilthetemplateisorientedthewayyouneed.
Tip:Tomodifythetemplatesize,pressthe<ALT>keywhiledrawingit.
Youcanalsousethetemplatestoaddstructuralfeaturestoexistingdrawings.
Toaddstructuralfeaturestoexistingdrawings:
1. Selecttherequiredtemplatefromthetemplatetoolbar.
2. Clickanatomorbondintheexistingdrawingtoaddthetemplatestructure.
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CustomizingTemplates
Youcanmodifyatemplatepalettetocreateyourownpalette.Whenyoucreateapalette,asetofemptytemplate
panesappearabovethedocumentwindow.Afteryousaveyourpalette,itcontainsthetemplatesyouhavedrawn.
YoucanthenselectyourpalettefromthepalettelistintheTemplatestool.Youcanalsostoretemplatesasgroups,or
evenintegralgroups,sothattheyaretreatedasanindividualentitywithinthedocumentsintowhichtheyaredropped.
Tocreateatemplatepalette:
1. NavigatetoFile>OpenTemplates>NewTemplates.
2. Clickatemplatepane.
3. Inthedocumentwindow,drawanewstructure.
4. Clickanothertemplatepaneanddrawanotherstructureasdesired.
5. Afteryoudrawallthetemplatesyouwant,gotoFile>Save.
Note:SaveyourpaletteintheChemDrawItemsfoldertoensureitappearsintheMaintoolbar.
6. Inanydrawing,selecttheTemplatetoolontheMaintoolbartouseyoupalette.
ModifyingaTemplate
1. NavigatetoFile>OpenTemplatesandchooseapalette.
2. Inthepalette,clickatemplatepane.Thetemplateappearsinthedocumentwindow.
3. Inthedocumentwindow,editthetemplate.
4. Savethetemplate.
Toaddordeleteapaletteroworcolumninapalette:
1. Inthepalette,clickacellintheroworcolumn.
2. SelecttheappropriateoptionintheEditmenu.
AddingaTemplate
Toaddatemplate,clickinanemptytemplatepaneanddrawthetemplateinthedocumentwindow.Navigateto
File>Save.
AnnotatingaTemplate
1. NavigatetoFile>OpenTemplatesandchooseapalette.
2. Right-clickonanemptyspaceinatemplatepane,andselectAnnotate.TheAnnotatedialogappears.
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3. SpecifyanewnameforthetemplateintheContenttextbox.
4. ClickOK.
5. ClickSave.Theannotationappearsasatooltip,whenyoupointtotheannotatedtemplate.
DeletingaTemplate
1. Selectthetemplatepaneforthetemplatetodelete.
2. Inthedocumentwindow,selecttheentiredrawing.
3. NavigatetoEdit>Clear.
4. NavigatetoFile>Save.
OrientingTemplates
Tomaketemplatesyoucreatesimpletouse,orientthetemplatestructuresothatyoucanmodifythebondsyouuse
mostoften.
ResizingTemplatePanes
ToresizetheTemplatepanesintheTemplatepanel,dragthelowerrightcorneroftheTemplatepanel.Ifnecessary,
firstclickanddragtheresizehandle.
DefiningNicknames
Anicknameisanalphanumericabbreviationthatrepresentsasubstructure1.Nicknamesareusefulfordrawinglarge
structures,orstructuresthatrepeatedlyusesimilarfeatures.Contractedlabelsaresimilartonicknames,buttheyare
forone-timeuseonly,inthecurrentdocument.
ChemBioDrawincludesalibraryofnicknamesofcommonfunctionalgroupsandmonomers.Forexample,ifyoutyp-
icallydrawproteinstructures,youmayconsiderusingaminoacidnicknamesinyourdrawingsratherthandrawing
eachaminoacid.
Thesubstructurethatanicknamerepresentsconnectstotherestofthestructureusingoneormoreattachment
points.Attachmentpointsmustbesinglebonds.Forsubstructureswithtwoormoreattachmentpoints,theattach-
mentpointnumberingsequencedeterminestheorderinwhichotherpartsofthestructureareattached.Forexample,
1
Asubstructurecanbeanypartofadrawnstructure.
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ifyouexpandthestructureH-Leu-OH,thehydrogenisbondedtothefirstattachmentpointinleucineandthehydroxyl
grouptothesecond.
Formoreinformation,see"UsingNicknames"onpage62.
Todefineanewnickname:
(Intheexamplebelow,ab-alaninestructureisused.)
1. Drawtheb-alaninestructure.
2. DrawabondtotheNH2group.
3. DeletethelabelontheOHgroup.
4. UsingtheAttachmentPointtool,addanattachmenttotheN-terminus.
5. AddanattachmenttotheC-terminus.
6. Selectthestructure,andnavigatetoStructure>DefineNickname.
7. Typeashortnameforthenickname.
Tip:Toavoidpossibleconflictswithelements,specifynameswithmorethantwocharacters.
8. ClickOK.
Note:Theattachmentpointorderisdeterminedbytheorderinwhichyouaddtheattachmentpointstothestruc-
ture.
Youcanalsodefinenicknamesfromastructurecontainingasingleradical.Attachmentpointsareaddedatthesiteof
theradical.
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Nicknamescanalsobedefinedbycarvingasubstructureoutofastructure.
NicknamesandAtomLabels
Ifyouuseanicknamethatisthesameasanelementname,amessageindicatesthattheelementisreplacedwith
thenickname.Forexample,usingAcforanacetylgroupreplacestheelementActinium.TheCheckStructurecom-
mandrecognizesthelabelasanacetylgroupratherthanActinium.
ThenicknameslistprovidestheseNickname/Elementconflicts:
Symbol
Nickname
Element
Ac
Acetyl
Actinium
Am
Amyl
Americium
Np
para-Nitrophenyl
Neptunium
Pr
Propyl
Praeseodymium
Note:IfyouusethePeriodicTabledialogtoinsertatomsintostructures,theelementswillpreferentiallybedepos-
ited.SelectingAcfromthePeriodicTableandclickingonanatomwillplaceActiniumratherthanAcetyl.
Toremovetheoverridingnicknames,navigatetoFile>ListNicknamesanddeletetheoverridingnicknamedefinition.
DeletingNicknames
Todeleteanicknamefromthenicknamelibrary:
1. NavigatetoFile>ListNicknames.
2. SelectthenicknameandclickDelete.
TroubleshootingNicknames
IftheDefineNicknamescommandisdisabled,checkforthefollowing:
Aconnectionpointthatisnotpresent
Morethantwoconnectionpointsthataredefined
Aconnectionpointthatisnotasinglebond
InFigureabelow,theentirefunctionalgroupwasselected.Becausethereisnoatomthatindicatesaconnection
point,youcannotdefineanickname.Whenasulfonamidegroupisattachedtoanunselectedbond,youcandefinea
nickname.
InFigureb,thereismorethanoneattachmentpointonasingleatominanickname.
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