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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
Youcandeterminetheorientationoftheresultingbondbydragging.Ifyouclicktoaddabond,thereareseveralpref-
erentialorientationsfortheresultingbondasoutlinedbelow.
Addingfromtheendofanatomlabelcreatesbondsthatarepreferentiallyhorizontal.
Addingfromthemiddleofanatomlabelcreatesbondsthatarepreferentiallyvertical.
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AddingfromthestartofanatomlabelcreatesbondsthattrytoattainthechainanglesettingintheDrawingSet-
tingsdialog.Ifthatanglecannotbeattained,thenextbestangleisused.
AttachmentPoints
Youcandrawpolyhaptostructuressuchasferrocene((Cp)
2
Fe),orabbreviatednotationsfordifferentpositionaliso-
mersofacompound,usingattachmentpoints.Theprocedureissimilar,andinbothcases,thestructureretainschem-
icalsignificance.Youcangenerateallpossiblestructuresfromanabbreviatedcombinatorialstructurebyusing
ExpandGenericStructurefeature.Formoreinformation,see"ExpandGenericStructures"onpage255.
Figure9.4:Drawingapolyhaptostructure
Multi-CenterAttachments
Toaddamulti-centerattachmentpointtoastructure:
1. Selectallorpartofthestructure.
2. NavigatetoStructure>AddMulti-CenterAttachment.Anasteriskindicatesamulti-centernode.
Todrawabondtoamulti-centerattachmentpoint:
1. Clickthebondtool.
2. Pointtotheasteriskandeitherclickordragtocreateabond.
Theasteriskisnotvisibleonceabondisdrawntoit.However,youcanviewtheattachmentpointusingabondor
selectiontool.
Tip:Iffixedlengthsisenabled,press<ALT>asyoudragthebond.
VariableAttachmentPoints
YoucanusetheAddVariableAttachmentcommandtodrawdifferentpositionalisomersofacompoundusingan
abbreviatednotationthatretainschemicalsignificance.
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Forexample,youcanexplicitlydrawthethreeisomersofdibromobenzene,asshownbelow.Alternately,youcan
expressallthreeisomersasasingleparentstructurebyusingavariableattachmentasshownbelow.
Abbreviated
notationfor:
Figure9.5:Isomersofdibromobenzene
Toaddavariableattachmentpointtoastructure:
1. Selectallorpartofthestructure.
2. NavigatetoStructure>AddVariableAttachment.
3. Pointtotheasteriskinthestructureanddragtodrawabond.
Note:EitherdisableortoggleFixedLengthstodrawthebondsothatitextendsfromthering.
Note:Todrawthestructurebelowyoushouldonlyselectthe5ringsatomthatdonotalreadyhaveabromine
atomboundtothem. Selectingtheentiremoleculewouldcauseavalenceproblemwiththetopmostcarbon.
Tip:Iffixedlengthsisenabled,press<ALT>asyoudragthebond.
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Note:Afteryoudrawabondfromanattachmentpoint,theasteriskdisappears.Toviewanattachmentpoint,pos-
itionthecursoroveritwitheitherabondtooloraselectiontool.
AtomNumbering
Youcanaddsequentialnumbersorletterstotheatomsinyourstructure.Youcanadd:
Numbers(1,2,3,andsoon)
Textendingwithanumber(atom1)
Greeklettersforalpha,beta,andsoon
Letters(a,b,c,andsoon)
Thedefaultindicatorisnumbers.
Tip:Tousetextinsteadofnumbers,numberanatom,andtheneditthenumber.See"FormattingAtomNumbers"
below.
ShowingAtomNumbers
1. Selectoneormoreatomstonumber.
2. Whilepointingtotheselectedatomsorstructure,dooneofthefollowing:
Right-click andselectAtom>ShowAtomnumberinthecontextmenu.
Typethehotkey‘(singlequote).
Tohideatomnumbers:
1. Selecttheatomsorstructure.
2. Right-click,pointtoAtom,anddeselectShowAtomNumber.
Note:Toremoveanatomnumberindicator,clicktheindicatorwiththeErasertool.
FormattingAtomNumbers
Toedittheatomnumbertextandstyle:
1. SelecttheTexttool.
2. Selecttheatomnumberandtypethenewtext.
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Note:Whenyoutypeanewindicator,thecounterresetstothenewstyleandyoucancontinuenumberinginthat
stylewiththestandardmeans.Forexample,ifyoutype
a
inatextbox,thenpointtoanotheratom,andusethe
contextmenuorhotkey,theatomislabeled
b.
Switchingtoanotherstructureresetsthecounter.
3. Toedittheatomnumberstyle,selecttheatomnumberwiththeTexttoolandusetheTextmenu,orTextformat-
tingtoolbar,tochangethestyle.
PositioningAtomNumbers
Youcanpositioneachatomnumberanywherearounditscorrespondingatomanditsdistancefromtheatom.
Torepositionanatomnumber:
1. Right-clicktheindicatortomoveandclickthePositioncommandonthecontextmenu.ThePositionIndicators
dialogappears.
2. Clicktheappropriatepositionoption,andenteravalue.
Toposition
TypeaValuefor
Position
Fromtheatomorbondcentertotheindicatorcen-
ter
Byangleorby
clock
Fromtheatomorbondcentertobottomleftof
indicatorbaseline
Byoffset—hori-
zontalandvertical
Atspecifiedcoordinates
Absolute—hori-
zontalandvertical
StructurePerspective
YoucantiltmoleculesorportionsofmoleculesthroughthreedimensionswiththeStructurePerspectivetool.
Totiltastructure:
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1. SelectthestructurewitheitheraselectiontoolortheStructurePerspectivetool.
2. WiththeStructurePerspectivetool,clickanddragtheselectedstructure.Placethecursorinsidethemarkedrect-
angleanddraginanydirection.
Tip:Use<SHIFT>+dragtolimittherotationtotheXorYaxesonly.
Youcanalsoselectpartofacomplexmoleculeandrotateitaroundaparticularbond.
Note:Youcannotapplystructureperspectivetoorbitals.
ToremovetheStructurePerspectiveTooleffect:
1. SelectthestructurewiththeMarqueeorLassoTool.
2. NavigatetoObject>Flatten.
Note:Flatteningthestructureremovesitsz-coordinateinformationbutdoesnotchangeitsappearance.
MassFragmentation
Massfragmentationmimicsthemolecularfragmentationinamassspectrometer.Whenyouapplythemassfrag-
mentationtooltoastructure,youcutthroughthestructure,severingitsbonds,andcreatingfragmentsfromtheori-
ginalstructure.Thisisnotapredictivetool,youmustspecifywhatbondsaretobebroken.
Tofragmentastructure,usetheMassFragmentationTooltodragthecursoracrossoneormorebonds.Whenyou
releasethemousebutton,bondsthatyoucrossarebroken.
Bydefault,thelineyoudrawdisappearswhenyoureleasethemousebutton.
Note:Todrawacurvedline,ortokeepthelinevisible,holddownthe<ALT>keywhiledrawing.
Whenthelinecrossesabond,theformulaandexactmassforthefragmentsoneithersideofthebondappearasifthe
bondwerehomolyticallybroken.Thatis,asinglebondturnsintoamonoradicaloneachfragment;adoublebondturns
intoapairofdiradicals.Ifmorethanonebondiscrossed,allfragmentsoneachsideofthelineareconsidered
together.Iftheonlybondcrossedisaringbond,asingleformula/masspairdisplays.
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Youcanrepositiontheformulaandmassdisplays,ordeletethem.
SynthesisandRetrosynthesis
ChemBioDrawincludestwotoolstohelpyoudrawsynthesisreactions.TheSynthesistooldrawsasynthesisreac-
tionbasedonaproductstructurethatyouspecify.Alternatively,theRetrosynthesistooldrawsthereactionwiththe
productontheleftandanarrowpointingtothereactants.Thesetoolsareinthefragmentationtoolspaletteofthemain
toolspalette.
Todemonstratethesefeatures,weusetheBeyerMethodforquinolines,startingwiththestructurebelow.
Youcancreateeithertypeofreactionusingtheappropriatetoolanddraggingthroughbondsindicatedbythedotted
line.Forexample,usetheRetrosynthesistooltocreatethisreaction:
Figure9.6:QuinolineRetrosynthesis
Quinlinesynthesis
DrawingReactions
Todemonstratehowtodrawreactions,wewillusethisexample:
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DrawinganArrow
Startingwith2-propanone(see"Tutorial1:DrawingaStructure"onpage298),drawthereactionarrow:
1. OntheArrowstoolbar,clickthethirdarrowfromtheleftinthetoprow,asshownbelow:
2. Inthedocumentwindow,clickanddragthemousehorizontallytotherightofthe2-propanonestructure.Thearrow
appears.
3. SelecttheText tool.
4. Clickabovethearrow.Atextboxappears.
5. TypeOHandpress<ESC>.Re-alignthetextboxasnecessaryusingaselectiontool.
Note:IfShowChemicalWarningsisturnedon(thedefault),aredboxwillappeararoundtheOHlabelwhenyou
changetoolsoropenanothertextboxindicatinganerror.Ignorethisfornow.
AddachargesymbolusingtheChemicalSymbolstoolpalette:
1. IntheMainTooltoolbar,clicktheChemicalSymboltool.
2. Holdingthemousebuttondown,selectthecircledCircleMinussymbol.
3. PointtothecenteroftheOHlabel.MovethecursorslightlyrightorlefttoselecttheO.
4. Withtheoxygenatomselected,dragthechargesymbolaroundtheatomtothedesiredposition.
ObjectsthatyouaddfromtheChemicalSymbolspaletteareassociatedchemicallywiththestructuretheyarenear.
Notethattheredvalenceerrorwarningdisappearswhenyouaddtheminuscharge.
DrawingtheProduct
Wenowcreate4-hydroxy-4-methyl-2-pentanoneusingacopyofthe2-propanonestructure.Youcancreatethe
productfromscratch,oryoucancopyanexistingstructure.
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Tocopyastructure:
1. Selectthe2-propanonestructureanditscaption.
2. Pressandholdthe<CTRL>key.
Thehandpointerwithaplussignindicatesthatyouareintheduplicationmodeofaselectiontool.
3. Dragtheselectionrectangletotherightandreleasethemousebutton.
Note:Tokeepthecopyalignedwiththeoriginal,pressthe<SHIFT>keywhiledragging.
Modifytheduplicatestructure:
1. SelecttheSolidBondtool.
2. Clickthefarrightbondofthecopiedstructure(Figurebelow).
3. Pointtoaterminalcarbon.
4. Clickthecarbonatomuntilthreebondsappear,allowingapausebetweeneachclick.
Note:Ifyouclicktoofast,theclickisinterpretedeitherasadouble-click,whichopensatextboxoratriple-click,
whichduplicatesyourlastatomlabel.
5. Pointtoaterminalcarbonatom.
6. TypeOH.
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Replacetheproductcaption:
1. SelectthecaptionwiththeTexttoolandtype4-hydroxy-4-methyl-2-pentanone,pressthe<ENTER> keyand
type 1mole.
2. UsingtheTexttool,add
2Mole
tothecaptionforthereactant.
CleanUpReactions
Afteryoudrawareaction,youcancleanthereactionusingtheCleanUpReactioncommandundertheStructure
menu.WhenyouapplytheCleanUpReactioncommand,thespacingbetweenthereactioncomponentsismod-
ified,thecomponentsareevenlydistributed,plussignsareinsertedwherevernecessary,andthelengthofthearrow
isadjusted.
Tocleanupareaction:
1. Selectthereaction.
2. NavigatetoStructure>CleanUpReaction.
Ifthereactionistoowideforthedocument,thereactioniswrappedtofillmultiplelines,asshownintheexample
below:
Figure9.7:ThereactionbeforeapplyingtheCleanUpReactioncommand
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