Where:
Uistheinternalenergy(SIunit:Joule)
pispressure(SIunit:Pascal)
Visvolume(SIunit:m
3
)
Tisthetemperature(SIunit:Kelvin)
Sistheentropy(SIunit:jouleperKelvin)
Histheenthalpy(SIunit:Joule)
Note:HandSarethermodynamicvaluesfoundatstandardtemperatureandpressure.
HeatofFormation
ReportedinKJ/mole,theheatofformationistheincreaseinenthalpyresultingfromtheformationofonemoleofasub-
stancefromitsconstituentelementsatconstantpressure.
Henry’sLawConstant
Aunitlessvalue,Henry'sLawConstantcanbeexpressedas:
Where‘p’isthepartialpressureofthesoluteinthegasabovethesolution,‘c’istheconcentrationofthesoluteand
‘k
H,pc
’isaconstantwiththedimensionsofpressuredividedbyconcentration.Theconstant,knownastheHenry's
lawconstant,dependsonthesolute,solvent,andtemperature.
LogP
Thepartitioncoefficientisaratioofconcentrationsofun-ionizedcompoundbetweentwosolutions.Tomeasurethe
partitioncoefficientofionizablesolutes,thepHoftheaqueousphaseisadjustedsothatthepredominantformofthe
compoundisun-ionized.Thelogarithmoftheratiooftheconcentrationsoftheun-ionizedsoluteinthesolventsis
calledLogP.
Normally,oneofthesolventschoseniswater;thesecondishydrophobic,suchasoctanol.
TheformulatocalculateLogPis:
LogS
LogSdeterminesthesolubilityofasubstance,measuredinmol/liter.
Theaqueoussolubilityofacompoundisknowntosignificantlyaffectabsorptionanddistributioncharacteristicsof
thatcompound.
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Note:LogScalculationsareavailableonlyinMicrosoftWindowsversionofChemBioDraw.
Meltingpoint
Isthetemperatureatwhichasolidbecomesaliquidatstandardatmosphericpressure.Atthemeltingpoint,thesolid
andliquidphaseexistinequilibrium.Theformulatocalculatemeltingpointis:
Where‘T’isthetemperatureatthemeltingpoint,‘
D
S’isthechangeinentropyofmelting,and‘
D
H’isthechangein
enthalpyofmelting.
MR
TheMolarRefractivityisestimatedbyCrippen'sfragmentationandViswanadhan'sfragmentationmethod.Additional
empiricalLogPdataappearsforselectedsubstancesinthereportfile.
pKa
pKaisthenegativelogoftheaciddissociationconstantK
a
.Itdescribesthetendencyofcompoundsorionstodis-
sociateinsolution.Itiscalculatedusingtheformula:
EmpiricalpKadataappearsforselectedsubstancesinthereportfile.
Note:pKacalculationsareavailableonlyinMicrosoftWindowsversionofChemBioDraw.
tPSA
Calculationofpolarsurfaceareabasedonfragmentcontributions.
PropertyPredictionsinChemDraw/Excel
ThePropertiesfeatureinChemDraw/Excelletsyouviewthevaluesofdifferentpropertiesforagivenstructure.Each
propertyiscalculatedusingthe“bestavailable”method.AlistofpropertiesavailableinChemDraw/Excelislistedin
thetablebelow.Formoreinformationontheseproperties,seeChemDraw/Excelonlinehelp,orvisitthePerkinElmer
Informatics
website
.
Thepropertiesavailableinclude:
B
F
MeltingPoint
ShapeAttribute
BalabanIndex
FormalCharge
MolarRefractivity
ShapeCoefficient
BoilingPoint
FreezingPoint
MolecularFormula
SumOfDegrees
C
G
MolecularWeight
SumofValence
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Degrees
ClusterCount
GibbsFreeEnergy
N
T
CriticalPressure
H
NumberofRotatable
Bonds
TotalConnectivity
CriticalTemperature
HeatofFormation
O
TopologicalDia-
meter
CriticalVolume
Henry'sLawConstant Ovality
TopologicalIndex
ConnollyAccessibleArea
I
P
TotalValenceCon-
nectivity
ConnollyMolecularSurface
Area
IdealGasThermal
Capacity
PrincipalMomentsof
Inertia(X,Y,Z)
V
ConnollySolventAccess-
ibleSurfaceArea
L
PolarSurfaceArea
VaporPressure
ConnollySolvent-Excluded
Volume
LogP
R
W
E
M
Radius
WaterSolubility
ExactMass
Mass
S
WienerIndex
PropertyPredictionsinChem3D
Chem3Dletsyoubuild,analyze,andcomputepropertiesveryeasily.Inadditiontoanalyzingstructurestocalculate
massandformula,predictingnumerousphysicalproperties,youcanalsoperformcalculationsformoleculartopology.
AlistofpropertiesavailableinChem3Dislistedinthetablebelow.Formoreinformationontheseproperties,see
Chem3DonlinehelporvisitthePerkinElmer
Informatics
website
.
B
G
MolWeight
SpinDensity
BalabanIndex
GibbsFreeEnergy
MolecularMass
SumOfDegrees
BoilingPoint
H
MolecularSurfaces
SumofValence
Degrees
C
HarmonicZeroPoint
Energy
MolecularTopological
Index
T
C
P
HeatCapacity
MolecularVolume
Thermodynamic
Energy
C
v
HeatofFormation
MullikenCharges
TopologicalDia-
meter
ClusterCount
Henry’sLawConstant MullikenPopulations
TotalConnectivity
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ConnollyAccessibleArea
HyperPolarizability
m/z
TotalEnergy
ConnollyMolecularArea
HyperfineCoupling
Constants
N
TotalValenceCon-
nectivity
ConnollySolventExcluded
Volume
I
NumRotatableBonds
V
CriticalPressure
IdealGasThermal
Capacity
O
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
ElectrostaticPotential
LogS
PotentialEnergy
ElementalAnalysis
LowdinCharges
PrincipalMoment
Enthalpy
LowdinPopulations
R
Entropy
M
Radius
ExactMass
Mass
RMSForce
F
MeltingPoint
S
FormalCharge
MolFormula
SCFEnergy
Frequencies
MolFormulaHTML
ShapeAttribute
MolRefractivity
ShapeCoefficient
ChemBioFinderProperties
ThepropertieslistedbelowcanbecalculatedinChemBioFinderUltraforChemBioOffice.Formoreinformationon
thesepropertiesandhowtocalculatethem,seetheChemBioFinderonlinehelp.
B
H
P
BalabanIndex
HeatofFormation
PartitionCoefficient
BoilingPoint
Henry’sLawConstant
pKa
C
I
PolarSurfaceArea
ChemicalName
IdealGasThermalCapacity
PrincipalMoment
ClusterCount
L
R
CriticalPressure
LogP
Radius
CriticalTemperature
LogS
S
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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
ViewingChemicalProperties
Toviewchemicalproperties:
1. Selectthestructurewhosepropertiesyouwanttoview.
2. NavigatetoView>ShowChemicalPropertiesWindow.TheChemicalPropertieswindowappears.
3. Topastethebasicpropertiesintoyourdocument,clickPaste.
4. Tocreateareportandviewresultsforotherfragmentationmethods,clickReport.
3DViewing
Asyoucreateyourdrawing,youcanviewitinthree-dimensions.TwofeaturesinChemBioDrawletyouviewstruc-
turesinthreedimensions.
Note:ChemBio3Dmustbeinstalledonyourcomputertopreviewstructuresinthreedimensions.
3DModel
Usea3Dmodeltopastea3Dversionofthestructureintoyourdrawing.
1. Selectthestructure.
2. NavigatetoEdit>Get3DModel.The3Dstructureappearsinthedocumentwindow.
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ToviewthemodelinChemBio3D,double-clickonit.
Note:3Dobjectsinsertedinthiswaycannotbetransferredbetweenplatforms.Formoreinformation,see"File
Formats"onpage273.
Note:Youcancopyamodelusing"CopyasCDX"fromChemBio3DandpasteintoChemBioDraw.Theresultis
aChemDrawstructurewith3Dcoordinates,anditispossibletorotatethisstructurein3Dusingthestructureper-
spectivetool.
ChemBio3DPreviewOptions
Thepreviewwindowdisplaysstructuresyouselectin3D,anddisplaysallstructuresifnoneareselected.ChemBio
3DPreviewworksonlyforchemicalstructures.
Toview,navigatetoView>ShowChemBio3DHotlinkWindow.Forexample:
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Withthepreviewwindowopen,youcanchangethestructure’sappearance,ineitherthedocumentwindow,orthepre-
viewwindow.
IntheDocumentWindow
Withthepreviewwindowopen,youcanstillchangeyourdrawinginthedocumentwindow.Thepreviewwindow
updatestoreflectthechanges.
InChemBio3DPreview
Thepreviewwindowoffersseveraloptionstoviewstructures.
Figure11.4:A)LaunchChem3D;B)Displaymode;C)Select;D)Translate;E)Rotate;F)Zoom;G)Spin;H)Rock.
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LaunchChem3D.ThestructurewillappearinChemBio3Dasamodelthatyoucanedit.
DisplayMode.Choosedisplayoptionsforthemodel:wireframe,stick,ball&stick,cylindricalbonds,andspace
filling.
Select.Selectthestructureorpartsofit.
Translate.Movethestructure.
Rotate.Rotatethestructureinthreedimensions(theimagerotatesonlyintheChemBio3DPreview).
Zoom.Enlargeorreducetheapparentsizeofthestructure.
Spin.Rotatethestructurehorizontallyinonedirection.
Rock.Rotatethestructurehorizontallybackandforth.
ReturningtotheDocumentWindow
ToexittheChemBio3DPreview,closethepreviewwindow.
Toeditthe3Dmodel:
1. Double-clickthe3Dstructure.ChemBio3Dopens.
2. EditthestructureandcloseChemBio3D.
TheeditedstructureappearsintheChemBioDrawdocumentwindow.
TLC
TheTLC (ThinLayerChromatography)Tool letsyoudepictthinlayerchromatographyplates.Thetoolcreatesarect-
angularplatewithanoriginline,solventfront,andoneormorelanes.Thelanescanbepopulatedwithspotsofdif-
ferentR
f
,size,shape,orcolor.
TocreateaTLCplate:
1. SelecttheTLCtoolfromtheChromatographytoolbar.
2. Draginanydirectionfromthepointoforigin.Thewidthoftheplatedeterminesthenumberoflanes.
Youcanmodifytheplateasfollows:
Ifyouwantto
Then
Changetheheightorwidthoftheplate.
Dragaborderorcorner.
Movetheoriginorsolventfront.
Clickanddragtheoriginorsolventfrontline.
Showorhidetheorigin,solventfront,borders,or
sideticks.
Right-clickintheplateandselecttheappropriate
action.
UsetheTransparentoptiontooverlaytheTLCplateon
ascannedplate.
Changetheorderoflanes.
Dragtheoriginticktothenewlocation.
Add,delete,orduplicatealane.
1. Positionthecursoronthelanetodeleteorduplicate
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Ifyouwantto
Then
(orbetweenlanestoadd).
2. Right-click in theplate.
3. Selecttheappropriateaction.
4. (Optional)Todeletealane,clickonitwiththeEraser
tool.
Moveaspot.
Dragthespot.TheR
f
displaysasyoudrag.
Duplicateaspot.
<CTRL>+dragthespottoadifferentlane.
Deleteaspot.
ClickthespotwiththeErasertool.Ifyoueraseallspots
inalane,thelaneisdeleted.
DisplayorsettheR
f
foraspot;addacustom
spot..
1. Right-click onaspot.
2. PointtoTLCSpots,andtaketheappropriateaction.
3. TodisplayR
f
forallspots,right-click intheplate
andselectShowRffromtheTLCSpotssubmenu.
Changethestyleorcolorofaspot.
1. Right-click
aspot
.
.
2. Choosethestyleorcolor.
Note:Keepingallstylesuncheckedcreatesahollow
spot.
3. Tochangethestyleforallspots,right-click inthe
plateandchoosethestylefromtheTLCSpotssub-
menu.
Enlargeor“smear”aspot.
<Shift>+dragthespot.Whenyoupositionthecursor
onaspotandpress<Shift>,thecursorassumesoneof
threeshapes,dependingonhowitispositioned:
Crossarrows,usedtoenlargeaspot
Horizontalarrow,usedtowidenaspot
Verticalarrow,usedtoelongateaspotorcreatea
crescent
RfDisplay
Right-clickaspotandselectShowRftoindicatethespot’sretentionvalue.Bydefault,thevalueofR
f
issettotwo
decimalplaces.
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MovingtheTag
EitherclickanddragthetagusingaselectiontoolorRight-click
thetagandchoose
Position.
Editthevaluesin
the
PositionIndicatorsbox.
EditingtheRfValue
SelectthetagwiththeTexttoolandeditthevalue.
IfyouchangetheR
f
thespotwillmovetothenewpositionindicated.
IfyouedittheR
f
tohavedifferentprecision,thatprecisionwillbepreserved.
ResizingSpots
Youcanresizespotsbyholdingdownthe<Shift>keywhilepointingatanedgeofthespot.Dragtheleftorrightsides
ofthespottoadjustthewidthonly.Dragfromthetoptoadjusttheheight.Dragfromthebottomtoadjustthetail.Drag
fromanyoftheotherfourcornerstoscaleallthreevalues.
CustomizingSpots
TheTLCtoolcancreatethemostcommonspotshapes.Othertypesofspots,suchassmears,canbereproducedas
customspots.TheSetCustomSpotcommandletsyouinsertagraphicfileforaspot.Typically,thesefileswould
beproducedbyscanningaTLCplateandsavingthespotsinalibraryofspotshapes.
Gelelectrophoresistool
GelElectrophoresistoolisavailableintheChromatographytoolbarandfunctionsmuchliketheTLCtool.Itconsists
ofaplatecontainingseverallaneswithoneormorebands.Thebandscanberesizedandmovedalongthelane.For
example,considerthefigurebelow:
Youcanperformthefollowingactiononaplate:
Option
Action
Showscale.
Ascalebarappearsontherightoftheplate.Bydefault,theunitis
displayedinkDa.HoweveryoucanchangeittoLog(Mass),
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