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1. TheLipinskiruleoffive.
2. TheGhosemodifications
3. TheCongreveRule-of-Three.
Lipinskiruleoffive
TheLipinskiruleusesfivecriteriatodeterminewhetherasubstanceisdruglike.Thesubstancemusthave:
FiveorfewerH-bonddonors.
TenorfewerH-bondacceptors.
Amolecularweightunder500daltons.
LogPlowerthan5.
Fewerthantwoviolationsoftheabovefourrules.
TodeterminewhetherthesubstancemeetstheLipinskirulerequirement:
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
TheGhosemodificationsusethesecriterias:
Atomcountbetween20and70.
Molarrefractivitybetween40and130.
Amolecularweightbetween160and480daltons.
LogPintherange-0.4to+5.6.
Fewerthantwoviolationsoftheabovefourrules.
TodeterminewhetherthesubstancemeetstheGhosemodificationrequirement:
1. Calculatethevalueofeachofthesefunctions:
CHEM.NUM.ATOMS()
CHEMPROPPRO.MOL.REFRACTIVITY()
CHEM.MOLWEIGHT()
CHEMPROPPRO.LOGP()
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2. VerifythatthevaluereturnedbythefunctionsmeetstheGhosemodificationcriteria.Forexample,ifthevalue
returnedbythefunctionCHEMPROPPRO.LOGP()forthatstructureiswithintherange-0.4to+5.6,itsatisfies
Ghosemodification’sfourthcriteria.
3. Calculatethenumberofcriteriasatisfied.Ifthenumberofviolationsislessthantwo,thentheGhosemodifications
requirementissatisfied.
Congreveruleofthree
The"CongreveRuleofThree"usesthesecriterias:
ThreeorfewerH-bonddonors.
ThreeorfewerH-bondacceptors.
Amolecularweightunder300daltons.
LogPlowerthan3.
Fewerthantwoviolationsoftheabovefourrules.
TodetermineifthesubstancemeetstheCongreveRule-of-Threerequirement:
1. Calculatethevalueofeachofthesefunctions:
CHEM.NUM.HBDONORS()
CHEM.NUM.HBACCEPTORS()
CHEM.MOLWEIGHT()
CHEMPROPPRO.LOGP()
2. VerifythatthevaluereturnedbythefunctionsmeetstheCongreveRule-of-Threecriteria.Forexample,iftheifthe
functionCHEMPROPPRO.LOGP()returnsavalueforthestructurethatis<3,itsatisfiesCongreveRule-of-
Three’sfourthcriteria.
3. Calculatethenumberofcriteriasatisfied.Ifthenumberofviolationsislessthantwo,thentheCongreveRule-of-
Threeissatisfied.
ChemicalProperties
ChemicalpropertypredictionisanimportantfeaturethatChemBioOfficeapplicationssupport.Itenablesyoutocal-
culatevaluesforawiderangeofmethodologies;forexample,topologicaldescriptorssuchastheWeinerindexand
Balabanindex,thermodynamicdescriptorssuchassolubility,meltingandboilingpoints,andpartitioncoefficients
suchasCLogP,propertiesrelatedtothethree-dimensionalshapeandvolumeofachemicalsuchastheConnollysur-
faceareaandvolume.Intotalyoucancalculatemorethan100chemicalpropertiesforagivenstructure.
Foralistofpropertiesavailableinanyspecificapplications,clicktherespectivelinkbelow.Formoreinformationon
thepropertiesavailableinanyspecificapplications,seetherespectiveonlinehelpavailableorvisitthePerkinElmer
Informatics
Web
site
.
"PropertypredictionsinChemDraw/Excel"onpage203.
"PropertyPredictionsinChemBioDraw"onpage158.
"PropertyPredictionsinChem3D"onpage163.
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PropertypredictionsinChemDraw/Excel
ChemDraw/Excelincludesavarietyoffunctionsforreportingpropertiesforagivenstructure.Eachpropertyiscal-
culatedusingthe“bestavailable”method.
Toviewthepropertiesforagivenstructure:
1. Selectthestructurecell.
2. Right-clickthecellandselectStructure>Propertiesfromthecontext-menu.ThePropertiesdialogboxdisplaying
variouspropertiesanditsvaluesappears.
Thepropertiesinclude:
B
F
MOLECULAR_NETWORKS_
LOGP
S
Balabanindex
Formalcharge
MOLECULAR_NETWORKS_
LOGS
Shapeattribute
Boilingpoint
Freezingpoint
MOLECULAR_NETWORKS_PKa
Shapecoefficient
C
G
Molecularformula
SumOfdegrees
Clustercount
Gibbsfreeenergy
Molecularweight
Sumofvalencedegrees
Connollyaccessiblearea
H
N
T
Connollymolecularsurfacearea
Heatofformation
Numrotatablebonds
Topologicaldiameter
Connollysolventaccessiblesur-
facearea
Henry’sLawconstant
O
Totalconnectivity
Connollysolventexcludedvolume
I
Ovality
TotalValenceCon-
nectivity
Criticalpressure
Idealgasthermalcapacity
P
V
Criticaltemperature
M
Polarsurfacearea
Vaporpressure
Criticalvolume
Mass
PrincipalmomentOfinertia
W
E
Meltingpoint
R
Watersolubility
Exactmass
Molarrefractivity
Radius
Wienerindex
Aboutmolecularnetworks
*MOSES.pKa,MOSES.logSandMOSES.logPforpredictingaciddissociationconstants,aqueouessolubilityand
octanol/waterdistributioncoefficientsofchemicalcompoundsarecomputationalcalculatormodulesbasedon
MolecularNetworks'chemoinformaticsplatformMOSES.MOSESisdeveloped,maintainedandownedbyMolecular
NetworksGmbH,Erlangen,Germany.Forfurtherinformationpleasevisitwww.molecular-
networks.com/moses
.All
rightsreserved.MolecularNetworksGmbH,Erlangen,Germany(www.molecular-
networks.com
).
Balabanindex
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Where:
qisthenumberofedgesinthemoleculargraph.
=(q-n+1)isthecyclomaticnumberofmoleculargraph.
nisthenumberofatomsinthemoleculargraph.
S
i
isthesumofallentriesinthei
th
row(orcolumn)ofthetopologicaldistancematrixofthemolecule.Thedistance
matrixstorestheshortestpathbetweenallpairsofatoms.
Boilingpoint
TheboilingpointisreportinKelvin.
Asolutionboilsataslightlyhighertemperaturethanthepuresolvent.Thechangeinboilingpointiscalculatedusing
theformula:
WhereK
b
isthemolalboilingpointconstant,mistheconcentrationofthesoluteexpressedasmolality,and
D
T
b
isthe
changeintemperature.
Clustercount
Isthenumberofpathsofagivenlengthinthedistancematrix.
Connollyaccessiblearea
Thisisthelocusofthecenterofasphericalprobe(representingthesolvent)asitisrolledoverthemolecularmodel.
Connollymolecularsurfacearea
Thecontactsurfacecreatedwhenasphericalprobe(representingthesolvent)isrolledoverthemolecularmodel.
UnitsAngstroms
2
.
Connollysolventaccessiblesurfacearea
Thelocusofthecenterofasphericalprobe(representingthesolvent)asitisrolledoverthemolecularmodel.Units
Angstroms
2
.
Connollysolventexcludedvolume
Thisisthevolumeofspaceboundedbythesolventaccessiblemolecularsurface.
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Criticalpressure
Reportedinbars,thisistheleastappliedpressurerequiredatthecriticaltemperaturetoliquefyagas.
Criticaltemperature
ReportedinKelvin,thisisthetemperatureabovewhichagascannotbeliquefied,regardlessofthepressureapplied.
Criticalvolume
Reportedincm
3
/mol,thisisthevolumeoccupiedbyonemoleofasubstanceatthecriticaltemperatureandpres-
sure.
Exactmass
Thisisthesumofthemassesoftheindividualisotopesinthemolecule.Forexample,theexactmassofwatercon-
tainingtwohydrogen-1(1H)andoneoxygen-16(16O)is1.0078+1.0078+15.9994=18.0106.Theexactmassof
heavywater,containingtwohydrogen-2(deuteriumor2H)andoneoxygen-16(16O)is2.014+2.014+15.9994=
20.027.
Formalcharge
Thisisthechargeassignedtoanatominamolecule,assumingthatelectronsinachemicalbondaresharedequally
betweenatoms,regardlessofrelativeelectronegativity.
Theformalchargeofanyatominamoleculecanbecalculatedusingtheformula:
FC=V-N-B/2
Where‘V’isthenumberofvalenceelectronsoftheatominisolation(atomingroundstate);‘N’isthenumberofnon-
bondingelectronsonthisatominthemolecule;and‘B’isthetotalnumberofelectronssharedincovalentbondswith
otheratomsinthemolecule.
Freezingpoint
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: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.
Idealgasthermalcapacity
Thethermalcapacityatconstantvolumeofanidealgasis:
Where:
c
V
isaconstantdependentontemperature
Uistheinternalenergy
Tistheabsolutetemperature
Visthevolume
nistheamountofsubstanceofthegas
Risthegasconstant(8.314J·K−1mol-1inSIunits)
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Nisthenumberofgasparticles
k
B
istheBoltzmannconstant(1.381×10−23J·K−1inSIunits)
Thethermalcapacityatconstantpressureofanidealgasis:
Where‘H’istheenthalpyofthegas,calculatedas:H=U+pV.
MOLECULAR_NETWORKS_LOGP
Thepartitioncoefficientisaratioofconcentrationsofun-ionizedcompoundbetweentwosolutions.Tomeasurethe
partitioncoefficientofionizablesolutes,thepHoftheaqueousphaseisadjustedsothatthepredominantformofthe
compoundisun-ionized.Thelogarithmoftheratiooftheconcentrationsoftheun-ionizedsoluteinthesolventsis
calledLogP.
Normally,oneofthesolventschoseniswater;thesecondishydrophobic,suchasoctanol.
MOLECULAR_NETWORKS_LOGS
MOLECULAR_NETWORKS_LogSdeterminesthesolubilityofasubstance,measuredinmol/liter.Theaqueoussol-
ubilityofacompoundisknowntosignificantlyaffectabsorptionanddistributioncharacteristicsofthatcompound.
MOLECULAR_NETWORKS_PKa
MOLECULAR_NETWORKS_PKaisthenegativelogoftheaciddissociationconstantKa.Itdescribesthetendency
ofcompoundsorionstodissociateinsolution.
Mass
Thisisthemassofonemoleculeofasubstance,relativetotheunifiedatomicmassunitu(equalto1/12themassof
oneatomof12C).Alsocalledmolecularmass.
Meltingpoint
Isthetemperatureatwhichasolidbecomesaliquidatstandardatmosphericpressure.Atthemeltingpoint,thesolid
andliquidphaseexistinequilibrium.Theformulatocalculatemeltingpointis:
Where‘T’isthetemperatureatthemeltingpoint,‘
D
S’isthechangeinentropyofmelting,and‘
D
H’isthechangein
enthalpyofmelting.
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Molarrefractivity
Isameasureofthetotalpolarizabilityofonemoleofasubstance.Itisdependentonthetemperature,indexofrefrac-
tion,andpressure.
Themolarrefractivity,‘A’isexpressedas:
Where‘N
A
’istheAvogadroconstantand
a
isthemeanpolarizability.
Molecularformula
Thisisthemolecularformulaofthecompound.
Molecularweight
Thisisthesumoftheatomicweightsofallatomsinamolecule.
Numrotatablebonds
Isthenumberofrotatablebondsinamolecule.Arotatablebondisdefinedasanacyclicbonddrawnasasinglebond
(amideC-Nbonds,O=C--N,arerotatable)wheretheatomoneachendhasatleastoneothernon-hydrogensub-
stituent.Thistopologicalparameterisameasureofmolecularflexibility.Unsaturatedbonds,andsinglebondscon-
nectedtohydrogensorterminalatoms,singlebondsofamides,sulphonamides,andthoseconnectingtwohindered
aromaticrings(havingatleastthreeorthosubstituents)areconsiderednon-rotatable.
Ovality
Thisreferstoameasureofhowtheshapeofamoleculeapproachesasphere(atoneextreme)oracigarshape(atthe
other).Ovalityisdescribedbyaratioofvolumetoarea:
Where‘A’isarea,‘V’isVolume,and‘O’isOvality.
Theovalityofaheliumatomis1.0andHC
24
H(12triplebonds)is~1.7(equivalentto1.7).
Polarsurfacearea
ThePolarSurfaceArea(PSA)isdefinedasthesurfacesumoverallpolaratoms
PrincipalmomentOfinertia
Thisreferstotheprincipalmomentsofinertiaabouttheprincipalaxesofamolecule.Themomentsofinertiaarecom-
putedforaseriesofstraightlinesthroughthecenterofmassusingtheformula:
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DistancesareestablishedalongeachlineproportionaltothereciprocalofthesquarerootofIoneithersideofthe
centerofmass.Thelocusofthesedistancesformsanellipsoidalsurface.Theprincipalmomentsareassociated
withtheprincipalaxesoftheellipsoid.
Ifallthreemomentsareequal,themoleculeisconsideredtobeasymmetricaltop.Ifnomomentsareequal,the
moleculeisconsideredtobeanasymmetricaltop.
Radius
Theeccentricityofanatomisthelargestvalueinitsrow(orcolumn)ofthedistancematrix,andrepresentshowfar
awayfromthemolecularcenteritresides.
Thediameter(D)isthemaximumsuchvalueforallatoms,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.
Shapeattribute
Theshapeattribute(kappa)measuresthebranchingofamolecule,andisscaledsoastofallbetweentheminimum
andmaximumvaluespossibleforthegivenorder.Thefirst-ordershapeattributecountsthenumberofone-bond
paths.Thesecond-orderattributecountsthenumberoftwo-bondpaths,andsoon.Thefirstthreeorders(1..3)are
available.
Shapecoefficient
Theshapecoefficient,Iisgivenby:
Wherethediameter(D)isthemaximumsuchvalueforallatoms,andisheldbythemostoutlyingatom(s).Theradius
(R)istheminimumsuchvalue,andisheldbythemostcentralatom(s).
ExamplesvaluesforD:methane=0;ethane=1;propane=2;n-butane=3.
ExamplevaluesforR:Radius:methane=0;ethane=1;propane=1;n-butane=2.
SumOfdegrees
Isthesumofdegreesofeveryatom.Anatom’sdegreeisthenumberofnonhydrogenatomstowhichitisbonded.
Sumofvalencedegrees
Isthesumofdegreesofeveryatom.Anatom’svalencedegreeisequaltothesumofitsadjacentbonds'orders,
includinghydrogens.
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Topologicaldiameter
Isthelongestdimensionofamolecule.
Totalconnectivity
Istheconnectivityconsideredoveralltheheteroatoms.
TotalValenceConnectivity
Isthevalenceconnectivityconsideredoveralltheheteroatoms.
Vaporpressure
Isthepressureexertedbyavaporinequilibriumwithitssolidorliquidphase.Vaporpressuremeasuresthecon-
centrationofsolventmoleculesinthegasphase.
VaporpressurecanbecalculatedusingRaoult’slaw.Theformulatocalculatevaporpressureis:
Where‘p’isvaporpressure,‘i’isacomponentindex,and‘
c
’isamolefraction.
Watersolubility
Isthemaximumamountofasubstancethatcanbedissolvedinwateratequilibriumatagiventemperatureandpres-
sure.Watersolubilityismeasuredinmg/L.
Wienerindex
Providesmeasureofbranchingdefinedas:
WhereD
ij
aretheoff-diagonalelementsofthedistancematrix.
GeneralPreferences
FromtheGeneralPreferencesdialog,youcancustomizeChemDrawforExcelforyourspecificworkneeds.
TocustomizeChemDrawforExcel:
1. NavigatetoChemOffice>Options>Preference.TheGeneralPreferencesdialogappears.
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