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1. Computational
chemistry
background
2. UsingGaussian(a) input(b)output
IntroductiontoGaussianComputationalchemistryusingtheArcticRegion
SupercomputingCenterinstallationofGaussian03
JohnKellerDepartmentofChemistry&Biochemistry
UniversityofAlaskaFairbanks
IntroductiontoGaussianComputationalchemistryusingtheArcticRegion
SupercomputingCenterinstallationofGaussian03
JohnKellerDepartmentofChemistry&Biochemistry
UniversityofAlaskaFairbanks
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Everyattempttoemploymathematicalmethodsinthestudyofchemicalquestionsmustbeconsideredprofoundlyirrationalandcontraryto
the
spirit
of
chemistry.
AugusteCompte,Frenchphilosopher,1830
Backintheday,itwasnotclearthatmathematicaltreatmentswouldeverbeusefulinchemistry!
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ChemometricsandIntelligentLaboratorySystems
ComputationalandTheoreticalPolymerScience
ElectronicJournalofTheoreticalChemistry
International
Journal
of
Quantum
ChemistryJournalofChemicalInformationandComputerSciences
JournalofChemicalTheoryandComputation
JournalofChemometrics
JournalofComputationalChemistry
JournalofComputerAidedChemistry
Journal
of
Mathematical
ChemistryJournalofMolecularGraphicsandModelling
JournalofMolecularModeling
JournalofMolecularStructure:THEOCHEM
JournaloftheChemicalComputingGroup
JournalofTheoreticalandComputationalChemistry
Macromolecular
Theory
and
SimulationsPerspectivesinDrugDiscoveryandDesign
ProteinsStructure,Function,andGenetics
StructuralChemistry
TheoreticalChemistryAccounts:Theory,Computation,andModeling(TheoreticalChimica
Acta)
Today computational chemistry is a standard tool of science. For
example, there are now >20 journals devoted to the subject.
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Gaussian03Gaussianutilities(e.g.,fmchk)GaussView04(UNIX)
GaussView03(UAsitelicense)HyperChemv8
KerberosFTP
Telnet
Iceberg
Midnight
UnivofAlaskaFairbanks/ARSCResources
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CapabilitiesofGaussian(similartootherlarge
scalecomputationalchemistrypackages):
Determinemoststable(optimum)moleculargeometryandenergy.(UsedtocalculateEandKeq.)*
Defineapotentialenergysurfacebysteppingthrougharangeofvaluesforageometrycoordinate,suchasbonddistanceortorsionangle
Predict IR,Raman,UV,NMR,andotherspectra
Optimizetransitionstates
Solvatemoleculesusingthepolarizedcontinuum(PCM) orothermodels.
Specialtoolsforoptimizingtransitionmetalcomplexes,andothermoleculescontaininglargeatoms.
ONIOM techniquefordefininglayerswithinonemoleculewherehigherandloweraccuracymethodscanbeapplied.
Modelsurfacesusinga2Dperiodicboundarycondition(PBC)method,orcrystalsusing3DPBC.
*JWK has used.
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GaussianandHyperChemResources
TheGaussianmanualisonlineathttp://www.gaussian.com/g_ur/g03mantop.htm
ARSCissuesrelatingtouseraccounts,connections,Kerberosetc arebest
answeredbyARSCconsultants.Emailatconsult@arsc.eduortelephone4508602
TechnicalquestionsonrunningGaussianarebestdirectedtoGaussianconsultantsat [email protected]
CurrentusersincludingJ.Keller([email protected])mayalsobeabletomakeconstructivesuggestions.
ThefullmanualofHyperChemmethodsandtheoryinpdf formatisinstalled
oneachcomputerinthechemistrycomputerlab.
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Computationalchemistrybackground
Basicallytwowaystocalculatemolecularstructure:
1. Molecularmechanics
2. Quantummechanics
BasissetsFourdifferentmethodsGeometryoptimizationComparingdifferentmethods&basissetswithanexample
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Molecularmechanics
Eachbondandbondangleisassignedapotentialfunctionbasedonexperimentalbonddistancesandangles.Theseareaddedup
andthenminimizedasthegeometryisadjusted.
Thesetofpotentialfunctionsiscalledaforcefield.
There
are
3
force
fields
available
in
Gaussian:
AMBER,
DREIDING,UFF.
Fast.Usedmainlyforlargemolecules.AMBERisthestandardforcefieldusedinproteinoptimizationandmoleculardynamics.
Majorlimitations:Noelectrondensity,vibrations,orotherspectroscopicresults.Majorlimitations:Noelectrondensity,vibrations,orotherspectroscopicresults.
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Quantum
mechanicsBasedontheSchrdingerEquation.
H=E
Hisenergyoperatorwhichdescribesthekineticandpotentialenergyofanelectroninfieldof
nucleiandotherelectrons.
Usuallythenucleiareassumedtobestationary.
(Electronsmoveat~c/3.
Nucleimoveat~c/25,000.)
isf(x,y,z)Asetofspatialdistributionsdescribing theprobabilityoffindingelectrons(orbitals).
istheproductofnspatialfunctions(s),oneforeachofnelectronsintheatomormolecule.
AsingleatomhasAOs.MoleculeshaveMOs.
E=sumoftheenergiesoftheorbitals,whichmaycontain1,oratmost2,electrons.
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Gaussianapproximatesorbitalshapesandorbitalenergiesofagivenmoleculargeometryusingamodel chemistryconsistingoftwoparts:
abasis set andamethod.
Gaussianapproximatesorbitalshapesandorbitalenergiesofagivenmoleculargeometryusingamodel chemistryconsistingoftwoparts:
abasis set andamethod.
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Molecularorbitals(MOs)areapproximatedaslinearcombinationsofbasisfunctions(thebasisset),which
mathematicallylooklikes,p,ordatomicorbitals.
Eachatomisassignedseveral(ormany)basisfunctions.
Inturn,eachbasissetfunctioniscomprisedofanumberofgaussianfunctionscalledprimitives.
Calculationsusinglargebasissetsaremoreaccuratebecausetheyarelessrestrictiveonthelocationoftheelectrons.
Suchcalculationsarealsomoreexpensivebecausetheyrequirecomputingmoreintegrals.
Calculationsusinglargebasissetsaremoreaccuratebecausetheyarelessrestrictiveonthelocationoftheelectrons.
Suchcalculationsarealsomoreexpensivebecausetheyrequirecomputingmoreintegrals.
Basis
Sets
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BasisSets,continued
SplitvalencebasissetsweredevelopedbyJohnPople,1998NobelPrizewinnerandfounderofGaussian,Inc.
Example: 631G basisset
The basissetnomenclaturedescribeshowthebasisfunctionsareconstructedfromthegaussianprimitives(thecontractionscheme.)
Thefirstnumberindicatesthe#ofgaussianprimitivesusedforcore(inner)electrons.
Thenumber ofdigits(2here)indicates
how
many
sub
orbitals
each
valence
atomicorbitalissplitinto.
Thevalues tellhowmanygaussianprimitivesmakeup
eachsuborbital.
A p-orbital in
the 6-31G
basis set is
split intoinnerand
outerp-type
sub-orbitals.
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BasisSets:addingpolarization anddiffuse basisfunctions
631G
Basisset
#andtypeofbasisfunctions
EachHatomgets: EachC,O,orFatomgets:
2(1s,1s) 9(1s,2s,2s,3p,3p)
631G(d) or631G*
631G(d,p) or631G**
631G+(d,p) or631+G**
631G++(d,p) or631++G**
2(1s,1s) 15(1s,2s,2s,3p,3p,6d)
5(1s,1s,3p) 15(1s,2s,2s,3p,3p,6d)
5(1s,1s,3p) 19(1s,2s,2s,2s+,3p,3p,3p+,6d)
6(1s,1s,1s+,3p) 19(1s,2s,2s,2s+,3p,3p,3p+,6d)
Diffuse functions extend further out from the nucleus, and are necessary for
modeling non-bonding or weakly-bonding systems.
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HartreeFock(HF) methodElectroncorrelationisignored.Themanyelectronwavefunction()isestimatedbytheselfconsistentfield(SCF)method.
0 0 0(1) (2) (3)o =
1 1 1 1(1) (2) (3) =
Then,whilealltheotherMOfunctionsareheldconstant(thefield),each isvariedsoastominimizethetotalenergy.Thisisthevariationalmethod. Thisgivesanew (1):
Thisprocessisrepeateduntilthechangeinenergyisclosetozero.Theseorbitals thencomprisetheselfconsistentfield.
Thisstartswithaninitialguessof (o),whichistheproductoftheinitialestimatesofthemolecularorbitals.
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MllerPlesset(MP)
Electroncorrelationisaccountedforallowingoneormoreelectronsto
occupy
higher
energy,
unoccupied
(anti
bonding)
MOs.
Thisresultsinanenergycorrectionthatlowersthetotalenergybecauseitlowerstheelectronelectronrepulsionenergy.
ThecommonlyusedMP2methodactuallyconsiderstheeffectof2electronsoccupyingantibondingorbitals.
MP2
is
more
expensive
than
HF
because
more
configurationsmustbecalculated.MP2
is
more
expensive
than
HF
because
more
configurationsmustbecalculated.
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DensityFunctionalTheory
Developed by Walter Kohn of UC-Santa Barbara and others.
Kohn shared the 1998 Nobel Prize with John Pople.
Gives nearly the same accuracy as MP2, but with the (lower)
computational cost of Hartree-Fock SCF.
Afunctiontransformsanumberintoanothernumber.
Afunctionaltransformsafunctionintoanumber.
ComputationalChemistry,E.Lewars,2003,Kluwers,p.388.
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DensityFunctionalTheory
HohenbergKohnTheorem:
Energyofamolecule= F
[electrondensity], whereelectrondensity=f(x,y,z))
HohenbergKohnTheorem:
Energyofamolecule
= F
[electrondensity], whereelectrondensity=f(x,y,z))
Thissaysthatthereexistsafunctionalthatwillcalculatemolecularenergyfromelectrondensity.
But
it
does
not
say
what
the
functional
is!DFTmethodsaccountforelectroncorrelationbyestimatingtheinteractionofanelectronwiththetotalelectrondensity.
DFTorbitals areformedfrombasisfunctionslikethoseusedinSCForMP2.
MostpopularDFTmethodisB3LYP.(Becke3Parametermethodforcalculatingthatpartofthemolecularenergyduetooverlappingorbitals,plustheLeeYangParrmethodofaccountingforcorrelation.)
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GeometryOptimization
InGaussian/GaussView,optimizationstepsare
visualized
by
querying
the
.log
output
file.
Geometry(dist/angles)
Energy
Gradient 0kcal/mol
PotentialEnergySurface
AMBERoptimizationstartingwithanonoptimalconformationoftheaspirinmolecule.VisualizedinrealtimewithHyperChem.
Optimizationadjustsgeometryto
decreasethetotalenergyuntilitreachesthenearestminimum.
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UsingdifferentmodelchemistriestoestimateOOdistancesintheformicacidtrifluoroacetic acidbimolecule.*
2.55
2.60
2.65
2.70
2.75
2.80
2.85
2.90
HF/3-21G
HF/6-31G
HF/D95
**
HF/6-31+G
(d)
HF/6-311G(d
,p)
HF/6-31++G(d
,p)
MP2/6-31G
MP2/6-31G(d)
MP2(Full)/6-31G
(d)
MP2/6-31(d,p
)
MP2/6-311(d,p
)
MP2/6-31++G(d
,p)
BLYP/6-31G(d)
BLYP/6-31G(d
,p)
B3LYP/6-31G(d)
B3LYP/6-31G(d
,p)
B3LYP/6-31+G(d
,p)
B3LYP/6-31++G(d
,p)
B3LYP/AUG-cc-pVDZ
B3LYP/AUG-cc-pVTZ
Exp(Martinach
e)
Exp(Costain)
Model Chemistry
O-OD
ist()
F O
O HFF
H O
H
O
*J. W. Keller,J. Physical Chemistry A 108, 4610-4618(2004) John W. Keller 2008
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Using Gaussian and GaussView
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GaussView:Buildmolecule
(oropenxx.mol).Createxx.com inputfile
HyperChem:Buildandoptimizemolecule,andsave
asxx.mol
MSWordorothertexteditor:Formatxx.com asUSASCII,LFOnly.Openxx.ll script.Editandsavein sameformat.
Filezilla:Uploadxx.com andxx.ll to/wrkdir/username/oniceberg.arsc.edu
Kerberos5:Obtainkerberos ticket
PuTTY:Submitxx.ll job
CreateandsubmitaGaussianinputfile
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Gaussianinputfile (AA631ppGssB3LYPOptFreq.com)
PBSscriptfile (AA631ppGssB3LYPOptFreq.cmd)
Suggestion:Uselongfilenamestokeeptrackofdifferentcomputationaljobs.
MoleculeBasissetMethodJobtype.com
Aceticacid
631++G**basisset
B3LYPmethod(themostcommonlyusedDFTmethod)
OptimizationandVibrational frequencycalculation John W. Keller 2008
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Gaussianinputfile(xx.com)canbetypedinmanually,orcreatedbyGaussView
OptionalLink0 linesforjobcontrol:***Names
checkpoint
file
(saves
output)****
SetsamountofsharedmemorySetsnumberofprocessors(noblanklineterminator) Routesection:keywordsdefine
typeofcalculation,method,
basisset,andoptionalsettings.
Blankline
Blankline Titlesection
MoleculespecificationNetcharge
Multiplicity(1 forevenelectronspeciessuchasmolecules;2 foroddelectronspeciessuchasNOmolecule)
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A script file is used to specify job details.
Iceberg uses the Loadleveler job queue software (xx.ll).Midnight uses the PBS job queue software (xx.cmd).
A script must be used for each job.
#!/bin/ksh#PBS -q standard
#PBS -l walltime=1:00:00
#PBS -l select=4:ncpus=4:node_type=4way
#PBS -j oe
# for midnight# standard class
# Change directory to where the script is submitted
cd $PBS_O_WORKDIR
# Set Location of Gaussian
export GAUSS_SCRDIR=$WRKDIRexport g03root=/usr/local/pkg/gaussian/current
. $g03root/g03/bsd/g03.profile
# run the calculation
g03 AA-631ppGssB3LYP-OptFreq.com
This should match the Link0 nproc line
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GaussView:openxx.logViewmolecule(&vibrations)
Filezilla:Downloadxx.log filefrom/wrkdir/username/
Kerberos5:Obtainkerberos ticket
SomeGaussianoutputiscontainedinthexx.log file.
Viewxx.log filedirectly
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Electrostaticpotentialoutputis
contained
in
the
xx.chk file.
Log on to Iceberg
cd / wr kdi r / user name/
l s (to get filename list)set env g03r oot / usr / l ocal / pkg/ gaussi an/ cur r ent
$g03r oot / g03/ f or mchk f i l ename. chk (paste it)
This should create the new file filename.fchk.
Transfer filename.fchk to your machine by FTP.
ThesesurfacesarecalculatedbyGaussView(onlocalorremotemachine)usingaformattedcheckpointfile asinput. Thisfileiscreatedfromthestandardcheckpointfile(xx.chk)bytheGaussianformchk utilityprogram,whichrunsonIcebergorMidnight.
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CalculatingandDisplayinganElectrostaticPotentialSurface
InGaussView,openthexx.fchk file.DoResults,Surface,CubeActions,NewCube,TotalDensity,Coarse,OK.SetIsovalue fornewsurfacetoabout
0.02(unitsofelectrons/3).UnderSurfaceActions,chooseNewMappedSurface,ESP.AdjustcolorscaleMin/Max
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(1)Acube ofelectrondensityiscreated.
(2)Theisosurface iscreatedbyconnectingboxesofequalelectrondensity(0.02e/3
here)
(3)Theelectrostaticpotentialiscalculatedateachpointonthe
electrondensitysurface.Thepotential valuesarepaintedonthesurfaceusingaredtobluescale.
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OneCurrentProject
investigates
the
stability
and
vibrational spectra
of
SO2
formic
acid
complexes.
C OHO
H
S
O
O
COH
O
HSO
O
1) ArethecomplexesstableenoughtoexistinnaturalSO2acidgasmixturessuchasvolcanogases?
2) Canweobservesuchcomplexesinthelaboratory?3) Howimportantarethe StoOdipolarinteractions?
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GaussiancalculationsonthesecomplexeswerecarriedoutbyBronwynHarrod, thenafreshmanchemistrymajor. Shepresentedaposteratthe2007MercuryConferenceonComputationalChemistry .
Sifat Chowdhury,aWestValleyH.S.student,workedonthisprojectasapartofhisAlaskaHighSchoolScienceSymposiumproject.
Students
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Acknowledgements
NationalScienceFoundationforpurchaseofHyperChemandGaussViewlicenses.
UniversityofAlaskaFoundation
ArcticRegionSupercomputingCenterforinstallingGaussian,andprovidingampleamountsofcomputertime.
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TheEnd
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Geometry optimization of aspirin
~4x faster
HyperChemv8 Gaussian03
WinXP/DualCoreCPU Iceberg/2Processors
Method PM3semiempirical PM3semiempirical
Finalgradient(kcal/mol)
0.00029 0.0000092
#Iterations 596 33
Heatofformation(kcal/mole)
145.2472 145.1500
Dipolemoment(Debyes)
4.742 4.7423
Wallclocktime 1min22sec 23sec
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CalculatingandDisplayingMolecularOrbitals
InGaussView,openthexx.fchk file.
DoResults,Surface,CubeActions,NewCube,MolecularOrbital,HOMO,Coarse,OK.
SetIsovalue fornewsurfacetoabout0.02(unitsofelectrons/3).
UnderSurfaceActions,chooseNewSurface,MO
(SurfacestyleissetusingFile,Preferences,Surface,Format.)
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Molecularorbitalschemecanbeviewedusingthe
MolecularOrbitalEditor
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Rotationalconstants(inGHz)aremeasuredbymicrowavespectroscopy
