IntroductiontoGaussian

ComputationalchemistryusingtheArcticRegion
SupercomputingCenterinstallationofGaussian03

JohnKeller
DepartmentofChemistry&Biochemistry
UniversityofAlaskaFairbanks

1. Computationalchemistrybackground
2. UsingGaussian
(a)input
(b)output
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Backintheday,itwasnotclearthatmathematical
treatmentswouldeverbeusefulinchemistry!

Everyattempttoemploymathematicalmethods
inthestudyofchemicalquestionsmustbe
consideredprofoundlyirrationalandcontraryto
thespiritofchemistry.
AugusteCompte,Frenchphilosopher,1830

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Today computational chemistry is a standard tool of science. For

example, there are now >20 journals devoted to the subject.
ChemometricsandIntelligentLaboratorySystems
ComputationalandTheoreticalPolymerScience
ElectronicJournalofTheoreticalChemistry
InternationalJournalofQuantumChemistry
JournalofChemicalInformationandComputerSciences
JournalofChemicalTheoryandComputation
JournalofChemometrics
JournalofComputationalChemistry
JournalofComputerAidedChemistry
JournalofMathematicalChemistry
JournalofMolecularGraphicsandModelling
JournalofMolecularModeling
JournalofMolecularStructure:THEOCHEM
JournaloftheChemicalComputingGroup
JournalofTheoreticalandComputationalChemistry
MacromolecularTheoryandSimulations
PerspectivesinDrugDiscoveryandDesign
ProteinsStructure,Function,andGenetics
StructuralChemistry
TheoreticalChemistryAccounts:Theory,Computation,andModeling(TheoreticalChimica
Acta)

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UnivofAlaskaFairbanks/ARSCResources

Midnight

'

Kerberos
FTP
Telnet

'
Iceberg
Gaussian03
Gaussianutilities(e.g.,fmchk)
GaussView04(UNIX)

GaussView03(UAsitelicense)
HyperChemv8
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CapabilitiesofGaussian(similartootherlarge
scalecomputationalchemistrypackages):
*JWK has used.

Determinemoststable(optimum)moleculargeometryandenergy.
(UsedtocalculateEandKeq.)*
Defineapotentialenergysurface bysteppingthrougharangeofvalues
forageometrycoordinate,suchasbonddistanceortorsionangle
Predict IR,Raman,UV,NMR,andotherspectra
Optimizetransitionstates
Solvatemoleculesusingthepolarizedcontinuum(PCM) orother
models.
Specialtoolsforoptimizingtransitionmetalcomplexes,andother
moleculescontaininglargeatoms.
ONIOM techniquefordefininglayerswithinonemoleculewhere
higherandloweraccuracymethodscanbeapplied.
Modelsurfacesusinga2Dperiodicboundarycondition(PBC)method,
orcrystalsusing3DPBC.
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GaussianandHyperChemResources
TheGaussianmanualisonlineat
http://www.gaussian.com/g_ur/g03mantop.htm
ARSCissuesrelatingtouseraccounts,connections,Kerberosetc arebest
answeredbyARSCconsultants.Emailatconsult@arsc.edu ortelephone
4508602
TechnicalquestionsonrunningGaussianarebestdirectedtoGaussian
consultantsathelp@gaussian.com
CurrentusersincludingJ.Keller(ffjwk@uaf.edu)mayalsobeabletomake
constructivesuggestions.
ThefullmanualofHyperChem methodsandtheoryinpdf formatisinstalled
oneachcomputerinthechemistrycomputerlab.

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Computationalchemistrybackground
Basicallytwowaystocalculatemolecularstructure:
1. Molecularmechanics
2. Quantummechanics
Basissets
Fourdifferentmethods
Geometryoptimization
Comparingdifferentmethods&basissetswithanexample

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Molecularmechanics
Eachbondandbondangleisassignedapotentialfunctionbasedon
experimentalbonddistancesandangles.Theseareaddedup
andthenminimizedasthegeometryisadjusted.
Thesetofpotentialfunctionsiscalledaforcefield.
Thereare3forcefieldsavailableinGaussian:AMBER,DREIDING,
UFF.
Fast.Usedmainlyforlargemolecules.AMBERisthestandardforce
fieldusedinproteinoptimizationandmoleculardynamics.
Majorlimitations:Noelectrondensity,vibrations,orotherspectroscopicresults.
Majorlimitations:Noelectrondensity,vibrations,orotherspectroscopicresults.

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Quantummechanics
BasedontheSchrdingerEquation.

H=E

Hisenergyoperatorwhichdescribesthekinetic
andpotentialenergyofanelectroninfieldof
nucleiandotherelectrons.
Usuallythenuclei areassumedtobestationary.
(Electronsmoveat~c/3.
Nucleimoveat~c/25,000.)

isf(x,y,z)
Asetofspatialdistributions
describingtheprobabilityof
findingelectrons(orbitals).
istheproductofn spatial
functions(s),oneforeachof
n electronsintheatomor
molecule.
AsingleatomhasAOs.
MoleculeshaveMOs.

E=sumoftheenergiesoftheorbitals,which
maycontain1,oratmost2,electrons.
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Gaussian approximatesorbitalshapesand
orbitalenergiesofagivenmoleculargeometry
usingamodel chemistry consistingoftwoparts:
abasis set andamethod.

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BasisSets
Molecularorbitals(MOs)areapproximatedaslinear
combinationsofbasisfunctions(thebasisset),which
mathematicallylooklikes,p,ordatomicorbitals.
Eachatomisassignedseveral(ormany)basisfunctions.
Inturn,eachbasissetfunctioniscomprisedofanumber
ofgaussianfunctionscalledprimitives.
Calculationsusing largebasissets aremoreaccuratebecause
theyarelessrestrictiveonthelocationoftheelectrons.
Suchcalculationsarealsomoreexpensive becausetheyrequire
computingmoreintegrals.
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BasisSets,continued
Splitvalencebasissets weredevelopedbyJohn
Pople,1998NobelPrizewinnerandfounderof
Gaussian,Inc.
Thebasissetnomenclature describeshowthe
basisfunctionsareconstructedfromthegaussian
primitives(thecontractionscheme.)

A p-orbital in
the 6-31G
basis set is
split into
inner and
outer p-type
sub-orbitals.

Example:631Gbasisset
Thenumber ofdigits(2here)indicates
howmanysuborbitalseachvalence
atomicorbital issplitinto.
Thefirstnumberindicatesthe#of
gaussianprimitivesusedforcore
(inner) electrons.
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Thevalues tellhowmany
gaussianprimitivesmakeup
eachsuborbital.

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BasisSets:addingpolarization anddiffuse basisfunctions

#andtypeofbasisfunctions

Basisset

EachHatomgets:

EachC,O,orFatomgets:

631G

2 (1s,1s)

631G(d)or631G*

2 (1s,1s)

15 (1s,2s,2s,3p,3p,6d)

631G(d,p)or631G**

5 (1s,1s,3p)

15 (1s,2s,2s,3p,3p,6d)

631G+(d,p)or631+G**

5 (1s,1s,3p)

19 (1s,2s,2s,2s+,3p,3p,3p+,6d)

9 (1s,2s,2s,3p,3p)

631G++(d,p)or631++G** 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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Methods
Thesediffermainlyaccordingtohow,orif,electron
correlation istreated.
Electroncorrelationisthetendencyofelectronstoavoideach
other,evenwithinthesameorbital.

Fourcommonquantummethods:
Semiempirical

Uses pre-calculated orbital functions for different

kinds of atoms. Fast, but less accurate.

HartreeFock(HF),
MllerPlessetn (MP2),
DensityFunctionalTheory(DFT)
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ab initio methods that require

significant computing power for
accurate results.

14

HartreeFock(HF) method
Electroncorrelationisignored.Themanyelectronwavefunction()isestimated
bytheselfconsistentfield(SCF) method.

Thisstartswithaninitialguess of (o),whichistheproductof
theinitialestimatesofthemolecularorbitals.

o = 0 (1) 0 (2) 0 (3)

Then,whilealltheotherMOfunctionsareheldconstant(thefield),each
isvariedsoastominimizethetotalenergy.Thisisthevariational
method. Thisgivesanew (1):

1 = 1 (1) 1 (2) 1 (3)

Thisprocessisrepeateduntilthechangeinenergyisclosetozero.
Theseorbitals thencomprisetheselfconsistentfield.
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MllerPlesset(MP)
Electroncorrelationisaccountedforallowingoneormoreelectronsto
occupyhigherenergy,unoccupied(antibonding)MOs.
Thisresultsinanenergycorrectionthatlowersthetotalenergy
becauseitlowerstheelectronelectronrepulsionenergy.
ThecommonlyusedMP2 methodactuallyconsiderstheeffectof2
electrons occupyingantibondingorbitals.
MP2ismoreexpensivethanHFbecausemore
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.
Afunction transformsanumber intoanothernumber.

Afunctional transformsafunction intoanumber.

ComputationalChemistry,E.Lewars,2003,Kluwers,p.388.

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DensityFunctionalTheory
HohenbergKohnTheorem:
Energyofamolecule
=F[electrondensity],whereelectrondensity=f(x,y,z))
Thissaysthatthereexists afunctionalthatwillcalculate
molecularenergyfromelectrondensity.
Butitdoesnotsaywhatthefunctionalis!
DFTmethodsaccountforelectroncorrelationbyestimatingtheinteractionofan
electronwiththetotalelectrondensity.
DFTorbitals areformedfrombasisfunctions likethoseusedinSCForMP2.
MostpopularDFTmethodisB3LYP.(Becke 3Parametermethodforcalculatingthat
partofthemolecularenergyduetooverlappingorbitals,plusthe LeeYangParr
methodofaccountingforcorrelation.)
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GeometryOptimization
AMBERoptimizationstartingwithanon
optimalconformationoftheaspirinmolecule.
VisualizedinrealtimewithHyperChem.
Energy

PotentialEnergySurface

Gradient 0kcal/mol

Geometry(dist/angles)
Optimizationadjustsgeometryto
decreasethetotalenergyuntilit
reachesthenearestminimum.

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InGaussian/GaussView, optimizationstepsare
visualizedbyqueryingthe.logoutputfile.

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Model Chemistry

Exp (Costain)

Exp (Martinache)

B3LYP/AUG-cc-pVTZ

B3LYP/AUG-cc-pVDZ

B3LYP/6-31++G(d,p)

2.85

B3LYP/6-31+G(d,p)

2.80

B3LYP/6-31G(d,p)

B3LYP/6-31G(d)

BLYP/6-31G(d,p)

BLYP/6-31G(d)

MP2/6-31++G(d,p)

MP2/6-311(d,p)

MP2/6-31(d,p)

MP2(Full)/6-31G(d)

MP2/6-31G(d)

MP2/6-31G

HF/6-31++G(d,p)

HF/6-311G(d,p)

HF/6-31+G(d)

HF/D95**

HF/6-31G

HF/3-21G

O-O Dist ()

Usingdifferentmodelchemistries toestimateOOdistancesin
theformicacidtrifluoroacetic acidbimolecule.*

2.90

O
H

O
H

O
H

2.75

2.70

2.65

2.60

2.55

*J. W. Keller, J. Physical Chemistry A 108, 4610-4618(2004)

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Using Gaussian and GaussView

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CreateandsubmitaGaussianinputfile
HyperChem:
Buildandoptimize
molecule,andsave
asxx.mol

GaussView:
Buildmolecule
(oropenxx.mol).
Createxx.com inputfile

MS Word orothertexteditor:
Formatxx.com as
USASCII,LFOnly.
Openxx.ll script.Editandsave
insameformat.

PuTTY:
Submitxx.ll job
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Kerberos5:
Obtainkerberos ticket

Filezilla:
Uploadxx.com andxx.ll to
/wrkdir/username/on
iceberg.arsc.edu
22

Suggestion:
Uselongfilenamestokeeptrackofdifferentcomputationaljobs.
MoleculeBasissetMethodJobtype.com
Gaussianinputfile(AA631ppGssB3LYPOptFreq.com)
PBSscriptfile(AA631ppGssB3LYPOptFreq.cmd)
Aceticacid
631++G**basisset
B3LYPmethod(themostcommonlyused
DFTmethod)
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OptimizationandVibrational frequencycalculation
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Gaussianinputfile(xx.com)canbetypedinmanually,or
createdbyGaussView
OptionalLink0 linesforjobcontrol:
***Namescheckpointfile(savesoutput)****
Setsamountofsharedmemory
Setsnumberofprocessors(noblanklineterminator) Routesection:keywordsdefine
typeofcalculation,method,
basisset,andoptionalsettings.
Blankline
Blankline

Titlesection

Netcharge

Moleculespecification
3-18-2008 Multiplicity(1 forevenelectronspeciessuchasmolecules;2 for
oddelectronspeciessuchasNOmolecule)

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John W. Keller 2008

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
This should
#PBS -q standard
#PBS -l walltime=1:00:00
#PBS -l select=4:ncpus=4:node_type=4way
#PBS -j oe

match the Link0 nproc line

# for midnight
# standard class
# Change directory to where the script is submitted
cd $PBS_O_WORKDIR
# Set Location of Gaussian
export GAUSS_SCRDIR=$WRKDIR
export g03root=/usr/local/pkg/gaussian/current
. $g03root/g03/bsd/g03.profile
# run the calculation
g03 AA-631ppGssB3LYP-OptFreq.com
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SomeGaussian outputiscontainedinthexx.log file.

Viewxx.log filedirectly

GaussView:
openxx.log
Viewmolecule(&vibrations)

Kerberos5:
Obtainkerberos ticket
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Filezilla:
Downloadxx.log filefrom
/wrkdir/username/
26

Electrostaticpotentialoutputis
containedinthexx.chk file.
Thesesurfacesarecalculatedby
GaussView(onlocalorremotemachine)
usingaformattedcheckpointfile as
input.Thisfileiscreatedfromthe
standardcheckpointfile(xx.chk)bythe
Gaussianformchk utilityprogram,which
runsonIcebergorMidnight.
Log on to Iceberg
cd /wrkdir/username/
ls
(to get filename list)
setenv g03root /usr/local/pkg/gaussian/current
$g03root/g03/formchk filename.chk
(paste it)
This should create the new file filename.fchk.
Transfer filename.fchk to your machine by FTP.
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CalculatingandDisplayingan
ElectrostaticPotentialSurface
InGaussView,openthexx.fchk file.
DoResults,Surface,CubeActions,
NewCube,TotalDensity,Coarse,OK.
SetIsovalue fornewsurfacetoabout
0.02(unitsofelectrons/3).
UnderSurfaceActions,chooseNew
MappedSurface,ESP.
AdjustcolorscaleMin/Max

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(1)Acube ofelectrondensityiscreated.
(2)Theisosurface iscreatedbyconnecting
boxesofequalelectrondensity(0.02e/3
here)

(3)Theelectrostaticpotentialis
calculatedateachpointonthe
electrondensitysurface.The
potentialvaluesarepainted on
thesurfaceusingaredtoblue
scale.
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OneCurrentProject
investigatesthestabilityandvibrational spectraofSO2formicacidcomplexes.

O
O

O
C

O
O

H
C
O

O
H

1) ArethecomplexesstableenoughtoexistinnaturalSO2acidgasmixtures
suchasvolcanogases?
2) Canweobservesuchcomplexesinthelaboratory?
3) Howimportantarethe StoOdipolarinteractions?

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Students
Gaussiancalculationsonthesecomplexeswerecarriedoutby
BronwynHarrod,thenafreshmanchemistrymajor.Shepresenteda
posteratthe2007MercuryConferenceonComputationalChemistry .
Sifat Chowdhury,aWestValleyH.S.student,workedonthisproject
asapartofhisAlaskaHighSchoolScienceSymposiumproject.

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Acknowledgements
NationalScienceFoundationforpurchaseofHyperChem and
GaussView licenses.
UniversityofAlaskaFoundation
ArcticRegionSupercomputingCenterforinstallingGaussian,and
providingampleamountsofcomputertime.

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TheEnd

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Geometry optimization of aspirin

HyperChemv8

Gaussian03

WinXP/DualCoreCPU

Iceberg/2Processors

PM3semiempirical

PM3semiempirical

0.00029

0.0000092

596

33

145.2472

145.1500

Dipolemoment
(Debyes)

4.742

4.7423

Wallclocktime

1min22sec

23sec

Method
Finalgradient
(kcal/mol)
#Iterations
Heatofformation
(kcal/mole)

~4x faster

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CalculatingandDisplaying
MolecularOrbitals
InGaussView,openthexx.fchk file.
DoResults,Surface,CubeActions,
NewCube,MolecularOrbital,HOMO,
Coarse,OK.
SetIsovalue fornewsurfacetoabout
0.02(unitsofelectrons/3).
UnderSurfaceActions,chooseNew
Surface,MO
(SurfacestyleissetusingFile,
Preferences,Surface,Format.)
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35

Molecularorbitalschemecanbeviewedusingthe
MolecularOrbitalEditor

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36

Rotationalconstants(inGHz)aremeasuredbymicrowavespectroscopy

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