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首页 Introduction to Computational Chemistry (2)

Introduction to Computational Chemistry (2).pdf

Introduction to Computational C…

alex
2011-08-04 0人阅读 举报 0 0 暂无简介

简介:本文档为《Introduction to Computational Chemistry (2)pdf》,可适用于高等教育领域

IntroductiontoComputationalChemistryByBenjaminLynchandPattonFastJune,AfewimportantareasAbinitiocalculationsQuantumdynamicsNanoparticlesBiochemistryAbinitiocalculations•“abinitio”isLatinfor“fromthebeginning”•Webeginwithfundamentalphysicalproperties,andwecalculatehowelectronsandnucleiinteract•MostoftenthisrequiressolvingapproximationstothetimeindependentSchödingerequation•OccasionallyweneedtosolvethetimedependentSchödingerequation(thiswillbecoveredlaterwhenwegettoquantumdynamics)•WhatcanwepredictwithmodernAbInitiomethods–Geometryofamolecule–Dipolemoment–Energyofreaction–Reactionbarrierheight–Vibrationalfrequencies–IRspectra–NMRspectra–Reactionrate–Partitionfunction–Freeenergy–AnyphysicalobservableofasmallmoleculeAbinitiocalculations•Theunderlyingphysicallawsnecessaryforthemathematicaltheoryofalargepartofphysicsandthewholeofchemistryarethuscompletelyknown,andthedifficultyisonlythatthattheexactapplicationoftheselawsleadstoequationsmuchtoocomplicatedtobesolvable–PAMDirac•Thechallengeincomputationalchemistryistosimplifythecalculationenoughtobesolvable,butstillaccurateenoughtopredictthedesiredphysicalquantity•Howaccuratelycanwepredictthosequantities•That’swhereyoucomein…–Thebestcompromiseofaccuracyandcomputationalcostrequiresaskilledcomputationalchemistatthehelm–Thereisanenormoustoolboxoftheoreticalmethodsavailable,anditwilltakeskillandcreativitytosolverealworldproblemsElectronicStructureTheory•Thisiswherewedescribethemotionoftheelectrons–Firstwedecideonamathematicalbasistodescribeourelectronicwavefunction•AsumofatomcenteredGaussianfunctionsisthemostcommonapproach!"=iriiec#$ElectronicStructureTheory•Aplanewavebasissetisacommonchoiceforpredictingpropertiesofacrystal•Otherfunctionscanbeusedtodescribethewavefunction,howevermostotherformshaveseverelimitations!=iiic)sin("#$!"=iriiec#$Choosingabasisset•Largebasissetshavemorefreedomtoproperlydescribetheelectronicstateofthesystem•Largebasissetscandrasticallyincreasethecostofacalculation,andoccasionallytheyintroducenewnumericalchallengesElectronicStructureTheory•Leveloftheory–Theleveloftheoryisthesetofapproximationsusedtosimplifythecomplexmotionoftheelectrons•Commonmethods–HF,MP,MP,CISD,CCSD,CCSD(T)ElectronicStructureTheory•Densityfunctionaltheory(DFT)–DFTisanalternativetowavefunctionbasedorexplicitlycorrelatedmethods–Thecorrelationenergyandtheexchangeenergyisexpressedasafunctionaloftheelectrondensity–Thefittingofthefunctionalisoftendonewithempiricaldata–Somedensityfunctionalscanbeconsideredabinitiobecausetheydonotfittoempiricaldata•Commonmethods–BLYP,MPWK,PBEHowcalculationsarerun•Inputfilesdescribethesystem,basisset,andtheleveloftheory•SystemrequirementswillalsosometimesappearintheinputfilesNPROC=MEM=MB#MPG*ThisisaGaussianInputFileOHrHrar=a=Howcalculationsarerun•CommandlineexecutionblynchgmyinputinpmyoutputoutblynchvimyoutputoutHowcalculationsarerun•GUI•GraphicalUserInterfacesaresometimesusefulAfterwehaveanelectronicwavefunction•Afterwehavesolvedforawavefunctionforoursystem,wecanextractanddisplaymanyproperties•TotherightisaplotofamolecularorbitalThesecanbeusedtobetterunderstandthenatureofchemicalbondinginvarioussystemsGeometryoptimization•Oncewehaveatheoryandabasisset,wecanstartpredictingenergies•Wecancalculatethefirstderivativeoftheenergywithrespecttothenuclearcoordinatestodetermineifthesystemisatalocalminimum•Wecancontinuetochangethepositionofthenucleitominimizetheenergy•LocalminimaandsaddlepointsoftencorrespondtoimportantstructuresGeometryoptimization•Afteroptimizingageometry,wecanpredictexperimentalstructuresPotentialEnergySurfaces•ThisisapictureofthepotentialenergyasafunctionofcoordinatesBornOppenheimerApproximation•ThepotentialsurfaceisaBornOppenheimerpotentialssurface,wherethepotentialenergyisafunctionofgeometryMotionofthenucleiisassumedtobeindependentofthemotionoftheelectronsTheseareallStationarypointsTransitionstatetheorycanbeusedtocalculatereactionratesCostofcalculations•Thecostofacalculationwilldeterminehowlargeofasystemcanbesimulated•ThescalingpropertiesofamethodareoftenexpressedasNXwhereNisthenumberofatomsinthesystem(ofthesametype)•HartreeFocktheory(HF)scalesasNDoublingthesizewillincreasethecostbyafactorof•CCSDTQscalesasNDoublingthesizewillincreasethecostbyafactorofPrograms•GAUSSIAN•GAMESS•Molpro•NWCHEM•Columbus•Manyothers•SometimeswecannotaccuratelydescribeasystemwiththeBornOppenheimerapproximation•Themotionofthenucleimaybecoupledtothemotionoftheelectrons•ThefollowingtechniquesarecommonlyappliedtophotochemicalreactionsQuantumDynamics•Somemethodspropagatewavepacketsandswarmsoftrajectoriesareusedtogaininsightintoreactionrates•Thesemethodsareincrediblyexpensive,andarelimitedto~atomsQuantumDynamics•Somelessexpensivealternativeshavealsobeendeveloped•Onetechniquethatcanbeusediscalledsurfacehopping•Apotentialsurfaceismappedoutfor(ormore)surfaceswhichhaveasmallseparationinenergy•Theseproblemscannotbesolvedwith“blackbox”software•Mostsoftwareisdevelopedbytheresearchgroupswhouseit•Fittingthesurfacesrequiresoptimizinghundredsofparameters,sometimeswithgeneticalgorithmsNanoparticles•Nanotechnologyisofincreasinginterest•Propertiesofnanoparticlescanbeexpensivetodetermineexperimentally•Applicationsincludeelectronics,catalysis,propellants,explosives,medicine,photonicmaterials,…Whatisananoparticle•Aparticlewithdimensionsbetween–mand–m•Aclusterofaluminumatomsis~nmindiameter•NanoparticleshavepropertiesthatrangefromatomliketobulklikeHowaresuchlargesystemshandled•Adifferentclassofmethodsarerequiredtohandlesuchlargesystems•Verysimpletheoriesareusedtodescribetheelectronicstructure–UsuallysemiempiricalmethodsNanoparticles•Calculationsonaninfinitecrystalcanbeusedtovalidateatheory•ThecalculatedpropertiescanbecomparedtomacroscopicphysicalpropertiesNanoparticles•Periodicboundaryconditionsandplanewavebasissetscanbeusedforaninfinitecrystal•Simple,parameterizedelectronicstructuremethodscanbeusedformoreirregularstructuresNanoparticles•Localizedelectronicstructuremethodsareveryuseful–Interactionsbeyondacertaindistancecanbeignored–ThesemethodsscalebetterthanmorecompletemethodsMorechallenges•Manynanomaterialshaveahighfractionofmetals•Metals,ingeneral,arequitedifficulttosimulateHowaresuchlargesystemshandled•Thisisahotareaofresearch•Manynewmethodsarerequired–Methodstodeterminereactionpaths•Manysimilarreactionchannelsmayexists–Methodsthatcanhandlemaingroupelementsaswellasmetals–Methodsthatcanpredictelectronicpropertiesofmetalnanoparticles–MethodsthatcanaccuratelypredictthermochemicalpropertiesChallengesinsimulatinglargesystems•Manysimilarreactionchannelsmayexistforasinglereaction•Longrangeelectrostaticscanhaveahighcomputationalcost•Surroundingmediummayplayanimportantrole(isthisnanoparticleinwater)•Allofthesechallengesarealsopresentinbiochemistryproblems•VASP•Crystal•Gaussianandotherabinitiopackages•TBandothertightbindingcodesProgramsBiochemistryMolecularMechanicsUsefulfor•Molecularsystemscontainingthousandsofatoms•Organics,oligonucleotides,peptides,etc•Vacuum,implicitsolvent,explicitsolventenvironments•Groundstate•Thermodynamicandkineticproperties(moleculardynamics)BallandSpringModelingMolecularMechanicsPrincipleassumptions•Nucleiandelectronsarelumpedintoballs(atomlikeparticles)•Ballsaresphericalandhaveanetcharge•Interactionsarebasedonspringsandclassicalpotentials•Interactionsarepreassignedtospecificsetsofatoms•InteractionsdeterminethespatialdistributionoftheballsandtheirenergyBallandSpringModelingMolecularMechanicsBallandSpringModelingfromtheNIHGuidetoMolecularModelingEnergy=StretchingBendingTorsionNonBondedMolecularMechanicsBallandSpringModeling!E=EbondEangleEdihedralEvdwEelec=Kbb"b()bonds#K$$"$()angles#Kcosn"()dihedrals#'r()*,"'r()*,qqDr:non"bonds#(shortrange)(longrange)QMMME=QMQMMMPolarizationBoundaryQMMMPu,Ma,Gao,Truhlar,JPhysChemB,(),NADPHNpreprotonatedDHFQMMMboundariesStructureDeterminationXrayCrystallographyProteinpreparationandanalysisProteinCrystallizationDiffractionDataPhaseEstimationModelBuildingandStructureRefinement•BenLynch–()•PattonFast–()•MSIHelpline–()

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