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HandbookofComputationalChemistry JerzyLeszczynski(Ed.) Handbook of Computational Chemistry WithFiguresandTables 123 Editor JerzyLeszczynski DepartmentofChemistryandBiochemistry JacksonStateUniversity Jackson,MS39217 USA [email protected] ISBN978-94-007-0710-8 e-ISBN978-94-007-0711-5 DOI10.1007/978-94-007-0711-5 ISBNBundle978-94-007-0712-2 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2011941760 ©SpringerScience+BusinessMediaB.V.2012 Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorbyanymeans, electronic,mechanical,photocopying,microfilming,recordingorotherwise,withoutwrittenpermissionfromthe Publisher,withtheexceptionofanymaterialsuppliedspecificallyforthepurposeofbeingenteredandexecuted onacomputersystem,forexclusiveusebythepurchaserofthework. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Ithas beenanamazingexperience towitness andcomprehendtransformation of chemistry duringthetwentiethcentury.Sinceitsancientbeginnings,chemistryhasbeenconsideredto beanexperimentalscience.However,duringthelastyearsithasbeenadvancingthrough noticeablecontributionsofcomputationalmethods.Thistransformationhasitsrootsinboth theoreticalbreakthroughs(Heisenberg’sandSchrodinger’sfirstpapersonquantum mechanics) as well as developmentof the first computer – Electronic Numerical Integrator andComputer(ENIAC)buildinfortheUSADepartmentoftheArmy.However,ittook abouttwentyyearsaftercreationofENIACcomputerstodelivercomputationalchemistrytech- niques to scientific community. Such early methods being semi-empirical in nature rely on thenumberofparametersderivedfromexperiments.Thoughsuchanapproachunitesexper- imental chemistry origins with new theoretical approaches, in some cases it also produced artificial computational results. Further, it also lacks reliable parameters for some elements. Thenext,successfulchapterforcomputationalchemistrystartedintheswithapplications of non-empirical ab initio methods. The first ab initio computer code popular among non- theoreticians–GAUSSIAN–wasdevelopedinthesbyJohnAPople’sgroup.Itinitiated acomputationalchemistryrevolutionthatfiredupintheswhensupercomputersbecame accessibletothegeneralscientificcommunity.Alsoduringthisperiod,theDensityFunctional Theoryapproachesgainedaprominentpositionamongefficientcomputationalmethods.The vitalroleofcomputationalchemistryinmanyresearchareaswasconvincinglyacknowledgedin whenthechemicalandphysicalcommunitycelebratedtheNobelPrizethatwasawarded to two leading computational experts. Walter Kohn and John A. Pople were recognized by the Nobel Committee for their contributions to the developmentof efficient computational methodsforquantumchemistry. Over the years, different methodsof theoretical chemistry have been successfully trans- formedintousefultoolsthatcouldbeappliedindiverseareasofscientificandtechnological research.Owingtothefundamentalmethodologicaldevelopmentsandcontinuedimpressive progressincomputationaltechnologiesinthelastquarterofthetwentiethcentury,severalfast anduser-friendlyprogramshavebeendevelopedandmadeaccessibletoawidecommunityof scientists.Thesenearlyautomaticcomputercodesindicatehowmethodsoftheoreticalchem- istrycouldbeappliedasbothdiagnosticandpredictiveresearchtoolswhichsupportefforts andevenguidedirections oftraditional experimentalapproaches.Theuser-friendlyfeatures ofcommercialcodescombinedwithefficientvisualizationmethodsmakethemaccessibleto researcherswithpracticallyanyeducationalbackground.Generally,onlyalimitedknowledge andalittleformalexperienceintheoreticalchemistryarerequiredtousesuchprogramsandto obtainsomenumericaldata.Thismightcauseunexpectedoutcomes.Mostofthemethodsof theoretical(quantum)chemistryhavealimitedrangeofapplicationsandtheirusebyaninexpe- riencedamateurwhoperformscomputationalstudieswithoutunderstandingsuchconstraint mayleadtoseriousproblemsandspuriousresults.Moreover,duetotheavailabilityofavariety ofmethodsofdifferentquality,auserwithoutagoodbackgroundintheoreticalchemistrymay feellostgiventhechoicesfromusuallyrichmenusofavailableprograms. vi Preface Thethreevolume“HandbookofComputationalChemistry”isprimarilyintendedasaguide thatcanhelptonavigateamongdifferentcomputationalmethodscurrentlyinuse.Inorderto accomplishthisgoal,wecollectedchaptersthatprovidecompactdescriptionofthebasisof computationalchemistrytechniquesalongwithvastexamplesofapplicationsofthesemethods invariousareas.Thehandbookisdesignedforresearcherswhoarejustbeingintroducedto computationalmethods,aswellasforthosewhoaresearchingforthebestchoiceforsolution tospecificproblemsinvolvingtheoreticalapproaches. Thefirstvolumebrieflydescribesdifferentmethodsusedincomputationalchemistrywith- out going into exhaustive details of theory. Basic assumptions common to the majority of computational methodsbased on eitherquantum or statistical mechanics are outlined. Par- ticularattentionispaidtothelimitsoftheirapplicability.Importantly,thisvolumealsoestab- lishesdefinitionsofavarietyofacronymsandterminologyusedintheareaofcomputational chemistry. Sinceweassumedthatthereadersofthisbookareinterestedinapplicationsofcomputa- tionalmethods,abroadrangeofthemostimportantapplicationsofcomputationalchemistry isprovidedinthesecondsectionofthefirstvolume.Theapplicationsincludedescriptionsof standardchemicalcalculationsformodelmoleculesundervariousconditions.TheHandbook providesinformationonthepredictionofvariousmolecularpropertiesaswellasinvestigations ofchemicalreactions. Therearetwoclassesofspecies:biomoleculesandnanomaterialsthatareofavitalinterest notonlytochemistsbutalsotophysicists,biologists,andmaterialscientists.Twovolumesare devotedtoadescriptionofspecificcomputationalmethodsthataredesignedtoinvestigatesuch species.Numerousexamplesofapplicationsaswellasdescriptionsofspecificresearchproblems andtheirsolutionsforvarioustypesofbiomoleculesandnanoparticlesaregiveninthesecond andthirdvolumesoftheHandbook.Thereviewedtopicswillattracttheattentionofallthose whoarealreadyworkingorplanningtostartresearchinvolvingcomputationalapproaches. Theideaofthishandbookcrystallizedafternumerousdiscussionswithadearfriendandthe leadingPolishquantumchemistsAndrzejJ.Sadlej.Andrzejwasalsoactivelyinvolvedinselect- ingthepotentialcontributorsandeditingthebook.Unfortunately,hepassedawaybeforethe bookwaspublished.Thoughtheisnolongerwithus,hewillalwaysberemembered.Andrzej’s intellectualcontributionswillcontinuetoliveonandthisHandbook,whichisdedicatedtohim, isintendedasatributetohismemoryforfriends,colleaguesandstudentstorememberhim. TheEditors Editorial Board TheoryandMethodology AnnaKaczmarek-Ke˛dzieraandAndrzejJ.Sadlej ApplicationsofComputationalMethodstoModelSystems AnnaKaczmarek-Ke˛dzieraandAndrzejJ.Sadlej SolidStatesandNanomaterials ManthosG.PapadopoulosandHeribertReis Biomolecules ManojK.Shukla Table of Contents Preface........................................................................................................... v EditorialBoard................................................................................................ vii ListofContributors.......................................................................................... xiii Volume  FromQuantumTheorytoComputationalChemistry.ABriefAccountof Developments...........................................................................................  LucjanPiela  ThePositionoftheClampedNucleiElectronicHamiltonianinQuantum Mechanics.................................................................................................  BrianSutcliffe ⋅R.GuyWoolley  RemarksonWaveFunctionTheoryandMethods............................................  DariuszKe˛dziera ⋅AnnaKaczmarek-Ke˛dziera  DirectionsforUseofDensityFunctionalTheory:AShortInstructionManual forChemists..............................................................................................  HeikoJacobsen ⋅LuigiCavallo  IntroductiontoResponseTheory..................................................................  ThomasBondoPedersen  IntermolecularInteractions.........................................................................  AlstonJ.Misquitta  MolecularDynamicsSimulation:From“AbInitio”to“CoarseGrained”................  ChrisLorenz ⋅NikosL.Doltsinis  StatisticalMechanicsofForce-InducedTransitionsofBiopolymers....................  SanjayKumar  MolecularMechanics:MethodandApplications..............................................  ValeriPoltev  MolecularStructureandVibrationalSpectra..................................................  JonBaker x TableofContents  MolecularElectric,Magnetic,andOpticalProperties.......................................  MichałJaszun´ski ⋅AntonioRizzo ⋅KennethRuud  WeakIntermolecularInteractions:ASupermolecularApproach.........................  MarkWaller ⋅StefanGrimme  ChemicalReactions:ThermochemicalCalculations..........................................  JohnD.Watts  CalculationofExcitedStates:MolecularPhotophysicsandPhotochemistryon Display.....................................................................................................  LuisSerrano-Andre´s ⋅JuanJose´Serrano-Pe´rez  SolventEffectsinQuantumChemistry...........................................................  GeraldMonard ⋅Jean-LouisRivail  AuxiliaryDensityFunctionalTheory:FromMoleculestoNanostructures............  PatriziaCalaminici ⋅Victor-DanielDomínguez-Soria ⋅RobertoFlores-Moreno ⋅GabrielUlises Gamboa-Martínez ⋅GeraldGeudtner ⋅AnnickGoursot ⋅DennisR.Salahub ⋅AndreasM.Ko¨ster  GuidetoProgramsforNon-relativisticQuantumChemistryCalculations............  TaoZeng ⋅MariuszKlobukowski Volume  FunctionalNanostructuresandNanocomposites–NumericalModeling ApproachandExperiment...........................................................................  MalgorzataMakowska-Janusik ⋅Abdel-HadiKassiba  StructuresandStabilityofFullerenes,Metallofullerenes,and TheirDerivatives........................................................................................  AlexeyA.Popov  StructuresandElectricPropertiesofSemiconductorclusters............................  PanaghiotisKaramanis  Structures,Energetics,andSpectroscopicFingerprintsof WaterClustersn=–...............................................................................  SoohaengYoo ⋅SotirisS.Xantheas  FundamentalStructural,Electronic,andChemicalPropertiesofCarbon Nanostructures:Graphene,Fullerenes,CarbonNanotubes,and TheirDerivatives........................................................................................  TandabanyC.Dinadayalane ⋅JerzyLeszczynski

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HandbookofComputationalChemistry JerzyLeszczynski(Ed.) Handbook of Computational Chemistry WithFiguresandTables 123 Editor JerzyLeszczynski DepartmentofChemistryandBiochemistry JacksonStateUniversity Jackson,MS39217 USA [email protected] ISBN978-94-007-0710-8 e-ISBN978-94-007-0711-5 DOI10.1007/978-94-007-0711-5 ISBNBundle978-94-007-0712-2 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2011941760 ©SpringerScience+BusinessMediaB.V.2012 Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorbyanymeans, electronic,mechanical,photocopying,microfilming,recordingorotherwise,withoutwrittenpermissionfromthe Publisher,withtheexceptionofanymaterialsuppliedspecificallyforthepurposeofbeingenteredandexecuted onacomputersystem,forexclusiveusebythepurchaserofthework. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Ithas beenanamazingexperience towitness andcomprehendtransformation of chemistry duringthetwentiethcentury.Sinceitsancientbeginnings,chemistryhasbeenconsideredto beanexperimentalscience.However,duringthelastyearsithasbeenadvancingthrough noticeablecontributionsofcomputationalmethods.Thistransformationhasitsrootsinboth theoreticalbreakthroughs(Heisenberg’sandSchrodinger’sfirstpapersonquantum mechanics) as well as developmentof the first computer – Electronic Numerical Integrator andComputer(ENIAC)buildinfortheUSADepartmentoftheArmy.However,ittook abouttwentyyearsaftercreationofENIACcomputerstodelivercomputationalchemistrytech- niques to scientific community. Such early methods being semi-empirical in nature rely on thenumberofparametersderivedfromexperiments.Thoughsuchanapproachunitesexper- imental chemistry origins with new theoretical approaches, in some cases it also produced artificial computational results. Further, it also lacks reliable parameters for some elements. Thenext,successfulchapterforcomputationalchemistrystartedintheswithapplications of non-empirical ab initio methods. The first ab initio computer code popular among non- theoreticians–GAUSSIAN–wasdevelopedinthesbyJohnAPople’sgroup.Itinitiated acomputationalchemistryrevolutionthatfiredupintheswhensupercomputersbecame accessibletothegeneralscientificcommunity.Alsoduringthisperiod,theDensityFunctional Theoryapproachesgainedaprominentpositionamongefficientcomputationalmethods.The vitalroleofcomputationalchemistryinmanyresearchareaswasconvincinglyacknowledgedin whenthechemicalandphysicalcommunitycelebratedtheNobelPrizethatwasawarded to two leading computational experts. Walter Kohn and John A. Pople were recognized by the Nobel Committee for their contributions to the developmentof efficient computational methodsforquantumchemistry. Over the years, different methodsof theoretical chemistry have been successfully trans- formedintousefultoolsthatcouldbeappliedindiverseareasofscientificandtechnological research.Owingtothefundamentalmethodologicaldevelopmentsandcontinuedimpressive progressincomputationaltechnologiesinthelastquarterofthetwentiethcentury,severalfast anduser-friendlyprogramshavebeendevelopedandmadeaccessibletoawidecommunityof scientists.Thesenearlyautomaticcomputercodesindicatehowmethodsoftheoreticalchem- istrycouldbeappliedasbothdiagnosticandpredictiveresearchtoolswhichsupportefforts andevenguidedirections oftraditional experimentalapproaches.Theuser-friendlyfeatures ofcommercialcodescombinedwithefficientvisualizationmethodsmakethemaccessibleto researcherswithpracticallyanyeducationalbackground.Generally,onlyalimitedknowledge andalittleformalexperienceintheoreticalchemistryarerequiredtousesuchprogramsandto obtainsomenumericaldata.Thismightcauseunexpectedoutcomes.Mostofthemethodsof theoretical(quantum)chemistryhavealimitedrangeofapplicationsandtheirusebyaninexpe- riencedamateurwhoperformscomputationalstudieswithoutunderstandingsuchconstraint mayleadtoseriousproblemsandspuriousresults.Moreover,duetotheavailabilityofavariety ofmethodsofdifferentquality,auserwithoutagoodbackgroundintheoreticalchemistrymay feellostgiventhechoicesfromusuallyrichmenusofavailableprograms. vi Preface Thethreevolume“HandbookofComputationalChemistry”isprimarilyintendedasaguide thatcanhelptonavigateamongdifferentcomputationalmethodscurrentlyinuse.Inorderto accomplishthisgoal,wecollectedchaptersthatprovidecompactdescriptionofthebasisof computationalchemistrytechniquesalongwithvastexamplesofapplicationsofthesemethods invariousareas.Thehandbookisdesignedforresearcherswhoarejustbeingintroducedto computationalmethods,aswellasforthosewhoaresearchingforthebestchoiceforsolution tospecificproblemsinvolvingtheoreticalapproaches. Thefirstvolumebrieflydescribesdifferentmethodsusedincomputationalchemistrywith- out going into exhaustive details of theory. Basic assumptions common to the majority of computational methodsbased on eitherquantum or statistical mechanics are outlined. Par- ticularattentionispaidtothelimitsoftheirapplicability.Importantly,thisvolumealsoestab- lishesdefinitionsofavarietyofacronymsandterminologyusedintheareaofcomputational chemistry. Sinceweassumedthatthereadersofthisbookareinterestedinapplicationsofcomputa- tionalmethods,abroadrangeofthemostimportantapplicationsofcomputationalchemistry isprovidedinthesecondsectionofthefirstvolume.Theapplicationsincludedescriptionsof standardchemicalcalculationsformodelmoleculesundervariousconditions.TheHandbook providesinformationonthepredictionofvariousmolecularpropertiesaswellasinvestigations ofchemicalreactions. Therearetwoclassesofspecies:biomoleculesandnanomaterialsthatareofavitalinterest notonlytochemistsbutalsotophysicists,biologists,andmaterialscientists.Twovolumesare devotedtoadescriptionofspecificcomputationalmethodsthataredesignedtoinvestigatesuch species.Numerousexamplesofapplicationsaswellasdescriptionsofspecificresearchproblems andtheirsolutionsforvarioustypesofbiomoleculesandnanoparticlesaregiveninthesecond andthirdvolumesoftheHandbook.Thereviewedtopicswillattracttheattentionofallthose whoarealreadyworkingorplanningtostartresearchinvolvingcomputationalapproaches. Theideaofthishandbookcrystallizedafternumerousdiscussionswithadearfriendandthe leadingPolishquantumchemistsAndrzejJ.Sadlej.Andrzejwasalsoactivelyinvolvedinselect- ingthepotentialcontributorsandeditingthebook.Unfortunately,hepassedawaybeforethe bookwaspublished.Thoughtheisnolongerwithus,hewillalwaysberemembered.Andrzej’s intellectualcontributionswillcontinuetoliveonandthisHandbook,whichisdedicatedtohim, isintendedasatributetohismemoryforfriends,colleaguesandstudentstorememberhim. TheEditors Editorial Board TheoryandMethodology AnnaKaczmarek-Ke˛dzieraandAndrzejJ.Sadlej ApplicationsofComputationalMethodstoModelSystems AnnaKaczmarek-Ke˛dzieraandAndrzejJ.Sadlej SolidStatesandNanomaterials ManthosG.PapadopoulosandHeribertReis Biomolecules ManojK.Shukla Table of Contents Preface........................................................................................................... v EditorialBoard................................................................................................ vii ListofContributors.......................................................................................... xiii Volume  FromQuantumTheorytoComputationalChemistry.ABriefAccountof Developments...........................................................................................  LucjanPiela  ThePositionoftheClampedNucleiElectronicHamiltonianinQuantum Mechanics.................................................................................................  BrianSutcliffe ⋅R.GuyWoolley  RemarksonWaveFunctionTheoryandMethods............................................  DariuszKe˛dziera ⋅AnnaKaczmarek-Ke˛dziera  DirectionsforUseofDensityFunctionalTheory:AShortInstructionManual forChemists..............................................................................................  HeikoJacobsen ⋅LuigiCavallo  IntroductiontoResponseTheory..................................................................  ThomasBondoPedersen  IntermolecularInteractions.........................................................................  AlstonJ.Misquitta  MolecularDynamicsSimulation:From“AbInitio”to“CoarseGrained”................  ChrisLorenz ⋅NikosL.Doltsinis  StatisticalMechanicsofForce-InducedTransitionsofBiopolymers....................  SanjayKumar  MolecularMechanics:MethodandApplications..............................................  ValeriPoltev  MolecularStructureandVibrationalSpectra..................................................  JonBaker x TableofContents  MolecularElectric,Magnetic,andOpticalProperties.......................................  MichałJaszun´ski ⋅AntonioRizzo ⋅KennethRuud  WeakIntermolecularInteractions:ASupermolecularApproach.........................  MarkWaller ⋅StefanGrimme  ChemicalReactions:ThermochemicalCalculations..........................................  JohnD.Watts  CalculationofExcitedStates:MolecularPhotophysicsandPhotochemistryon Display.....................................................................................................  LuisSerrano-Andre´s ⋅JuanJose´Serrano-Pe´rez  SolventEffectsinQuantumChemistry...........................................................  GeraldMonard ⋅Jean-LouisRivail  AuxiliaryDensityFunctionalTheory:FromMoleculestoNanostructures............  PatriziaCalaminici ⋅Victor-DanielDomínguez-Soria ⋅RobertoFlores-Moreno ⋅GabrielUlises Gamboa-Martínez ⋅GeraldGeudtner ⋅AnnickGoursot ⋅DennisR.Salahub ⋅AndreasM.Ko¨ster  GuidetoProgramsforNon-relativisticQuantumChemistryCalculations............  TaoZeng ⋅MariuszKlobukowski Volume  FunctionalNanostructuresandNanocomposites–NumericalModeling ApproachandExperiment...........................................................................  MalgorzataMakowska-Janusik ⋅Abdel-HadiKassiba  StructuresandStabilityofFullerenes,Metallofullerenes,and TheirDerivatives........................................................................................  AlexeyA.Popov  StructuresandElectricPropertiesofSemiconductorclusters............................  PanaghiotisKaramanis  Structures,Energetics,andSpectroscopicFingerprintsof WaterClustersn=–...............................................................................  SoohaengYoo ⋅SotirisS.Xantheas  FundamentalStructural,Electronic,andChemicalPropertiesofCarbon Nanostructures:Graphene,Fullerenes,CarbonNanotubes,and TheirDerivatives........................................................................................  TandabanyC.Dinadayalane ⋅JerzyLeszczynski

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