Fragmentation : toward accurate calculations on complex molecular systems

364 Pages·2017·12.64 MB·English

by  Gordon

Fragmentation
Fragmentation
TowardAccurateCalculationson
ComplexMolecularSystems
Editedby
MarkS.Gordon
IowaStateUniversity,USA
Thiseditionfirstpublished2017
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LibraryofCongressCataloging-in-PublicationData
Names:Gordon,M.S.(MarkS.),editor.
Title:Fragmentation:towardaccuratecalculationsoncomplexmolecularsystems/editedbyProfessorMarkS.
Gordon,IowaStateUniversity,USA.
Description:Chichester,UK;Hoboken,NJ:JohnWiley&Sons,Inc.,2017.|Includesbibliographicalreferencesand
index.
Identifiers:LCCN2016057161(print)|LCCN2016058050(ebook)|ISBN9781119129240(cloth)|ISBN
9781119129257(pdf)|ISBN9781119129264(epub)
Subjects:LCSH:Fragmentationreactions.|Electronconfiguration.
Classification:LCCQD281.F7F7382017(print)|LCCQD281.F7(ebook)|DDC547/.128–dc23
LCrecordavailableathttps://lccn.loc.gov/2016057161
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Setin10/12ptWarnockProbyAptaraInc.,NewDelhi,India
10 9 8 7 6 5 4 3 2 1
v
Contents
ListofContributors xi
Preface xv
 ExplicitlyCorrelatedLocalElectronCorrelationMethods 1
Hans-JoachimWerner,ChristophKo¨ppl,QianliMa,andMaxSchwilk
1.1 Introduction 1
1.2 BenchmarkSystems 3
1.3 Orbital-InvariantMP2Theory 6
1.4 PrinciplesofLocalCorrelation 9
1.5 OrbitalLocalization 10
1.6 LocalVirtualOrbitals 12
1.6.1 Pseudo-CanonicalPair-SpecificOrbitals 12
1.6.2 ProjectedAtomicOrbitals 16
1.6.3 PairNaturalOrbitals 18
1.6.4 LinearScalingPNOGeneration 22
1.6.5 Orbital-SpecificVirtuals(OSVs) 23
1.7 ChoiceofDomains 24
1.8 ApproximationsforDistantPairs 26
1.8.1 BipolarMultipoleApproximationsofElectronRepulsionIntegrals 26
1.8.2 ApproximationsofDistantPairEnergies 29
1.9 LocalCoupled-ClusterMethods(LCCSD) 33
1.9.1 WeakPairApproximations 35
1.9.2 Long-RangeCancellationsofTermsintheLCCSDEquations 36
1.9.3 ProjectionApproximations 39
1.10 TripleExcitations 41
1.11 LocalExplicitlyCorrelatedMethods 41
1.11.1 PNO-LMP2-F12 42
1.11.2 PNO-LCCSD-F12 49
1.12 TechnicalAspects 53
1.12.1 LocalDensityFitting 53
1.12.2 Parallelization 56
1.13 ComparisonofLocalCorrelationandFragmentMethods 57
1.14 Summary 60
AppendixA:TheLCCSDEquations 63
vi Contents
AppendixB:DerivationoftheInteractionMatrices 65
References 67
 DensityandPotentialFunctionalEmbedding:TheoryandPractice 81
KuangYu,CarolineM.Krauter,JohannesM.Dieterich,andEmilyA.Carter
2.1 Introduction 81
2.2 TheoreticalBackground 82
2.3 DensityFunctionalEmbeddingTheory 84
2.3.1 BasicTheory 84
2.3.1.1 DefinitionoftheEmbeddingPotential 85
2.3.1.2 OptimizationProcedure 85
2.3.2 EmbeddingPotentialConstruction—ImplementationsinPlanewave
Codes 86
2.3.2.1 ImplementationwithPseudopotentialsinABINIT 87
2.3.2.2 ImplementationwithPAWinVASP 87
2.3.2.3 PenaltyFunctions—DampingtheUnphysicalOscillations 91
2.3.2.4 IllustrativeExample 93
2.3.3 EmbeddedClusterCalculations 94
2.3.3.1 CalculationofEmbeddingIntegrals 94
2.3.3.2 EvaluationoftheTotalEnergy 96
2.3.3.3 Examples 97
2.4 PotentialFunctionalEmbeddingTheory 101
2.4.1 BasicTheoriesandTechnicalDetails 102
2.4.1.1 DefinitionofEnergies 102
2.4.1.2 OptimizedEffectivePotential(OEP)SchemeforExactKineticEnergy 103
2.4.1.3 EnergyGradient 104
2.4.1.4 SummaryoftheCodeStructure 105
2.4.2 IllustrativeExamples 106
2.4.2.1 AlPDiatomic 107
2.4.2.2 H OonMgO(001) 108
2
2.5 SummaryandOutlook 109
Acknowledgments 111
References 111
 ModelingandVisualizationfortheFragmentMolecularOrbital
MethodwiththeGraphicalUserInterfaceFU,andAnalysesof
Protein–LigandBinding 119
DmitriG.FedorovandKazuoKitaura
3.1 Introduction 119
3.2 OverviewofFMO 120
3.3 Methodology 120
3.3.1 FMO/PCMFormulationinthePresenceofDummyAtoms 120
3.3.2 NewAnalysesDefiningtheDesolvationPenaltyinthe
Protein–LigandBinding 122
3.3.2.1 AsymmetricBindingAnalysis(ABA) 122
3.3.2.2 SymmetricBindingAnalysis(SBA) 123
3.3.2.3 SymmetricBindingAnalysiswithSeparatedCavitation(SBAC) 123
Contents vii
3.3.2.4 Fragment-WiseElaborationofSBAinFMO 124
3.3.2.5 Fragment-WiseElaborationofSBAC 127
3.3.3 ApplicationofAnalysestoProtein–LigandBinding 127
3.4 GUIDevelopment 128
3.4.1 OutlineofFU 128
3.4.2 ModelingandResultVisualization 129
3.4.2.1 ModelingofanFKBPProteinComplex 129
3.4.2.2 CreatingFMOInput 129
3.4.2.3 RunningFMOinGAMESS 131
3.4.2.4 VisualizingFMOResults 131
3.4.3 AnOverviewofUsingFUforaComplexSystem 133
3.4.4 ExamplesofScriptinginFU 133
3.4.4.1 ConvertingMultiplePDBFilesintoZ-matrixFiles 133
3.4.4.2 DrawingDipoleMomentswithArrows 135
3.5 Conclusions 136
Acknowledgments 137
References 137
 Molecules-in-MoleculesFragment-BasedMethod
fortheAccurateEvaluationofVibrationalandChiroptical
SpectraforLargeMolecules 141
K.V.JovanJoseandKrishnanRaghavachari
4.1 Introduction 141
4.2 ComputationalMethodsandTheory 142
4.3 ResultsandDiscussion 146
4.3.1 MIMMethodforGeometryOptimization 146
4.3.2 MIMMethodforEvaluatingIRSpectra(MIM-IR) 146
4.3.3 MIMMethodforEvaluatingRamanSpectra(MIM-Raman) 149
4.3.4 MIMMethodforEvaluatingVCDSpectra(MIM-VCD) 151
4.3.5 MIMMethodforEvaluatingROASpectra(MIM-ROA) 154
4.3.6 Two-Step-MIMSchemeforEvaluatingRamanandROASpectra 156
4.4 Summary 157
4.5 Conclusions 158
Acknowledgments 159
References 159
 EffectiveFragmentMolecularOrbitalMethod 165
CasperSteinmannandJanH.Jensen
5.1 Introduction 165
5.1.1 EffectiveFragmentPotentials 166
5.1.2 FragmentMolecularOrbitalMethod 167
5.2 EffectiveFragmentMolecularOrbitalMethod 168
5.2.1 CorrelationEnergiesintheEFMOMethod 170
5.2.2 TheEFMOGradient 172
5.2.3 TimingsandComputationalEfficiency 173
5.2.4 BiochemistrywithEFMO 174
5.2.5 FullyIntegratedEFMO 178
viii Contents
5.2.6 Remarks,Notes,andComments 179
5.3 SummaryandFutureDevelopments 180
References 180
 EffectiveFragmentPotentialMethod:Past,Present,andFuture 183
LyudmilaV.SlipchenkoandPradeepK.Gurunathan
6.1 OverviewoftheEFPMethod 183
6.2 MilestonesintheDevelopmentoftheEFPMethod 185
6.2.1 EFP1WaterModel 185
6.2.2 EFP(EFP2)GeneralModel 187
6.3 Present:ChemistryatInterfacesandPhotobiology 192
6.3.1 OHRadicalSolvatedinWater 192
6.3.2 EFPforMacromoleculesandPolymers 198
6.4 FutureDirectionsandOutlook 202
References 203
 NucleationUsingtheEffectiveFragmentPotentialandTwo-Level
Parallelism 209
AjithaDevarajan,AlexanderGaenko,MarkS.Gordon,andTheresaL.Windus
7.1 Introduction 209
7.2 Methods 211
7.2.1 BriefOverviewofDNTMC 211
7.2.2 BriefOverviewofEFP 213
7.2.3 OverviewoftheTwo-LevelParallelismApproach 215
7.3 Results 217
7.3.1 EvaporationRateofWaterHexamerClusterat243K 217
7.3.2 IonMediatedNucleation 218
7.3.3 EvaporationRateofSulfuricAcidfromNeutralSulfuricAcidDimer
Clusters 219
7.3.4 Two-LevelParallelDNTEFPPerformanceAnalysis 221
7.4 Conclusions 223
Acknowledgments 223
References 224
 FiveYearsofDensityMatrixEmbeddingTheory 227
SebastianWouters,CarlosA.Jime´nez-Hoyos,andGarnetK.L.Chan
8.1 QuantumEntanglement 227
8.2 DensityMatrixEmbeddingTheory 228
8.3 BathOrbitalsfromaSlaterDeterminant 230
8.4 TheEmbeddingHamiltonian 232
8.5 Self-Consistency 234
8.6 Green’sFunctions 236
8.7 OverviewoftheLiterature 237
8.8 TheOne-BandHubbardModelontheSquareLattice 237
8.9 DissociationofaLinearHydrogenChain 240
8.10 Summary 240
Contents ix
Acknowledgments 241
References 241
 AbinitioIce,DryIce,andLiquidWater 245
SoHirata,KandisGilliard,XiaoHe,MuratKec¸eli,JinjinLi,MichaelA.Salim,
OlaseniSode,andKiyoshiYagi
9.1 Introduction 245
9.2 ComputationalMethod 247
9.2.1 InternalEnergy 248
9.2.2 StructureandPhonons 250
9.2.3 Spectra 251
9.2.4 PressureEffects 252
9.2.5 TemperatureEffects 253
9.2.6 Born–OppenheimerMolecularDynamics 255
9.3 CaseStudies 256
9.3.1 Ice-Ih 256
9.3.2 Ice-HDA 259
9.3.3 Ice-VIII 262
9.3.4 LiquidWater 266
9.3.5 CO -I:PressureTuningofFermiResonance 272
2
9.3.6 CO -IandIII:Solid–SolidPhaseTransition 277
2
9.3.7 CO -I:ThermalExpansion 280
2
9.4 ConcludingRemarks 284
9.5 Disclaimer 284
Acknowledgments 284
References 285
 ALinear-ScalingDivide-and-ConquerQuantumChemicalMethodfor
Open-ShellSystemsandExcitedStates 297
TakeshiYoshikawaandHiromiNakai
10.1 Introduction 297
10.2 TheoriesfortheDivide-and-ConquerMethod 298
10.2.1 ReviewofDC-SCFandDC-BasedCorrelationTheories 298
10.2.1.1 DC-HF/DFT 298
10.2.1.2 DC-BasedCorrelationTheory 300
10.2.1.3 Dual-BufferDC-BasedCorrelationMethod 301
10.2.2 Linear-ScalingDivide-and-ConquerMethodforOpen-ShellSystems 302
10.2.2.1 DC-USCFandDC-UMP2 302
̂
10.2.2.2 ExpectedValueoftheSquaredSpinOperatorS2 304
10.2.3 Linear-ScalingDivide-and-ConquerMethodforExcited-State
Calculations 304
10.2.3.1 DC-CIS/TDDFT 304
10.2.3.2 DC-SAC/SACCI 305
10.3 AssessmentoftheDivide-and-ConquerMethod 307
10.3.1 Divide-and-ConquerCalculationsforOpen-ShellSystems 307
10.3.1.1 DC-USCFandDC-UMP2 307
10.3.2 Excited-StateCalculationsbasedontheDivide-and-ConquerMethod 313
x Contents
10.3.2.1 ConjugatedAldehyde 313
10.3.2.2 PhotoactiveYellowProtein 315
10.4 Conclusion 318
References 319
 MFCC-BasedFragmentationMethodsforBiomolecules 323
JinfengLiu,TongZhu,XiaoHe,andJohnZ.H.Zhang
11.1 Introduction 323
11.2 TheoryandApplications 324
11.2.1 TheMFCCApproach 324
11.2.2 ElectronDensityandTotalEnergy 326
11.2.3 TheEE-GMFCCMethodforEnergyCalculation 328
11.2.4 TheEE-GMFCC-CPCMMethodforProteinSolvationEnergy 331
11.2.5 TheEE-GMFCC-CPCMMethodforProtein–LigandBindingEnergy 337
11.2.6 TheEE-GMFCCMethodforGeometryOptimizationand
VibrationalSpectrumofProteins 338
11.2.7 TheEE-GMFCC-BasedAbInitioMolecularDynamicsforProteins 340
11.3 Conclusion 345
Acknowledgments 346
References 346
Index 349
xi
ListofContributors
EmilyA.Carter MarkS.Gordon
SchoolofEngineeringandApplied AmesLaboratoryofUnitedStates
Science,PrincetonUniversity,USA DepartmentofEnergy,USA
DepartmentofChemistry,IowaState
GarnetK.L.Chan
University,USA
FrickChemistryLaboratory,
DepartmentofChemistry,Princeton PradeepK.Gurunathan
University,USA
DepartmentofChemistry,Purdue
University,USA
AjithaDevarajan
OfficeofUniversityDevelopment, XiaoHe
UniversityofMichigan,USA SchoolofChemistryandMolecular
Engineering,EastChinaNormal
JohannesM.Dieterich
University,China
DepartmentofMechanicaland
NYU-ECNUCenterforComputational
AerospaceEngineering,Princeton
Chemistry,NYUShanghai,China
University,USA
SoHirata
DmitriG.Fedorov
DepartmentofChemistry,Universityof
ResearchCenterforComputational
IllinoisatUrbana–Champaign,USA
DesignofAdvancedFunctional
Materials(CD-FMat),National JanH.Jensen
InstituteofAdvancedIndustrial
DepartmentofChemistry,Universityof
ScienceandTechnology(AIST),
Copenhagen,Denmark
Tsukuba,Japan
CarlosA.Jime´nez-Hoyos
AlexanderGaenko FrickChemistryLaboratory,
AdvancedResearchComputing, DepartmentofChemistry,Princeton
UniversityofMichigan,USA University,USA
KandisGilliard K.V.JovanJose∗
DepartmentofChemistry,Universityof DepartmentofChemistry,Indiana
IllinoisatUrbana–Champaign,USA University,USA
∗Currentaddress:SchoolofChemistry,UniversityofHyderabad,India