Table Of ContentMolecularSpectroscopy
Molecular Spectroscopy
AQuantumChemistryApproach
Editedby
YukihiroOzaki
MarekJanuszWójcik
JürgenPopp
Volume1
Molecular Spectroscopy
AQuantumChemistryApproach
Editedby
YukihiroOzaki
MarekJanuszWójcik
JürgenPopp
Volume2
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v
ContentstoVolume1
Preface xiii
1 InterpretabilityMeetsAccuracyinComputational
Spectroscopy:TheVirtualMultifrequencySpectrometer 1
VincenzoBaroneandCristinaPuzzarini
1.1 Introduction 2
1.2 TheVirtualMultifrequencySpectrometer 3
1.2.1 TheVMSFramework 3
1.2.2 TheVMSFramework:SpectroscopiesandTheoreticalBackground 4
1.2.2.1 RotationalSpectroscopy 4
1.2.2.2 VibrationalSpectroscopy 5
1.2.2.3 VibronicSpectroscopy 8
1.2.2.4 MagneticSpectroscopy 10
1.2.3 TheVMSFramework:QuantumChemicalMethods 12
1.3 TheVMSFrameworkatWork 14
1.3.1 RotationalSpectroscopy 14
1.3.2 VibrationalSpectroscopy 16
1.3.3 VibronicSpectroscopy 19
1.3.4 MagneticSpectroscopy 22
1.4 TheVMSFramework:Applications 25
1.4.1 ACompleteSpectroscopicCharacterization:TheGlycineCase
Study 26
1.4.2 VibrationalSpectroscopyofaChiralMolecule:TheMethyloxirane
CaseStudy 28
1.4.3 FromMolecularStructuretoElectronicSpectrum:ThePyrimidine
CaseStudy 30
1.4.4 EPRSpectruminDifferentSolvents:TheTOACCaseStudy 35
1.5 Conclusions 37
Acknowledgments 38
References 38
2 ExcitedStateDynamicsinNTChem 43
TakehiroYonehara,NoriyukiMinezawa,andTakahitoNakajima
2.1 NTChem 43
2.2 ElectronDynamicsinaMolecularAggregateUnderaLightField 44
vi Contents
2.2.1 TheoreticalBackground 45
2.2.1.1 OverviewofElectronDynamicsCalculation 45
2.2.1.2 SchemesBasedonMultistateMulti-electronWavefunctions 46
2.2.1.3 SchemesBasedontheElectronDensityMatrix 48
2.2.2 GroupDiabaticFockScheme 49
2.2.2.1 GroupDiabaticFockMatrix 49
2.2.2.2 TransformationofObservable,Fock,andDensityMatrices 50
2.2.2.3 TimePropagationofDensityMatrixinGDRepresentation 51
2.2.2.4 InitialDensityMatrix:LocalExcitationandElectronFilling 51
2.2.3 NumericalDemonstration 52
2.2.3.1 ChargeMigrationDynamics:NPTL–TCNEDimer 53
2.2.3.2 UnpairedElectronDynamics:20-merEthylene 54
2.3 TrajectorySurfaceHoppingMolecularDynamicsSimulation 59
2.3.1 TheoreticalBackground 60
2.3.1.1 ConicalIntersection 60
2.3.1.2 NonadiabaticMolecularDynamicsSimulation 61
2.3.1.3 ElectronicStructureMethod 62
2.3.2 TheoreticalMethod 63
2.3.2.1 TSHApproach 63
2.3.2.2 LR-TDDFT 63
2.3.2.3 NonadiabaticCoupling 64
2.3.3 Example:PhotodynamicsofCoumarin 65
2.3.3.1 ComputationalDetails 66
2.3.3.2 ResultsandDiscussion 66
2.3.4 FutureDirection 69
2.3.4.1 EffectsofEnvironment 69
2.3.4.2 AccurateDescriptionofS /S Crossing 69
0 1
2.3.4.3 Spin-ForbiddenTransition 70
2.4 Summary 70
Acknowledgment 72
References 72
3 QuantumChemistryforStudyingElectronicSpectroscopyand
DynamicsofComplexMolecularSystems 79
HyunWooKim,KyungminKim,SooWanPark,andYoungMinRhee
3.1 OverviewofQuantumChemicalToolsforStudyingElectronic
Spectroscopy 80
3.2 Examples:QuantumChemicalCalculationsofSimpleSystems 88
3.3 SpectralLineShape 93
3.4 Examples:ComplexSystems 95
3.4.1 SingleChromophoreCase:RetinalinRhodopsin 95
3.4.1.1 IsolatedRetinal:EarlyStudies 96
3.4.1.2 RetinalinProtein:AbsorptionPredictions 97
3.4.1.3 MDSimulationswithQM/MM 99
3.4.1.4 RhodopsinVariants 100
3.4.1.5 2DElectronicSpectra 100
3.4.2 MultipleChromophoreCase:BacteriochlorophyllsinLH2 102
Contents vii
3.4.2.1 ExcitedStateEnergies 103
3.4.2.2 CouplingBetweenExcitedStates 104
3.4.2.3 DynamicsSimulations 105
References 107
4 TheoreticalandExperimentalMolecularSpectroscopyofthe
Far-UltravioletRegion 119
MasahiroEharaandYusukeMorisawa
4.1 Introduction 119
4.2 Method 120
4.2.1 TheoryandComputationalDetails 120
4.2.2 ATR-FUVSpectroscopy 123
4.3 ResultsandDiscussion 124
4.3.1 FUVSpectraofn-AlkanesintheLiquidandSolidPhases 124
4.3.2 Amides 130
4.3.3 Nylons 136
4.4 Summary 141
References 142
5 WeightAveragedAnharmonicVibrationalCalculations:
ApplicationstoPolypeptide,LipidBilayers,andPolymer
Materials 147
KiyoshiYagi,HirokiOtaki,Pai-ChiLi,BoThomsen,andYujiSugita
5.1 Introduction 147
5.2 Method 149
5.2.1 WeightAverageMethod 149
5.2.2 ElectronicStructureCalculationsforaClusterandLocalModes 150
5.2.3 VibrationalQuasi-degeneratePerturbationTheory 151
5.2.4 ComputationalProcedure 153
5.3 Applications 153
5.3.1 Pentapeptide:SIVSF 153
5.3.2 SphingomyelinBilayer 157
5.3.3 HydrationofNylon6 160
5.4 ConcludingRemarksandOutlook 163
Acknowledgments 164
References 165
6 ChiralRecognitionbyMolecularSpectroscopy 171
MagdalenaPeculandJoannaSadlej
6.1 Introduction 171
6.2 ThePhysicalManifestationofOpticalActivityinChiroptical
SpectroscopicMethods:TheoryoftheChiropticalProperties 172
6.2.1 GeneralBackground 173
6.2.2 CalculationsofVCDSpectra 173
6.2.2.1 PracticalSimulationofVCDSpectra 173
6.2.3 CalculationsofROASpectra 175
viii Contents
6.2.4 CalculationsofECDandCPLSpectra 176
6.2.5 CalculationsofCPLSpectra 177
6.2.5.1 Spin-ForbiddenCircularDichroismandCircularlyPolarized
Phosphorescence(CPP) 177
6.2.6 ElectronicStructureMethods,BasisSetRequirements,andProgram
Packages 179
6.2.6.1 VibrationalOpticalActivity 180
6.2.6.2 ElectronicStructureMethods:ECD,CPL,andCPP 181
6.2.6.3 TheBasisSetRequirements:VCD,ROA,ECD,andCPL 181
6.2.6.4 Software 182
6.3 SelectedCaseStudies 182
6.3.1 TakingintoAccountChemicalEnvironment,Conformational
Flexibility,andVibrationalCorrectionsintheCalculationof
ChiropticalSpectra 182
6.3.1.1 Matrix-IsolationCDSpectra 183
6.3.1.2 ModelingofSolventEffectsintheChiropticalSpectra 183
6.3.1.3 Environment-InducedCDandCPLActivity 184
6.3.1.4 ConformationalAveragingoftheChiropticalSpectra 185
6.3.1.5 TheConceptofRobustness 185
6.3.2 ModelingofAnharmonicityinVCDandROASpectra 186
6.3.2.1 ComputationalApproachestoAnharmonicity 186
6.3.2.2 TheRoleofAnharmonicityinVCDandROASpectra:Examples 186
6.3.3 TheInducedVCDIntensityMonitoredbyExperimentalorCalculated
VCDSpectra 187
6.4 Perspective 189
References 191
7 QuantumApproachofIRLineShapesofCarboxylicAcidsUsing
theLinearResponseTheory 199
PaulBlaise,OlivierHenri-Rousseau,andAdinaVelcescu
7.1 Introduction 199
7.2 TheCharacteristicsoftheInfraredSpectraofHydrogen-Bonded
Species 199
7.2.1 RecallontheGeneralFeaturesoftheIRSpectraofSystemsContaining
HydrogenBonds 199
7.2.2 TheLinearResponseTheory 201
7.2.3 ConditionsforaQuantitativeTheory 202
7.3 TheStrongCouplingTheoryofAnharmonicity 203
7.3.1 SpectralDensity 203
7.3.2 TheModelforIRSpectraofCentrosymmetricDimers 207
7.3.3 TheLineShape 208
7.3.4 LimitSituations 210
7.3.5 Examples 211
7.3.5.1 AceticAcid 211
7.3.5.2 FormicAcid 211
7.4 Conclusion 212
References 212
Contents ix
8 TheoreticalCalculationsAreaStrongToolintheInvestigation
ofStrongIntramolecularHydrogenBonds 215
PoulErikHansen,AnetaJezierska,JarosławJ.Panek,andJensSpanget-Larsen
8.1 IntroductionandDefinitionofTypesofIntramolecularHydrogen
Bonds 215
8.2 DefinitionsofStrongIntramolecularHydrogenBonds 215
8.3 CalculationofStructuralParameters 217
8.4 HydrogenBondStrength 218
8.5 CalculationofEnergies 220
8.6 Tautomerism 223
8.6.1 2DApproachestoHydrogenBondPotentials 223
8.6.2 PotentialEnergyandFreeEnergySurfaces 223
8.7 CalculationofIRSpectraofStronglyHydrogen-BondedSystems 226
8.7.1 TheHarmonicApproximation 226
8.7.2 GoingBeyondtheHarmonicApproximation 228
8.7.2.1 Simplified,StaticProcedures 228
8.7.2.2 AdvancedCalculationsonSmallSystems:Malonaldehydeand
Acetylacetone 229
8.7.3 LargerSystems 232
8.7.3.1 Car–ParrinelloMolecularDynamicsSimulations 232
8.8 NMR 234
8.8.1 Introduction 234
8.8.2 CalculationofOHChemicalShifts 235
8.8.3 EstimationofRingCurrentandAnisotropyEffectsonOHChemical
Shifts 236
8.8.4 EstimationofOtherEffectsonOHChemicalShifts 237
8.8.5 CalculationofChemicalShiftsinChargedSystems 237
8.8.6 CalculationofDeuteriumIsotopeEffectsonNuclearShieldings 238
8.8.6.1 JamesonApproach 238
8.8.6.2 Car–ParrinelloandTwo-DimensionalSamplingofChemical
Shifts 239
8.9 PrincipalComponentAnalysis 240
8.10 SolventEffects 240
8.11 Conclusions 241
References 242
9 SpectralSimulationforFlexibleMoleculesinSolutionwith
QuantumChemicalCalculations 253
YukiteruKatsumoto
9.1 Introduction 253
9.2 SelectionoftheCalculationLevelforSpectralSimulationsofFlexible
Molecules 254
9.3 SimulationofIRSpectraObservedinSolutionPhase 257
9.4 CompetitionBetweenIntramolecularandIntermolecular
Interactions 261
9.5 ConformationalDiversityandSolvationintheVibrational
Spectrum 265
