Computational Modeling for Homogeneous and Enzymatic Catalysis: A Knowledge-Base for Designing Efficient Catalysts

398 Pages·2008·4.631 MB·English

ComputationalModeling
forHomogeneousand
EnzymaticCatalysis
Editedby
KeijiMorokumaand
DjamaladdinG.Musaev
ComputationalModelingforHomogeneousandEnzymaticCatalysis.
AKnowledge-BaseforDesigningEfficientCatalysts. K.MorokumaandD.G.Musaev(Eds.)
Copyright62008WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:978-3-527-31843-8
Further Reading
vanSanten,R.A.,Neurock,M.
Molecular Heterogeneous Catalysis
AConceptualandComputationalApproach
2006
ISBN978-3-527-29662-0
Dronskowski,R.
Computational Chemistry of Solid State Materials
AGuideforMaterialsScientists,Chemists,Physicistsandothers
2006
ISBN978-3-527-31410-2
Computational Modeling for Homogeneous
and Enzymatic Catalysis
A Knowledge-Base for Designing Efficient Catalysts
Edited by
Keiji Morokuma and Djamaladdin G. Musaev
TheEditors 9 AllbookspublishedbyWiley-VCHarecarefully
produced.Nevertheless,authors,editors,and
Prof.Dr.KeijiMorokuma publisherdonotwarranttheinformation
EmoryUniversity containedinthesebooks,includingthisbook,
DepartmentofChemistry tobefreeoferrors.Readersareadvisedtokeep
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Atlanta,GA30322 fromtheBritishLibrary.
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publicationintheDeutscheNational-
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availableintheInternetat3http://dnb.d-nb.de4.
ª2008WILEY-VCHVerlagGmbH&Co.
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ISBN 978-3-527-31843-8
DedicatedtoEiko,Matanat,MikiandAiten

VII
Contents
Preface XV
ListofContributors XVII
1 ComputationalInsightsintotheStructuralPropertiesandCatalytic
FunctionsofSelenoproteinGlutathionePeroxidase(GPx) 1
RajeevPrabhakar,KeijiMorokuma,andDjamaladdinG.Musaev
1.1 Introduction 1
1.2 CatalyticFunctions 3
1.2.1 PeroxidaseActivity 3
1.2.2 ReductaseActivity 3
1.3 ComputationalDetails 5
1.3.1 ComputationalMethods 5
1.3.2 ComputationalModels 5
1.4 ResultsandDiscussion 6
1.4.1 RefinementoftheActiveSite 6
1.4.2 CatalyticFunctions:PeroxidaseActivity 8
1.4.3 CatalyticFunctions:EffectoftheSurroundingProteinonthe
PeroxidaseActivity 12
1.4.3.1 HydrogenPeroxideCoordination 12
1.4.3.2 FormationofSelenenicAcid[EaSeaOH] 14
1.4.4 CatalyticFunctions:ReductaseActivity 16
1.4.4.1 Peroxynitrite/PeroxynitrousAcid(ONOO(cid:1)/ONOOH)Coordination 17
1.4.4.2 OxidationPathway 17
1.4.4.3 NitrationPathways 20
1.5 Summary 23
References 24
ComputationalModelingforHomogeneousandEnzymaticCatalysis.
AKnowledge-BaseforDesigningEfficientCatalysts. K.MorokumaandD.G.Musaev(Eds.)
Copyright62008WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:978-3-527-31843-8
VIII Contents
2 AComparisonofTetrapyrroleCofactorsinNatureandtheirTuningby
AxialLigands 27
KasperP.Jensen,PatrikRydberg,JimmyHeimdal,andUlfRyde
2.1 Introduction 27
2.2 Methodology 29
2.3 ComparisonoftheIntrinsicChemicalPropertiesofthe
Tetrapyrroles 31
2.3.1 Introduction 31
2.3.2 SpinStates 32
2.3.3 TetrapyrrolesPreferTheirNativeIons 33
2.3.4 CavitySizeandFlexibilityoftheTetrapyrroles 33
2.3.5 Cytochrome-likeElectronTransfer 35
2.3.6 StabilityofaMetalaCarbonBond 36
2.3.7 MetallationReaction 37
2.4 TuningofTetrapyrroleStructureandFunctionbyAxialLigands 38
2.4.1 Introduction 38
2.4.2 ImportanceoftheLowerAxialLigandforB Chemistry 38
12
2.4.3 LowerAxialLigandinCofactorF430 41
2.4.4 ImportanceofAxialLigandsfortheGlobins 42
2.4.5 RoleofAxialLigandsfortheCytochromes 42
2.4.6 RoleoftheAxialLigandinHemeEnzymes 44
2.4.7 TuningtheHisLigandbyHydrogenBondsinHemeProteins 47
2.4.8 AxialLigandinChlorophylls 50
2.5 ConcludingRemarks 51
References 53
3 ModelingofMechanismsforMetalloenzymeswhereProtonsand
ElectronsEnterorLeave 57
PerE.M.SiegbahnandMargaretaR.A.Blomberg
3.1 Introduction 57
3.2 EnergyDiagrams 59
3.2.1 PhotosystemII 59
3.2.2 CytochromecOxidase 64
3.2.3 NitricOxideReduction 70
3.2.4 NiFe-hydrogenase 72
3.2.5 MolybdenumCODehydrogenase 76
3.3 Conclusions 79
References 80
4 PrinciplesofDinitrogenHydrogenation:ComputationalInsights 83
DjamaladdinG.Musaev,PetiaBobadova-Parvanova,andKeijiMorokuma
4.1 Introduction 83
4.2 ReactionMechanismoftheCoordinatedDinitrogenMoleculein
Di-zirconocene-N ComplexeswithaHydrogenMolecule 87
2
Contents IX
4.2.1 MechanismoftheReaction(3) 87
4.2.2 MechanismsoftheReactions(4)and(5) 89
4.3 FactorsControllingtheN CoordinationModesintheDi-zirconocene-
2
N Complexes 91
2
4.4 Whythe[(h5-C5MenH5(cid:1)n)2Ti]2(m2,h2,h2-N2)ComplexCannotAddaH2
MoleculetotheSide-onCoordinatedN ,whileitsZr-andHf-analogs
2
Can 95
4.4.1 RelativeStabilityoftheLowestSinglet(S)andTriplet(T)Electronic
StatesoftheComplexes[(h5-C5MenH5(cid:1)n)2M]2(m2,h2,h2-N2),II_M
(forM¼Ti,Zr,andHf,andn¼0and4) 96
4.4.2 ReactivityoftheLowestSingletandTripletStatesoftheComplexes
[(h5-C5MenH5(cid:1)n)2M]2(m2,h2,h2-N2),II_M,(forM¼Ti,Zr,andHf,and
n¼0and4)towardsH Molecules 99
2
4.5 WhyDizirconium-dinitrogenComplexeswithbis(Amidophosphine)
(P2N2)andCyclopentadienyl(Cp)LigandsReactdifferentlywiththe
HydrogenMolecule:RoleofLigandEnvironmentoftheZr
Centers 101
4.6 SeveralNecessaryConditionsforSuccessfulHydrogenationofa
CoordinatedDinitrogenMolecule 103
Appendix:ComputationalDetails 105
References 106
5 MechanismofPalladium-catalyzedCross-couplingReactions 109
AtaualpaA.C.Braga,GregoriUjaque,andFeliuMaseras
5.1 Introduction 109
5.2 OxidativeAddition 112
5.3 Transmetalation 114
5.3.1 Suzuki–MiyauraReaction 114
5.3.1.1 RoleoftheBase 115
5.3.1.2 CisversusTransSpeciesinbis(Phosphine)Systems 118
5.3.1.3 MonophosphineSystems 120
5.3.2 StilleReaction 122
5.4 ReductiveElimination 125
5.5 Isomerization 126
5.6 ConcludingRemarks 128
References 129
6 TransitionMetalCatalyzedCarbonxCarbonBondFormation:TheKeyof
HomogeneousCatalysis 131
ValentineP.Ananikov,DjamaladdinG.Musaev,andKeijiMorokuma
6.1 Introduction 131
6.1.1 CatalyticCaCBondFormationviatheReductiveElimination
Pathway 131
6.1.2 ReductiveEliminationofAlkylGroups(Alkyl–AlkylCoupling) 133
X Contents
6.2 CaCCouplingofUnsaturatedLigands 133
6.2.1 ReductiveEliminationfromtheSymmetricalR M(PH )
2 32
Complexes 134
6.2.2 ReductiveEliminationfromtheAsymmetricalRR0M(PH )
32
Complexes 137
6.2.3 HomocouplingversusHeterocouplingPathwaysviaCaCReductive
Elimination 140
6.2.4 MetalEffectonCaCReductiveEliminationReaction 141
6.2.5 LigandEffectonCaCReductiveEliminationReaction 142
6.2.6 DissociativeMechanismofCaCBondFormation 142
6.2.7 SolventEffectonCaCReductiveEliminationReaction 144
6.2.8 ReductiveEliminationofUnsaturatedOrganicMoleculesInvolving
CyanoandCarbonylGroups 144
6.3 Conclusions 145
References 145
7 OlefinPolymerizationUsingHomogeneousGroupIVMetallocenes 149
RobertD.J.Froese
7.1 Introduction 149
7.2 ComputationalDetails 152
7.3 ResultsandDiscussion 152
7.3.1 ChainPropagation 152
7.3.2 b-HydrideElimination 164
7.3.3 Chain-transfer-to-monomer 166
7.3.4 Chain-transfer-to-hydrogen 168
7.3.5 AbsoluteRatesofReactions 170
7.3.6 KineticConsiderations 173
7.4 Conclusions 176
References 177
8 GroupTransferPolymerizationofAcrylateswithMonoNuclearEarly
d-andf-blockMetallocenes.ADFTStudy 181
SimoneTomasiandTomZiegler
8.1 Introduction 181
8.2 ComputationalDetails 182
8.3 Discussion 184
8.3.1 PolymerizationMechanism 184
8.3.1.1 Initiation:FormationofaMetallocene-enolateComplex 184
8.3.1.2 ConformationsoftheMetallocene-acrylate-enolateComplexes 185
8.3.1.3 TransitionStatesoftheCouplingReaction 188
8.3.1.4 Ring-openingReactions 190
8.3.2 KineticSchemeforthePredictionofStereoregularity 195
8.3.3 SideReactionsInvolvingMetallacycles 198
8.3.3.1 BackbitingReactioninZr-andSm-eight-memberedMetallacycles 200