Hydrogen transfer reactions: 4 Biological aspects III - V
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2007
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| 245 | 1 | 0 | |a Hydrogen transfer reactions |n 4 |p Biological aspects III - V |c ed. by James T. Hynes ... |
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| 300 | |a XLIV, S. 1207 - 1559 |b Ill., graph. Darst. | ||
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| 700 | 1 | |a Hynes, James T. |e Sonstige |4 oth | |
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| adam_text | Contents
Foreword V
Preface XXXVU
Preface to Volumes 1 and 2 XXXIX
List of Contributors to Volumes 1 and 2 XLI
I Physical and Chemical Aspects, Parts I Ill
Part I Hydrogen Transfer in Isolated Hydrogen Bonded Molecules, Complexes
and Clusters 1
1 Coherent Proton Tunneling in Hydrogen Bonds
of Isolated Molecules: Malonaldehyde and Tropolone 3
Richard L. Redington
1.1 Introduction 3
1.2 Coherent Tunneling Splitting Phenomena in Malonaldehyde 5
1.3 Coherent Tunneling Phenomena in Tropolone 13
1.4 Tropolone Derivatives 26
1.5 Concluding Remarks 27
Acknowledgments 28
References 29
2 Coherent Proton Tunneling in Hydrogen Bonds of Isolated Molecules:
Carboxylic Dimers 33
Martina Havenith
2.1 Introduction 33
2.2 Quantum Tunneling versus Classical Over Barrier Reactions 34
2.3 Carboxylic Dimers 35
2.4 Benzoic Acid Dimer 38
2.4.1 Introduction 38
Hydrogen Transfer Reactions. Edited by J. T. Hynes, J. P. Klinman. H. H. Limbach, and R. L. Schowen
Copyright © 2007 WILEY VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978 3 527 30777 7
X I Contents
2.4.2 Determination of the Structure 38
2.4.3 Barriers and Splittings 39
2.4.4 Infrared Vibrational Spectroscopy 41
2.5 Formic Add Dimer 42
2.5.1 Introduction 42
2.5.2 Determination of the Structure 42
2.5.3 Tunneling Path 43
2.5.4 Barriers and Tunneling Splittings 44
2.5.5 Infrared Vibrational Spectroscopy 45
2.5.6 Coherent Proton Transfer in Formic Acid Dimer 46
2.6 Condusion 49
References 50
3 Gas Phase Vibrational Spectroscopy of Strong Hydrogen Bonds 53
Knut R. Asmis, Daniel M. Neumark, andjoel M. Bowman
3.1 Introduction 53
3.2 Methods 55
3.2.1 Vibrational Spectroscopy of Gas Phase Ions 55
3.2.2 Experimental Setup 56
3.2.3 Potential Energy Surfaces 58
3.2.4 Vibrational Calculations 59
3.3 Selected Systems 60
3.3.1 Bihalide Anions 60
3.3.2 The Protonated Water Dimer (H2O H OH2)+ 65
3.3.2.1 Experiments 65
3.3.2.2 Calculations 70
3.4 Outlook 75
Acknowledgments 76
References 77
4 Laser driven Ultrafast Hydrogen Transfer Dynamics 79
Oliver Kühn and Leticia Gonzalez
4.1 Introduction 79
4.2 Theory 80
4.3 Laser Control 83
4.3.1 Laser driven Intramolecular Hydrogen Transfer 83
4.3.2 Laser driven H Bond Breaking 90
4.4 Conclusions and Outlook 100
Acknowledgments 203
References 101
Contents I XI
Part II Hydrogen Transfer in Condensed Phases 105
5 Proton Transfer from Alkane Radical Cations to Alkanes 107
Jan Ceulemans
5.1 Introduction 308
5.2 Electronic Absorption of Alkane Radical Cations 108
5.3 Paramagnetic Properties of Alkane Radical Cations 109
5.4 The Bransted Acidity of Alkane Radical Cations 110
5.5 The a Basicity of Alkanes 112
5.6 Powder EPR Spectra of Alkyl Radicals 114
5.7 Symmetrie Proton Transfer from Alkane Radical Cations to Alkanes:
An Experimental Study in y Irradiated n Alkane Nanoparticles
Embedded in a Cryogenic CC13F Matrix 317
5.7.1 Mechanismofthe Radiolytic Process 117
5.7.2 Physical State of Alkane Aggregates in CC13F 118
5.7.3 Evidence for Proton donor and Proton acceptor Site Selectivity in the
Symmetrie Proton Transfer from Alkane Radical Cations to Alkane
Molecules 121
5.7.3.1 Proton donor Site Selectivity 121
5.7.3.2 Proton acceptor Site Selectivity 122
5.7.4 Comparison with Results on Proton Transfer and Deprotonation in
Other Systems 124
5.8 Asymmetrie Proton Transfer from Alkane Radical Cations to Alkanes:
An Experimental Study in y Irradiated Mixed Alkane Crystals 125
5.8.1 Mechanismofthe Radiolytic Process 125
5.8.2 Evidence for Proton donor and Proton acceptor Site Selectivity in the
Asymmetrie Proton Transfer from Alkane Radical Cations to
Alkanes 128
References 131
6 Single and Multiple Hydrogen/Deuterium Transfer Reactions in Liquids
and Solids 135
Hans Heinrich Limbach
6.1 Introduction 136
6.2 Theoretical 138
6.2.1 Coherent vs. Incoherent Tunneling 338
6.2.2 The Bigeleisen Theory 140
6.2.3 Hydrogen Bond Compression Assisted H transfer 141
6.2.4 Reduction of a Two dimensional to a One dimensional Tunneling
Model 143
6.2.5 The Beil Limbach Tunneling Model 146
6.2.6 Concerted Multiple Hydrogen Transfer 151
6.2.7 Multiple Stepwise Hydrogen Transfer 152
6.2.7.1 HH rransfer 153
XII I Contents
6.2.7.2 Degenerate Stepwise HHH transfer 159
6.2.7.3 Degenerate Stepwise HHHH transfer 161
6.2.8 Hydrogen Transfers Involving Pre equilibria 165
6.3 Applications 368
6.3.1 H transfers Coupled to Minor Heavy Atom Motions 174
6.3.1.1 Symmetrie Porphyrins and Porphyrin Analogs 174
6.3.1.2 Unsymmetrically Substituted Porphyrins 181
6.3.1.3 Hydroporphyrins 184
6.3.1.4 Intramolecular Single and Stepwise Double Hydrogen Transfer in
H bonds of Medium Strength 185
6.3.1.5 Dependence on the Environment 187
6.3.1.6 Intermolecular Multiple Hydrogen Transfer in H bonds of Medium
Strength 188
6.3.1.7 Dependence of the Barrier on Molecular Structure 193
6.3.2 H transfers Coupled to Major Heavy Atom Motions 197
6.3.2.1 H transfers Coupled to Conformational Changes 197
6.3.2.2 H transfers Coupled to Conformational Changes and Hydrogen Bond
Pre equilibria 203
6.3.2.3 H transfers in Complex Systems 212
6.4 Conclusions 216
Acknowledgments 217
References 217
7 Intra and Intermolecular Proton Transfer and Related Processes in
Confined Cyclodextrin Nanostructures 223
Abderrazzak Douhal
7.1 Introduction and Concept of Femtochemistry in Nanocavities 223
7.2 Overview of the Photochemistry and Photophysics of Cyclodextrin
Complexes 224
7.3 Picosecond Studies of Proton Transfer in Cyclodextrin
Complexes 225
7.3.1 l Hydroxy,2 acetonaphthone 225
7.3.2 1 Naphthol and 1 Aminopyrene 228
7.4 Femtosecond Studies of Proton Transfer in Cyclodextrin
Complexes 230
7.4.1 Coumarins 460 and 480 230
7.4.2 Bound and Free Water Molecules 231
7.5.3 2 (2 Hydroxyphenyl) 4 methyloxazole 236
7.5.4 Orange II 239
7.6 Concluding Remarks 240
Acknowledgment 241
References 241
Contents I XIII
8 Tautomerization in Porphycenes 245
Jacek Waluk
8.1 Introduction 245
8.2 Tautomerization in the Ground Electronic State 247
8.2.1 Structural Data 247
8.2.2 NMR Studies of Tautomerism 251
8.2.3 Supersonic Jet Studies 253
8.2.4 The Nonsymmetric Case: 2,7,12,17 Tetra n propyl 9
acetoxyporphycene 256
8.2.5 Calculations 258
8.3 Tautomerization in the Lowest Excited Singlet State 258
8.3.1 Tautomerization as a Tool to Determine Transition Moment
Directions in Low Symmetry Molecules 260
8.3.2 Determination of Tautomerization Rates from Anisotropy
Measurements 262
8.4 Tautomerization in the Lowest Excited Triplet State 265
8.5 Tautomerization in Single Molecules of Porphycene 266
8.6 Summary 267
Acknowledgments 268
References 269
9 Proton Dynamics in Hydrogen bonded Crystals 273
Mikhail V. Vener
9.1 Introduction 273
9.2 Tentative Study of Proton Dynamics in Crystals with Quasi linear
H bonds 274
9.2.1 A Model 2D Hamiltonian 275
9.2.2 Specific Features of H bonded Crystals with a Quasi symmetric
O H O Fragment 277
9.2.3 Proton Transfer Assisted by a Low frequency Mode
Excitation 279
9.2.3.1 Crystals with Moderate H bonds 280
9.2.3.2 Crystals with Streng H bonds 283
9.2.3.3 Limitations of the Model 2D Treatment 284
9.2.4 Vibrational Spectra of H bonded Crystals: IR versus INS 285
9.3 DFT Calculations with Periodic Boundary Conditions 286
9.3.1 Evaluation of the Vibrational Spectra Using Classical MD
Simulations 287
9.3.2 Effects of Crystalline Environment on Strong H bonds:
the H5O2+ Ion 288
9.3.2.1 The Structure and Harmonie Frequencies 288
9.3.2.2 The PESoftheO H O Fragment 291
9.3.2.3 Anharmonic INS and IR Spectra 293
XIV I Contents
9.4 Conclusions 296
Acknowledgments 297
References 217
Part IM Hydrogen Transfer in Polar Environments 301
10 Theoretical Aspects of Proton Transfer Reactions
in a Polar Environment 303
Philip M. Kiefer and James T. Hynes
10.1 Introduction 303
10.2 Adiabatic Proton Transfer 309
10.2.1 General Picture 309
10.2.2 Adiabatic Proton Transfer Free Energy Relationship (FER) 315
10.2.3 Adiabatic Proton Transfer Kinetic Isotope Effects 320
10.2.3.1 KIE Arrhenius Behavior 321
10.2.3.2 KIE Magnitude and Variation with Reaction Asymmetry 321
10.2.3.3 Swain Schaad Relationship 323
10.2.3.4 Further Discussion of Nontunneling Kinetic Isotope Effects 323
10.2.3.5 Transition State Geometrie Structure in the Adiabatic PT Picture 324
10.2.4 Temperature Solvent Polarity Effects 325
10.3 Nonadiabatic Tunneling Proton Transfer 326
10.3.1 General Nonadiabatic Proton Transfer Perspective and Rate
Constant 327
10.3.2 Nonadiabatic Proton Transfer Kinetic Isotope Effects 333
10.3.2.1 Kinetic Isotope Effect Magnitude and Variation
with Reaction Asymmetry 333
10.3.2.2 Temperature Behavior 337
10.3.2.3 Swain Schaad Relationship 340
10.4 Concluding Remarks 341
Acknowledgments 343
References 345
11 Direct Observation of Nuclear Motion during
Ultra fast Intramolecular Proton Transfer 349
Stefan Lochbrunner, Christian Schriever, and Eberhard Riedle
11.1 Introduction 349
11.2 Time resolved Absorption Measurements 352
11.3 SpectralSignaturesofUltrafastESIPT 353
11.3.1 Characteristic Features of the Transient Absorption 354
11.3.2 Analysis 356
11.3.3 Ballistic Wavepacket Motion 357
11.3.4 Coherently Excited Vibrations in Product Modes 359
11.4 Reaction Mechanism 362
11.4.1 Reduction of Donor Acceptor Distance by Skeletal Motions 362
Contents I XV
11.4.2 Multidimensional ESIPT Model 363
11.4.3 Micro irreversibility 365
11.4.4 Topology of the PES and Turns in the Reaction Path 366
11.4.5 Comparison with Ground State Hydrogen Transfer Dynamics 368
11.4.6 Internal Conversion 368
11.5 Reaction Path Specific Wavepacket Dynamics in Double Proton
Transfer Molecules 370
11.6 Conclusions 372
Acknowledgment 373
References 373
12 Solvent Assisted Photoacidity 377
Dina Pines and Ehud Pines
12.1 Introduction 377
12.2 Photoacids, Photoacidity and Förster Cyde 378
12.2.1 Photoacids and Photobases 378
12.2.2 Use of the Förster Cyde to Estimate the Photoacidity of
Photoacids 379
12.2.3 Direct Methods for Determining the Photoacidity of Photoacids 387
12.3 Evidence for the General Validity of the Förster Cycle and the
K*a Scale 389
12.3.1 Evidence for the General Validity of the Förster Cycle Based on Time
resolved and Steady State Measurements of Excited state Proton
Transfer of Photoacids 389
12.3.2 Evidence Based on Free Energy Correlations 393
12.4 Factors Affecting Photoacidity 397
12.4.1 General Considerations 397
12.4.2 Comparing the Solvent Effect on the Photoacidities of Neutral and
Cationic Photoacids 398
12.4.3 The Effect of Substituents on the Photoacidity of Aromatic Alcohols 400
12.5 Solvent Assisted Photoacidity: The 1LO, lLb Paradigm 404
12.6 Summary 410
Acknowledgments 411
References 411
13 Design and Implementation of Super Photoacids 417
Laren M. Tolbert and Kyril M. Solntsev
13.1 Introduction 417
13.2 Excited state Proton Transfer (ESPT) 420
13.2.1 1 Naphthol vs. 2 Naphthol 420
13.2.2 Super Photoacids 422
13.2.3 Fluorinated Phenols 426
13.3 Natureof the Solvent 426
13.3.1 Hydrogen Bonding and Solvatochromism in Super Photoacids 426
XVI I Contents
13.3.2 Dynamics in Water and Mixed Solvents 427
13.3.3 Dynamics in Nonaqueous Solvents 428
13.3.4 ESPT in the Gas Phase 431
13.3.5 Stereochemistry 433
13.4 ESPT in Biological Systems 433
13.4.1 The Green Fluorescent Protein (GFP) or ESPT in a Box 435
13.5 Conclusions 436
Acknowledgments 436
References 437
Foreword V
Preface XXXVII
Preface to Volumes 1 and 2 XXXIX
List of Contributors to Volumes 1 and 2 XII
I Physical and Chemical Aspects, Parts IV—VII
Part IV Hydrogen Transfer in Protic Systems 441
14 Bimolecular Proton Transfer in Solution 443
Erik T. J. Nibbering and Ehud Pines
14.1 Intermolecular Proton Transfer in the Liquid Phase 443
14.2 Photoacids as Ultrafast Optical Triggers for Proton Transfer 445
14.3 Proton Recombination and Acid Base Neutralization 448
14.4 Reaction Dynamics Probing with Vibrational Marker Modes 449
Acknowledgment 455
References 455
15 Coherent Low frequency Motions in Condensed Phase Hydrogen Bonding
and Transfer 459
Thomas Elsaesser
15.1 Introduction 459
15.2 Vibrational Excitations of Hydrogen Bonded Systems 460
15.3 Low frequency Wavepacket Dynamics of Hydrogen Bonds in the
Electronic Ground State 463
15.3.1 Intramolecular Hydrogen Bonds 463
15.3.2 Hydrogen Bonded Dimers 466
15.4 Low frequency Motions in Excited State Hydrogen Transfer 471
15.5 Conclusions 475
Acknowledgments 476
References 476
Contents I XVII
16 Proton Coupled Electron Transfer: Theoretical Formulation
and Applications 479
Sharon Hammes Schiffer
16.1 Introduction 479
16.2 Theoretical Formulation for PCET 480
16.2.1 Fundamental Concepts 480
16.2.2 Proton Donor Acceptor Motion 483
16.2.3 Dynamical Effects 485
16.2.3.1 Dielectric Continuum Representation of the Environment 486
16.2.3.2 Molecular Representation of the Environment 490
16.3 Applications 492
16.3.1 PCET in Solution 492
16.3.2 PCET in a Protein 498
16.4 Conclusions 500
Acknowledgments 500
References 501
17 The Relation between Hydrogen Atom Transfer and Proton coupled Electron
Transfer in Model Systems 503
Justin M. Hodgkiss, Joel Rosenthal, and Daniel C. Nocera
17.1 Introduction 503
17.1.1 Formulation of HAT as a PCET Reaction 504
17.1.2 ScopeofChapter 507
17.1.2.1 Unidirectional PCET 508
17.1.2.2 Bidirectional PCET 508
17.2 Methods of HAT and PCET Study 509
17.2.1 Free Energy Correlations 510
17.2.2 Solvent Dependence 511
17.2.3 Deuterium Kinetic Isotope Effects 511
17.2.4 Temperature Dependence 512
17.3 Unidirectional PCET 512
17.3.1 Type A: Hydrogen Abstraction 512
17.3.2 Type B: Site Differentiated PCET 523
17.3.2.1 PCET across Symmetrie Hydrogen Bonding Interfaces 523
17.3.2.2 PCET across Polarized Hydrogen Bonding Interfaces 527
17.4 Bidirectional PCET 537
17.4.1 Type C: Non Specific 3 Point PCET 538
17.4.2 Type D: Site Specified 3 Point PCET 543
17.5 The Different Types of PCET in Biology 548
17.6 Application of Emerging Ultrafast Spectroscopy to PCET 554
Acknowledgment 556
References 556
XVIII I Contents
Part V Hydrogen Transfer in Organic and Organometallic Reactions 563
18 Formation of Hydrogen bonded Carbanions as Intermediates in Hydron
Transfer between Carbon and Oxygen 565
Heinz F. Koch
18.1 Proton Transfer from Carbon Acids to Methoxide Ion 565
18.2 Proton Transfer from Methanol to Carbanion Intermediates 573
18.3 Proton Transfer Associated with Methoxide Promoted
Dehydrohalogenation Reactions 576
18.4 Conclusion 580
References 581
19 Theoretical Simulations of Free Energy Relationships in
Proton Transfer 583
lan H. Williams
19.1 Introduction 583
19.2 Qualitative Models for FERs 584
19.2.1 What is Meant by Reaction Coordinate ? 588
19.2.2 The Bransted a as a Measure of TS Structure 589
19.3 FERs from MO Calculations of PESs 590
19.3.1 Energies and Transition States 590
19.4 FERs from VB Studies of Free Energy Changes for PT in Condensed
Phases 597
19.5 Concluding Remarks 600
References 600
20 The Extraordinary Dynamic Behavior and Reactivity of Dihydrogen and
Hydride in the Coordination Sphere of Transition Metals 603
GregoryJ. Kubas
20.1 Introduction 603
20.1.1 Structure, Bonding, and Activation of Dihydrogen Complexes 603
20.1.2 Extraordinary Dynamics of Dihydrogen Complexes 606
20.1.2 Vibrational Motion of Dihydrogen Complexes 608
20.1.3 Elongated Dihydrogen Complexes 609
20.1.4 Cleavage of the H H Bond in Dihydrogen Complexes 620
20.2 H2 Rotation in Dihydrogen Complexes 615
20.2.1 Determination of the Barrier to Rotation of Dihydrogen 616
20.3 NMR Studies of H2 Activation, Dynamics, and Transfer
Processes 637
20.3.1 Solution NMR 617
20.3.2 Solid State NMR of H2 Complexes 621
Contents I XIX
20.4 Intramolecular Hydrogen Rearrangement and Exchange 623
20.4.1 Extremely Facile Hydrogen Transfer in IrXH2(H2)(PR3)2 and Other
Systems 627
20.4.2 Quasielastic Neutron Scattering Studies of H2 Exchange with cis
Hydrides 632
20.5 Summary 633
Acknowledgments 634
References 634
21 Dihydrogen Transfer and Symmetry: The Role of Symmetry in the Chemistry
of Dihydrogen Transfer in the Light of N M R Spectroscopy 639
Gerd Buntkowsky and Hans Heinrich Limbach
21.1 Introduction 639
21.2 Tunneling and Chemical Kinetics 641
21.2.1 The Role of Symmetry in Chemical Exchange Reactions 641
21.2.1.1 Coherent Tunneling 642
21.2.1.2 The Density Matrix 648
21.2.1.3 The Transition from Coherent to Incoherent Tunneling 649
21.2.2 Incoherent Tunneling and the Bell Model 653
21.3 Symmetry Effects on NMR Lineshapes of Hydration Reactions 655
21.3.1 Analytical Solution for the Lineshape of PHIP Spectra Without
Exchange 657
21.3.2 Experimental Examples of PHIP Spectra 662
21.3.2.1 PHIP under ALTADENA Conditions 662
21.3.2.2 PHIP Studies of Stereoselective Reactions 662
21.3.2.3 13C PHIP NMR 664
21.3.3 Effects of Chemical Exchange on the Lineshape of PHIP Spectra 665
21.4 Symmetry Effects on NMR Lineshapes of Intramolecular Dihydrogen
Exchange Reactions 670
21.4.1 Experimental Examples 670
21.4.1.1 Slow Tunneling Determined by *H Liquid State
NMR Spectroscopy 671
21.4.1.2 Slow to Intermediate Tunneling Determined by
2H Solid State NMR 671
21.4.1.3 Intermediate to Fast Tunneling Determined by
2H Solid State NMR 673
21.4.1.4 Fast Tunneling Determined by Incoherent Neutron Scattering 675
21.4.2 Kinetic Data Obtained from the Experiments 675
21.4.2.1 Ru D2 Complex 676
21.4.2.2 W(PCy)3(CO)3 (*7 H2 ) Complex 677
21.5 Summary and Conclusion 678
Acknowledgments 679
References 679
XX I Contents
Part VI Proton Transfer in Solids and Surfaces 683
22 Proton Transfer in Zeolites 685
Joachim Sauer
22.1 Introduction The Active Sites ofAcidic Zeolite Catalysts 685
22.2 Proton Transfer to Substrate Molecules within Zeolite Cavities 686
22.3 Formation of NH4+ions on NH3 adsorption 688
22.4 Methanol Molecules and Dimers in Zeolites 692
22.5 Water Molecules and Clusters in Zeolites 694
22.6 Proton Jumps in Hydrated and Dry Zeolites 700
22.7 Stability ofCarbenium Ions in Zeolites 703
References 706
23 Proton Conduction in Fuel Cells 709
Klaus Dieter Kreuer
23.1 Introduction 709
23.2 Proton Conducting Electrolytes and Their Application in Fuel Cells 710
23.3 Long range Proton Transport of Protonic Charge Carriers in
Homogeneous Media 714
23.3.1 Proton Conduction in Aqueous Environments 715
23.3.2 Phosphoric Acid 719
23.3.3 Heterocycles (Imidazole) 720
23.4 Confinement and Interfacial Effects 723
23.4.1 Hydrated Acidic Polymers 723
23A.2 Adducts of Basic Polymers with Oxo acids 727
23.4.3 Separated Systems with Covalently Bound Proton Solvents 728
23.5 Concluding Remarks 731
Acknowledgment 733
References 733
24 Proton Diffusion in Ice Bifayers 737
Katsutoshi Aoki
24.1 Introduction 737
24.1.1 Phase Diagram and Crystal Structure of Ice 737
24.1.2 Molecular and Protonic Diffusion 739
24.1.3 Protonic Diffusion at High Pressure 740
24.2 Experimental Method 741
24.2.1 Diffusion Equation 741
24.2.2 High Pressure Measurement 742
24.2.3 Infrared Reflection Spectra 743
24.2.4 Thermal Activation of Diffusion Motion 744
24.3 Spectral Analysis of the Diffusion Process 745
24.3.1 Protonic Diffusion 745
Contents I XXI
24.3.2 Molecular Diffusion 746
24.3.3 Pressure Dependence of Protonic Diffusion Coefficient 747
24.4 Summary 749
References 749
25 Hydrogen Transfer on Metal Surfaces 751
Klaus Christmann
25.1 Introduction 751
25.2 The Principles of the Interaction of Hydrogen with Surfaces: Terms
and Definitions 755
25.3 The Transfer of Hydrogen on Metal Surfaces 761
25.3.1 Hydrogen Surface Diffusion on Homogeneous Metal Surfaces 762
25.3.2 Hydrogen Surface Diffusion and Transfer on Heterogeneous Metal
Surfaces 771
25.4 Alcohol and Water on Metal Surfaces: Evidence of H Bond Formation
and H Transfer 775
25.4.1 Alcohols on Metal Surfaces 775
25.4.2 Water on Metal Surfaces 778
25.5 Conclusion 783
Acknowledgments 783
References 783
26 Hydrogen Motion in Metals 787
RolfHempelmann and Alexander Skripov
26.1 Survey 787
26.2 Experimental Methods 788
26.2.1 Anelastic Relaxation 788
26.2.2 Nuclear Magnetic Resonance 790
26.2.3 Quasielastic Neutron Scattering 792
26.2.4 Other Methods 795
26.3 Experimental Results on Diffusion Coefficients 796
26.4 Experimental Results on Hydrogen Jump Diffusion Mechanisms 801
26.4.1 Binary Metal Hydrogen Systems 802
26.4.2 Hydrides of Alloys and Intermetallic Compounds 804
26.4.3 Hydrogen in Amorphous Metals 810
26.5 Quantum Motion of Hydrogen 812
26.5.1 Hydrogen Tunneling in Nb Doped with Impurities 824
26.5.2 Hydrogen Tunneling in a MnHx 827
26.5.3 Rapid Low temperarure Hopping of Hydrogen in a ScH^(Dx) and
TaV2H%(Dx) 822
26.6 Concluding Remarks 825
Acknowledgment 825
References 826
XXII I Contents
Part VII Special Features of Hydrogen Transfer Reactions 831
27 Variational Transition State Theory in the Treatment of Hydrogen Transfer
Reactions 833
Donald G. Truhlar and Bruce C. Garrett
27.1 Introduction 833
27.2 Incorporation of Quantum Mechanical Effects in VTST 835
27.2.1 Adiabatic Theory of Reactions 837
27.2.2 Quantum Mechanical Effects on Reaction Coordinate Motion 840
27.3 H atom Transfer in Bimolecular Gas phase Reactions 843
27.3.1 H + H2andMu + H2 843
27.3.2 Cl + HBr 849
27.3.3 Cl + CH4 853
21A Intramolecular Hydrogen Transfer in Unimolecular Gas phase
Reactions 857
27.4.1 Intramolecular H transfer in 1,3 Pentadiene 858
27.4.2 1,2 Hydrogen Migration in Methylchlorocarbene 860
27.5 Liquid phase and Enzyme catalyzed Reactions 860
27.5.1 Separable Equilibrium Solvation 862
27.5.2 Equilibrium Solvation Path 864
27.5.3 Nonequilibrium Solvation Path 864
27.5.4 Potential of mean force Method 865
27.5.5 Ensemble averaged Variational Transition State Theory 865
27.6 Examplesof Condensed phase Reactions 867
27.6.1 H + Methanol 867
27.6.2 Xylose Isomerase 868
27.6.3 Dihydrofolate Reductase 868
27.7 Another Perspective 869
27.8 Concluding Remarks 869
Acknowledgments 871
References 871
28 Quantum Mechanical Tunneling of Hydrogen Atoms in
Some Simple Chemical Systems 875
K. U. Ingold
28.1 Introduction 875
28.2 Unimolecular Reactions 876
28.2.1 Isomerization of Sterically Hindered Phenyl Radicals 876
28.2.1.1 2,4,6 Tri tert butylphenyl 876
28.2.1.2 Other Sterically Hindered Phenyl Radicals 881
28.2.2 Inversion of Nonplanar, Cydic, Carbon Centered Radicals 883
28.2.2.1 Cydopropyl and 1 Methylcyclopropyl Radicals 883
28.2.2.2 The Oxiranyl Radical 884
28.2.2.3 The Dioxolanyl Radical 886
Contents I XXIII
28.2.2.4 Summary 887
28.3 Bimolecular Reactions 887
28.3.1 H Atom Abstraction by Methyl Radicals in Organic Glasses 887
28.3.2 H Atom Abstraction by Bis(trifluoromethyl) Nitroxide in the Liquid
Phase 890
References 892
29 Multiple Proton Transfer: From Stepwise to Concerted 895
Zorka Smedarchina, Willem Siebrand, and Antonio Fernündez Ramos
29.1 Introduction 895
29.2 Basic Model 897
29.3 Approaches to Proton Tunneling Dynamics 904
29.4 Tunneling Dynamics for Two Reaction Coordinates 908
29.5 Isotope Effects 914
29.6 Dimeric Formic Acid and Related Dimers 918
29.7 Other Dimeric Systems 922
29.8 Intramolecular Double Proton Transfer 926
29.9 Proton Conduits 932
29.10 Transfer of More Than Two Protons 939
29.11 Conclusion 940
Acknowledgment 943
References 943
Foreword V
Preface XXXVII
Preface to Volumes 3 and 4 XXXIX
List of Contributors to Volumes 3 and 4 XII
II Biological Aspects, Parts •—11
Part I Models for Biological Hydrogen Transfer 947
1 Proton Transfer to and from Carbon in Model Reactions 949
Tina L Amyes and John P. Richard
1.1 Introduction 949
1.2 Rate and Equilibrium Constants for Carbon Deprotonation in
Water 949
1.2.1 Rate Constants for Carbanion Formation 951
1.2.2 Rate Constants for Carbanion Protonation 953
1.2.2.1 Protonation by Hydronium Ion 953
XXIV I Contents
1.2.2.2 Protonation by Buffer Acids 954
1.2.2.3 Protonation by Water 955
1.2.3 The Bürden Borne by Enzyme Catalysts 955
1.3 Substituent Effects on Equilibrium Constants for Deprotonation of
Carbon 957
1.4 Substituent Effects on Rate Constants for Proton Transfer at
Carbon 958
IAA The Marcus Equation 958
1.4.2 Marcus Intrinsic Barriers for Proton Transfer at Carbon 960
1.4.2.1 Hydrogen Bonding 960
1.4.2.2 Resonance Effects 962
1.5 Small Molecule Catalysis of Proton Transfer at Carbon 965
1.5.1 General Base Catalysis 966
1.5.2 Electrophilic Catalysis 967
1.6 Comments on Enzymatic Catalysis of Proton Transfer 970
Acknowledgment 970
References 971
2 General Acid Base Catalysis in Model Systems 975
AnthonyJ. Kirby
2.1 Introduction 975
2.1.1 Kinetics 975
2.1.2 Mechanism 977
2.1.3 Kinetic Equivalence 979
2.2 Strucrural Requirements and Mechanism 981
2.2.1 General Acid Catalysis 982
2.2.2 Classical General Base Catalysis 983
2.2.3 General Base Catalysis of Cyclization Reactions 984
2.2.3.1 Nucleophilic Substitution 984
2.2.3.2 Ribonuclease Models 985
2.3 Intramolecular Reactions 987
2.3.1 Introduction 987
2.3.2 Efficient Intramolecular General Acid Base Catalysis 988
2.3.2.1 Aliphatic Systems 992
2.3.3 Intramolecular General Acid Catalysis of Nucleophilic Catalysis 993
2.3.4 Intramolecular General Acid Catalysis of Intramolecular Nucleophilic
Catalysis 998
2.3.5 Intramolecular General Base Catalysis 999
2.4 Proton Transfers to and from Carbon 2000
2.4.1 Intramolecular General Acid Catalysis 2002
2.4.2 Intramolecular General Base Catalysis 2004
2.4.3 Simple Enzyme Models 2006
2.5 Hydrogen Bonding, Mechanism and Reactivity 1007
References 2020
Contents I XXV
3 Hydrogen Atom Transfer in Model Reactions 1013
Christian Schöneich
3.1 Introduction 1013
3.2 Oxygen centered Radicals 1013
3.3 Nitrogen dentered Radicals 1017
3.3.1 Generation of Aminyl and Amidyl Radicals 1017
3.3.2 Reactions of Aminyl and Amidyl Radicals 1018
3.4 Sulfur centered Radicals 1019
3.4.1 Thiols and Thiyl Radicals 1020
3.4.1.1 Hydrogen Transfer from Thiols 1020
3.4.1.2 Hydrogen Abstraction by Thiyl Radicals 1023
3.4.2 Sulfide Radical Cations 1029
3.5 Conclusion 1032
Acknowledgment 1032
References 1032
4 Model Studies of Hydride transfer Reactions 1037
Richard L Schowen
4.1 Introduction 1037
4.1.1 Nicotinamide Coenzymes: Basic Features 1038
4.1.2 Flavin Coenzymes: Basic Features 1039
4.1.3 Quinone Coenzymes: Basic Features 1039
4.1.4 Matters Not Treated in This Chapter 1039
4.2 The Design ofSuitable Model Reactions 1040
4.2.1 The Anchor Principle of Jencks 1042
4.2.2 The Proximity Effectof Bruice 1044
4.2.3 Environmental Considerations 3045
4.3 The Role of Model Reactions in Mechanistic Enzymology 1045
4.3.1 Kinetic Baselines for Estimations of Enzyme Catalytic Power 1045
4.3.2 Mechanistic Baselines and Enzymic Catalysis 1047
4.4 Models for Nicotinamide mediated Hydrogen Transfer 1048
4.4.1 Events in the Course of Formal Hydride Transfer 1048
4.4.2 Electron transfer Reactions and H atom transfer Reactions 1049
4.4.3 Hydride transfer Mechanisms in Nicotinamide Models 3052
4.4.4 Transition state Structure in Hydride Transfer The Kreevoy
Model 1054
4.4.5 Quantum Tunneling in Model Nicotinamide mediated Hydride
Transfer 3060
4.4.6 Intramolecular Models for Nicotinamide mediated Hydride
Transfer 3063
4.4.7 Summary 1063
4.5 Models for Flavin mediated Hydride Transfer 3064
4.5.1 Differences between Flavin Reactions and Nicotinamide
Reactions 3064
XXVI I Contents
4.5.2 The Hydride transfer Process in Model Systems 1065
4.6 Models for Quinone mediated Reactions 1068
4.7 Summary and Condusions 1071
4.8 Appendix: The Use of Model Reactions to Estimate Enzyme Catalytic
Power 1071
References 1074
5 Acid Base Catalysis in Designed Peptides 1079
Lars Baltzer
5.1 Designed Polypeptide Catalysts 1079
5.1.1 Protein Design 1080
5.1.2 Catalyst Design 1083
5.1.3 Designed Catalysts 1085
5.2 Catalysis of Ester Hydrolysis 1089
5.2.1 Design ofa Folded Polypeptide Catalyst for Ester Hydrolysis 1089
5.2.2 The HisH+ His Pair 1091
5.2.3 Reactivity According to the Brönsted Equation 1093
5.2.4 Cooperative Nucleophilic and General acid Catalysis in Ester
Hydrolysis 1094
5.2.5 Why General acid Catalysis? 1095
5.3 Limits of Activity in Surface Catalysis 1096
5.3.1 Optimal Organization of His Residues for Catalysis of Ester
Hydrolysis 1097
5.3.2 Substrate and Transition State Binding 1098
5.3.3 His Catalysis in Re engineered Proteins 1099
5.4 Computational Catalyst Design 1100
5.4.1 Ester Hydrolysis 1101
5.4.2 Triose Phosphate Isomerase Activity by Design 1101
5.5 Enzyme Design 1102
References 3102
Part II General Aspects of Biological Hydrogen Transfer 1105
6 Enzymatic Catalysis of Proton Transfer at Carbon Atoms 1107
John A. Cerlt
6.1 Introduction 1107
6.2 The Kinetic Problems Associated with Proton Abstraction from
Carbon 1108
6.2.1 Marcus Formalism for Proton Transfer 1110
6.2.2 AG°, the Thermodynamic Barrier 1111
6.2.3 AG*!,,,, the Intrinsic Kinetic Barrier 1112
6.3 Structural Strategies for Reduction of AG° 1114
6.3.1 Proposais for Understanding the Rates of Proton Transfer 1114
6.3.2 Short Strang Hydrogen Bonds 1115
Contents I XXVII
6.3.3 Electrostatic Stabilization of Enolate Anion Intermediates 2225
6.3.4 Experimental Measure of Differential Hydrogen Bond Strengths 1116
6.4 Experimental Paradigms for Enzyme catalyzed Proton Abstraction
from Carbon 1118
6.4.1 Triose Phosphate Isomerase 1118
6.4.2 Ketosteroid Isomerase 1125
6.4.3 Enoyl CoA Hydratase (Crotonase) 2327
6.4.4 Mandelate Racemase and Enolase 1131
6.5 Summary 1134
References 1135
7 Multiple Hydrogen Transfers in Enzyme Action 1139
M. Ashley Spies and Michael D. Toney
7.1 Introduction 1139
7.2 Cofactor Dependent with Activated Substrates 1139
7.2.1 Alanine Racemase 1139
7.2.2 Broad Specificity Amino Acid Racemase 1151
7.2.3 Serine Racemase 1152
7.2.4 Mandelate Racemase 1152
7.2.5 ATP Dependent Racemases 1154
7.2.6 Methylmalonyl CoA Epimerase 1156
7.3 Cofactor Dependent with Unactivated Substrates 1157
7.4 Cofactor Independent with Activated Substrates 2 257
7.4.1 Proline Racemase 2257
7.4.2 Glutamate Racemase 2262
7.4.3 DAP Epimerase 2262
7.4.4 Sugar Epimerases 2 265
7.5 Cofactor Independent with Unactivated Substrates 2265
7.6 Summary 2266
References 2267
8 Computer Simulations of Proton Transfer in Proteins and Solutions 2272
Sonja Braun Sand, Mats H. M. Olsson, Janez Mavri, and Arieh Warshel
8.1 Introduction 2 272
8.2 Simulating PT Reactions by the EVB and other QM/MM
Methods 2272
8.3 Simulating the Flucruations of the Environment and Nuclear
Quantum Mechanical Effects 2277
8.4 The EVB asa Basis for LFERofPT Reactions J285
8.5 Demonstrating the Applicability of the Modified Marcus
Equation 2288
8.6 General Aspects of Enzymes that Catalyze PT Reactions 2294
8.7 Dynamics, Tunneling and Related Nuclear Quantum Mechanical
Effects 2 295
XXVIII I Contents
8.8 Concluding Remarks 1198
Acknowledgements 1199
Abbreviations 1199
References 1200
Foreword V
Preface XXXVII
Preface to Volumes 3 and 4 XXXIX
List of Contributors to Volumes 3 and 4 XU
II Biological Aspects, Parts Ill V
Part III Quantum Tunneling and Protein Dynamics 1207
9 The Quantum Kramers Approach to Enzymatic Hydrogen Transfer
Protein Dynamics as it Couples to Catalysis 1209
Steven D. Schwartz
9.1 Introduction 1209
9.2 The Derivation of the Quantum Kramers Method 1210
9.3 Promoting Vibrations and the Dynamics of Hydrogen Transfer 1213
9.3.1 Promoting Vibrations and The Symmetry of Coupling 1213
9.3.2 Promoting Vibrations Corner Cutting and the Masking of
KIEs 1215
9.4 Hydrogen Transfer and Promoting Vibrations Alcohol
Dehydrogenase 1217
9.5 Promoting Vibrations and the Kinetic Control of Enzymes
Lactate Dehydrogenase 1223
9.6 The Quantum Kramers Model and Proton Coupled Electron
Transfer 1231
9.7 Promoting Vibrations and Electronic Polarization 1233
9.8 Conclusions 1233
Acknowledgment 1234
References 1234
10 Nuclear Tunneling in the Condensed Phase: Hydrogen Transfer
in Enzyme Reactions 1241
Michael J. Knapp, Matthew Meyer, and Judith P. Klinman
10.1 Introduction 1241
10.2 Enzyme Kinetics: Extracting Chemistry from Complexity 1242
10.3 Methodology for Detecting Nonclassical H Transfers 1245
Contents I XXIX
10.3.1 Bond Stretch KIE Model: Zero point Energy Effects 1245
10.3.1.1 Primary Kinetic Isotope Effects 3246
10.3.1.2 Secondary Kinetic Isotope Effects 1247
10.3.2 Methods to Measure Kinetic Isotope Effects 1247
10.3.2.1 Noncompetitive Kinetic Isotope Effects: fecat or kC3t/KM 1247
10.3.2.2 Competitive Kinetic Isotope Effects: kat/KM 1248
10.3.3 Diagnostics for Nonclassical H Transfer 1249
10.3.3.1 The Magnitude of Primary KIEs: feH/feD 8 at Room
Temperature 1249
10.3.3.2 Discrepant Predictions of Transition state Structure and
Inflated Secondary KIEs 1251
10.3.3.3 Exponential Breakdown: Rule of the Geometrie Mean and
Swain Schaad Relationships 1252
10.3.3.4 Variable Temperature KIEs: AH/AD » 1 or AH/AD « 1 1254
10.4 Concepts and Theories Regarding Hydrogen Tunneling 1256
10.4.1 Conceptual View of Tunneling 1256
10.4.2 Tunnel Corrections to Rates: Static Barriers 2258
10.4.3 Fluctuating Barriers: Reproducing Temperature Dependences 1260
10.4.4 Overview 1264
10.5 Experimental Systems 1265
10.5.1 Hydride Transfers 3265
10.5.1.1 Alcohol Dehydrogenases 3265
10.5.1.2 Glucose Oxidase 2270
10.5.2 Amine Oxidases 1273
10.5.2.1 Bovine Serum Amine Oxidase 1273
10.5.2.2 Monoamine Oxidase B 1275
10.5.3 Hydrogen Atom (H*) Transfers 1276
10.5.3.1 Soybean Lipoxygense 1 1276
10.5.3.2 Peptidylglycine a Hydroxylating Monooxygenase (PHM) and
Dopamine /3 Monooxygenase (D/?M) 2279
10.6 Concluding Comments 2280
References 3282
11 Multiple isotope Probesof Hydrogen Tunneling 1285
W. Phillip Huskey
11.1 Introduction 2285
11.2 Background: H/D Isotope Effects as Probes of Tunneling 1287
11.2.1 One frequency Models 1287
11.2.2 Temperature Dependence of Isotope Effects 1289
11.3 Swain Schaad Exponents: H/D/T Rate Comparisons 1290
11.3.1 Swain Schaad Limits in the Absence of Tunneling 2293
11.3.2 Swain Schaad Exponents for Tunneling Systems 2292
11.3.3 Swain Schaad Exponents from Computational Studies that
Include Tunneling 2293
XXX I Contents
11.3.4 Swain Schaad Exponents for Secondary Isotope Effects 1294
11.3.5 Effects of Mechanistic Complexity on Swain Schaad
Exponents 1294
11.4 Ruie of the Geometrie Mean: Isotope Effects on Isotope
Effects 1297
11.4.1 RGM Breakdown from Intrinsic Nonadditivity 1298
11.4.2 RGM Breakdown from Isotope sensitive Effective States 1300
11.4.3 RGM Breakdown as Evidence for Tunneling 1303
11.5 Saunders Exponents: Mixed Multiple Isotope Probes 1304
11.5.1 Experimental Considerations 2304
11.5.2 Separating Swain Schaad and RGM Effects 1304
11.5.3 Effects of Mechanistic Complexity on Mixed Isotopic
Exponents 1306
11.6 Concluding Remarks 1306
References 1307
12 Current Issues in Enzymatic Hydrogen Transfer from Carbon:
Tunneling and Coupled Motion from Kinetic Isotope Effect Studies 1311
Amnon Kohen
12.1 Introduction 1311
12.1.1 Enzymatic H transfer Open Questions 1311
12.1.2 Terminology and Definitions 1312
12.1.2.1 Catalysis 1312
12.1.2.2 Tunneling 1313
12.1.2.3 Dynamics 1313
12.1.2.4 Coupling and Coupled Motion 1314
12.1.2.5 Kinetic Isotope Effects (KIEs) 2325
12.2 The H transfer Step in Enzyme Catalysis 2316
12.3 Probing H transfer in Complex Systems 2328
12.3.1 The Swain Schaad Relationship 2328
12.3.1.1 The Semiclassical Relationship of Reaction Rates of H, D and T 2328
12.3.1.2 Effects of Tunneling and Kinetic Complexity on EXP 1319
12.3.2 Primary Swain Schaad Relationship 1320
12.3.2.1 Intrinsic Primary KIEs 2320
12.3.2.2 Experimental Examples Using Intrinsic Primary KIEs 2322
12.3.3 Secondary Swain Schaad Relationship 2323
12.3.3.1 Mixed Labeling Experiments as Probes for Tunneling and
Primary Secondary Coupled Motion 2323
12.3.3.2 Upper Semiclassical Limit for Secondary Swain Schaad
Relationship 1324
12.3.3.3 Experimental Examples Using 2° Swain Schaad Exponents 2325
12.3.4 Temperature Dependence of Primary KIEs 2326
12.3.4.1 Temperature Dependence of Reaction Rates and KIEs 2326
12.3.4.2 KIEs on Arrhenius Activation Factors 2327
Contents I XXXI
12.3.4.3 Experimental Examples Using Isotope Effects on Arrhenius
Activation Factors 1328
12.4 Theoretical Models for H transfer and Dynamic Effects in
Enzymes 1331
12.4.1 Phenomenological Marcus like Models 1332
12.4.2 MM/QM Models and Simulations 1334
12.5 Concluding Comments 1334
Acknowledgments 1335
References 1335
13 Hydrogen Tunneling in Enzyme catalyzed Hydrogen Transfer:
Aspects from Flavoprotein Catalysed Reactions 1341
Jasivir Basran, Parvinder Hothi, Laura Masgrau, MichaelJ. Sutcliffe,
and Nigel S. Scrutton
13.1 Introduction 1341
13.2 Stopped flow Methods to Access the Half reactions of
Flavoenzymes 1343
13.3 Interpreting Temperature Dependence of Isotope Effects in
Terms of H Tunneling 1343
13.4 H Tunneling in Morphinone Reductase and Pentaerythritol
Tetranitrate Reductase 1347
13.4.1 Reductive Half reaction in MR and PETN Reductase 1348
13.4.2 Oxidative Half reaction in MR 1349
13.5 H Tunneling in Flavoprotein Amine Dehydrogenases:
Heterotetrameric Sarcosine Oxidase and Engineering Gated
Motion in Trimethylamine Dehydrogenase 1350
13.5.1 Heterotetrameric Sarcosine Oxidase 1351
13.5.2 Trimethylamine Dehydrogenase 1351
13.5.2.1 Mechanism of Substrate Oxidation in Trimethylamine
Dehydrogenase 2351
13.5.2.2 H Tunneling in Trimethylamine Dehydrogenase 1353
13.6 Concluding Remarks 3356
Acknowledgments 1357
References 1357
14 Hydrogen Exchange Measurements in Proteins 1361
Thomas Lee, Carrie H. Croy, Katheryn A. Resing, and Natalie C. Ahn
14.1 Introduction 1361
14.1.1 Hydrogen Exchange in Unstructured Peptides 1361
14.1.2 Hydrogen Exchange in Native Proteins 1363
14.1.3 Hydrogen Exchange and Protein Motions 1364
14.2 Methods and Instrumentation 1365
14.2.1 Hydrogen Exchange Measured by Nuclear Magnetic Resonance (NMR)
Spectroscopy 2365
XXXII I Contents
14.2.2 Hydrogen Exchange Measured by Mass Spectrometry 1367
14.2.3 Hydrogen Exchange Measured by Fourier transform Infrared (FT IR)
Spectroscopy 1369
14.3 Applications of Hydrogen Exchange to Study Protein Conformations
and Dynamics 1371
14.3.1 Protein Folding 1371
14.3.2 Protein Protein, Protein DNA Interactions 1374
14.3.3 Macromolecular Complexes 1378
14.3.4 Protein Ligand Interactions 1379
14.3.5 Allostery 1381
14.3.6 Protein Dynamics 1382
14.4 Future Developments 3386
References 1387
15 Spectroscopic Probes of Hydride Transfer Activation by Enzymes 1393
Robert Callender and Hua Deng
15.1 Introduction 1393
15.2 Substrate Activation for Hydride Transfer 1395
15.2.1 Substrate C 0 Bond Activation 1395
15.2.1.1 Hydrogen Bond Formation with the C O Bond of Pyruvate in
LDH 1395
15.2.1.2 Hydrogen Bond Formation with the C 0 Bond of Substrate in
LADH 1397
15.2.2 Substrate C N Bond Activation 1398
15.2.2.1 N5 Protonation of 7,8 Dihydrofolate in DHFR 1398
15.3 NAD(P) Cofactor Activation for Hydride Transfer by
Enzymes 1401
15.3.1 Ring Puckering of Reduced Nicotinamide and Hydride
Transfer 1401
15.3.2 Effects of the Carboxylamide Orientation on the Hydride
Transfer 1403
15.3.3 Spectroscopic Signatures of Entropie Activation of Hydride
Transfer 2404
15.3.4 Activation ofCHbonds in NAD(P)+or NAD(P)H 1405
15.4 Dynamics of Protein Catalysis and Hydride Transfer
Activation 3406
15.4.1 The Approach to the Michaelis Complex: the Binding of
Ligands 1407
15.4.2 Dynamics of Enzymic Bound Substrate Product
Interconversion 1410
Acknowledgments 1412
Abbreviations 1412
References 1412
Contents I XXXIII
Part IV Hydrogen Transfer in the Action ofSpecific Enzyme Systems 1417
16 Hydrogen Transfer in the Action of Thiamin Diphosphate Enzymes 1419
Gerhard Hühner, Ralph Golbik, and Kai Tittmann
16.1 Introduction 1419
16.2 The Mechanism of the C2 H Deprotonation of Thiamin
Diphosphate in Enzymes 1421
16.2.1 Deprotonation Rate of the C2 H of Thiamin Diphosphate in
Pyruvate Decarboxylase 1422
16.2.2 Deprotonation Rate of the C2 H of Thiamin Diphosphate in
Transketolase from Saccharomyces cerevisiae 1424
16.2.3 Deprotonation Rate of the C2 H of Thiamin Diphosphate in the
Pyruvate Dehydrogenase Multienzyme Complex from Escherichia
coli 1425
16.2.4 Deprotonation Rate of the C2 H of Thiamin Diphosphate in the
Phosphate dependent Pyruvate Oxidase from Lactobacillus
plantarum 1425
16.2.5 Suggested Mechanism of the C2 H Deprotonation of Thiamin
Diphosphate in Enzymes 1427
16.3 Proton Transfer Reactions during Enzymic Thiamin Diphosphate
Catalysis 1428
16.4 Hydride Transfer in Thiamin Diphosphate dependent
Enzymes 1432
References 1436
17 Dihydrofolate Reductase: Hydrogen Tunneling and Protein Motion 1439
StephenJ. Benkovic and Sharon Hammes Schiffer
17.1 Reaction Chemistry and Catalysis 1439
17.1.1 Hydrogen Tunneling 1441
17.1.2 Kinetic Analysis 1443
17.2 Structural Features ofDHFR 1443
17.2.1 The Active Site ofDHFR 1444
17.2.2 Role of Interloop Interactions in DHFR Catalysis 1446
17.3 Enzyme Motion in DHFR Catalysis 2447
17.4 Conclusions 1452
References 1452
18 Proton Transfer During Catalysis by Hydrolases 1455
Ross L. Stein
18.1 Introduction 1455
18.1.1 Classification of Hydrolases 1455
18.1.2 Mechanistic Strategies in Hydrolase Chemistry 1456
18.1.2.1 Heavy Atom Rearrangement and Kinetic Mechanism 1457
XXXIV I Contents
18.1.2.2 Proton Bridging and the Stabilization of Chemical Transition
States 2458
18.1.3 Focus and Organization of Chapter 2458
18.2 Proton Abstraction Activation of Water or Amino Acid
Nucleophiles 1459
18.2.1 Activation of Nucleophile First Step of Double Displacement
Mechanisms 1459
18.2.2 Activation of Active site Water 1462
18.2.2.1 Double displacement Mechanisms Second Step 1462
18.2.2.2 Single Displacement Mechanisms 3464
18.3 Proton Donation Stabilization of Intermediates or Leaving
Groups 2466
18.3.1 Proton Donation to Stabilize Formation of Intermediates 3466
18.3.2 Proton Donation to Facilitate Leaving Group Departure 1467
18.3.2.1 Double displacement Mechanisms 3467
18.3.2.2 Single displacement Mechanisms 2468
18.4 Proton Transfer in Physical Steps of Hydrolase catalyzed
Reactions 2468
18.4.1 Product Release 2468
18.4.2 Protein Conformational Changes 3469
References 3469
19 Hydrogen Atom Transfers in B12 Enzymes 1473
Ruma Banerjee, Donald C. Truhlar, Agnieszka Dybala Defratyka,
and Piotr Paneth
19.1 Introduction to B12 Enzymes 1473
19.2 Overall Reaction Mechanisms oflsomerases 2475
19.3 Isotope Effects in B12 Enzymes 2478
19.4 Theoretical Approaches to Mechanisms of H transfer in Bi2
Enzymes 2480
19.5 Free Energy Profile for Cobalt Carbon Bond Cleavage and H atom
Transfer Steps 2487
19.6 Model Reactions 1488
19.7 Summary 1489
Acknowledgments 2489
References 2489
Part V Proton Conduction in Biology 1497
20 Proton Transfer at the Protein/Water Interface 1499
Menachem Cutman and Esther Nachliel
20.1 Introduction 2499
20.2 The Membrane/Protein Surface as a Special Environment 2501
20.2.1 TheEffectof Dielectric Boundary 2502
Contents I XXXV
20.2.2 The Ordering of the Water by the Surface 1501
20.2.2.1 The Effect of Water on the Rate of Proton Dissociation 1502
20.2.2.2 The Effect of Water Immobilization on the Diffusion of a
Proton 1503
20.3 The Electrostatic Potential Near the Surface 1504
20.4 The Effect of the Geometry on the Bulk surface Proton Transfer
Reaction 1505
20.5 Direct Measurements of Proton Transfer at an Interface 1509
20.5.1 A Model System: Proton Transfer Between Adjacent Sites on
Fluorescein 1509
20.5.1.1 The Rate Constants of Proton Transfer Between Nearby Sites 1509
20.5.1.2 Proton Transfer Inside the Coulomb Cage 1511
20.5.2 Direct Measurements of Proton Transfer Between Bulk and Surface
Groups 1514
20.6 Proton Transfer at the Surface of a Protein 1517
20.7 The Dynamics of Ionsatan Interface 1518
20.8 Concluding Remarks 1522
Acknowledgments 152.2
References 1522
Index 1527
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| adam_txt |
Contents
Foreword V
Preface XXXVU
Preface to Volumes 1 and 2 XXXIX
List of Contributors to Volumes 1 and 2 XLI
I Physical and Chemical Aspects, Parts I Ill
Part I Hydrogen Transfer in Isolated Hydrogen Bonded Molecules, Complexes
and Clusters 1
1 Coherent Proton Tunneling in Hydrogen Bonds
of Isolated Molecules: Malonaldehyde and Tropolone 3
Richard L. Redington
1.1 Introduction 3
1.2 Coherent Tunneling Splitting Phenomena in Malonaldehyde 5
1.3 Coherent Tunneling Phenomena in Tropolone 13
1.4 Tropolone Derivatives 26
1.5 Concluding Remarks 27
Acknowledgments 28
References 29
2 Coherent Proton Tunneling in Hydrogen Bonds of Isolated Molecules:
Carboxylic Dimers 33
Martina Havenith
2.1 Introduction 33
2.2 Quantum Tunneling versus Classical Over Barrier Reactions 34
2.3 Carboxylic Dimers 35
2.4 Benzoic Acid Dimer 38
2.4.1 Introduction 38
Hydrogen Transfer Reactions. Edited by J. T. Hynes, J. P. Klinman. H. H. Limbach, and R. L. Schowen
Copyright © 2007 WILEY VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978 3 527 30777 7
X I Contents
2.4.2 Determination of the Structure 38
2.4.3 Barriers and Splittings 39
2.4.4 Infrared Vibrational Spectroscopy 41
2.5 Formic Add Dimer 42
2.5.1 Introduction 42
2.5.2 Determination of the Structure 42
2.5.3 Tunneling Path 43
2.5.4 Barriers and Tunneling Splittings 44
2.5.5 Infrared Vibrational Spectroscopy 45
2.5.6 Coherent Proton Transfer in Formic Acid Dimer 46
2.6 Condusion 49
References 50
3 Gas Phase Vibrational Spectroscopy of Strong Hydrogen Bonds 53
Knut R. Asmis, Daniel M. Neumark, andjoel M. Bowman
3.1 Introduction 53
3.2 Methods 55
3.2.1 Vibrational Spectroscopy of Gas Phase Ions 55
3.2.2 Experimental Setup 56
3.2.3 Potential Energy Surfaces 58
3.2.4 Vibrational Calculations 59
3.3 Selected Systems 60
3.3.1 Bihalide Anions 60
3.3.2 The Protonated Water Dimer (H2O H OH2)+ 65
3.3.2.1 Experiments 65
3.3.2.2 Calculations 70
3.4 Outlook 75
Acknowledgments 76
References 77
4 Laser driven Ultrafast Hydrogen Transfer Dynamics 79
Oliver Kühn and Leticia Gonzalez
4.1 Introduction 79
4.2 Theory 80
4.3 Laser Control 83
4.3.1 Laser driven Intramolecular Hydrogen Transfer 83
4.3.2 Laser driven H Bond Breaking 90
4.4 Conclusions and Outlook 100
Acknowledgments 203
References 101
Contents I XI
Part II Hydrogen Transfer in Condensed Phases 105
5 Proton Transfer from Alkane Radical Cations to Alkanes 107
Jan Ceulemans
5.1 Introduction 308
5.2 Electronic Absorption of Alkane Radical Cations 108
5.3 Paramagnetic Properties of Alkane Radical Cations 109
5.4 The Bransted Acidity of Alkane Radical Cations 110
5.5 The a Basicity of Alkanes 112
5.6 Powder EPR Spectra of Alkyl Radicals 114
5.7 Symmetrie Proton Transfer from Alkane Radical Cations to Alkanes:
An Experimental Study in y Irradiated n Alkane Nanoparticles
Embedded in a Cryogenic CC13F Matrix 317
5.7.1 Mechanismofthe Radiolytic Process 117
5.7.2 Physical State of Alkane Aggregates in CC13F 118
5.7.3 Evidence for Proton donor and Proton acceptor Site Selectivity in the
Symmetrie Proton Transfer from Alkane Radical Cations to Alkane
Molecules 121
5.7.3.1 Proton donor Site Selectivity 121
5.7.3.2 Proton acceptor Site Selectivity 122
5.7.4 Comparison with Results on Proton Transfer and "Deprotonation" in
Other Systems 124
5.8 Asymmetrie Proton Transfer from Alkane Radical Cations to Alkanes:
An Experimental Study in y Irradiated Mixed Alkane Crystals 125
5.8.1 Mechanismofthe Radiolytic Process 125
5.8.2 Evidence for Proton donor and Proton acceptor Site Selectivity in the
Asymmetrie Proton Transfer from Alkane Radical Cations to
Alkanes 128
References 131
6 Single and Multiple Hydrogen/Deuterium Transfer Reactions in Liquids
and Solids 135
Hans Heinrich Limbach
6.1 Introduction 136
6.2 Theoretical 138
6.2.1 Coherent vs. Incoherent Tunneling 338
6.2.2 The Bigeleisen Theory 140
6.2.3 Hydrogen Bond Compression Assisted H transfer 141
6.2.4 Reduction of a Two dimensional to a One dimensional Tunneling
Model 143
6.2.5 The Beil Limbach Tunneling Model 146
6.2.6 Concerted Multiple Hydrogen Transfer 151
6.2.7 Multiple Stepwise Hydrogen Transfer 152
6.2.7.1 HH rransfer 153
XII I Contents
6.2.7.2 Degenerate Stepwise HHH transfer 159
6.2.7.3 Degenerate Stepwise HHHH transfer 161
6.2.8 Hydrogen Transfers Involving Pre equilibria 165
6.3 Applications 368
6.3.1 H transfers Coupled to Minor Heavy Atom Motions 174
6.3.1.1 Symmetrie Porphyrins and Porphyrin Analogs 174
6.3.1.2 Unsymmetrically Substituted Porphyrins 181
6.3.1.3 Hydroporphyrins 184
6.3.1.4 Intramolecular Single and Stepwise Double Hydrogen Transfer in
H bonds of Medium Strength 185
6.3.1.5 Dependence on the Environment 187
6.3.1.6 Intermolecular Multiple Hydrogen Transfer in H bonds of Medium
Strength 188
6.3.1.7 Dependence of the Barrier on Molecular Structure 193
6.3.2 H transfers Coupled to Major Heavy Atom Motions 197
6.3.2.1 H transfers Coupled to Conformational Changes 197
6.3.2.2 H transfers Coupled to Conformational Changes and Hydrogen Bond
Pre equilibria 203
6.3.2.3 H transfers in Complex Systems 212
6.4 Conclusions 216
Acknowledgments 217
References 217
7 Intra and Intermolecular Proton Transfer and Related Processes in
Confined Cyclodextrin Nanostructures 223
Abderrazzak Douhal
7.1 Introduction and Concept of Femtochemistry in Nanocavities 223
7.2 Overview of the Photochemistry and Photophysics of Cyclodextrin
Complexes 224
7.3 Picosecond Studies of Proton Transfer in Cyclodextrin
Complexes 225
7.3.1 l' Hydroxy,2' acetonaphthone 225
7.3.2 1 Naphthol and 1 Aminopyrene 228
7.4 Femtosecond Studies of Proton Transfer in Cyclodextrin
Complexes 230
7.4.1 Coumarins 460 and 480 230
7.4.2 Bound and Free Water Molecules 231
7.5.3 2 (2' Hydroxyphenyl) 4 methyloxazole 236
7.5.4 Orange II 239
7.6 Concluding Remarks 240
Acknowledgment 241
References 241
Contents I XIII
8 Tautomerization in Porphycenes 245
Jacek Waluk
8.1 Introduction 245
8.2 Tautomerization in the Ground Electronic State 247
8.2.1 Structural Data 247
8.2.2 NMR Studies of Tautomerism 251
8.2.3 Supersonic Jet Studies 253
8.2.4 The Nonsymmetric Case: 2,7,12,17 Tetra n propyl 9
acetoxyporphycene 256
8.2.5 Calculations 258
8.3 Tautomerization in the Lowest Excited Singlet State 258
8.3.1 Tautomerization as a Tool to Determine Transition Moment
Directions in Low Symmetry Molecules 260
8.3.2 Determination of Tautomerization Rates from Anisotropy
Measurements 262
8.4 Tautomerization in the Lowest Excited Triplet State 265
8.5 Tautomerization in Single Molecules of Porphycene 266
8.6 Summary 267
Acknowledgments 268
References 269
9 Proton Dynamics in Hydrogen bonded Crystals 273
Mikhail V. Vener
9.1 Introduction 273
9.2 Tentative Study of Proton Dynamics in Crystals with Quasi linear
H bonds 274
9.2.1 A Model 2D Hamiltonian 275
9.2.2 Specific Features of H bonded Crystals with a Quasi symmetric
O H O Fragment 277
9.2.3 Proton Transfer Assisted by a Low frequency Mode
Excitation 279
9.2.3.1 Crystals with Moderate H bonds 280
9.2.3.2 Crystals with Streng H bonds 283
9.2.3.3 Limitations of the Model 2D Treatment 284
9.2.4 Vibrational Spectra of H bonded Crystals: IR versus INS 285
9.3 DFT Calculations with Periodic Boundary Conditions 286
9.3.1 Evaluation of the Vibrational Spectra Using Classical MD
Simulations 287
9.3.2 Effects of Crystalline Environment on Strong H bonds:
the H5O2+ Ion 288
9.3.2.1 The Structure and Harmonie Frequencies 288
9.3.2.2 The PESoftheO H O Fragment 291
9.3.2.3 Anharmonic INS and IR Spectra 293
XIV I Contents
9.4 Conclusions 296
Acknowledgments 297
References 217
Part IM Hydrogen Transfer in Polar Environments 301
10 Theoretical Aspects of Proton Transfer Reactions
in a Polar Environment 303
Philip M. Kiefer and James T. Hynes
10.1 Introduction 303
10.2 Adiabatic Proton Transfer 309
10.2.1 General Picture 309
10.2.2 Adiabatic Proton Transfer Free Energy Relationship (FER) 315
10.2.3 Adiabatic Proton Transfer Kinetic Isotope Effects 320
10.2.3.1 KIE Arrhenius Behavior 321
10.2.3.2 KIE Magnitude and Variation with Reaction Asymmetry 321
10.2.3.3 Swain Schaad Relationship 323
10.2.3.4 Further Discussion of Nontunneling Kinetic Isotope Effects 323
10.2.3.5 Transition State Geometrie Structure in the Adiabatic PT Picture 324
10.2.4 Temperature Solvent Polarity Effects 325
10.3 Nonadiabatic 'Tunneling' Proton Transfer 326
10.3.1 General Nonadiabatic Proton Transfer Perspective and Rate
Constant 327
10.3.2 Nonadiabatic Proton Transfer Kinetic Isotope Effects 333
10.3.2.1 Kinetic Isotope Effect Magnitude and Variation
with Reaction Asymmetry 333
10.3.2.2 Temperature Behavior 337
10.3.2.3 Swain Schaad Relationship 340
10.4 Concluding Remarks 341
Acknowledgments 343
References 345
11 Direct Observation of Nuclear Motion during
Ultra fast Intramolecular Proton Transfer 349
Stefan Lochbrunner, Christian Schriever, and Eberhard Riedle
11.1 Introduction 349
11.2 Time resolved Absorption Measurements 352
11.3 SpectralSignaturesofUltrafastESIPT 353
11.3.1 Characteristic Features of the Transient Absorption 354
11.3.2 Analysis 356
11.3.3 Ballistic Wavepacket Motion 357
11.3.4 Coherently Excited Vibrations in Product Modes 359
11.4 Reaction Mechanism 362
11.4.1 Reduction of Donor Acceptor Distance by Skeletal Motions 362
Contents I XV
11.4.2 Multidimensional ESIPT Model 363
11.4.3 Micro irreversibility 365
11.4.4 Topology of the PES and Turns in the Reaction Path 366
11.4.5 Comparison with Ground State Hydrogen Transfer Dynamics 368
11.4.6 Internal Conversion 368
11.5 Reaction Path Specific Wavepacket Dynamics in Double Proton
Transfer Molecules 370
11.6 Conclusions 372
Acknowledgment 373
References 373
12 Solvent Assisted Photoacidity 377
Dina Pines and Ehud Pines
12.1 Introduction 377
12.2 Photoacids, Photoacidity and Förster Cyde 378
12.2.1 Photoacids and Photobases 378
12.2.2 Use of the Förster Cyde to Estimate the Photoacidity of
Photoacids 379
12.2.3 Direct Methods for Determining the Photoacidity of Photoacids 387
12.3 Evidence for the General Validity of the Förster Cycle and the
K*a Scale 389
12.3.1 Evidence for the General Validity of the Förster Cycle Based on Time
resolved and Steady State Measurements of Excited state Proton
Transfer of Photoacids 389
12.3.2 Evidence Based on Free Energy Correlations 393
12.4 Factors Affecting Photoacidity 397
12.4.1 General Considerations 397
12.4.2 Comparing the Solvent Effect on the Photoacidities of Neutral and
Cationic Photoacids 398
12.4.3 The Effect of Substituents on the Photoacidity of Aromatic Alcohols 400
12.5 Solvent Assisted Photoacidity: The 1LO, lLb Paradigm 404
12.6 Summary 410
Acknowledgments 411
References 411
13 Design and Implementation of "Super" Photoacids 417
Laren M. Tolbert and Kyril M. Solntsev
13.1 Introduction 417
13.2 Excited state Proton Transfer (ESPT) 420
13.2.1 1 Naphthol vs. 2 Naphthol 420
13.2.2 "Super" Photoacids 422
13.2.3 Fluorinated Phenols 426
13.3 Natureof the Solvent 426
13.3.1 Hydrogen Bonding and Solvatochromism in Super Photoacids 426
XVI I Contents
13.3.2 Dynamics in Water and Mixed Solvents 427
13.3.3 Dynamics in Nonaqueous Solvents 428
13.3.4 ESPT in the Gas Phase 431
13.3.5 Stereochemistry 433
13.4 ESPT in Biological Systems 433
13.4.1 The Green Fluorescent Protein (GFP) or "ESPT in a Box" 435
13.5 Conclusions 436
Acknowledgments 436
References 437
Foreword V
Preface XXXVII
Preface to Volumes 1 and 2 XXXIX
List of Contributors to Volumes 1 and 2 XII
I Physical and Chemical Aspects, Parts IV—VII
Part IV Hydrogen Transfer in Protic Systems 441
14 Bimolecular Proton Transfer in Solution 443
Erik T. J. Nibbering and Ehud Pines
14.1 Intermolecular Proton Transfer in the Liquid Phase 443
14.2 Photoacids as Ultrafast Optical Triggers for Proton Transfer 445
14.3 Proton Recombination and Acid Base Neutralization 448
14.4 Reaction Dynamics Probing with Vibrational Marker Modes 449
Acknowledgment 455
References 455
15 Coherent Low frequency Motions in Condensed Phase Hydrogen Bonding
and Transfer 459
Thomas Elsaesser
15.1 Introduction 459
15.2 Vibrational Excitations of Hydrogen Bonded Systems 460
15.3 Low frequency Wavepacket Dynamics of Hydrogen Bonds in the
Electronic Ground State 463
15.3.1 Intramolecular Hydrogen Bonds 463
15.3.2 Hydrogen Bonded Dimers 466
15.4 Low frequency Motions in Excited State Hydrogen Transfer 471
15.5 Conclusions 475
Acknowledgments 476
References 476
Contents I XVII
16 Proton Coupled Electron Transfer: Theoretical Formulation
and Applications 479
Sharon Hammes Schiffer
16.1 Introduction 479
16.2 Theoretical Formulation for PCET 480
16.2.1 Fundamental Concepts 480
16.2.2 Proton Donor Acceptor Motion 483
16.2.3 Dynamical Effects 485
16.2.3.1 Dielectric Continuum Representation of the Environment 486
16.2.3.2 Molecular Representation of the Environment 490
16.3 Applications 492
16.3.1 PCET in Solution 492
16.3.2 PCET in a Protein 498
16.4 Conclusions 500
Acknowledgments 500
References 501
17 The Relation between Hydrogen Atom Transfer and Proton coupled Electron
Transfer in Model Systems 503
Justin M. Hodgkiss, Joel Rosenthal, and Daniel C. Nocera
17.1 Introduction 503
17.1.1 Formulation of HAT as a PCET Reaction 504
17.1.2 ScopeofChapter 507
17.1.2.1 Unidirectional PCET 508
17.1.2.2 Bidirectional PCET 508
17.2 Methods of HAT and PCET Study 509
17.2.1 Free Energy Correlations 510
17.2.2 Solvent Dependence 511
17.2.3 Deuterium Kinetic Isotope Effects 511
17.2.4 Temperature Dependence 512
17.3 Unidirectional PCET 512
17.3.1 Type A: Hydrogen Abstraction 512
17.3.2 Type B: Site Differentiated PCET 523
17.3.2.1 PCET across Symmetrie Hydrogen Bonding Interfaces 523
17.3.2.2 PCET across Polarized Hydrogen Bonding Interfaces 527
17.4 Bidirectional PCET 537
17.4.1 Type C: Non Specific 3 Point PCET 538
17.4.2 Type D: Site Specified 3 Point PCET 543
17.5 The Different Types of PCET in Biology 548
17.6 Application of Emerging Ultrafast Spectroscopy to PCET 554
Acknowledgment 556
References 556
XVIII I Contents
Part V Hydrogen Transfer in Organic and Organometallic Reactions 563
18 Formation of Hydrogen bonded Carbanions as Intermediates in Hydron
Transfer between Carbon and Oxygen 565
Heinz F. Koch
18.1 Proton Transfer from Carbon Acids to Methoxide Ion 565
18.2 Proton Transfer from Methanol to Carbanion Intermediates 573
18.3 Proton Transfer Associated with Methoxide Promoted
Dehydrohalogenation Reactions 576
18.4 Conclusion 580
References 581
19 Theoretical Simulations of Free Energy Relationships in
Proton Transfer 583
lan H. Williams
19.1 Introduction 583
19.2 Qualitative Models for FERs 584
19.2.1 What is Meant by "Reaction Coordinate"? 588
19.2.2 The Bransted a as a Measure of TS Structure 589
19.3 FERs from MO Calculations of PESs 590
19.3.1 Energies and Transition States 590
19.4 FERs from VB Studies of Free Energy Changes for PT in Condensed
Phases 597
19.5 Concluding Remarks 600
References 600
20 The Extraordinary Dynamic Behavior and Reactivity of Dihydrogen and
Hydride in the Coordination Sphere of Transition Metals 603
GregoryJ. Kubas
20.1 Introduction 603
20.1.1 Structure, Bonding, and Activation of Dihydrogen Complexes 603
20.1.2 Extraordinary Dynamics of Dihydrogen Complexes 606
20.1.2 Vibrational Motion of Dihydrogen Complexes 608
20.1.3 Elongated Dihydrogen Complexes 609
20.1.4 Cleavage of the H H Bond in Dihydrogen Complexes 620
20.2 H2 Rotation in Dihydrogen Complexes 615
20.2.1 Determination of the Barrier to Rotation of Dihydrogen 616
20.3 NMR Studies of H2 Activation, Dynamics, and Transfer
Processes 637
20.3.1 Solution NMR 617
20.3.2 Solid State NMR of H2 Complexes 621
Contents I XIX
20.4 Intramolecular Hydrogen Rearrangement and Exchange 623
20.4.1 Extremely Facile Hydrogen Transfer in IrXH2(H2)(PR3)2 and Other
Systems 627
20.4.2 Quasielastic Neutron Scattering Studies of H2 Exchange with cis
Hydrides 632
20.5 Summary 633
Acknowledgments 634
References 634
21 Dihydrogen Transfer and Symmetry: The Role of Symmetry in the Chemistry
of Dihydrogen Transfer in the Light of N M R Spectroscopy 639
Gerd Buntkowsky and Hans Heinrich Limbach
21.1 Introduction 639
21.2 Tunneling and Chemical Kinetics 641
21.2.1 The Role of Symmetry in Chemical Exchange Reactions 641
21.2.1.1 Coherent Tunneling 642
21.2.1.2 The Density Matrix 648
21.2.1.3 The Transition from Coherent to Incoherent Tunneling 649
21.2.2 Incoherent Tunneling and the Bell Model 653
21.3 Symmetry Effects on NMR Lineshapes of Hydration Reactions 655
21.3.1 Analytical Solution for the Lineshape of PHIP Spectra Without
Exchange 657
21.3.2 Experimental Examples of PHIP Spectra 662
21.3.2.1 PHIP under ALTADENA Conditions 662
21.3.2.2 PHIP Studies of Stereoselective Reactions 662
21.3.2.3 13C PHIP NMR 664
21.3.3 Effects of Chemical Exchange on the Lineshape of PHIP Spectra 665
21.4 Symmetry Effects on NMR Lineshapes of Intramolecular Dihydrogen
Exchange Reactions 670
21.4.1 Experimental Examples 670
21.4.1.1 Slow Tunneling Determined by *H Liquid State
NMR Spectroscopy 671
21.4.1.2 Slow to Intermediate Tunneling Determined by
2H Solid State NMR 671
21.4.1.3 Intermediate to Fast Tunneling Determined by
2H Solid State NMR 673
21.4.1.4 Fast Tunneling Determined by Incoherent Neutron Scattering 675
21.4.2 Kinetic Data Obtained from the Experiments 675
21.4.2.1 Ru D2 Complex 676
21.4.2.2 W(PCy)3(CO)3 (*7 H2 ) Complex 677
21.5 Summary and Conclusion 678
Acknowledgments 679
References 679
XX I Contents
Part VI Proton Transfer in Solids and Surfaces 683
22 Proton Transfer in Zeolites 685
Joachim Sauer
22.1 Introduction The Active Sites ofAcidic Zeolite Catalysts 685
22.2 Proton Transfer to Substrate Molecules within Zeolite Cavities 686
22.3 Formation of NH4+ions on NH3 adsorption 688
22.4 Methanol Molecules and Dimers in Zeolites 692
22.5 Water Molecules and Clusters in Zeolites 694
22.6 Proton Jumps in Hydrated and Dry Zeolites 700
22.7 Stability ofCarbenium Ions in Zeolites 703
References 706
23 Proton Conduction in Fuel Cells 709
Klaus Dieter Kreuer
23.1 Introduction 709
23.2 Proton Conducting Electrolytes and Their Application in Fuel Cells 710
23.3 Long range Proton Transport of Protonic Charge Carriers in
Homogeneous Media 714
23.3.1 Proton Conduction in Aqueous Environments 715
23.3.2 Phosphoric Acid 719
23.3.3 Heterocycles (Imidazole) 720
23.4 Confinement and Interfacial Effects 723
23.4.1 Hydrated Acidic Polymers 723
23A.2 Adducts of Basic Polymers with Oxo acids 727
23.4.3 Separated Systems with Covalently Bound Proton Solvents 728
23.5 Concluding Remarks 731
Acknowledgment 733
References 733
24 Proton Diffusion in Ice Bifayers 737
Katsutoshi Aoki
24.1 Introduction 737
24.1.1 Phase Diagram and Crystal Structure of Ice 737
24.1.2 Molecular and Protonic Diffusion 739
24.1.3 Protonic Diffusion at High Pressure 740
24.2 Experimental Method 741
24.2.1 Diffusion Equation 741
24.2.2 High Pressure Measurement 742
24.2.3 Infrared Reflection Spectra 743
24.2.4 Thermal Activation of Diffusion Motion 744
24.3 Spectral Analysis of the Diffusion Process 745
24.3.1 Protonic Diffusion 745
Contents I XXI
24.3.2 Molecular Diffusion 746
24.3.3 Pressure Dependence of Protonic Diffusion Coefficient 747
24.4 Summary 749
References 749
25 Hydrogen Transfer on Metal Surfaces 751
Klaus Christmann
25.1 Introduction 751
25.2 The Principles of the Interaction of Hydrogen with Surfaces: Terms
and Definitions 755
25.3 The Transfer of Hydrogen on Metal Surfaces 761
25.3.1 Hydrogen Surface Diffusion on Homogeneous Metal Surfaces 762
25.3.2 Hydrogen Surface Diffusion and Transfer on Heterogeneous Metal
Surfaces 771
25.4 Alcohol and Water on Metal Surfaces: Evidence of H Bond Formation
and H Transfer 775
25.4.1 Alcohols on Metal Surfaces 775
25.4.2 Water on Metal Surfaces 778
25.5 Conclusion 783
Acknowledgments 783
References 783
26 Hydrogen Motion in Metals 787
RolfHempelmann and Alexander Skripov
26.1 Survey 787
26.2 Experimental Methods 788
26.2.1 Anelastic Relaxation 788
26.2.2 Nuclear Magnetic Resonance 790
26.2.3 Quasielastic Neutron Scattering 792
26.2.4 Other Methods 795
26.3 Experimental Results on Diffusion Coefficients 796
26.4 Experimental Results on Hydrogen Jump Diffusion Mechanisms 801
26.4.1 Binary Metal Hydrogen Systems 802
26.4.2 Hydrides of Alloys and Intermetallic Compounds 804
26.4.3 Hydrogen in Amorphous Metals 810
26.5 Quantum Motion of Hydrogen 812
26.5.1 Hydrogen Tunneling in Nb Doped with Impurities 824
26.5.2 Hydrogen Tunneling in a MnHx 827
26.5.3 Rapid Low temperarure Hopping of Hydrogen in a ScH^(Dx) and
TaV2H%(Dx) 822
26.6 Concluding Remarks 825
Acknowledgment 825
References 826
XXII I Contents
Part VII Special Features of Hydrogen Transfer Reactions 831
27 Variational Transition State Theory in the Treatment of Hydrogen Transfer
Reactions 833
Donald G. Truhlar and Bruce C. Garrett
27.1 Introduction 833
27.2 Incorporation of Quantum Mechanical Effects in VTST 835
27.2.1 Adiabatic Theory of Reactions 837
27.2.2 Quantum Mechanical Effects on Reaction Coordinate Motion 840
27.3 H atom Transfer in Bimolecular Gas phase Reactions 843
27.3.1 H + H2andMu + H2 843
27.3.2 Cl + HBr 849
27.3.3 Cl + CH4 853
21A Intramolecular Hydrogen Transfer in Unimolecular Gas phase
Reactions 857
27.4.1 Intramolecular H transfer in 1,3 Pentadiene 858
27.4.2 1,2 Hydrogen Migration in Methylchlorocarbene 860
27.5 Liquid phase and Enzyme catalyzed Reactions 860
27.5.1 Separable Equilibrium Solvation 862
27.5.2 Equilibrium Solvation Path 864
27.5.3 Nonequilibrium Solvation Path 864
27.5.4 Potential of mean force Method 865
27.5.5 Ensemble averaged Variational Transition State Theory 865
27.6 Examplesof Condensed phase Reactions 867
27.6.1 H + Methanol 867
27.6.2 Xylose Isomerase 868
27.6.3 Dihydrofolate Reductase 868
27.7 Another Perspective 869
27.8 Concluding Remarks 869
Acknowledgments 871
References 871
28 Quantum Mechanical Tunneling of Hydrogen Atoms in
Some Simple Chemical Systems 875
K. U. Ingold
28.1 Introduction 875
28.2 Unimolecular Reactions 876
28.2.1 Isomerization of Sterically Hindered Phenyl Radicals 876
28.2.1.1 2,4,6 Tri tert butylphenyl 876
28.2.1.2 Other Sterically Hindered Phenyl Radicals 881
28.2.2 Inversion of Nonplanar, Cydic, Carbon Centered Radicals 883
28.2.2.1 Cydopropyl and 1 Methylcyclopropyl Radicals 883
28.2.2.2 The Oxiranyl Radical 884
28.2.2.3 The Dioxolanyl Radical 886
Contents I XXIII
28.2.2.4 Summary 887
28.3 Bimolecular Reactions 887
28.3.1 H Atom Abstraction by Methyl Radicals in Organic Glasses 887
28.3.2 H Atom Abstraction by Bis(trifluoromethyl) Nitroxide in the Liquid
Phase 890
References 892
29 Multiple Proton Transfer: From Stepwise to Concerted 895
Zorka Smedarchina, Willem Siebrand, and Antonio Fernündez Ramos
29.1 Introduction 895
29.2 Basic Model 897
29.3 Approaches to Proton Tunneling Dynamics 904
29.4 Tunneling Dynamics for Two Reaction Coordinates 908
29.5 Isotope Effects 914
29.6 Dimeric Formic Acid and Related Dimers 918
29.7 Other Dimeric Systems 922
29.8 Intramolecular Double Proton Transfer 926
29.9 Proton Conduits 932
29.10 Transfer of More Than Two Protons 939
29.11 Conclusion 940
Acknowledgment 943
References 943
Foreword V
Preface XXXVII
Preface to Volumes 3 and 4 XXXIX
List of Contributors to Volumes 3 and 4 XII
II Biological Aspects, Parts •—11
Part I Models for Biological Hydrogen Transfer 947
1 Proton Transfer to and from Carbon in Model Reactions 949
Tina L Amyes and John P. Richard
1.1 Introduction 949
1.2 Rate and Equilibrium Constants for Carbon Deprotonation in
Water 949
1.2.1 Rate Constants for Carbanion Formation 951
1.2.2 Rate Constants for Carbanion Protonation 953
1.2.2.1 Protonation by Hydronium Ion 953
XXIV I Contents
1.2.2.2 Protonation by Buffer Acids 954
1.2.2.3 Protonation by Water 955
1.2.3 The Bürden Borne by Enzyme Catalysts 955
1.3 Substituent Effects on Equilibrium Constants for Deprotonation of
Carbon 957
1.4 Substituent Effects on Rate Constants for Proton Transfer at
Carbon 958
IAA The Marcus Equation 958
1.4.2 Marcus Intrinsic Barriers for Proton Transfer at Carbon 960
1.4.2.1 Hydrogen Bonding 960
1.4.2.2 Resonance Effects 962
1.5 Small Molecule Catalysis of Proton Transfer at Carbon 965
1.5.1 General Base Catalysis 966
1.5.2 Electrophilic Catalysis 967
1.6 Comments on Enzymatic Catalysis of Proton Transfer 970
Acknowledgment 970
References 971
2 General Acid Base Catalysis in Model Systems 975
AnthonyJ. Kirby
2.1 Introduction 975
2.1.1 Kinetics 975
2.1.2 Mechanism 977
2.1.3 Kinetic Equivalence 979
2.2 Strucrural Requirements and Mechanism 981
2.2.1 General Acid Catalysis 982
2.2.2 Classical General Base Catalysis 983
2.2.3 General Base Catalysis of Cyclization Reactions 984
2.2.3.1 Nucleophilic Substitution 984
2.2.3.2 Ribonuclease Models 985
2.3 Intramolecular Reactions 987
2.3.1 Introduction 987
2.3.2 Efficient Intramolecular General Acid Base Catalysis 988
2.3.2.1 Aliphatic Systems 992
2.3.3 Intramolecular General Acid Catalysis of Nucleophilic Catalysis 993
2.3.4 Intramolecular General Acid Catalysis of Intramolecular Nucleophilic
Catalysis 998
2.3.5 Intramolecular General Base Catalysis 999
2.4 Proton Transfers to and from Carbon 2000
2.4.1 Intramolecular General Acid Catalysis 2002
2.4.2 Intramolecular General Base Catalysis 2004
2.4.3 Simple Enzyme Models 2006
2.5 Hydrogen Bonding, Mechanism and Reactivity 1007
References 2020
Contents I XXV
3 Hydrogen Atom Transfer in Model Reactions 1013
Christian Schöneich
3.1 Introduction 1013
3.2 Oxygen centered Radicals 1013
3.3 Nitrogen dentered Radicals 1017
3.3.1 Generation of Aminyl and Amidyl Radicals 1017
3.3.2 Reactions of Aminyl and Amidyl Radicals 1018
3.4 Sulfur centered Radicals 1019
3.4.1 Thiols and Thiyl Radicals 1020
3.4.1.1 Hydrogen Transfer from Thiols 1020
3.4.1.2 Hydrogen Abstraction by Thiyl Radicals 1023
3.4.2 Sulfide Radical Cations 1029
3.5 Conclusion 1032
Acknowledgment 1032
References 1032
4 Model Studies of Hydride transfer Reactions 1037
Richard L Schowen
4.1 Introduction 1037
4.1.1 Nicotinamide Coenzymes: Basic Features 1038
4.1.2 Flavin Coenzymes: Basic Features 1039
4.1.3 Quinone Coenzymes: Basic Features 1039
4.1.4 Matters Not Treated in This Chapter 1039
4.2 The Design ofSuitable Model Reactions 1040
4.2.1 The Anchor Principle of Jencks 1042
4.2.2 The Proximity Effectof Bruice 1044
4.2.3 Environmental Considerations 3045
4.3 The Role of Model Reactions in Mechanistic Enzymology 1045
4.3.1 Kinetic Baselines for Estimations of Enzyme Catalytic Power 1045
4.3.2 Mechanistic Baselines and Enzymic Catalysis 1047
4.4 Models for Nicotinamide mediated Hydrogen Transfer 1048
4.4.1 Events in the Course of Formal Hydride Transfer 1048
4.4.2 Electron transfer Reactions and H atom transfer Reactions 1049
4.4.3 Hydride transfer Mechanisms in Nicotinamide Models 3052
4.4.4 Transition state Structure in Hydride Transfer The Kreevoy
Model 1054
4.4.5 Quantum Tunneling in Model Nicotinamide mediated Hydride
Transfer 3060
4.4.6 Intramolecular Models for Nicotinamide mediated Hydride
Transfer 3063
4.4.7 Summary 1063
4.5 Models for Flavin mediated Hydride Transfer 3064
4.5.1 Differences between Flavin Reactions and Nicotinamide
Reactions 3064
XXVI I Contents
4.5.2 The Hydride transfer Process in Model Systems 1065
4.6 Models for Quinone mediated Reactions 1068
4.7 Summary and Condusions 1071
4.8 Appendix: The Use of Model Reactions to Estimate Enzyme Catalytic
Power 1071
References 1074
5 Acid Base Catalysis in Designed Peptides 1079
Lars Baltzer
5.1 Designed Polypeptide Catalysts 1079
5.1.1 Protein Design 1080
5.1.2 Catalyst Design 1083
5.1.3 Designed Catalysts 1085
5.2 Catalysis of Ester Hydrolysis 1089
5.2.1 Design ofa Folded Polypeptide Catalyst for Ester Hydrolysis 1089
5.2.2 The HisH+ His Pair 1091
5.2.3 Reactivity According to the Brönsted Equation 1093
5.2.4 Cooperative Nucleophilic and General acid Catalysis in Ester
Hydrolysis 1094
5.2.5 Why General acid Catalysis? 1095
5.3 Limits of Activity in Surface Catalysis 1096
5.3.1 Optimal Organization of His Residues for Catalysis of Ester
Hydrolysis 1097
5.3.2 Substrate and Transition State Binding 1098
5.3.3 His Catalysis in Re engineered Proteins 1099
5.4 Computational Catalyst Design 1100
5.4.1 Ester Hydrolysis 1101
5.4.2 Triose Phosphate Isomerase Activity by Design 1101
5.5 Enzyme Design 1102
References 3102
Part II General Aspects of Biological Hydrogen Transfer 1105
6 Enzymatic Catalysis of Proton Transfer at Carbon Atoms 1107
John A. Cerlt
6.1 Introduction 1107
6.2 The Kinetic Problems Associated with Proton Abstraction from
Carbon 1108
6.2.1 Marcus Formalism for Proton Transfer 1110
6.2.2 AG°, the Thermodynamic Barrier 1111
6.2.3 AG*!,,,, the Intrinsic Kinetic Barrier 1112
6.3 Structural Strategies for Reduction of AG° 1114
6.3.1 Proposais for Understanding the Rates of Proton Transfer 1114
6.3.2 Short Strang Hydrogen Bonds 1115
Contents I XXVII
6.3.3 Electrostatic Stabilization of Enolate Anion Intermediates 2225
6.3.4 Experimental Measure of Differential Hydrogen Bond Strengths 1116
6.4 Experimental Paradigms for Enzyme catalyzed Proton Abstraction
from Carbon 1118
6.4.1 Triose Phosphate Isomerase 1118
6.4.2 Ketosteroid Isomerase 1125
6.4.3 Enoyl CoA Hydratase (Crotonase) 2327
6.4.4 Mandelate Racemase and Enolase 1131
6.5 Summary 1134
References 1135
7 Multiple Hydrogen Transfers in Enzyme Action 1139
M. Ashley Spies and Michael D. Toney
7.1 Introduction 1139
7.2 Cofactor Dependent with Activated Substrates 1139
7.2.1 Alanine Racemase 1139
7.2.2 Broad Specificity Amino Acid Racemase 1151
7.2.3 Serine Racemase 1152
7.2.4 Mandelate Racemase 1152
7.2.5 ATP Dependent Racemases 1154
7.2.6 Methylmalonyl CoA Epimerase 1156
7.3 Cofactor Dependent with Unactivated Substrates 1157
7.4 Cofactor Independent with Activated Substrates 2 257
7.4.1 Proline Racemase 2257
7.4.2 Glutamate Racemase 2262
7.4.3 DAP Epimerase 2262
7.4.4 Sugar Epimerases 2 265
7.5 Cofactor Independent with Unactivated Substrates 2265
7.6 Summary 2266
References 2267
8 Computer Simulations of Proton Transfer in Proteins and Solutions 2272
Sonja Braun Sand, Mats H. M. Olsson, Janez Mavri, and Arieh Warshel
8.1 Introduction 2 272
8.2 Simulating PT Reactions by the EVB and other QM/MM
Methods 2272
8.3 Simulating the Flucruations of the Environment and Nuclear
Quantum Mechanical Effects 2277
8.4 The EVB asa Basis for LFERofPT Reactions J285
8.5 Demonstrating the Applicability of the Modified Marcus'
Equation 2288
8.6 General Aspects of Enzymes that Catalyze PT Reactions 2294
8.7 Dynamics, Tunneling and Related Nuclear Quantum Mechanical
Effects 2 295
XXVIII I Contents
8.8 Concluding Remarks 1198
Acknowledgements 1199
Abbreviations 1199
References 1200
Foreword V
Preface XXXVII
Preface to Volumes 3 and 4 XXXIX
List of Contributors to Volumes 3 and 4 XU
II Biological Aspects, Parts Ill V
Part III Quantum Tunneling and Protein Dynamics 1207
9 The Quantum Kramers Approach to Enzymatic Hydrogen Transfer
Protein Dynamics as it Couples to Catalysis 1209
Steven D. Schwartz
9.1 Introduction 1209
9.2 The Derivation of the Quantum Kramers Method 1210
9.3 Promoting Vibrations and the Dynamics of Hydrogen Transfer 1213
9.3.1 Promoting Vibrations and The Symmetry of Coupling 1213
9.3.2 Promoting Vibrations Corner Cutting and the Masking of
KIEs 1215
9.4 Hydrogen Transfer and Promoting Vibrations Alcohol
Dehydrogenase 1217
9.5 Promoting Vibrations and the Kinetic Control of Enzymes
Lactate Dehydrogenase 1223
9.6 The Quantum Kramers Model and Proton Coupled Electron
Transfer 1231
9.7 Promoting Vibrations and Electronic Polarization 1233
9.8 Conclusions 1233
Acknowledgment 1234
References 1234
10 Nuclear Tunneling in the Condensed Phase: Hydrogen Transfer
in Enzyme Reactions 1241
Michael J. Knapp, Matthew Meyer, and Judith P. Klinman
10.1 Introduction 1241
10.2 Enzyme Kinetics: Extracting Chemistry from Complexity 1242
10.3 Methodology for Detecting Nonclassical H Transfers 1245
Contents I XXIX
10.3.1 Bond Stretch KIE Model: Zero point Energy Effects 1245
10.3.1.1 Primary Kinetic Isotope Effects 3246
10.3.1.2 Secondary Kinetic Isotope Effects 1247
10.3.2 Methods to Measure Kinetic Isotope Effects 1247
10.3.2.1 Noncompetitive Kinetic Isotope Effects: fecat or kC3t/KM 1247
10.3.2.2 Competitive Kinetic Isotope Effects: kat/KM 1248
10.3.3 Diagnostics for Nonclassical H Transfer 1249
10.3.3.1 The Magnitude of Primary KIEs: feH/feD 8 at Room
Temperature 1249
10.3.3.2 Discrepant Predictions of Transition state Structure and
Inflated Secondary KIEs 1251
10.3.3.3 Exponential Breakdown: Rule of the Geometrie Mean and
Swain Schaad Relationships 1252
10.3.3.4 Variable Temperature KIEs: AH/AD » 1 or AH/AD « 1 1254
10.4 Concepts and Theories Regarding Hydrogen Tunneling 1256
10.4.1 Conceptual View of Tunneling 1256
10.4.2 Tunnel Corrections to Rates: Static Barriers 2258
10.4.3 Fluctuating Barriers: Reproducing Temperature Dependences 1260
10.4.4 Overview 1264
10.5 Experimental Systems 1265
10.5.1 Hydride Transfers 3265
10.5.1.1 Alcohol Dehydrogenases 3265
10.5.1.2 Glucose Oxidase 2270
10.5.2 Amine Oxidases 1273
10.5.2.1 Bovine Serum Amine Oxidase 1273
10.5.2.2 Monoamine Oxidase B 1275
10.5.3 Hydrogen Atom (H*) Transfers 1276
10.5.3.1 Soybean Lipoxygense 1 1276
10.5.3.2 Peptidylglycine a Hydroxylating Monooxygenase (PHM) and
Dopamine /3 Monooxygenase (D/?M) 2279
10.6 Concluding Comments 2280
References 3282
11 Multiple isotope Probesof Hydrogen Tunneling 1285
W. Phillip Huskey
11.1 Introduction 2285
11.2 Background: H/D Isotope Effects as Probes of Tunneling 1287
11.2.1 One frequency Models 1287
11.2.2 Temperature Dependence of Isotope Effects 1289
11.3 Swain Schaad Exponents: H/D/T Rate Comparisons 1290
11.3.1 Swain Schaad Limits in the Absence of Tunneling 2293
11.3.2 Swain Schaad Exponents for Tunneling Systems 2292
11.3.3 Swain Schaad Exponents from Computational Studies that
Include Tunneling 2293
XXX I Contents
11.3.4 Swain Schaad Exponents for Secondary Isotope Effects 1294
11.3.5 Effects of Mechanistic Complexity on Swain Schaad
Exponents 1294
11.4 Ruie of the Geometrie Mean: Isotope Effects on Isotope
Effects 1297
11.4.1 RGM Breakdown from Intrinsic Nonadditivity 1298
11.4.2 RGM Breakdown from Isotope sensitive Effective States 1300
11.4.3 RGM Breakdown as Evidence for Tunneling 1303
11.5 Saunders'Exponents: Mixed Multiple Isotope Probes 1304
11.5.1 Experimental Considerations 2304
11.5.2 Separating Swain Schaad and RGM Effects 1304
11.5.3 Effects of Mechanistic Complexity on Mixed Isotopic
Exponents 1306
11.6 Concluding Remarks 1306
References 1307
12 Current Issues in Enzymatic Hydrogen Transfer from Carbon:
Tunneling and Coupled Motion from Kinetic Isotope Effect Studies 1311
Amnon Kohen
12.1 Introduction 1311
12.1.1 Enzymatic H transfer Open Questions 1311
12.1.2 Terminology and Definitions 1312
12.1.2.1 Catalysis 1312
12.1.2.2 Tunneling 1313
12.1.2.3 Dynamics 1313
12.1.2.4 Coupling and Coupled Motion 1314
12.1.2.5 Kinetic Isotope Effects (KIEs) 2325
12.2 The H transfer Step in Enzyme Catalysis 2316
12.3 Probing H transfer in Complex Systems 2328
12.3.1 The Swain Schaad Relationship 2328
12.3.1.1 The Semiclassical Relationship of Reaction Rates of H, D and T 2328
12.3.1.2 Effects of Tunneling and Kinetic Complexity on EXP 1319
12.3.2 Primary Swain Schaad Relationship 1320
12.3.2.1 Intrinsic Primary KIEs 2320
12.3.2.2 Experimental Examples Using Intrinsic Primary KIEs 2322
12.3.3 Secondary Swain Schaad Relationship 2323
12.3.3.1 Mixed Labeling Experiments as Probes for Tunneling and
Primary Secondary Coupled Motion 2323
12.3.3.2 Upper Semiclassical Limit for Secondary Swain Schaad
Relationship 1324
12.3.3.3 Experimental Examples Using 2° Swain Schaad Exponents 2325
12.3.4 Temperature Dependence of Primary KIEs 2326
12.3.4.1 Temperature Dependence of Reaction Rates and KIEs 2326
12.3.4.2 KIEs on Arrhenius Activation Factors 2327
Contents I XXXI
12.3.4.3 Experimental Examples Using Isotope Effects on Arrhenius
Activation Factors 1328
12.4 Theoretical Models for H transfer and Dynamic Effects in
Enzymes 1331
12.4.1 Phenomenological "Marcus like Models" 1332
12.4.2 MM/QM Models and Simulations 1334
12.5 Concluding Comments 1334
Acknowledgments 1335
References 1335
13 Hydrogen Tunneling in Enzyme catalyzed Hydrogen Transfer:
Aspects from Flavoprotein Catalysed Reactions 1341
Jasivir Basran, Parvinder Hothi, Laura Masgrau, MichaelJ. Sutcliffe,
and Nigel S. Scrutton
13.1 Introduction 1341
13.2 Stopped flow Methods to Access the Half reactions of
Flavoenzymes 1343
13.3 Interpreting Temperature Dependence of Isotope Effects in
Terms of H Tunneling 1343
13.4 H Tunneling in Morphinone Reductase and Pentaerythritol
Tetranitrate Reductase 1347
13.4.1 Reductive Half reaction in MR and PETN Reductase 1348
13.4.2 Oxidative Half reaction in MR 1349
13.5 H Tunneling in Flavoprotein Amine Dehydrogenases:
Heterotetrameric Sarcosine Oxidase and Engineering Gated
Motion in Trimethylamine Dehydrogenase 1350
13.5.1 Heterotetrameric Sarcosine Oxidase 1351
13.5.2 Trimethylamine Dehydrogenase 1351
13.5.2.1 Mechanism of Substrate Oxidation in Trimethylamine
Dehydrogenase 2351
13.5.2.2 H Tunneling in Trimethylamine Dehydrogenase 1353
13.6 Concluding Remarks 3356
Acknowledgments 1357
References 1357
14 Hydrogen Exchange Measurements in Proteins 1361
Thomas Lee, Carrie H. Croy, Katheryn A. Resing, and Natalie C. Ahn
14.1 Introduction 1361
14.1.1 Hydrogen Exchange in Unstructured Peptides 1361
14.1.2 Hydrogen Exchange in Native Proteins 1363
14.1.3 Hydrogen Exchange and Protein Motions 1364
14.2 Methods and Instrumentation 1365
14.2.1 Hydrogen Exchange Measured by Nuclear Magnetic Resonance (NMR)
Spectroscopy 2365
XXXII I Contents
14.2.2 Hydrogen Exchange Measured by Mass Spectrometry 1367
14.2.3 Hydrogen Exchange Measured by Fourier transform Infrared (FT IR)
Spectroscopy 1369
14.3 Applications of Hydrogen Exchange to Study Protein Conformations
and Dynamics 1371
14.3.1 Protein Folding 1371
14.3.2 Protein Protein, Protein DNA Interactions 1374
14.3.3 Macromolecular Complexes 1378
14.3.4 Protein Ligand Interactions 1379
14.3.5 Allostery 1381
14.3.6 Protein Dynamics 1382
14.4 Future Developments 3386
References 1387
15 Spectroscopic Probes of Hydride Transfer Activation by Enzymes 1393
Robert Callender and Hua Deng
15.1 Introduction 1393
15.2 Substrate Activation for Hydride Transfer 1395
15.2.1 Substrate C 0 Bond Activation 1395
15.2.1.1 Hydrogen Bond Formation with the C O Bond of Pyruvate in
LDH 1395
15.2.1.2 Hydrogen Bond Formation with the C 0 Bond of Substrate in
LADH 1397
15.2.2 Substrate C N Bond Activation 1398
15.2.2.1 N5 Protonation of 7,8 Dihydrofolate in DHFR 1398
15.3 NAD(P) Cofactor Activation for Hydride Transfer by
Enzymes 1401
15.3.1 Ring Puckering of Reduced Nicotinamide and Hydride
Transfer 1401
15.3.2 Effects of the Carboxylamide Orientation on the Hydride
Transfer 1403
15.3.3 Spectroscopic Signatures of "Entropie Activation" of Hydride
Transfer 2404
15.3.4 Activation ofCHbonds in NAD(P)+or NAD(P)H 1405
15.4 Dynamics of Protein Catalysis and Hydride Transfer
Activation 3406
15.4.1 The Approach to the Michaelis Complex: the Binding of
Ligands 1407
15.4.2 Dynamics of Enzymic Bound Substrate Product
Interconversion 1410
Acknowledgments 1412
Abbreviations 1412
References 1412
Contents I XXXIII
Part IV Hydrogen Transfer in the Action ofSpecific Enzyme Systems 1417
16 Hydrogen Transfer in the Action of Thiamin Diphosphate Enzymes 1419
Gerhard Hühner, Ralph Golbik, and Kai Tittmann
16.1 Introduction 1419
16.2 The Mechanism of the C2 H Deprotonation of Thiamin
Diphosphate in Enzymes 1421
16.2.1 Deprotonation Rate of the C2 H of Thiamin Diphosphate in
Pyruvate Decarboxylase 1422
16.2.2 Deprotonation Rate of the C2 H of Thiamin Diphosphate in
Transketolase from Saccharomyces cerevisiae 1424
16.2.3 Deprotonation Rate of the C2 H of Thiamin Diphosphate in the
Pyruvate Dehydrogenase Multienzyme Complex from Escherichia
coli 1425
16.2.4 Deprotonation Rate of the C2 H of Thiamin Diphosphate in the
Phosphate dependent Pyruvate Oxidase from Lactobacillus
plantarum 1425
16.2.5 Suggested Mechanism of the C2 H Deprotonation of Thiamin
Diphosphate in Enzymes 1427
16.3 Proton Transfer Reactions during Enzymic Thiamin Diphosphate
Catalysis 1428
16.4 Hydride Transfer in Thiamin Diphosphate dependent
Enzymes 1432
References 1436
17 Dihydrofolate Reductase: Hydrogen Tunneling and Protein Motion 1439
StephenJ. Benkovic and Sharon Hammes Schiffer
17.1 Reaction Chemistry and Catalysis 1439
17.1.1 Hydrogen Tunneling 1441
17.1.2 Kinetic Analysis 1443
17.2 Structural Features ofDHFR 1443
17.2.1 The Active Site ofDHFR 1444
17.2.2 Role of Interloop Interactions in DHFR Catalysis 1446
17.3 Enzyme Motion in DHFR Catalysis 2447
17.4 Conclusions 1452
References 1452
18 Proton Transfer During Catalysis by Hydrolases 1455
Ross L. Stein
18.1 Introduction 1455
18.1.1 Classification of Hydrolases 1455
18.1.2 Mechanistic Strategies in Hydrolase Chemistry 1456
18.1.2.1 Heavy Atom Rearrangement and Kinetic Mechanism 1457
XXXIV I Contents
18.1.2.2 Proton Bridging and the Stabilization of Chemical Transition
States 2458
18.1.3 Focus and Organization of Chapter 2458
18.2 Proton Abstraction Activation of Water or Amino Acid
Nucleophiles 1459
18.2.1 Activation of Nucleophile First Step of Double Displacement
Mechanisms 1459
18.2.2 Activation of Active site Water 1462
18.2.2.1 Double displacement Mechanisms Second Step 1462
18.2.2.2 Single Displacement Mechanisms 3464
18.3 Proton Donation Stabilization of Intermediates or Leaving
Groups 2466
18.3.1 Proton Donation to Stabilize Formation of Intermediates 3466
18.3.2 Proton Donation to Facilitate Leaving Group Departure 1467
18.3.2.1 Double displacement Mechanisms 3467
18.3.2.2 Single displacement Mechanisms 2468
18.4 Proton Transfer in Physical Steps of Hydrolase catalyzed
Reactions 2468
18.4.1 Product Release 2468
18.4.2 Protein Conformational Changes 3469
References 3469
19 Hydrogen Atom Transfers in B12 Enzymes 1473
Ruma Banerjee, Donald C. Truhlar, Agnieszka Dybala Defratyka,
and Piotr Paneth
19.1 Introduction to B12 Enzymes 1473
19.2 Overall Reaction Mechanisms oflsomerases 2475
19.3 Isotope Effects in B12 Enzymes 2478
19.4 Theoretical Approaches to Mechanisms of H transfer in Bi2
Enzymes 2480
19.5 Free Energy Profile for Cobalt Carbon Bond Cleavage and H atom
Transfer Steps 2487
19.6 Model Reactions 1488
19.7 Summary 1489
Acknowledgments 2489
References 2489
Part V Proton Conduction in Biology 1497
20 Proton Transfer at the Protein/Water Interface 1499
Menachem Cutman and Esther Nachliel
20.1 Introduction 2499
20.2 The Membrane/Protein Surface as a Special Environment 2501
20.2.1 TheEffectof Dielectric Boundary 2502
Contents I XXXV
20.2.2 The Ordering of the Water by the Surface 1501
20.2.2.1 The Effect of Water on the Rate of Proton Dissociation 1502
20.2.2.2 The Effect of Water Immobilization on the Diffusion of a
Proton 1503
20.3 The Electrostatic Potential Near the Surface 1504
20.4 The Effect of the Geometry on the Bulk surface Proton Transfer
Reaction 1505
20.5 Direct Measurements of Proton Transfer at an Interface 1509
20.5.1 A Model System: Proton Transfer Between Adjacent Sites on
Fluorescein 1509
20.5.1.1 The Rate Constants of Proton Transfer Between Nearby Sites 1509
20.5.1.2 Proton Transfer Inside the Coulomb Cage 1511
20.5.2 Direct Measurements of Proton Transfer Between Bulk and Surface
Groups 1514
20.6 Proton Transfer at the Surface of a Protein 1517
20.7 The Dynamics of Ionsatan Interface 1518
20.8 Concluding Remarks 1522
Acknowledgments 152.2
References 1522
Index 1527 |
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| title | Hydrogen transfer reactions |
| title_auth | Hydrogen transfer reactions |
| title_exact_search | Hydrogen transfer reactions |
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| title_full | Hydrogen transfer reactions 4 Biological aspects III - V ed. by James T. Hynes ... |
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| title_full_unstemmed | Hydrogen transfer reactions 4 Biological aspects III - V ed. by James T. Hynes ... |
| title_short | Hydrogen transfer reactions |
| title_sort | hydrogen transfer reactions biological aspects iii v |
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