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  Contents  
 
  Foreword V
  Preface XXXVII
  Preface to Volumes 1 and 2 XXXIX
   List of Contributors to Volumes 1 and 2 XLI
I Physical and Chemical Aspects, Parts I-III  
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
Richard L. Redington 		3
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
Martina Havenith 		33
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
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 Acid 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 Conclusion 49
References 50
3 Gas Phase Vibrational Spectroscopy of Strong Hydrogen Bonds
Knut R. Asmis, Daniel M. Neumark, and Joel M. Bowman 		53
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 (H2OHOH2)+ 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
Oliver Kühn and Leticia González 		79
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 101
References 101
Part II Hydrogen Transfer in Condensed Phases 105
5 Proton Transfer from Alkane Radical Cations to Alkanes
Jan Ceulemans 		107
5.1 Introduction 108
5.2 Electronic Absorption of Alkane Radical Cations 108
5.3 Paramagnetic Properties of Alkane Radical Cations 109
5.4 The Brønsted Acidity of Alkane Radical Cations 110
5.5 The -Basicity of Alkanes 112
5.6 Powder EPR Spectra of Alkyl Radicals 114
5.7 Symmetric Proton Transfer from Alkane Radical Cations to Alkanes: An Experimental Study in -Irradiated n-Alkane Nanoparticles Embedded in a Cryogenic CCl3F Matrix 117
5.7.1 Mechanism of the Radiolytic Process 117
5.7.2 Physical State of Alkane Aggregates in CCl3F 118
5.7.3 Evidence for Proton-donor and Proton-acceptor Site Selectivity in the Symmetric 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 Asymmetric Proton Transfer from Alkane Radical Cations to Alkanes: An Experimental Study in -Irradiated Mixed Alkane Crystals 125
5.8.1 Mechanism of the Radiolytic Process 125
5.8.2 Evidence for Proton-donor and Proton-acceptor Site Selectivity in the Asymmetric Proton Transfer from Alkane Radical Cations to Alkanes 128
References 131
6 Single and Multiple Hydrogen/Deuterium Transfer Reactions in Liquids and Solids
Hans-Heinrich Limbach 		135
6.1 Introduction 136
6.2 Theoretical 138
6.2.1 Coherent vs. Incoherent Tunneling 138
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 Bell-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-transfer 153
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 168
6.3.1 H-transfers Coupled to Minor Heavy Atom Motions 174
6.3.1.1 Symmetric 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
Abderrazzak Douhal 		223
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 1´-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
8 Tautomerization in Porphycenes
Jacek Waluk 		245
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
Mikhail V. Vener 		273
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 OHO 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 Strong 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 Harmonic Frequencies 288
9.3.2.2 The PES of the OHO Fragment 291
9.3.2.3 Anharmonic INS and IR Spectra 293
9.4 Conclusions 296
Acknowledgments 297
References 217
Part III Hydrogen Transfer in Polar Environments 301
10 Theoretical Aspects of Proton Transfer Reactions in a Polar Environment
Philip M. Kiefer and James T. Hynes 		303
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 Geometric 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 Ultrafast Intramolecular Proton Transfer
Stefan Lochbrunner, Christian Schriever, and Eberhard Riedle 		349
11.1 Introduction 349
11.2 Time-resolved Absorption Measurements 352
11.3 Spectral Signatures of Ultrafast ESIPT 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
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
Dina Pines and Ehud Pines 		377
12.1 Introduction 377
12.2 Photoacids, Photoacidity and Förster Cycle 378
12.2.1 Photoacids and Photobases 378
12.2.2 Use of the Förster Cycle 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 1La, 1Lb Paradigm 404
12.6 Summary 410
Acknowledgments 411
References 411
13 Design and Implementation of "Super" Photoacids
Laren M. Tolbert and Kyril M. Solntsev 		417
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 Nature of the Solvent 426
13.3.1 Hydrogen Bonding and Solvatochromism in Super Photoacids 426
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 XLI
I Physical and Chemical Aspects, Parts IV-VII  
Part IV Hydrogen Transfer in Protic Systems 441
14 Bimolecular Proton Transfer in Solution
Erik T. J. Nibbering and Ehud Pines 		443
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
Thomas Elsaesser 		459
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
16 Proton-Coupled Electron Transfer: Theoretical Formulation and Applications
Sharon Hammes-Schiffer 		479
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
Justin M. Hodgkiss, Joel Rosenthal, and Daniel G. Nocera 		503
17.1 Introduction 503
17.1.1 Formulation of HAT as a PCET Reaction 504
17.1.2 Scope of Chapter 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 Symmetric 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
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
Heinz F. Koch 		565
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
Ian H. Williams 		583
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 Brønsted 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
Gregory J. Kubas 		603
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 610
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 617
20.3.1 Solution NMR 617
20.3.2 Solid State NMR of H2 Complexes 621
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 NMR Spectroscopy
Gerd Buntkowsky and Hans-Heinrich Limbach 		639
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 1H 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 (-H2 ) Complex 677
21.5 Summary and Conclusion 678
Acknowledgments 679
References 679
Part VI Proton Transfer in Solids and Surfaces 683
22 Proton Transfer in Zeolites
Joachim Sauer 		685
22.1 Introduction - The Active Sites of Acidic 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 691
22.5 Water Molecules and Clusters in Zeolites 694
22.6 Proton Jumps in Hydrated and Dry Zeolites 700
22.7 Stability of Carbenium Ions in Zeolites 703
References 706
23 Proton Conduction in Fuel Cells
Klaus-Dieter Kreuer 		709
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
23.4.2 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 Bilayers
Katsutoshi Aoki 		737
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
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
Klaus Christmann 		751
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 761
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
Rolf Hempelmann and Alexander Skripov 		787
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 814
26.5.2 Hydrogen Tunneling in -MnHx 817
26.5.3 Rapid Low-temperature Hopping of Hydrogen in -ScHx(Dx) and TaV2Hx(Dx) 821
26.6 Concluding Remarks 825
Acknowledgment 825
References 826
Part VII Special Features of Hydrogen-Transfer Reactions 831
27 Variational Transition State Theory in the Treatment of Hydrogen Transfer Reactions
Donald G. Truhlar and Bruce C. Garrett 		833
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 + H2 and Mu + H2 843
27.3.2 Cl + HBr 849
27.3.3 Cl + CH4 853
27.4 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 Examples of 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
K. U. Ingold 		875
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, Cyclic, Carbon-Centered Radicals 883
28.2.2.1 Cyclopropyl and 1-Methylcyclopropyl Radicals 883
28.2.2.2 The Oxiranyl Radical 884
28.2.2.3 The Dioxolanyl Radical 886
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
Zorka Smedarchina, Willem Siebrand, and Antonio Fernández-Ramos 		895
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 XLI
II Biological Aspects, Parts I-II  
Part I Models for Biological Hydrogen Transfer 947
1 Proton Transfer to and from Carbon in Model Reactions
Tina L. Amyes and John P. Richard 		949
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
1.2.2.2 Protonation by Buffer Acids 954
1.2.2.3 Protonation by Water 955
1.2.3 The Burden 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
1.4.1 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 961
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
Anthony J. Kirby 		975
2.1 Introduction 975
2.1.1 Kinetics 975
2.1.2 Mechanism 977
2.1.3 Kinetic Equivalence 979
2.2 Structural 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 991
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 1000
2.4.1 Intramolecular General Acid Catalysis 1002
2.4.2 Intramolecular General Base Catalysis 1004
2.4.3 Simple Enzyme Models 1006
2.5 Hydrogen Bonding, Mechanism and Reactivity 1007
References 1010
3 Hydrogen Atom Transfer in Model Reactions
Christian Schöneich 		1013
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
Richard L. Schowen 		1037
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 of Suitable Model Reactions 1040
4.2.1 The Anchor Principle of Jencks 1042
4.2.2 The Proximity Effect of Bruice 1044
4.2.3 Environmental Considerations 1045
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 1052
4.4.4 Transition-state Structure in Hydride Transfer: The Kreevoy Model 1054
4.4.5 Quantum Tunneling in Model Nicotinamide-mediated Hydride Transfer 1060
4.4.6 Intramolecular Models for Nicotinamide-mediated Hydride Transfer 1061
4.4.7 Summary 1063
4.5 Models for Flavin-mediated Hydride Transfer 1064
4.5.1 Differences between Flavin Reactions and Nicotinamide Reactions 1064
4.5.2 The Hydride-transfer Process in Model Systems 1065
4.6 Models for Quinone-mediated Reactions 1068
4.7 Summary and Conclusions 1071
4.8 Appendix: The Use of Model Reactions to Estimate Enzyme Catalytic Power 1071
References 1074
5 Acid-Base Catalysis in Designed Peptides
Lars Baltzer 		1079
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 of a 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 1102
Part II General Aspects of Biological Hydrogen Transfer 1105
6 Enzymatic Catalysis of Proton Transfer at Carbon Atoms
John A. Gerlt 		1107
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 Go, the Thermodynamic Barrier 1111
6.2.3 Gint, the Intrinsic Kinetic Barrier 1112
6.3 Structural Strategies for Reduction of Go 1114
6.3.1 Proposals for Understanding the Rates of Proton Transfer 1114
6.3.2 Short Strong Hydrogen Bonds 1115
6.3.3 Electrostatic Stabilization of Enolate Anion Intermediates 1115
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) 1127
6.4.4 Mandelate Racemase and Enolase 1131
6.5 Summary 1134
References 1135
7 Multiple Hydrogen Transfers in Enzyme Action
M. Ashley Spies and Michael D. Toney 		1139
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 1157
7.4.1 Proline Racemase 1157
7.4.2 Glutamate Racemase 1161
7.4.3 DAP Epimerase 1162
7.4.4 Sugar Epimerases 1165
7.5 Cofactor-Independent with Unactivated Substrates 1165
7.6 Summary 1166
References 1167
8 Computer Simulations of Proton Transfer in Proteins and Solutions
Sonja Braun-Sand, Mats H. M. Olsson, Janez Mavri, and Arieh Warshel 		1171
8.1 Introduction 1171
8.2 Simulating PT Reactions by the EVB and other QM/MM Methods 1171
8.3 Simulating the Fluctuations of the Environment and Nuclear Quantum Mechanical Effects 1177
8.4 The EVB as a Basis for LFER of PT Reactions 1185
8.5 Demonstrating the Applicability of the Modified Marcus´ Equation 1188
8.6 General Aspects of Enzymes that Catalyze PT Reactions 1194
8.7 Dynamics, Tunneling and Related Nuclear Quantum Mechanical Effects 1195
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 XLI
II Biological Aspects, Parts III-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
Steven D. Schwartz 		1209
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
Michael J. Knapp, Matthew Meyer, and Judith P. Klinman 		1241
10.1 Introduction 1241
10.2 Enzyme Kinetics: Extracting Chemistry from Complexity 1242
10.3 Methodology for Detecting Nonclassical H-Transfers 1245
10.3.1 Bond Stretch KIE Model: Zero-point Energy Effects 1245
10.3.1.1 Primary Kinetic Isotope Effects 1246
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: kcat or kcat/KM 1247
10.3.2.2 Competitive Kinetic Isotope Effects: kcat/KM 1248
10.3.3 Diagnostics for Nonclassical H-Transfer 1249
10.3.3.1 The Magnitude of Primary KIEs: kH/kD > 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 Geometric 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 1258
10.4.3 Fluctuating Barriers: Reproducing Temperature Dependences 1260
10.4.4 Overview 1264
10.5 Experimental Systems 1265
10.5.1 Hydride Transfers 1265
10.5.1.1 Alcohol Dehydrogenases 1265
10.5.1.2 Glucose Oxidase 1270
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 -Hydroxylating Monooxygenase (PHM) and Dopamine -Monooxygenase (DM) 1279
10.6 Concluding Comments 1280
References 1281
11 Multiple-isotope Probes of Hydrogen Tunneling
W. Phillip Huskey 		1285
11.1 Introduction 1285
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 1291
11.3.2 Swain-Schaad Exponents for Tunneling Systems 1292
11.3.3 Swain-Schaad Exponents from Computational Studies that Include Tunneling 1293
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 Rule of the Geometric 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 1304
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
Amnon Kohen 		1311
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) 1315
12.2 The H-transfer Step in Enzyme Catalysis 1316
12.3 Probing H-transfer in Complex Systems 1318
12.3.1 The Swain-Schaad Relationship 1318
12.3.1.1 The Semiclassical Relationship of Reaction Rates of H, D and T 1318
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 1320
12.3.2.2 Experimental Examples Using Intrinsic Primary KIEs 1322
12.3.3 Secondary Swain-Schaad Relationship 1323
12.3.3.1 Mixed Labeling Experiments as Probes for Tunneling and Primary-Secondary Coupled Motion 1323
12.3.3.2 Upper Semiclassical Limit for Secondary Swain-Schaad Relationship 1324
12.3.3.3 Experimental Examples Using 2º Swain-Schaad Exponents 1325
12.3.4 Temperature Dependence of Primary KIEs 1326
12.3.4.1 Temperature Dependence of Reaction Rates and KIEs 1326
12.3.4.2 KIEs on Arrhenius Activation Factors 1327
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
Jaswir Basran, Parvinder Hothi, Laura Masgrau, Michael J. Sutcliffe, and Nigel S. Scrutton 		1341
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 1351
13.5.2.2 H-Tunneling in Trimethylamine Dehydrogenase 1353
13.6 Concluding Remarks 1356
Acknowledgments 1357
References 1357
14 Hydrogen Exchange Measurements in Proteins
Thomas Lee, Carrie H. Croy, Katheryn A. Resing, and Natalie G. Ahn 		1361
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 1365
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 1386
References 1387
15 Spectroscopic Probes of Hydride Transfer Activation by Enzymes
Robert Callender and Hua Deng 		1393
15.1 Introduction 1393
15.2 Substrate Activation for Hydride Transfer 1395
15.2.1 Substrate C-O 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-O 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 "Entropic Activation" of Hydride Transfer 1404
15.3.4 Activation of CH bonds in NAD(P)+ or NAD(P)H 1405
15.4 Dynamics of Protein Catalysis and Hydride Transfer Activation 1406
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
Part IV Hydrogen Transfer in the Action of Specific Enzyme Systems 1417
16 Hydrogen Transfer in the Action of Thiamin Diphosphate Enzymes
Gerhard Hübner, Ralph Golbik, and Kai Tittmann 		1419
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
Stephen J. Benkovic and Sharon Hammes-Schiffer 		1439
17.1 Reaction Chemistry and Catalysis 1439
17.1.1 Hydrogen Tunneling 1441
17.1.2 Kinetic Analysis 1443
17.2 Structural Features of DHFR 1443
17.2.1 The Active Site of DHFR 1444
17.2.2 Role of Interloop Interactions in DHFR Catalysis 1446
17.3 Enzyme Motion in DHFR Catalysis 1447
17.4 Conclusions 1452
References 1452
18 Proton Transfer During Catalysis by Hydrolases
Ross L. Stein 		1455
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
18.1.2.2 Proton Bridging and the Stabilization of Chemical Transition States 1458
18.1.3 Focus and Organization of Chapter 1458
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 1464
18.3 Proton Donation - Stabilization of Intermediates or Leaving Groups 1466
18.3.1 Proton Donation to Stabilize Formation of Intermediates 1466
18.3.2 Proton Donation to Facilitate Leaving Group Departure 1467
18.3.2.1 Double-displacement Mechanisms 1467
18.3.2.2 Single-displacement Mechanisms 1468
18.4 Proton Transfer in Physical Steps of Hydrolase-catalyzed Reactions 1468
18.4.1 Product Release 1468
18.4.2 Protein Conformational Changes 1469
References 1469
19 Hydrogen Atom Transfers in B12 Enzymes
Ruma Banerjee, Donald G. Truhlar, Agnieszka Dybala-Defratyka, and Piotr Paneth 		1473
19.1 Introduction to B12 Enzymes 1473
19.2 Overall Reaction Mechanisms of Isomerases 1475
19.3 Isotope Effects in B12 Enzymes 1478
19.4 Theoretical Approaches to Mechanisms of H-transfer in B12 Enzymes 1480
19.5 Free Energy Profile for Cobalt-Carbon Bond Cleavage and H-atom Transfer Steps 1487
19.6 Model Reactions 1488
19.7 Summary 1489
Acknowledgments 1489
References 1489
Part V Proton Conduction in Biology 1497
20 Proton Transfer at the Protein/Water Interface
Menachem Gutman and Esther Nachliel 		1499
20.1 Introduction 1499
20.2 The Membrane/Protein Surface as a Special Environment 1501
20.2.1 The Effect of Dielectric Boundary 1501
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 Ions at an Interface 1518
20.8 Concluding Remarks 1522
Acknowledgments 1522
References 1522
  Index 1527

 
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