Theory and applications of the empirical valence bond approach : from physical chemistry to chemical biology / edited by Fernanda Duarte, Shina Caroline Lynn Kamerlin ; with a foreword by Arieh Warshel.

Format:

Book

Contributor:

Duarte, Fernanda (Fernanda Duarte Gonzalez), editor.

Kamerlin, Shina Caroline Lynn, 1981- editor.

Language:

English

Subjects (All):

Valence (Theoretical chemistry).

Chemical processes.

Physical Description:

xix, 241 pages, 18 unnumbered pages of plates : illustrations (some color) ; 26 cm

Place of Publication:

Chichester, West Sussex : John Wiley & Sons Ltd, 2017.

Summary:

Over the past two decades, empirical valence bond approaches have become one of the key tools for studying chemical processes in condensed phases and proteins. This book provides a comprehensive overview of these advances, recent applications, and extension of the original empirical valence bond approach to a variety of different areas of research, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems. Written by leading scientists in the field, the book provides a concise yet comprehensive introduction to the basic concepts and historical background of valence bond theory in general and the empirical valence bond approach specifically. In addition to fundamental theoretical background, it also highlights a broad range of applications from chemical physics to computational biology, including studies of chemical reaction mechanisms, reaction dynamics, and enzyme design, to name just a few examples. The book will be of primary interest to researchers and students working on computational modeling, theoretical chemistry, and chemical physics. Book jacket.

Contents:

1 Modelling Chemical Reactions Using Empirical Force Fields / Tibor Nagy Nagy, Tibor, Markus Meuwly Meuwly, Markus 1

1.1 Introduction 1

1.2 Computational Approaches 3

1.3 Molecular Mechanics with Proton Transfer 3

1.4 Adiabatic Reactive Molecular Dynamics 4

1.5 The Multi-Surface ARMD Method 6

1.6 Empirical Valence Bond 8

1.7 ReaxFF 9

1.8 Other Approaches 10

1.9 Applications 10

1.9.1 Protonated Water and Ammonia Dimer 10

1.9.2 Charge Transfer in N₂ - N⁺₂ 12

1.9.3 Vibrationally Induced Photodissociation of Sulfuric Acid 12

1.9.4 Proton Transfer in Malonaldehyde and Acetyl-Ace tone 15

1.9.5 Rebinding Dynamics in MbNO 16

1.9.6 NO Detoxification Reaction in Truncated Hemoglobin (trHbN) 16

1.9.7 Outlook 18

Acknowledgements 19

References 19

2 Introduction to the Empirical Valence Bond Approach / Fernanda Duarte Duarte, Fernanda, Anna Pabis Pabis, Anna, Shina Caroline Lynn Kamerlin Kamerlin, Shina Caroline Lynn 27

2.1 Introduction 27

2.2 Historical Overview 28

2.2.1 From Molecular Mechanics to QM/MM Approaches 28

2.2.2 Molecular Orbital (MO) vs. Valence Bond (VB) Theory 29

2.3 Introduction to Valence Bond Theory 30

2.4 The Empirical Valence Bond Approach 32

2.4.1 Constructing an EVB Potential Surface for an S_N2 Reaction in Solution 33

2.4.2 Evaluation of Free Energies 36

2.5 Technical Considerations 38

2.5.1 Reliability of the Parametrization of the EVB Surfaces 38

2.5.2 The EVB Off-diagonal Elements 39

2.5.3 The Choice of the Energy Gap Reaction Coordinate 39

2.5.4 Accuracy of the EVB Approach For Computing Detailed Rate Quantities 40

2.6 Examples of Empirical Valence Bond Success Stories 40

2.6.1 The EVB Approach as a Tool to Explore Electrostatic Contributions to Catalysis: Staphylococcal Nuclease as a Showcase System 40

2.6.2 Using EVB to Assess the Contribution of Nuclear Quantum Effects to Catalysis 42

2.6.3 Using EVB to Explore the Role of Dynamics in Catalysis 42

2.6.4 Exploring Enantioselectivity Using the EVB Approach 43

2.6.5 Moving to Large Biological Systems: Using the EVB Approach in Studies of Chemical Reactivity on the Ribosome 44

2.7 Other Empirical Valence Bond Models 47

2.7.1 Chang-Miller Formalism 47

2.7.2 Approximate Valence Bond (AVB) Approach 47

2.7.3 Multistats Empirical Valence Bond (MS-EVB) 48

2.7.4 Multiconfiguration Molecular Mechanics (MCMM) 48

2.7.5 Other VB Approaches for Studying Complex Systems 49

2.8 Conclusions and Future Perspectives 50

References 52

3 Using Empirical Valence Bond Constructs as Reference Potentials For High-Level Quantum Mechanical Calculations / Nikoloy V. Plotnikov Plotnikov, Nikoloy V. 63

3.1 Context 64

3.2 Concept 68

3.3 Challenges 69

3.3.1 Different Reference and Target Reaction Paths 69

3.3.2 Convergence of the Free Energy Estimates 70

3.4 Implementation of the Reference Potential Methods 71

3.4.1 Locating the Target Reaction Path 71

3.4.2 Low-accuracy Target Free Energy Surface from Non-equilibrium Distribution 71

3.4.3 Obtaining a Low-Accuracy Target Free Energy Surface from Free Energy Perturbation 72

3.4.4 Pre-Computing the Reaction Path 73

3.4.5 Reference Potential Refinement: the Paradynamics Model 74

3.4.6 Moving From the Reference to the Target Free Energy Surface at the TS Using Constraints on the Reaction Coordinate 74

3.4.7 High-Accuracy Local PMF Regions from Targeted Sampling 76

3.4.8 Improving Accuracy of Positioning the Local PMF Regions 77

3.5 EVB as a Reference Potential 77

3.5.1 EVB Parameter Refinement 80

3.5.2 EVB Functional Refinement 81

3.6 Estimation of the Free Energy Perturbation 82

3.6.1 Exponential Average 83

3.6.2 Linear Response Approximation (LRA) 84

3.6.3 Bennet's Acceptance Ratio 84

3.6.4 Free Energy Interpolation 85

3.7 Overcoming Some Limitations of EVB Approach as a Reference Potential 86

3.8 Final Remarks 86

References 87

4 Empirical Valence Bond Methods for Exploring Reaction Dynamics in the Gas Phase and in Solution / Jeremy N. Harvey Harvey, Jeremy N., Michael O'Connor O'Connor, Michael, David Ft. Glowacki Glowacki, David Ft. 93

4.1 Introduction 93

4.2 EVB and Related Methods for Describing Potential Energy Surfaces 94

4.3 Methodology 97

4.4 Recent Applications 100

4.4.1 CI + CH₄ in the Gas Phase 100

4.4.2 CN + c-C₆H₁₂ (CH₂Cl₂ Solvent) 102

4.4.3 CN + Tetrahydrofuran (Tetrahydrofuran Solvent) 103

4.4.4 F + CD₃CN (CD₃CN Solvent) 104

4.4.5 Diazocyclopropane Ring Opening 107

4.5 Software Implementation Aspects 108

4.5.1 CPU Parallelization Using MPI 109

4.5.2 GPU Parallelization 111

4.6 Conclusions and Perspectives 115

References 117

5 Empirical Valence-Bond Models Based on Polarizable Force Fields for Infrared Spectroscopy / Florian Thaunay Thaunay, Florian, Florent Caívo Caívo, Florent, Gilles Dhanessian Dhanessian, Gilles, Carine Clavaguéra Clavaguéra, Carine 121

5.1 Introduction 121

5.2 Infrared Spectra of Aspartate and Non-Reactive Calculations 123

5.2.1 Experimental Approach 123

5.2.2 Quantum Chemical Calculations 124

5.2.3 Finite Temperature IR Spectra Based on AMOEBA 126

5.2.3.1 The AMOEBA Force Field 126

5.2.3.2 Infrared Spectra From Molecular Dynamics Simulations 126

5.2.3.3 Role of the Multipoles 127

5.3 Empirical Valence-Bond Modeling of Proton Transfer 130

5.3.1 Two-State EVB Model 130

5.3.1.1 Implementation of EVB Model with AMOEBA 131

5.3.1.2 Coupling Between Diabatic States 131

5.3.2 Dynamics Under the EVB-AMOEBA Potential 133

5.3.3 Infrared Spectra with the EVB-AMOEBA Approach 136

5.4 Concluding Remarks 140

Acknowledgements 140

References 140

6 Empirical Valence Bond Simulations of Biological Systems / Avital Shurki Shurki, Avital 145

6.1 Introduction 145

6.2 EVB as a Tool to Unravel Reaction Mechanisms in Biological Systems 147

6.2.1 Hydrolysis of Organophosphate Compounds in BChE 147

6.2.2 Hydrolysis of GTP in Ras/RasGAP 150

6.3 EVB a Comparative Tool 152

6.3.1 Guided Reaction Paths 152

6.3.2 Studies of the Same Reaction in Different Environments 155

6.3.2.1 The Effect of Conformational Changes 155

6.3.2.2 Mutational Studies 156

6.4 EVB - A Sampling Tool 157

6.4.1 EVB - An Efficient Way to Run an Enormous Number of Calculations 157

6.4.2 EVB - An Efficient Way to Sample Conformations for Other QM/MM Approaches 159

6.4.2.1 Copper-Chaperones 159

6.4.2.2 Hybrid Ab Initio VB/MM Approach 161

6.4.2.3 EVB - An Efficient Reference Potential 161

6.5 EVB Provides Simple Yet Superior Definition of Reaction Coordinate 163

6.6 EVB - A Tool with Great Insight 164

6.7 Concluding Remarks 166

Acknowledgements 166

References 166

7 The Empirical Valence Bond Approach as a Tool for Designing Artificial Catalysts / Monika Fuxreiter Fuxreiter, Monika, Letif Mones Mones, Letif 173

7.1 Introduction 173

7.2 Proposals for the Origin of the Catalytic Effect 174

7.3 Reorganization Energy 177

7.4 Conventional In Silico Enzyme Design 179

7.5 Computational Analysis of Kemp Eliminases 183

7.6 Using the Empirical Valence Bond Approach to Determine Catalytic Effects 184

7.6.1 General EVB Framework 184

7.6.2 Computing Free Energy Profiles Within the EVB Framework 185

7.7 Computing the Reorganization Energy 186

7.8 E_gap: A General Reaction Coordinate and its Application on Other PES 187

7.9 Contribution of Individual Residues 189

7.10 Improving Rational Enzyme Design by Incorporating the Reorganization Energy 190

7.11 Conclusions and Outlook 191

Acknowledgements 193

References 193

8 EVB Simulations of the Catalytic Activity of Monoamine Oxidases: From Chemical Physics to Neurodegeneration / Robert Vianello Vianello, Robert, Janez Mavri Mavri, Janez 199

8.1 Introduction 199

8.2 Pharmacology of Monoamine Oxidases 200

8.3 Structures of MAO A and MAO B Isoforms 201

8.4 Mechanistic Studies of MAO 202

8.5 Cluster Model of MAO Catalysis 204

8.6 Protonation States of MAO Active Site Residues 211

8.7 EVB Simulation of the Rate Limiting Hydride-Abstraction Step for Various Substrates 215

8.8 Nuclear Quantum Effects in MAO Catalysis 218

8.9 Relevance of MAO Catalyzed Reactions for Neurodegeneration 221

8.10 Conclusion and Perspectives 223

Acknowledgements 223

References 224.

Notes:

Includes bibliographical references and index.

Other Format:

Online version: Theory and applications of the empirical valence bond approach.

ISBN:

9781119245391

1119245397

OCLC:

957455059