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.

Warshel, Arieh, writer of foreword.

Language:

English

Subjects (All):

Valence (Theoretical chemistry).

Chemical processes.

Physical Description:

1 online resource (282 pages) : illustrations (some color)

Edition:

1st ed.

Place of Publication:

Chichester, England : Wiley, 2017.

Summary:

A comprehensive overview of current empirical valence bond (EVB) theory and applications, one of the most powerful tools for studying chemical processes in the condensed phase and in enzymes. * Discusses the application of EVB models to a broad range of molecular systems of chemical and biological interest, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems * Edited by a rising star in the field of computational enzymology * Foreword by Nobel laureate Arieh Warshel, who first developed the EVB approach

Contents:

Cover

Title Page

Copyright

Contents

List of Contributors

Foreword

Acknowledgements

Chapter 1 Modelling Chemical Reactions Using Empirical Force Fields

1.1 Introduction

1.2 Computational Approaches

1.3 Molecular Mechanics with Proton Transfer

1.4 Adiabatic Reactive Molecular Dynamics

1.5 The Multi-Surface ARMD Method

1.6 Empirical Valence Bond

1.7 ReaxFF

1.8 Other Approaches

1.9 Applications

1.9.1 Protonated Water and Ammonia Dimer

1.9.2 Charge Transfer in N2-N2+

1.9.3 Vibrationally Induced Photodissociation of Sulfuric Acid

1.9.4 Proton Transfer in Malonaldehyde and Acetyl-Acetone

1.9.5 Rebinding Dynamics in MbNO

1.9.6 NO Detoxification Reaction in Truncated Hemoglobin (trHbN)

1.9.7 Outlook

References

Chapter 2 Introduction to the Empirical Valence Bond Approach

2.1 Introduction

2.2 Historical Overview

2.2.1 From Molecular Mechanics to QM/MM Approaches

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

2.3 Introduction to Valence Bond Theory

2.4 The Empirical Valence Bond Approach

2.4.1 Constructing an EVB Potential Surface for an SN2 Reaction in Solution

2.4.2 Evaluation of Free Energies

2.5 Technical Considerations

2.5.1 Reliability of the Parametrization of the EVB Surfaces

2.5.2 The EVB Off-diagonal Elements

2.5.3 The Choice of the Energy Gap Reaction Coordinate

2.5.4 Accuracy of the EVB Approach For Computing Detailed Rate Quantities

2.6 Examples of Empirical Valence Bond Success Stories

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

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

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

2.6.4 Exploring Enantioselectivity Using the EVB Approach

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

2.7 Other Empirical Valence Bond Models

2.7.1 Chang-Miller Formalism

2.7.2 Approximate Valence Bond (AVB) Approach

2.7.3 Multistate Empirical Valence Bond (MS-EVB)

2.7.4 Multiconfiguration Molecular Mechanics (MCMM)

2.7.5 Other VB Approaches for Studying Complex Systems

2.8 Conclusions and Future Perspectives

Chapter 3 Using Empirical Valence Bond Constructs as Reference Potentials For High-Level Quantum Mechanical Calculations

3.1 Context

3.2 Concept

3.3 Challenges

3.3.1 Different Reference and Target Reaction Paths

3.3.2 Convergence of the Free Energy Estimates

3.4 Implementation of the Reference Potential Methods

3.4.1 Locating the Target Reaction Path

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

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

3.4.4 Pre-Computing the Reaction Path

3.4.5 Reference Potential Refinement: the Paradynamics Model

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

3.4.7 High-Accuracy Local PMF Regions from Targeted Sampling

3.4.8 Improving Accuracy of Positioning the Local PMF Regions

3.5 EVB as a Reference Potential

3.5.1 EVB Parameter Refinement

3.5.2 EVB Functional Refinement

3.6 Estimation of the Free Energy Perturbation

3.6.1 Exponential Average

3.6.2 Linear Response Approximation (LRA)

3.6.3 Bennet's Acceptance Ratio

3.6.4 Free Energy Interpolation

3.7 Overcoming Some Limitations of EVB Approach as a Reference Potential

3.8 Final Remarks

References.

Chapter 4 Empirical Valence Bond Methods for Exploring Reaction Dynamics in the Gas Phase and in Solution

4.1 Introduction

4.2 EVB and Related Methods for Describing Potential Energy Surfaces

4.3 Methodology

4.4 Recent Applications

4.4.1 Cl + CH4 in the Gas Phase

4.4.2 CN + c-C6H12 (CH2Cl2 Solvent)

4.4.3 CN + Tetrahydrofuran (Tetrahydrofuran Solvent)

4.4.4 F + CD3CN (CD3CN Solvent)

4.4.5 Diazocyclopropane Ring Opening

4.5 Software Implementation Aspects

4.5.1 CPU Parallelization Using MPI

4.5.2 GPU Parallelization

4.6 Conclusions and Perspectives

Chapter 5 Empirical Valence-Bond Models Based on Polarizable Force Fields for Infrared Spectroscopy

5.1 Introduction

5.2 Infrared Spectra of Aspartate and Non-Reactive Calculations

5.2.1 Experimental Approach

5.2.2 Quantum Chemical Calculations

5.2.3 Finite Temperature IR Spectra Based on AMOEBA

5.3 Empirical Valence-Bond Modeling of Proton Transfer

5.3.1 Two-State EVB Model

5.3.2 Dynamics Under the EVB-AMOEBA Potential

5.3.3 Infrared Spectra with the EVB-AMOEBA Approach

5.4 Concluding Remarks

Chapter 6 Empirical Valence Bond Simulations of Biological Systems

6.1 Introduction

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

6.2.1 Hydrolysis of Organophosphate Compounds in BChE

6.2.2 Hydrolysis of GTP in Ras/RasGAP

6.3 EVB a Comparative Tool

6.3.1 Guided Reaction Paths

6.3.2 Studies of the Same Reaction in Different Environments

6.4 EVB - A Sampling Tool

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

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

6.5 EVB Provides Simple Yet Superior Definition of Reaction Coordinate

6.6 EVB - A Tool with Great Insight.

6.7 Concluding Remarks

Chapter 7 The Empirical Valence Bond Approach as a Tool for Designing Artificial Catalysts

7.1 Introduction

7.2 Proposals for the Origin of the Catalytic Effect

7.3 Reorganization Energy

7.4 Conventional In Silico Enzyme Design

7.5 Computational Analysis of Kemp Eliminases

7.6 Using the Empirical Valence Bond Approach to Determine Catalytic Effects

7.6.1 General EVB Framework

7.6.2 Computing Free Energy Profiles Within the EVB Framework

7.7 Computing the Reorganization Energy

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

7.9 Contribution of Individual Residues

7.10 Improving Rational Enzyme Design by Incorporating the Reorganization Energy

7.11 Conclusions and Outlook

Chapter 8 EVB Simulations of the Catalytic Activity of Monoamine Oxidases: From Chemical Physics to Neurodegeneration

8.1 Introduction

8.2 Pharmacology of Monoamine Oxidases

8.3 Structures of MAO A and MAO B Isoforms

8.4 Mechanistic Studies of MAO

8.5 Cluster Model of MAO Catalysis

8.6 Protonation States of MAO Active Site Residues

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

8.8 Nuclear Quantum Effects in MAO Catalysis

8.9 Relevance of MAO Catalyzed Reactions for Neurodegeneration

8.10 Conclusion and Perspectives

Index

Supplemental Images

EULA.

Notes:

Includes bibliographical references at the end of each chapters and index.

Description based on print version record.

ISBN:

9781119245452

1119245451

9781119245544

1119245540

OCLC:

975222755