Theory and Applications of the Empirical Valence Bond Approach : From Physical Chemistry to Chemical Biology.

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 -- Acknowledgements -- 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 -- References -- 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 -- References -- 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 -- Acknowledgements -- References -- 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 -- Acknowledgements -- References -- 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 -- Acknowledgements -- References -- 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 -- Acknowledgements -- References -- Index -- Supplemental Images -- EULA.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.