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Theory and Applications of the Empirical Valence Bond Approach : From Physical Chemistry to Chemical Biology.
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 int...
| Clasificación: | Libro Electrónico |
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| Autor principal: | |
| Otros Autores: | , |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Somerset :
John Wiley & Sons, Incorporated,
2017.
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| Temas: | |
| Acceso en línea: | Texto completo |
Tabla de Contenidos:
- 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-Acetone1.9.5 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 Energies2.5 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 Catalysis2.6.4 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 Calculations3.1 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.