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Informationen zum Autor Lynn Kamerlin, Professor, Department of Cell and Molecular Biology, Uppsala University Professor Kamerlin is a full?Professor?of Structural Biology at Uppsala University, as well as an ERC Starting Independent Researcher and a Wallenberg Academy Fellow. She is also the current Chair of the Young Academy of Europe (YAE). Her research interests span theoretical physical organic chemistry, phosphate and sulfate chemistry, the mechanisms of enzyme reactivity, specificity, promiscuity and catalysis, and computational directed evolution. Fernanda Duarte, Department of Cell and Molecular Biology, Uppsala University Dr Duarte is the Newton Fellow at University of Oxford, UK. In November 2015, she was awarded a ?100,000 grant for research into Plagiarizing Proteins: In Silico Evolution of Catalysts for Selective Chemical Synthesis. Klappentext 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 Zusammenfassung 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. Inhaltsverzeichnis List of Contributors xi Foreword xiii Acknowledgements xix 1 Modelling Chemical Reactions Using Empirical Force Fields 1 Tibor Nagy and Markus Meuwly 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 ProtonatedWater 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-Acetone 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 27 Fernanda Duarte, Anna Pabis and Shina Caroline Lynn Kamerlin 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 BondTheory 30 2.4 The Empirical Valence Bond Approach 32 2.4.1 Constructing an EVB Potential Surface for an SN2 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 B...
