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" Quantum tunnelling in enzyme-catalysed reactions / "
edited by Rudolf K. Allemann, Nigel S. Scrutton.
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BL
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988127
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b742497
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| Title & Author
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Quantum tunnelling in enzyme-catalysed reactions /\ edited by Rudolf K. Allemann, Nigel S. Scrutton.
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| Publication Statement
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Cambridge :: Royal Society of Chemistry,, ©2009.
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| Series Statement
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RSC Biomolecular Sciences ;; 18
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1 online resource (xxv, 385 pages) :: illustrations (some color)
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| ISBN
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0854041222
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: 1847559972
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: 9780854041220
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: 9781847559975
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Includes bibliographical references and index.
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| Contents
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Introduction. Preface: Beyond the Historical Perspective on Hydrogen and Electron Transfers. Chapter 1: The Transition State Theory Description of Enzyme Catalysis for Classically Activated Reactions: Introduction-- Quantifying the Catalytic Activity of Enzymes-- Free Energy Analysis of Enzyme Catalysis-- Transition State Stabilisation or Ground State Destabilisation?-- Selective Stabilisation of Transition Structures by Enzymes-- Enzyme Flexibility and Dynamics. Chapter 2: Introduction to Quantum Behavior -- A Primer: Introduction-- Classical Mechanics-- Quantum Mechanics-- Heisenberg Uncertainty Principle-- The Schrodinger Equation-- Electronic Structure Calculations-- Born-Oppenheimer Approximation-- Hartree-Fock Theory-- Basis sets-- Zero-point Energy-- Density Functional Theory-- DFT Calculations of Free Energies of Activation of Enzyme Models-- DFT Calculations of Kinetic Isotope Effects-- Quantum Mechanics/Molecular Mechanics Methods-- Summary and Outlook. Chapter 3: Quantum Catalysis in Enzymes: Introduction-- Theory-- Variational Transition State Theory-- The Transmission Coefficient-- One-Dimensional Tunneling-- Multidimensional Tunneling-- Ensemble Averaging-- Examples-- Liver Alcohol Dehydrogenase-- Dihydrofolate Reductase-- Soybean-Lipoxygenase-1 and Methylmalonyl-CoA Mutase-- Other Systems and Perspectives-- Concluding Remarks. Chapter 4: Selected Theoretical Models and Computational Methods for Enzymatic Tunneling: Introduction-- Vibronically Nonadiabatic Reactions: Proton-coupled Electron Transfer-- Theory-- Application to Lipoxygenase-- Predominantly Adiabatic Reactions: Proton and Hydride Transfer-- Theory-- Application to Dihydrofolate Reductase-- Emerging Concepts About Enzyme Catalysis. Chapter 5: Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations: Introduction-- Theoretical Background-- Path Integral Quantum Transition State Theory-- Centroid Path Integral Simulations-- Kinetic Isotope Effects-- Sequential Centroid Path Integral and Umbrella Sampling (PI/UM)-- The PI-FEP/UM Method-- Kleinert's Variational Perturbation (KP) Theory-- Potential Energy Surface-- Combined QM/MM Potentials-- The MOVB Potential-- Computational Details-- Illustrative Examples-- Proton Transfer between Viscosity-- Multiple Reactive Configurations and a Place for Single-Molecule Measurements. Chapter 10. Computational Simulations of Tunnelling Reactions in Enzymes-- Introduction-- Molecular Mechanical Methods-- Quantum Mechanical Methods-- Combined Quantum Mechanical/Molecular Mechanical Methods-- Improving Semiempirical QM Calculations-- Calculation of Potential Energy Surfaces and Free Energy Surfaces-- Simulation of the H-tunnelling Event-- Calculation of H-tunnelling Rates and Kinetic Isotope Effects-- Analysing Molecular Dynamics Trajectories-- A Case Study: Aromatic Amine Dehydrogenase (AADH)-- Preparation of the System-- Analysis of the H-tunnelling Step in AADH-- Analysis of the Role of Promoting Motions in Driving Tunnelling-- Comparison of Short-range Motions in AADH with Long Range Motions in Dihydrofolate Reductase-- Summary. Chapter 11. Tunneling Does Not Contribute Significantly to Enzyme Catalysis, But Studying Temperature Dependence of Isotope Effects is Useful-- Introduction-- Methods-- Simulating Temperature Dependence of KIEs in Enzymes-- Concluding Remarks. Chapter 12: The Use of X-Ray Crystallography to Study Enzymic H-Tunnelling-- Introduction-- X-Ray Crystallography: A Brief Overview-- Accuracy of X-Ray Diffraction Structures-- Dynamic Information from X-Ray Crystallography-- Examples of H-tunnelling Systems Studied by Crystallography-- Crystallographic Studies of AADH Catalytic Mechanism-- Crystallographic Studies of MR-- Conclusions. Chapter 13: The Strengths and Weaknesses of Model Reactions for the Assessment of Tunneling in Enzymic Reactions-- Model Reactions for Biochemical Processes-- Model Reactions Relevant to Enzymic Tunneling-- Isotope Effect Temperature Dependences and the Configurational-Search Framework (CSF) for their Interpretation-- The Traditionally Dependent Category-- The Underdependent Tunneling Category-- The Overdependent Tunneling Category-- Example 1. Hydride Transfer in a Thermophilic Alcohol Dehydrogenase-- The Kirby-Walwyn Intramolecular Model Reaction-- The Powell-Bruice Tunneling Model Reaction-- Enzymic Tunneling in Alcohol Dehydrogenases-- Model Reactions and the Catalytic Power of Alcohol Dehydrogenase-- Example 2. Hydrogen-atom Transfer in Methylmalonyl Coenzyme A Mutase (MCM)-- Non-enzymic Tunneling in the Finke Model Reactions for MCM-- Enzymic Tunneling in MCM-- Model Reactions and MCM Catalytic Power-- The Roles of Theory in the Comparison of Model and Enzymic Reactions-- Model Reactions, Enzymic Accelerations, and Quantum Tunneling. Chapter 14: Long-Distance Electron Tunneling in Proteins: Introduction-- Electronic Coupling and Tunneling Pathways-- Direct Method-- Avoided Crossing-- Application of Koopmans' Theorem-- Generalized Mulliken-Hush Method-- The Propagator Method-- Protein Pruning-- Tunneling Pathways-- The Method of Tunneling Currents-- General Relations-- Many-Electron Picture-- Calculation of Current Density. Hartree-Fock Approximation-- Interatomic Tunneling Currents-- Many-Electron Aspects-- One Tunneling Orbital (OTO) Approximation and Polarization Effects-- The Limitation of the SCF Description of Many-Electron Tunneling-- Correlation Effects. Polarization Cloud Dynamics. Beyond Hartree-Fock Methods-- Quantum Interference Effects. Quantized Vertices-- Electron Transfer or Hole Transfer? Exchange Effects-- Dynamical Aspects. Chapter 15. Proton-coupled Electron Transfer: The Engine that Drives Radical Transport and Catalysis in Biology-- Introduction-- PCET Model Systems-- Unidirectional PCET Networks-- Bidirectional PCET Networks-- PCET Biocatalysis-- PCET in Enzymes: A Study of Ribonucleotide Reductase-- The PCET Pathway in RNR-- PCET in the?2 Subunit of RNR-- PCET in?2 Subunit of RNR: PhotoRNRs-- A Model for PCET in RNR-- Concluding Remarks.
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| Abstract
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This accessible introduction to modern theories of enzyme catalysis presents the latest methods for studying quantum tunnelling in biological systems.
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Catalysis.
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Enzymes.
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Quantum biochemistry.
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Tunneling (Physics)
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Analytical, Diagnostic and Therapeutic Techniques and Equipment
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Chemicals and Drugs
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Computer Simulation.
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Computing Methodologies.
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Disciplines and Occupations
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Enzymes and Coenzymes
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Enzymes.
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Information Science.
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Investigative Techniques
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Models, Chemical.
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Models, Molecular.
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Models, Theoretical.
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Natural Science Disciplines.
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Nuclear Physics.
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Physics.
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Quantum Theory.
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Catalysis.
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Enzymes.
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Quantum biochemistry.
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SCIENCE-- Physics-- Condensed Matter.
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Tunneling (Physics)
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| Dewey Classification
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530.416
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| LC Classification
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QC176.8.T8Q368 2009
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| Added Entry
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Allemann, Rudolf K., (Rudolf Konrad)
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Scrutton, Nigel S.
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