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The Resource Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton
Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton
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The item Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton represents a specific, individual, material embodiment of a distinct intellectual or artistic creation found in University of Oklahoma Libraries.This item is available to borrow from all library branches.
Resource Information
The item Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton represents a specific, individual, material embodiment of a distinct intellectual or artistic creation found in University of Oklahoma Libraries.
This item is available to borrow from all library branches.
 Summary
 This accessible introduction to modern theories of enzyme catalysis presents the latest methods for studying quantum tunnelling in biological systems.
 Language
 eng
 Extent
 1 online resource (xxv, 385 pages)
 Contents

 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 BornOppenheimer Approximation HartreeFock Theory Basis sets Zeropoint 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 OneDimensional Tunneling Multidimensional Tunneling Ensemble Averaging Examples Liver Alcohol Dehydrogenase Dihydrofolate Reductase SoybeanLipoxygenase1 and MethylmalonylCoA Mutase Other Systems and Perspectives Concluding Remarks. Chapter 4: Selected Theoretical Models and Computational Methods for Enzymatic Tunneling: Introduction Vibronically Nonadiabatic Reactions: Protoncoupled 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 PIFEP/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 SingleMolecule 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 Htunnelling Event Calculation of Htunnelling Rates and Kinetic Isotope Effects Analysing Molecular Dynamics Trajectories A Case Study: Aromatic Amine Dehydrogenase (AADH) Preparation of the System Analysis of the Htunnelling Step in AADH Analysis of the Role of Promoting Motions in Driving Tunnelling Comparison of Shortrange 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 XRay Crystallography to Study Enzymic HTunnelling Introduction XRay Crystallography: A Brief Overview Accuracy of XRay Diffraction Structures Dynamic Information from XRay Crystallography Examples of Htunnelling 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 ConfigurationalSearch 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 KirbyWalwyn Intramolecular Model Reaction The PowellBruice Tunneling Model Reaction Enzymic Tunneling in Alcohol Dehydrogenases Model Reactions and the Catalytic Power of Alcohol Dehydrogenase Example 2. Hydrogenatom Transfer in Methylmalonyl Coenzyme A Mutase (MCM) Nonenzymic 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: LongDistance Electron Tunneling in Proteins: Introduction Electronic Coupling and Tunneling Pathways Direct Method Avoided Crossing Application of Koopmans' Theorem Generalized MullikenHush Method The Propagator Method Protein Pruning Tunneling Pathways The Method of Tunneling Currents General Relations ManyElectron Picture Calculation of Current Density. HartreeFock Approximation Interatomic Tunneling Currents ManyElectron Aspects One Tunneling Orbital (OTO) Approximation and Polarization Effects The Limitation of the SCF Description of ManyElectron Tunneling Correlation Effects. Polarization Cloud Dynamics. Beyond HartreeFock Methods Quantum Interference Effects. Quantized Vertices Electron Transfer or Hole Transfer? Exchange Effects Dynamical Aspects. Chapter 15. Protoncoupled 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
 Isbn
 9781847559975
 Label
 Quantum tunnelling in enzymecatalysed reactions
 Title
 Quantum tunnelling in enzymecatalysed reactions
 Statement of responsibility
 edited by Rudolf K. Allemann, Nigel S. Scrutton
 Subject

 Analytical, Diagnostic and Therapeutic Techniques and Equipment
 Catalysis
 Chemicals and Drugs
 Computer Simulation
 Computing Methodologies
 Disciplines and Occupations
 Enzymes
 Enzymes and Coenzymes
 Information Science
 Investigative Techniques
 Models, Chemical
 Models, Molecular
 Models, Theoretical
 Natural Science Disciplines
 Nuclear Physics
 Physics
 Quantum Theory
 Quantum biochemistry
 Tunneling (Physics)
 Language
 eng
 Summary
 This accessible introduction to modern theories of enzyme catalysis presents the latest methods for studying quantum tunnelling in biological systems.
 Cataloging source
 UKRSC
 Dewey number
 530.416
 Illustrations
 illustrations
 Index
 index present
 LC call number
 QC176.8.T8
 LC item number
 Q368 2009
 Literary form
 non fiction
 NAL call number
 QC176.8.T8
 NAL item number
 Q83 2009
 Nature of contents

 dictionaries
 bibliography
 http://library.link/vocab/relatedWorkOrContributorName

 Allemann, Rudolf K.
 Scrutton, Nigel S
 Series statement
 RSC Biomolecular Sciences
 Series volume
 18
 http://library.link/vocab/subjectName

 Tunneling (Physics)
 Quantum biochemistry
 Enzymes
 Catalysis
 Computer Simulation
 Quantum Theory
 Enzymes
 Models, Chemical
 Models, Molecular
 Models, Theoretical
 Nuclear Physics
 Computing Methodologies
 Enzymes and Coenzymes
 Information Science
 Investigative Techniques
 Physics
 Chemicals and Drugs
 Analytical, Diagnostic and Therapeutic Techniques and Equipment
 Natural Science Disciplines
 Disciplines and Occupations
 Summary expansion
 In recent years, there has been an explosion in knowledge and research associated with the field of enzyme catalysis and Htunneling. Rich in its breath and depth, this introduction to modern theories and methods of study is suitable for experienced researchers those new to the subject. Edited by two leading experts, and bringing together the foremost practitioners in the field, this uptodate account of a rapidly developing field sits at the interface between biology, chemistry and physics. It covers computational, kinetic and structural analysis of tunnelling and the synergy in combining these methods (with a major focus on Htunneling reactions in enzyme systems). The book starts with a brief overview of proton and electron transfer history by Nobel Laureate, Rudolph A. Marcus. The reader is then guided through chapters covering almost every aspect of reactions in enzyme catalysis ranging from descriptions of the relevant quantum theory and quantum/classical theoretical methodology to the description of experimental results. The theoretical interpretation of these large systems includes both quantum mechanical and statistical mechanical computations, as well as simple more approximate models. Most of the chapters focus on enzymatic catalysis of hydride, proton and H" transfer, an example of the latter being proton coupled electron transfer. There is also a chapter on electron transfer in proteins. This is timely since the theoretical framework developed fifty years ago for treating electron transfers has now been adapted to Htransfers and electron transfers in proteins. Accessible in style, this book is suitable for a wide audience but will be particularly useful to advanced level undergraduates, postgraduates and early postdoctoral workers
 Label
 Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton
 Bibliography note
 Includes bibliographical references and index
 Carrier category
 online resource
 Carrier category code

 cr
 Carrier MARC source
 rdacarrier
 Color
 multicolored
 Content category
 text
 Content type code

 txt
 Content type MARC source
 rdacontent
 Contents
 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 BornOppenheimer Approximation HartreeFock Theory Basis sets Zeropoint 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 OneDimensional Tunneling Multidimensional Tunneling Ensemble Averaging Examples Liver Alcohol Dehydrogenase Dihydrofolate Reductase SoybeanLipoxygenase1 and MethylmalonylCoA Mutase Other Systems and Perspectives Concluding Remarks. Chapter 4: Selected Theoretical Models and Computational Methods for Enzymatic Tunneling: Introduction Vibronically Nonadiabatic Reactions: Protoncoupled 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 PIFEP/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 SingleMolecule 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 Htunnelling Event Calculation of Htunnelling Rates and Kinetic Isotope Effects Analysing Molecular Dynamics Trajectories A Case Study: Aromatic Amine Dehydrogenase (AADH) Preparation of the System Analysis of the Htunnelling Step in AADH Analysis of the Role of Promoting Motions in Driving Tunnelling Comparison of Shortrange 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 XRay Crystallography to Study Enzymic HTunnelling Introduction XRay Crystallography: A Brief Overview Accuracy of XRay Diffraction Structures Dynamic Information from XRay Crystallography Examples of Htunnelling 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 ConfigurationalSearch 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 KirbyWalwyn Intramolecular Model Reaction The PowellBruice Tunneling Model Reaction Enzymic Tunneling in Alcohol Dehydrogenases Model Reactions and the Catalytic Power of Alcohol Dehydrogenase Example 2. Hydrogenatom Transfer in Methylmalonyl Coenzyme A Mutase (MCM) Nonenzymic 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: LongDistance Electron Tunneling in Proteins: Introduction Electronic Coupling and Tunneling Pathways Direct Method Avoided Crossing Application of Koopmans' Theorem Generalized MullikenHush Method The Propagator Method Protein Pruning Tunneling Pathways The Method of Tunneling Currents General Relations ManyElectron Picture Calculation of Current Density. HartreeFock Approximation Interatomic Tunneling Currents ManyElectron Aspects One Tunneling Orbital (OTO) Approximation and Polarization Effects The Limitation of the SCF Description of ManyElectron Tunneling Correlation Effects. Polarization Cloud Dynamics. Beyond HartreeFock Methods Quantum Interference Effects. Quantized Vertices Electron Transfer or Hole Transfer? Exchange Effects Dynamical Aspects. Chapter 15. Protoncoupled 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
 Dimensions
 unknown
 Extent
 1 online resource (xxv, 385 pages)
 Form of item
 online
 Isbn
 9781847559975
 Media category
 computer
 Media MARC source
 rdamedia
 Media type code

 c
 Other control number
 10.1039/9781847559975
 Other physical details
 illustrations (some color).
 Specific material designation
 remote
 System control number

 (OCoLC)429669105
 (OCoLC)ocn429669105
 Label
 Quantum tunnelling in enzymecatalysed reactions, edited by Rudolf K. Allemann, Nigel S. Scrutton
 Bibliography note
 Includes bibliographical references and index
 Carrier category
 online resource
 Carrier category code

 cr
 Carrier MARC source
 rdacarrier
 Color
 multicolored
 Content category
 text
 Content type code

 txt
 Content type MARC source
 rdacontent
 Contents
 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 BornOppenheimer Approximation HartreeFock Theory Basis sets Zeropoint 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 OneDimensional Tunneling Multidimensional Tunneling Ensemble Averaging Examples Liver Alcohol Dehydrogenase Dihydrofolate Reductase SoybeanLipoxygenase1 and MethylmalonylCoA Mutase Other Systems and Perspectives Concluding Remarks. Chapter 4: Selected Theoretical Models and Computational Methods for Enzymatic Tunneling: Introduction Vibronically Nonadiabatic Reactions: Protoncoupled 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 PIFEP/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 SingleMolecule 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 Htunnelling Event Calculation of Htunnelling Rates and Kinetic Isotope Effects Analysing Molecular Dynamics Trajectories A Case Study: Aromatic Amine Dehydrogenase (AADH) Preparation of the System Analysis of the Htunnelling Step in AADH Analysis of the Role of Promoting Motions in Driving Tunnelling Comparison of Shortrange 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 XRay Crystallography to Study Enzymic HTunnelling Introduction XRay Crystallography: A Brief Overview Accuracy of XRay Diffraction Structures Dynamic Information from XRay Crystallography Examples of Htunnelling 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 ConfigurationalSearch 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 KirbyWalwyn Intramolecular Model Reaction The PowellBruice Tunneling Model Reaction Enzymic Tunneling in Alcohol Dehydrogenases Model Reactions and the Catalytic Power of Alcohol Dehydrogenase Example 2. Hydrogenatom Transfer in Methylmalonyl Coenzyme A Mutase (MCM) Nonenzymic 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: LongDistance Electron Tunneling in Proteins: Introduction Electronic Coupling and Tunneling Pathways Direct Method Avoided Crossing Application of Koopmans' Theorem Generalized MullikenHush Method The Propagator Method Protein Pruning Tunneling Pathways The Method of Tunneling Currents General Relations ManyElectron Picture Calculation of Current Density. HartreeFock Approximation Interatomic Tunneling Currents ManyElectron Aspects One Tunneling Orbital (OTO) Approximation and Polarization Effects The Limitation of the SCF Description of ManyElectron Tunneling Correlation Effects. Polarization Cloud Dynamics. Beyond HartreeFock Methods Quantum Interference Effects. Quantized Vertices Electron Transfer or Hole Transfer? Exchange Effects Dynamical Aspects. Chapter 15. Protoncoupled 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
 Dimensions
 unknown
 Extent
 1 online resource (xxv, 385 pages)
 Form of item
 online
 Isbn
 9781847559975
 Media category
 computer
 Media MARC source
 rdamedia
 Media type code

 c
 Other control number
 10.1039/9781847559975
 Other physical details
 illustrations (some color).
 Specific material designation
 remote
 System control number

 (OCoLC)429669105
 (OCoLC)ocn429669105
Subject
 Analytical, Diagnostic and Therapeutic Techniques and Equipment
 Catalysis
 Chemicals and Drugs
 Computer Simulation
 Computing Methodologies
 Disciplines and Occupations
 Enzymes
 Enzymes and Coenzymes
 Information Science
 Investigative Techniques
 Models, Chemical
 Models, Molecular
 Models, Theoretical
 Natural Science Disciplines
 Nuclear Physics
 Physics
 Quantum Theory
 Quantum biochemistry
 Tunneling (Physics)
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