Chapter 1 Elementary Reactions: Rate Constants     1  (33)
and their Temperature-Dependence
          Ian W. M. Smith
    1.1 Introduction                               1  (2)
    1.2 A Little History                           3  (2)
    1.3 Potential Energy Surfaces and              5  (8)
    Transition State Theory
    1.4 Comparisons between Experimental and       13 (16)
    Theoretical Results for Selected Reactions
      1.4.1 Dissociation and Association           13 (8)
      Reactions
      1.4.2 Bimolecular Reactions                  21 (6)
      1.4.3 Reactions between Radicals and         27 (2)
      Unsaturated Molecules
    1.5 Concluding Remarks                         29 (1)
    Acknowledgements                               30 (1)
    References                                     30 (4)
Chapter 2 Rate Constant Calculation of             34 (21)
Benzylperoxy Radical Isomerization
          S. Canneaux
          C. Hammaecher
          F. Louis
          M. Ribaucour
    2.1 Introduction                               34 (4)
    2.2 Computational Methods                      38 (2)
    2.3 Results and Discussion                     40 (9)
      2.3.1 Geometric Parameters                   40 (3)
      2.3.2 Energetics                             43 (5)
      2.3.3 Kinetic Parameter Calculations         48 (1)
    2.4 Conclusions                                49 (1)
    Acknowledgements                               49 (1)
    References                                     50 (5)
Chapter 3 Rate Constants and the Kinetic           55 (22)
Isotope Effects in Multi-Proton Transfer
Reactions: A Case Study of ClONO2 + HCl->HNO3 +
Cl2 Reactions with Water Clusters with
Canonical Variational Transition State Theory
using a Direct Ab Initio Dynamics Approach
          Yongho Kim
    3.1 Introduction                               55 (3)
    3.2 Computational Methods                      58 (1)
    3.3 Results and Discussion                     59 (13)
      3.3.1 Electronic Structures at the           59 (3)
      Stationary Points
      3.3.2 Reaction Dynamics of Multi-Proton      62 (4)
      Transfers
      3.3.3 Rate Constants, Tunneling and          66 (2)
      Kinetic Isotope Effects
      3.3.4 Breakdown of the Rule of Geometric     68 (4)
      Mean
    3.4 Conclusions                                72 (1)
    Acknowledgements                               73 (1)
    References                                     73 (4)
Chapter 4 Statisticodynamical and Multiscale       77 (22)
Modeling of Cluster Dissociation
          F. Calvo
          P. Parneix
    4.1 Introduction                               77 (3)
      4.1.1 Cluster Physics and Chemistry          77 (1)
      4.1.2 Dissociation as a Multiscale Process   78 (2)
    4.2 Time Multiscale Modeling                   80 (6)
      4.2.1 Basic Principles                       80 (1)
      4.2.2 Connecting Atomistic Dynamics with     81 (5)
      Rate Theories
    4.3 Validating and Exploiting Rate Theories    86 (4)
      4.3.1 Probability Distributions              86 (1)
      4.3.2 An Integrated Kinetic Modeling of      87 (3)
      Sequential Dissociation
    4.4 Applications                               90 (5)
      4.4.1 Dissociation Induced by Electron       90 (1)
      Impact: Cationic Argon Clusters
      4.4.2 Thermalization along the               91 (2)
      Dissociative Chain and the Decay of
      Fullerenes
      4.4.3 Laser-Induced Spectroscopy of a        93 (2)
      Messenger-Tagged Ionic Cluster
    4.5 Conclusions                                95 (1)
    References                                     96 (3)
Chapter 5 A Mixed Quantum-Classical View to the    99 (34)
Kinetics of Chemical Reactions Involving
Multiple Electronic States
          Aurelien de la Lande
          Bernard L騅y
          Isabelle Demachy
    5.1 Introduction                               99 (2)
    5.2 A Mixed Quantum-Classical Framework for    101(9)
    Multiple PES Reactions
      5.2.1 Time Evolution of a Molecular          101(2)
      System using a Time-Dependent Schr?dinger
      Equation
      5.2.2 Simplification of the                  103(4)
      Nuclear-Electronic Dynamics Problem
      5.2.3 Mixed Quantum-Classical Kinetics       107(3)
      Theory
    5.3 Atomistically Resolved Decoherence in      110(18)
    Molecular Systems
      5.3.1 Modeling Decoherence from              111(4)
      Semi-Classical Molecular Dynamics
      Simulations
      5.3.2 Activation of Dioxygen by Cuprous      115(6)
      Complexes
      5.3.3 Decoherence and Long-Range Electron    121(7)
      Transfers
    5.4 Conclusions                                128(2)
    References                                     130(3)
Chapter 6 Adiabatic Treatment of Torsional         133(21)
Anharmonicity and Mode Coupling in Molecular
Partition Functions and Statistical Rate
Coefficients: Application to Hydrogen Peroxide
          Zeb C. Kramer
          Rex T. Skodje
    6.1 Introduction                               133(3)
    6.2 Adiabatic Theory of Molecular State        136(4)
    Density for Non-Separable Large Amplitude
    Motion: Bound Motion
    6.3 Adiabatic Theory for Reactive Systems      140(2)
    6.4 Results for HOOH and HOOD                  142(9)
    6.5 Conclusions                                151(1)
    Acknowledgements                               152(1)
    References                                     152(2)
Chapter 7 Dynamics of Chemical Reaction around     154(26)
a Saddle Point: What Divides Reacting and
Non-Reacting Trajectories?
          Shinnosuke Kawai
          Tamiki Komatsuzaki
    7.1 Introduction                               154(3)
    7.2 Phase Space Picture of Chemical            157(5)
    Reaction Systems in the Saddle Region
      7.2.1 Quadratic Approximation                157(2)
      7.2.2 Effect of Anharmonicities              159(3)
    7.3 Canceling the Effect of Coupling:          162(7)
    Normal Form Theory
      7.3.1 Lie Transformation                     162(3)
      7.3.2 Hierarchy of Reaction Dynamics         165(4)
    7.4 Calculation of Reaction Probabilities      169(6)
      7.4.1 Semi-Classical Reaction Rate Formula   169(4)
      7.4.2 Instanton Trajectories                 173(2)
    7.5 Conclusions                                175(1)
    References                                     176(4)
Chapter 8 Derivation of Rate Constants from        180(33)
Accurate Quantum Wave Packet Theory for
Nonadiabatic and Adiabatic Chemical Reactions
          Tianshu Chu
          Keli Han
    8.1 Introduction                               180(3)
    8.2 Accurate Nonadiabatic Quantum Dynamics     183(16)
    Methods
      8.2.1 Nonadiabatic State-to-State Real       183(7)
      Wave Packet Theory for Tri-Atomic
      Reaction of A+BC->AB+C
      8.2.2 Nonadiabatic Wave Packet Theory for    190(7)
      Tetra-Atomic Reaction of AB + CD->ABC + D
      or AB + CD
      8.2.3 Diabatic Potential Energy Surfaces     197(1)
      for Nonadiabatic Tri-Atomic and
      Tetra-Atomic Reactions
      8.2.4 Derivation of Rate Constants from      198(1)
      Quantum Wave Packet Calculation
    8.3 Application to Nonadiabatic and            199(9)
    Adiabatic Processes in Tri-Atomic and
    Tetra-Atomic and Polyatomic Reaction Systems
      8.3.1 Rate Constant Computations for         199(5)
      Nonadiabatic Reactions
      8.3.2 Rate Constant Computations for         204(4)
      Adiabatic Reactions
    8.4 Conclusions and Prospects                  208(1)
    References                                     209(4)
Chapter 9 Understanding Reactivity with Reduced    213(20)
Potential Energy Landscapes: Recent Advances
and New Directions
          Bryan R. Goldsmith
          Anthony Fong
          Baron Peters
    9.1 Introduction                               213(1)
    9.2 Background                                 214(3)
    9.3 Reduced Potential Energy Surface           217(2)
    9.4 RPES Algorithm to Study Catalysis on       219(9)
    Amorphous Supports
      9.4.1 Sequential Nonlinear Programming       221(3)
      Algorithm Formulation
      9.4.2 Model Energy Landscape                 224(1)
      9.4.3 Cluster Model of Proton Transfer       225(1)
      between Anchored Amine and Oxo Ligand
      9.4.4 Ethene Insertion During                226(2)
      Polymerization on the Phillips Catalyst
    9.5 Conclusions                                228(1)
    Acknowledgements                               228(1)
    References                                     229(4)
Chapter 10 Quantum-Classical Lionville Dynamics    233(27)
of Condensed Phase Quantum Processes
          Gabriel Hanna
          Raymond Kapral
    10.1 Introduction                              233(2)
    10.2 Nonadiabatic Dynamics                     235(2)
    10.3 Quantum-Classical Liouville Dynamics      237(2)
    10.4 Simulation of Quantum-Classical           239(1)
    Dynamics
    10.5 Proton Transfer Reactions                 240(4)
    10.6 Linear and Nonlinear Vibrational          244(10)
    Spectra
      10.6.1 Linear Optical Response               247(2)
      10.6.2 Third Order Optical Response          249(1)
      10.6.3 1D- and 2D-IR Spectroscopy of a       250(4)
      Solvated Hydrogen-Bonded Complex
    10.7 Concluding Remarks and Perspectives       254(1)
    References                                     255(5)
Chapter 11 Free Energetics and Kinetics of         260(23)
Charge Transfer and Shift Reactions in
Room-Temperature Ionic Liquids
          Youngseon Shim
          Hyung J. Kim
    11.1 Introduction                              260(1)
    11.2 Formulation of Unimolecular ET            261(3)
    Reactions
      11.2.1 ET Free Energetics                    261(2)
      11.2.2 ET Kinetics                           263(1)
    11.3 Electron-Exchange Reaction                264(8)
      11.3.1 Simulation Models and Methods         264(1)
      11.3.2 ET Reaction Free Energy               265(1)
      11.3.3 Barrier Crossing                      266(2)
      11.3.4 Activation and Deactivation           268(3)
      11.3.5 Overall ET Kinetics                   271(1)
    11.4 SN1 Ionization Reaction                   272(5)
      11.4.1 Models and Methods                    272(2)
      11.4.2 Ionization Free Energy and Pathway    274(2)
      11.4.3 Barrier Crossing Dynamics             276(1)
    11.5 Conclusions                               277(1)
    Acknowledgements                               278(1)
    References                                     278(5)
Chapter 12 Semi-Classical Treatments of            283(36)
Electron Transfer Rate from Weak to Strong
Electronic Coupling Regime
          Yi Zhao
    12.1 Introduction                              283(2)
    12.2 Nonadiabatic Transition State Theory      285(6)
    for Electron Transfer
    12.3 Electron Transfer Rate Theory             291(10)
    Incorporated Solvent Dynamic Effect
      12.3.1 Quantum Kramer-Like Theory            292(5)
      12.3.2 Extended Sumi-Marcus Theory           297(4)
    12.4 Time-Dependent Wavepacket Diffusion       301(6)
    Approach
    12.5 Applications                              307(6)
      12.5.1 Electron Transfer within              307(1)
      Charge-Localized Dinitroaromatic Radical
      Anions
      12.5.2 Ab Initio Calculations on the         308(2)
      Intramolecular Electron Transfer Rates of
      a Bis(hydrazine) Radical Cation
      12.5.3 Electron Mobilities of N-type         310(3)
      Organic Semiconductors from
      Time-Dependent Wavepacket Diffusion
      Method: Pentacenequinone Derivatives
    12.6 Conclusions                               313(1)
    Acknowledgements                               313(1)
    References                                     313(6)
Chapter 13 Modified Zusman Equation for Quantum    319(18)
Solvation Dynamics and Rate Processes
          Hou-Dao Zhang
          Jian Xu
          Rui-Xue Xu
          YiJing Yan
    13.1 Introduction                              319(2)
    13.2 Zusman Equation via the Conventional      321(4)
    Approach
      13.2.1 Caldeira-Leggett's Master Equation    321(2)
      13.2.2 The Zusman Equation                   323(2)
    13.3 Modified Zusman Equation versus HEOM      325(4)
      13.3.1 The HEOM Formalism                    325(1)
      13.3.2 The Equivalent Modified ZE            326(2)
      13.3.3 Accuracy Control Criterion            328(1)
    13.4 Kinetic Rates via Hierarchy Green's       329(5)
    Functions
      13.4.1 Kinetic Rate Equation versus          329(1)
      Quantum Dissipative Dynamics
      13.4.2 Formalism of the Hierarchy.Green's    330(2)
      Functions
      13.4.3 Analytical Solutions to Kinetics      332(2)
      Rate Between Two States
    13.5 Conclusions                               334(1)
    Acknowledgements                               335(1)
    References                                     335(2)
Chapter 14 Time-Dependent Treatment of SVRT        337(15)
Model for Polyatom-Polyatom Reaction
          John Z.H. Zhang
    14.1 Introduction                              337(1)
    14.2 The SVRT Model for a Polyatom-Polyatom    338(7)
    Reaction
      14.2.1 Hamiltonian for the Target            339(2)
      Molecule T
      14.2.2 Hamiltonian for the Reactant          341(1)
      Molecule R
      14.2.3 SVRT Hamiltonian for the              341(1)
      Polyatom-Polyatom Collision System
      14.2.4 Molecular Rotation Eigenfunction      342(3)
    14.3 TD Wavepacket Treatment                   345(3)
      14.3.1 Basis Set Expansion                   345(1)
      14.3.2 Total Angular Momentum                345(1)
      Eigenfunction
      14.3.3 Propagation of the Wavefunction       346(2)
    14.4 The ASVRT Model for a                     348(2)
    Polyatom-Polyatom Reaction
    14.5 Conclusions                               350(1)
    References                                     350(2)
Chapter 15 Role of Water in Radical Reactions:     352(27)
Molecular Simulation and Modelling
          Dorota Swiatla-Wojcik
    15.1 Introduction                              352(2)
    15.2 Physical and Solvent Properties of        354(1)
    Water
    15.3 Hydrogen Bonds in Water Solvent           355(10)
      15.3.1 Definitions of H-Bond in Molecular    358(2)
      Simulations
      15.3.2 H-Bonds from Ambient to               360(1)
      Supercritical Conditions
      15.3.3 H-Bonding Effect on Solutes           361(4)
    15.4 Applications                              365(8)
      15.4.1 Modelling Rate Constants by the       365(7)
      Noyes Relationship
      15.4.2 Radical Reactions Involving Water     372(1)
      as a Reactant
    15.5 Conclusions                               373(1)
    References                                     374(5)
Chapter 16 Molecular Modelling of Proton           379(29)
Transfer Kinetics in Biological Systems
          Patrick Bertrand
    16.1 Introduction                              379(1)
    16.2 Biological Proton Transfers               380(2)
      16.2.1 Biological Systems Involving          380(1)
      Proton Transfers
      16.2.2 Kinetic Data                          381(1)
    16.3 Modelling Biological Proton Transfers:    382(8)
    Basic Ingredients
      16.3.1 Introduction                          382(2)
      16.3.2 Molecular Dynamics: Quantum           384(1)
      Mechanics/Molecular Mechanics Methods
      16.3.3 Free-Energy Calculations              385(3)
      16.3.4 Nuclear Quantum-Mechanical Effects    388(1)
      16.3.5 Simulation of Proton Transfer         389(1)
      Chain Kinetics
    16.4 The Gramicidin Channel: a Paradigm for    390(3)
    Water Wires in Proteins?
      16.4.1 Proton Diffusion in Water: the        391(1)
      Grotthuss Mechanism
      16.4.2 Proton Conductance of the             391(1)
      Gramicidin Channel
      16.4.3 Modelling Proton Transfer in          392(1)
      Gramicidin
    16.5 Intramolecular Proton Transfer in         393(3)
    Carbonic Anhydrase
      16.5.1 Kinetic Data Obtained with CAII       394(1)
      16.5.2 Modelling Proton Transfers in         394(2)
      Carbonic Anhydrase
    16.6 Bacteriorhodopsin: A Light-Driven         396(4)
    Proton Pump
      16.6.1 Introduction                          396(1)
      16.6.2 Rate Constants                        397(1)
      16.6.3 Modelling Proton Transfers in         398(2)
      Bacteriorhodopsin
    16.7 Electron Coupled Proton Transfers         400(3)
      16.7.1 The Bacterial Photosynthetic          400(1)
      Reaction Centre
      16.7.2 Cytochrome c Oxidase                  401(2)
    16.8 Conclusions                               403(1)
    Acknowledgements                               403(1)
    References                                     403(5)
Chapter 17 Putting Together the Pieces: A          408(38)
Global Description of Valence and Long-Range
Forces via Combined Hyperbolic Inverse Power
Representation of the Potential Energy Surface
          A.J.C. Varandas
    17.1 Introduction                              408(7)
    17.2 The CHIPR Method                          415(6)
      17.2.1 The Underlying Many-Body Expansion    415(2)
      17.2.2 Coordinates and n-Body                417(3)
      Representations
      17.2.3 Primitives versus Contracted Basis    420(1)
    17.3 Case Studies                              421(17)
      17.3.1 Two-Body Systems                      421(2)
      17.3.2 Three-Body Systems                    423(15)
    17.4 Conclusions                               438(1)
    Acknowledgements                               438(1)
    References                                     439(7)
Chapter 18 Extension of Marcus Rate Theory to      446(16)
Electron Transfer Reactions with Large
Solvation Changes
          Guillaume Jeanmairet
          Daniel Borgis
          Anne Boutin
          Rodolphe Vuilleumier
    18.1 Introduction                              446(2)
    18.2 Marcus Theory: A Gaussian Solvation       448(3)
    (GS) Model
    18.3 Extension to a Non-Gaussian Solvation     451(2)
    (NGS) Model
    18.4 Incidence of the NGS Model on Marcus      453(1)
    Rate Theory
    18.5 Application to Realistic Electron         454(5)
    Transfer Systems
    18.6 Conclusions                               459(1)
    References                                     460(2)
Chapter 19 Theoretical Studies on Mechanism and    462(32)
Kinetics of Atmospheric Chemical Reactions
          L. Sandhiya
          K. Senthilkumar
    19.1 Introduction                              462(1)
    19.2 Potential Energy Hypersurfaces            463(2)
    19.3 Reaction Path and Reaction Phases         465(1)
    19.4 Thermodynamic Parameters                  466(1)
    19.5 Reaction Rate Theory                      467(3)
    19.6 Tropospheric Chemistry                    470(1)
    19.7 Example: Understanding the Reactivity     471(18)
    of 2,3-Dimethylphenol with OH Radical in
    the Atmosphere
      19.7.1 Computational Methodology             472(1)
      19.7.2 Results and Discussions               473(16)
    19.8 Conclusions and Outlook                   489(1)
    References                                     490(4)
Chapter 20 Computation of Intrinsic RRKM and       494(36)
Non-RRKM Unimolecular Rate Constants
          Amit Kumar Paul
          Sujitha Kolakkandy
          Subha Pratihar
          William L. Hase
    20.1 Introduction                              494(1)
    20.2 The RRKM Rate Constant for a              495(3)
    Microcanonical Ensemble
      20.2.1 Derivation of the RRKM Rate           495(2)
      Constant
      20.2.2 The RRKM Rate Constant as an          497(1)
      Average Flux
    20.3 Intrinsic RRKM and Non-RRKM               498(11)
    Unimolecular Dynamics
      20.3.1 Rate Expressions                      498(2)
      20.3.2 Phase Space Structure and Dynamics    500(3)
      20.3.3 Vibrational/Rotational Energy         503(4)
      Levels
      20.3.4 Phase Space Dynamics and Energy       507(2)
      Levels, Classical/Quantum Correspondence,
      and RRKM Theory
    20.4 Examples of Intrinsic Non-RRKM Dynamics   509(4)
      20.4.1 Experiments                           509(1)
      20.4.2 Simulations                           510(3)
    20.5 Calculating an Accurate RRKM Rate         513(6)
    Constant
      20.5.1 Variational RRKM Theory               513(2)
      20.5.2 Anharmonic Correction                 515(4)
    20.6 Quantum Dynamics                          519(6)
      20.6.1 Isolated Resonances                   519(2)
      20.6.2 Overlapping Resonances                521(4)
    References                                     525(5)
Chapter 21 Molecular Dynamics Simulation of        530(20)
Kinetic Isotope Effects in Enzyme-Catalyzed
Reactions
          Jiali Gao
    21.1 Introduction                              530(3)
    21.2 Methods                                   533(5)
      21.2.1 Quantum Transition State Theory       533(2)
      and Path Integral Simulations
      21.2.2 Potential Energy Surface              535(1)
      21.2.3 Integrated Path Integral-Free         536(2)
      Energy Perturbation/Umbrella Sampling
      (PI-FEP/UM) Method for Computing KIEs
    21.3 Illustrative Examples                     538(8)
      21.3.1 Alanine Racemase                      538(1)
      21.3.2 Nitroalkane Oxidase                   539(3)
      21.3.3 Dihydrofolate Reductase               542(4)
    21.4 Concluding Remarks                        546(1)
    Acknowledgements                               546(1)
    References                                     546(4)
Subject Index                                      550