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The Resource Reaction Rate Theory and Rare Events

Reaction Rate Theory and Rare Events

Label
Reaction Rate Theory and Rare Events
Title
Reaction Rate Theory and Rare Events
Creator
Subject
Language
eng
Cataloging source
MiAaPQ
Literary form
non fiction
Nature of contents
dictionaries
Reaction Rate Theory and Rare Events
Label
Reaction Rate Theory and Rare Events
Link
http://libproxy.rpi.edu/login?url=https://ebookcentral.proquest.com/lib/rpi/detail.action?docID=4827690
Publication
Copyright
Related Contributor
Related Location
Related Agents
Related Authorities
Related Subjects
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
  • Front Cover -- Reaction Rate Theory and Rare Events -- Copyright -- Contents -- Preface -- 1 Introduction -- 1.1 Motivation for this book -- 1.2 Why are rare events important? -- 1.3 The role of computation and simulation -- Quantitative rate predictions -- Two types of kinetic trends, two different applications -- In silico experiments -- Mechanistic hypothesis testing -- 1.4 Polemics -- Units -- On the value of results that disagree with experiment -- Quests of questionable value -- On the proliferation and testing of new methods -- On corrections to transition state theory -- On science priority and impact metrics -- References -- 2 Chemical equilibrium -- 2.1 Chemical potential and activity -- Gas mixtures -- Liquid solutions -- Electrolytes -- Pure solids and liquids -- 2.2 Equilibrium constants and compositions -- Multireaction equilibria -- Exercises -- References -- 3 Rate laws -- 3.1 Rates, mass balances, and reactors -- 3.2 Reaction order and elementary reactions -- Elementary reactions -- 3.3 Initial rates and integrated rate laws -- Excess reagents and ooding -- 3.4 Reversible reactions -- 3.5 Multistep reactions -- 3.6 The pseudo-steady-state approximation -- 3.7 Rate determining steps and quasi-equilibrated steps -- Exercises -- References -- 4 Catalysis -- 4.1 Acid-base catalysis -- Acid/base pre-equilibrium -- 4.2 Enzymes -- Phenomenological enzyme catalysis models -- 4.3 Heterogeneous catalysis -- Modeling heterogeneous catalysts -- Sabatier's principle -- 4.4 Microkinetic models -- One-site mechanisms -- Multi-site mechanisms -- 4.5 Degree-of-rate-control -- 4.6 Catalysts with non-uniform sites -- Kinetics with quenched disorder -- Exercises -- References -- 5 Diffusion control -- 5.1 Complete diffusion control -- 5.2 Partial diffusion control -- 5.3 Diffusion control with long range interactions
  • 5.4 Diffusion control for irregularly shaped reactants -- Exercises -- References -- 6 Collision theory -- 6.1 Hard spheres: Trautz and Lewis -- Collision theory for atom exchange reactions -- 6.2 Cross sections and rate constants -- Collision theory for atom exchange reactions -- Exercises -- References -- 7 Potential energy surfaces and dynamics -- 7.1 Molecular potential energy surfaces -- 7.2 Atom-exchange reactions -- 7.3 Mass weighted coordinates and normal modes -- 7.4 Features of molecular potential energy surfaces -- 7.5 Reaction path Hamiltonian -- 7.6 Empirical valence bond models -- 7.7 Disconnectivity graphs -- Exercises -- References -- 8 Saddles on the energy landscape -- 8.1 Newton-Raphson -- 8.2 Cerjan-Miller algorithm -- 8.3 Partitioned-Rational Function Optimization -- 8.4 The dimer method -- 8.5 Reduced landscape algorithms -- 8.6 Coordinate driving -- 8.7 Nudged elastic band -- Exercises -- References -- 9 Unimolecular reactions -- 9.1 Lindemann-Christiansen mechanism -- 9.2 Hinshelwood and RRK theories -- Rice-Ramsperger-Kassels theory -- 9.3 RRKM theory -- 9.4 Transition state theory from RRKM theory -- Exercises -- References -- 10 Transition state theory -- 10.1 Foundations -- 10.2 Statistical mechanics for chemical equilibria -- 10.3 Harmonic transition state theory -- Q{u2021} excludes the reaction coordinate -- 10.4 Thermodynamic formulation -- 10.5 Flux across a dividing surface -- 10.6 Variational transition state theory -- VTST for the intrinsic arclength reaction coordinate -- Limitations -- 10.7 Harmonic TST with internal coordinates -- 10.8 Non-idealities -- Exercises -- References -- 11 Landau free energies and restricted averages -- 11.1 Monte Carlo, molecular dynamics, and hybrid sampling -- MD-based sampling methods -- Hybrid sampling methods -- 11.2 Thermodynamic perturbation theory -- 11.3 Projections
  • 11.4 Non-Boltzmann sampling -- Umbrella sampling with windows between hard walls -- Umbrella sampling with harmonic restraints -- 11.5 Thermodynamic integration -- Conditional average -- Hitting points average -- Constrained dynamics average -- 11.6 Other methods for computing free energies -- Adiabatic partitioning methods -- Flooding, metadynamics, and related methods -- Adaptive biasing force -- 11.7 Cautionary notes -- Exercises -- References -- 12 Tunneling -- 12.1 One-dimensional tunneling models -- Parabolic barrier -- The truncated parabolic barrier -- The asymmetric Eckart barrier -- 12.2 Kinetic isotope effects -- 12.3 Tunneling or tunnel splitting -- 12.4 Multidimensional tunneling models -- Small curvature tunneling models -- Large curvature tunneling models -- Exercises -- References -- 13 Reactive ux -- 13.1 Phenomenological rate laws and time correlations -- 13.2 Reactive ux formalism -- Timescale separation -- Non-equilibrium effects -- Reactive ux calculations -- 13.3 Effective positive ux -- 13.4 Quantum dynamical correlation functions -- Quantum dynamics from classical simulations -- Exercises -- References -- 14 Discrete stochastic variables -- 14.1 Basic de nitions -- Markov property -- Temporal homogeneity -- Ergodicity -- Stationary and equilibrium distributions -- Time reversal properties -- Metastability -- 14.2 The master equation -- 14.3 Classical nucleation theory -- 14.4 Kinetic Monte Carlo -- 14.5 Markov state models -- Formal properties -- Constructing an MSM -- Applications of MSMs -- Limitations of MSMs -- 14.6 Spectral theory -- Variational two-state theory (V2ST) -- Exercises -- References -- 15 Continuous stochastic variables -- 15.1 Inertial Langevin dynamics -- 15.2 Overdamped Langevin dynamics -- 15.3 Fokker-Planck equations -- Fokker-Planck equation from the master equation
  • Detailed balance and the Smoluchowski equation -- Fokker-Planck equations from simulation data -- 15.4 From discrete models to Fokker-Planck equations -- 15.5 Stationary solutions of Fokker-Planck equations -- 15.6 Spectral theory revisited -- Exercises -- References -- 16 Kramers theory -- 16.1 Intermediate and high friction -- 16.2 Low friction: the energy diffusion limit -- 16.3 Insights and limitations -- Exercises -- References -- 17 Grote-Hynes theory -- 17.1 The Grote-Hynes equations -- 17.2 Multidimensional models and interpretations -- Exercises -- References -- 18 Diffusion over barriers -- 18.1 The forward and backward equations -- 18.2 Mean rst passage times -- 18.3 Langer's multidimensional theory -- 18.4 Committors (splitting probabilities) -- 18.5 Berezhkovskii and Szabo: back to one dimension -- 18.6 Classical nucleation theory revisited -- 18.7 Rates from the committor -- 18.8 Discrete committors and rates -- Rates from discrete committor -- Exercises -- References -- 19 Transition path sampling -- 19.1 The transition path ensemble -- 19.2 Transition path sampling -- 19.3 Basin de nitions and foliations -- 19.4 Rate constants from transition path sampling -- 19.5 Transition interface sampling -- 19.6 Forward ux sampling -- Exercises -- References -- 20 Reaction coordinates and mechanisms -- 20.1 Properties of an ideal reaction coordinate -- Requirement 1. Purely con gurational -- Requirement 2. Foliation -- Requirement 3. Suf cient to predict committor[3] -- Desideratum: A clear mechanistic interpretation -- 20.2 Variational theories and eigenfunctions -- Variational TST -- KLBS theory -- Eigenfunctions of the master equation -- 20.3 Committor analysis -- 20.4 Square error minimization -- 20.5 Likelihood maximization -- Occam's razor -- Need for an independent test -- 20.6 Inertial likelihood maximization -- Exercises
  • References -- 21 Nonadiabatic reactions -- 21.1 Diabatic and adiabatic representations -- 21.2 Spin-forbidden reactions -- 21.3 Electron transfer -- Marcus' parabolas -- Rate calculation -- Inverted regime -- Predictions for cross electron transfer -- 21.4 Classical MD methods for electron transfer -- Driving force and Zwanzig-Bennett relation -- 21.5 Nonadiabatic models of enzyme catalysis -- Exercises -- References -- 22 Free energy relationships -- 22.1 BEP relations and the Bronsted catalysis law -- 22.2 The Marcus equation -- 22.3 Externally controlled driving forces -- Closing remarks -- Exercises -- References -- Index -- Glossary of acronyms and constants -- Back Cover
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Extent
1 online resource (636 pages)
Form of item
online
Isbn
9780444594709
Media category
computer
Media MARC source
rdamedia
Media type code
c
Sound
unknown sound
Specific material designation
remote

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