Classical trajectory simulations of post-transition state dynamics

Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl− ··· CH3Br → ClCH3 + Br− and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl− ··· CH3Cl complexes mediating the Cl− + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH− + CH3F and F− + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.

[1]  S. Meroueh,et al.  Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation† , 2002 .

[2]  D. Truhlar,et al.  Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters , 1991 .

[3]  P. Houston,et al.  Photodissociation of acetaldehyde as a second example of the roaming mechanism , 2006, Proceedings of the National Academy of Sciences.

[4]  Stephen K. Gray,et al.  Symplectic integrators for large scale molecular dynamics simulations: A comparison of several explicit methods , 1994 .

[5]  S. Chapman,et al.  An exploratory study of reactant vibrational effects in CH3 + H2 and its isotopic variants , 1975 .

[6]  Claude Leforestier,et al.  Classical trajectories using the full abinitio potential energy surface H−+CH4→CH4+H− , 1978 .

[7]  W. Hase,et al.  Non-RRKM kinetics in gas-phase SN2 nucleophilic substitution , 1990 .

[8]  C. Wittig,et al.  IR multiple photon dissociation of fluorinated ethanes and ethylenes: HF vibrational energy distributions , 1980 .

[9]  H. Bernhard Schlegel,et al.  Ab initio classical trajectories on the Born–Oppenheimer surface: Updating methods for Hessian-based integrators , 1999 .

[10]  Upakarasamy Lourderaj,et al.  A direct dynamics trajectory study of F- + CH(3)OOH reactive collisions reveals a major non-IRC reaction path. , 2007, Journal of the American Chemical Society.

[11]  W. Miller,et al.  Eigenstate‐resolved unimolecular reaction dynamics: Ergodic character of S0 formaldehyde at the dissociation threshold , 1990 .

[12]  Kihyung Song,et al.  Post-transition state dynamics for propene ozonolysis: Intramolecular and unimolecular dynamics of molozonide. , 2006, The Journal of chemical physics.

[13]  Haobin Wang,et al.  Trajectory Studies of SN2 Nucleophilic Substitution. 4. Intramolecular and Unimolecular Dynamics of the Cl----CH3Br and ClCH3---Br- Complexes , 1994 .

[14]  Gilles H. Peslherbe,et al.  Monte Carlo Sampling for Classical Trajectory Simulations , 2007 .

[15]  S. Leone,et al.  Theoretical and Experimental Investigation of the Dynamics of the Production of CO from the CH 3 + O and CD 3 + O Reactions , 2001 .

[16]  W. Hase,et al.  Ab initio direct dynamics trajectory simulation of C2H5F-->C2H4 + HF product energy partitioning. , 2004, The Journal of chemical physics.

[17]  W. Hase,et al.  Complete multidimensional analytic potential energy surface for chloride + chloroform SN2 nucleophilic substitution , 1990 .

[18]  H. Schlegel,et al.  Ab initio classical trajectory study of H2CO+H2 + CO dissociation , 1994 .

[19]  Haobin Wang,et al.  Trajectory studies of SN2 nucleophilic substitution. IX. Microscopic reaction pathways and kinetics for Cl-+CH3Br , 2003 .

[20]  William L. Hase,et al.  DIRECT DYNAMICS SIMULATION OF THE LIFETIME OF TRIMETHYLENE , 1996 .

[21]  Michael T. Bowers,et al.  The nonstatistical dissociation dynamics of chloride(bromomethane) Cl-(CH3Br): evidence for vibrational excitation in the products of gas-phase SN2 reactions , 1991 .

[22]  Robert A. Morris,et al.  Kinetics of the gas-phase reactions of chloride anion, Cl- with CH3Br and CD3Br: experimental evidence for nonstatistical behavior? , 1992 .

[23]  J. Ross,et al.  Franck–Condon factors in studies of dynamics of chemical reactions. I. General theory, application to collinear atom–diatom reactions , 1977 .

[24]  John E. Adams,et al.  Reaction path Hamiltonian for polyatomic molecules , 1980 .

[25]  S. Benson.  Reaction of Cyclopropane with Iodine and Some Observations on the Isomerization of Cyclopropane , 1961 .

[26]  W. Hase,et al.  Trajectory studies of SN2 nucleophilic substitution. III. Dynamical stereochemistry and energy transfer pathways for the Cl−+CH3Cl association and direct substitution reactions , 1993 .

[27]  D. Lu,et al.  Classical mechanics of intramolecular vibrational energy flow in benzene. IV. Models with reduced dimensionality , 1988 .

[28]  R. Hoffmann.  Trimethylene and the addition of methylene to ethylene , 1968 .

[29]  D. J. Mann,et al.  Ab initio direct dynamics study of cyclopropyl radical ring-opening. , 2002, Journal of the American Chemical Society.

[30]  T. Mcmahon,et al.  Non-Statistical Effects in the Gas Phase SN2 Reaction , 2000 .

[31]  Josep Maria Bofill,et al.  Updated Hessian matrix and the restricted step method for locating transition structures , 1994, J. Comput. Chem..

[32]  William L. Hase,et al.  Dynamics of ethyl radical decomposition. II. Applicability of classical mechanics to large‐molecule unimolecular reaction dynamics , 1982 .

[33]  William L. Hase,et al.  An analytic function describing the H+C2H4?C2H5 potential energy surface , 1978 .

[34]  Haobin Wang,et al.  Statistical Rate Theory Calculations of the Cl- + CH3Br .fwdarw. ClCH3 + Br- Rate Constant Versus Temperature, Translational Energy, and H(D) Isotopic Substitution , 1995 .

[35]  J. Light,et al.  Reactions of large molecules proceeding through an intermediate complex: I. Theory , 1977 .

[36]  D. M. Hirst,et al.  Thermal Rate Constants for H + CH3 CH4 Recombination. II. Comparison of Experiment and Canonical Variational Transition State Theory , 1987 .

[37]  M. Head‐Gordon,et al.  Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: convergence toward Born-Oppenheimer trajectories. , 2004, The Journal of chemical physics.

[38]  H. W. Chang,et al.  Nonequilibrium unimolecular reactions and collisional deactivation of chemically activated fluoroethane and 1,1,1-trifluoroethane , 1972 .

[39]  R. Levine,et al.  Molecular Reaction Dynamics and Chemical Reactivity , 1987 .

[40]  Jan E. Szulejko,et al.  High-Pressure Mass Spectrometric Investigations of the Potential Energy Surfaces of Gas-Phase SN2 Reactions , 1996 .

[41]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[42]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[43]  W. Gentry,et al.  Classical trajectory treatment of inelastic scattering in collisions ofH+withH2, HD, andD2 , 1974 .

[44]  David E. Bernholdt,et al.  High performance computational chemistry: An overview of NWChem a distributed parallel application , 2000 .

[45]  M. Bowers,et al.  Chapter 4 – Statistical methods in reaction dynamics , 1979 .

[46]  C. Doubleday,et al.  Direct Dynamics Quasiclassical Trajectory Study of the Thermal Stereomutations of Cyclopropane , 1998 .

[47]  Michael A. Collins,et al.  Molecular potential energy surfaces by interpolation in Cartesian coordinates , 1998 .

[48]  C. Doubleday,et al.  Isomerisation of deuterated cyclopropanes : The possibility for stereochemical control , 1997 .

[49]  W. Miller,et al.  A simple model for correcting the zero point energy problem in classical trajectory simulations of polyatomic molecules , 1989 .

[50]  M. Bowers,et al.  Vibrational Excitation in Products of Nucleophilic Substitution: The Dissociation of Metastable X-(CH3Y) in the Gas Phase , 1994 .

[51]  M. Hartmann.  Molecular mechanics. Von ULRICH BURKERT und NORMAN L. ALLINGER. ACS Monograph 177. Washington: American Chemical Society 1982. 430 S., US $ 77.95 , 1984 .

[52]  K. M. Ervin,et al.  Gas-phase SN2 and bromine abstraction reactions of chloride ion with bromomethane: reaction cross sections and energy disposal into products. , 2003, Journal of the American Chemical Society.

[53]  Peter Pulay,et al.  Fock matrix dynamics , 2004 .

[54]  W. Hase.  Unimolecular and intramolecular dynamics. Relationship to potential energy surface properties , 1986 .

[55]  M. J. Perona,et al.  Comparison of energy partitioning from three-centered processes. Bimolecular transfer and unimolecular elimination reactions , 1971 .

[56]  W. Hase,et al.  A quasiclassical trajectory calculation of the atomic hydrogen + ethylene .fwdarw. ethyl bimolecular rate constant , 1983 .

[57]  Tamar Schlick,et al.  A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications , 1997, SIAM J. Sci. Comput..

[58]  D. J. Mann,et al.  Trajectory Studies of SN2 Nucleophilic Substitution. 6. Translational Activation of the Cl- + CH3Cl Reaction , 1998 .

[59]  C. Doubleday,et al.  Dynamics of the biradical mediating vinylcyclopropane–cyclopentene rearrangement , 2002 .

[60]  K. Fukui.  Formulation of the reaction coordinate , 1970 .

[61]  D. Lu,et al.  The role of state specificity in unimolecular rate theory , 1989 .

[62]  J. I. Brauman,et al.  Gas-Phase Ion Chemistry , 1985, Science.

[63]  William L. Hase,et al.  DIRECT DYNAMICS SIMULATIONS OF REACTIVE SYSTEMS , 1998 .

[64]  T. Yan,et al.  A PM3-SRP + Analytic Function Potential Energy Surface Model for O(3P) Reactions with Alkanes. Application to O(3P) + Ethane† , 2004 .

[65]  Stefan L. Debbert,et al.  The iconoclastic dynamics of the 1,2,6-heptatriene rearrangement. , 2002, Journal of the American Chemical Society.

[66]  F. Suits,et al.  The roaming atom pathway in formaldehyde decomposition. , 2006, The Journal of chemical physics.

[67]  G. J. Hoffman,et al.  Kinetics of thermal geometric isomerizations of three sets of isotopically labeled cyclopropanes followed by tunable diode laser spectroscopy , 1992 .

[68]  I. Prigogine.  Chemical Kinetics and Dynamics , 2003, Annals of the New York Academy of Sciences.

[69]  J. Tully,et al.  Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2 , 1971 .

[70]  J. A. Berson,et al.  Thermal stereomutation of cyclopropanes , 1976 .

[71]  P. Kollman,et al.  Encyclopedia of computational chemistry , 1998 .

[72]  W. Hase,et al.  Trajectory studies of SN2 nucleophilic substitution. II. Nonstatistical central barrier recrossing in the Cl−+CH3Cl system , 1992 .

[73]  J. I. Brauman,et al.  Phase-Shifting Acceleration of Ions in an Ion Cyclotron Resonance Spectrometer: Kinetic Energy Distribution and Reaction Dynamics , 1997 .

[74]  W. Miller,et al.  Theories of intramolecular vibrational energy transfer , 1991 .

[75]  E. Arunan,et al.  Hydrogen fluoride/hydrogen chloride vibrational and rotational distributions from three- and four-centered unimolecular elimination reactions , 1991 .

[76]  W. Hase,et al.  A direct mechanism for SN2 nucleophilic substitution enhanced by mode selective vibrational excitation , 1989 .

[77]  M. Stumpf,et al.  Theoretical study of the unimolecular dissociation HO2→H+O2. II. Calculation of resonant states, dissociation rates, and O2 product state distributions , 1996 .

[78]  A. Untch,et al.  The vibrational predissociation of cis‐methyl nitrite in the S1 state: A comparison of exact quantum mechanical wave packet calculations with classical trajectory calculations and detailed experimental results , 1993 .

[79]  W. Miller,et al.  Model studies of mode specificity in unimolecular reaction dynamics , 1980 .

[80]  Scott F. Smith,et al.  SN2 reaction profiles in the gas phase and aqueous solution , 1984 .

[81]  Donald L Thompson,et al.  Modern Methods for Multidimensional Dynamics Computations in Chemistry , 1998 .

[82]  W. Hase,et al.  Unimolecular reaction dynamics : theory and experiments , 1996 .

[83]  John M Herbert,et al.  Accelerated, energy-conserving Born-Oppenheimer molecular dynamics via Fock matrix extrapolation. , 2005, Physical chemistry chemical physics : PCCP.

[84]  Mark S. Gordon,et al.  Direct dynamics simulations , 2003, Comput. Sci. Eng..

[85]  M. Karplus,et al.  Dyanmics of organic reactions , 1973 .

[86]  W. Hase,et al.  A Hamiltonian with a Subset of Normal Modes for Studying Mode-Specific Energy Transfer in Intermolecular Collisions† , 2001 .

[87]  Gilles H. Peslherbe,et al.  Semiempirical MNDO, AM1, and PM3 direct dynamics trajectory studies of formaldehyde unimolecular dissociation , 1996 .

[88]  S. K. Lee,et al.  The Roaming Atom: Straying from the Reaction Path in Formaldehyde Decomposition , 2004, Science.

[89]  A. Seiter,et al.  High-order symplectic integration: an assessment , 2000 .

[90]  F. Smith.  Isomerization of Sym‐Cyclopropane‐d2 , 1958 .

[91]  D. Hrovat,et al.  Investigation of Cyclopropane Stereomutation by Quasiclassical Trajectories on an Analytical Potential Energy Surface , 1997 .

[92]  M. Quack,et al.  Specific Rate Constants of Unimolecular Processes II. Adiabatic Channel Model , 1974 .

[93]  B. C. Garrett,et al.  Variational Transition State Theory , 1980 .

[94]  A. Seiter,et al.  Symplectic Integration of Classical Trajectories: A Case Study , 1998 .

[95]  Upakarasamy Lourderaj,et al.  Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms. , 2007, The Journal of chemical physics.

[96]  W. Hase,et al.  Dynamics of ethyl radical decomposition. 3. Effect of chemical activation vs. microcanonical sampling , 1983 .

[97]  R. Zare,et al.  Reaction products with internal energy beyond the kinematic limit result from trajectories far from the minimum energy path: an example from H + HBr --> H2 + Br. , 2005, Journal of the American Chemical Society.

[98]  G. Schatz,et al.  A Quasiclassical Trajectory Study of the Cl + HCN → HCl + CN Reaction Dynamics. Microscopic Reaction Mechanism of the H(Cl) + HCN → H2(HCl) + CN Reactions† , 2001 .

[99]  K. Song,et al.  Comparison of levels of electronic structure theory in direct dynamics simulations of C2H5F --> HF + C2H4 product energy partitioning. , 2006, The journal of physical chemistry. A.

[100]  J. Polanyi.  Concepts in reaction dynamics , 1972 .

[101]  W. Hase,et al.  A classical trajectory study of the F+C2H4→C2H4F→H+C2H3F reaction dynamics , 1981 .

[102]  A. Sudbø.  THREE AND FOUR CENTER ELIMINATION OF HC1 IN THE MULTIPHOTON DISSOCIATION OF HALOGENATED HYDROCARBONS , 1978 .

[103]  Sean C. Smith.  Unimolecular Reaction Dynamics , 2002 .

[104]  Michel Dupuis,et al.  Dynamics-Driven Reaction Pathway in an Intramolecular Rearrangement , 2003, Science.

[105]  Kihyung Song,et al.  Trajectory Studies of SN2 Nucleophilic Substitution. 8. Central Barrier Dynamics for Gas Phase Cl- + CH3Cl , 2001 .

[106]  Stephen J Blanksby,et al.  Direct evidence for base-mediated decomposition of alkyl hydroperoxides (ROOH) in the gas phase. , 2002, Journal of the American Chemical Society.

[107]  Gilles H. Peslherbe,et al.  UNIMOLECULAR DYNAMICS OF CL-...CH3CL INTERMOLECULAR COMPLEXES FORMED BY CL-CH3CL ASSOCIATION , 1995 .

[108]  William L. Hase,et al.  An ab initio quasi-classical direct dynamics investigation of the F + C2H4 → C2H3F + H product energy distributions , 1999 .

[109]  Rudolph A. Marcus,et al.  On the Analytical Mechanics of Chemical Reactions. Classical Mechanics of Linear Collisions , 1966 .

[110]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[111]  K. Song,et al.  Use of a single trajectory to study product energy partitioning in unimolecular dissociation: mass effects for halogenated alkanes. , 2006, The Journal of chemical physics.

[112]  Xiche Hu,et al.  Use of microclusters to simulate cage, trapping, and chaperon effects in association reactions , 1992 .

[113]  B. E. Holmes,et al.  Unimolecular rate constants for ring rupture and hydrochloric acid elimination from chemically activated 1-, 2-, and 3-methylchlorocyclobutane and chloromethylcyclobutane , 1978 .

[114]  R. Levine,et al.  Energy disposal in unimolecular elimination reactions , 1980 .

[115]  Matt Challacombe,et al.  Time-reversible Born-Oppenheimer molecular dynamics. , 2006, Physical review letters.

[116]  D. Truhlar,et al.  Quantum mechanical methods for enzyme kinetics. , 2003, Annual review of physical chemistry.

[117]  K. Song,et al.  Central barrier recrossing dynamics of the Cl−+CD3Cl SN2 reaction , 2006 .

[118]  Wei Chen,et al.  Ab initio classical trajectories on the Born–Oppenheimer surface: Hessian-based integrators using fifth-order polynomial and rational function fits , 1999 .

[119]  C. Doubleday,et al.  Direct Dynamics Study of the Stereomutation of Cyclopropane , 1997 .

[120]  W. Hase,et al.  Comparison of models for calculating the RRKM unimolecular rate constant k(E, J) , 1990 .

[121]  W. Hase,et al.  Trajectory studies of SN2 nucleophilic substitution. I. Dynamics of Cl−+CH3Cl reactive collisions , 1990 .

[122]  B. Carpenter,et al.  Intramolecular Dynamics for the Organic Chemist , 1992 .

[123]  Trygve Helgaker,et al.  Integration of the classical equations of motion on ab initio molecular potential energy surfaces using gradients and Hessians: application to translational energy release upon fragmentation , 1990 .

[124]  W. Hase,et al.  Born–Oppenheimer Direct Dynamics Classical Trajectory Simulations , 2003 .

[125]  W. Hase,et al.  Simulations of Gas-Phase Chemical Reactions: Applications to SN2 Nucleophilic Substitution , 1994, Science.

[126]  Terry Beyer,et al.  Algorithm 448: number of multiply-restricted partitions , 1973, CACM.

[127]  C. Bamford,et al.  Comprehensive Chemical Kinetics , 1976 .

[128]  M. Bowers.  Gas phase ion chemistry , 1979 .

[129]  William L. Hase,et al.  On non‐RRKM unimolecular kinetics: Molecules in general, and CH3NC in particular , 1973 .

[130]  Kihyung Song,et al.  A SN2 Reaction That Avoids Its Deep Potential Energy Minimum , 2002, Science.

[131]  W. Miller,et al.  Time averaging the semiclassical initial value representation for the calculation of vibrational energy levels , 2003 .

[132]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[133]  Wei Chen,et al.  Comparison of models for treating angular momentum in RRKM calculations with vibrator transition states: pressure and temperature dependence of chlorine atom + acetylene association , 1993 .

[134]  E. Aubanel,et al.  Role of angular momentum in statistical unimolecular rate theory , 1991 .

[135]  W. Hase.  Some Recent Advances and Remaining Questions Regarding Unimolecular Rate Theory , 1998 .

[136]  T. Schlick.  Molecular modeling and simulation , 2002 .