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Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
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In this paper, the authors used time correlation function methods to discuss classical isomerization reactions of small nonrigid molecules in liquid solvents and derived molecular expressions for a macroscopic phenomenological rate constant.Abstract:
In this article, time correlation function methods are used to discuss classical isomerization reactions of small nonrigid molecules in liquid solvents. Molecular expressions are derived for a macroscopic phenomenological rate constant. The form of several of these equations depend upon what ensemble is used when performing averages over initial conditions. All of these formulas, however, reduce to one final physical expression whose value is manifestly independent of ensemble. The validity of the physical expression hinges on a separation of time scales and the plateau value problem. The approximations needed to obtain transition state theory are described and the errors involved are estimated. The coupling of the reaction coordinate to the liquid medium provides the dissipation necessary for the existence of a plateau value for the rate constant, but it also leads to failures of Wigner’s fundamental assumption for transition state theory. We predict that for many isomerization reactions, the transmissio...read more
Citations
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CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
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Reaction-rate theory: fifty years after Kramers
TL;DR: In this paper, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry.
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Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.
Journal ArticleDOI
Current status of transition-state theory
TL;DR: In this article, the authors present an overview of the current status of transition-state theory and its generalizations, including recent improvements in available methodology for calculations on complex systems, including the interface with electronic structure theory, progress in the theory and application of transitionstate theory to condensed-phase reactions, and insight into the relation of transition state theory to accurate quantum dynamics.
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TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark
TL;DR: This article reviews the concepts and methods of transition path sampling, which allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states.
References
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Lectures in Theoretical Physics
Book
Hydrodynamic Fluctuations, Broken Symmetry and Correlation Functions
TL;DR: In this article, a simple example of spin diffusion is presented, where the normal fluid and the memory function formalism are combined with Brownian motion and spin wave propagation in Ferromagnets.
BookDOI
Dynamics of Molecular Collisions
TL;DR: In this paper, the potential energy surfaces and their effect on collision processes are discussed. But the authors focus on the nonadiabatic processes in collision theory and not on the classical trajectories of trajectories.