Journal ArticleDOI
The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models
Richard F. Grote,James T. Hynes +1 more
TLDR
In this paper, the stable states picture (SSP) was used to derive the time correlation function (tcf) for the rate constant κ for a wide variety of gas and solution phase reaction models.Abstract:
The time correlation function (tcf) formulas for rate constants κ derived via the stable states picture (SSP) of chemical reactions are applied to a wide variety (a–d) of gas and solution phase reactionmodels. (a) For gas phase bimolecular reactions, we show that the flux tcf governing κ corresponds to standard numerical trajectory calculation methods. Alternate formulas for κ are derived which focus on saddle point surfaces, thus increasing computational efficiency. Advantages of the SSP formulas for κ are discussed. (b) For gas phase unimolecular reactions, simple results for κ are found in both the strong and weak coupling collision limits; the often ignored role of product stabilization is exposed for reversible isomerizations. The SSP results correct some standard weak coupling rate constant results by as much as 50%. (c) For barrier crossing reactions in solution, we evaluate κ for a generalized (non‐Markovian) Langevin description of the dynamics. For several realistic models of time dependent friction, κ differs dramatically from the popular Kramers constant friction predictions; this has important implications for the validity of transition state theory. (d) For solutionreactions heavily influenced by spatial diffusion, we show that the SSP isolates short range reaction dynamics of interest and includes important barrier region effects in structural isomerizations often missed in standard descriptions.read more
Citations
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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.
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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.
Journal ArticleDOI
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw,David E. Shaw,Paul Maragakis,Kresten Lindorff-Larsen,Stefano Piana,Ron O. Dror,Michael P. Eastwood,Joseph A. Bank,John M. Jumper,John K. Salmon,Yibing Shan,Willy Wriggers +11 more
TL;DR: Simulation of the folding of a WW domain showed a well-defined folding pathway and simulation of the dynamics of bovine pancreatic trypsin inhibitor showed interconversion between distinct conformational states.
References
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Journal ArticleDOI
Efficient trajectory simulation methods for diffusional barrier crossing processes
TL;DR: In this paper, the authors explored two trajectories, activated and branching-activated trajectory methods, which circumvent the problem of sample barrier crossing events inefficiently since the system spends most of its time in low-energy configurations.
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Vibrational Nonequilibrium Effects in the (H2, H2) Reactive System
TL;DR: In this article, a numerical solution of a nonlinear Master equation is proposed to calculate the decrease in the forward rate of the (H2, H2) reaction from its equilibrium value due to perturbation of the vibrational distribution function by reaction.
Journal ArticleDOI
Dynamics of collinear A + BC systems
TL;DR: In this paper, a pair of coordinates, one along the minimum reaction path and one normal to it, is employed to treat the collinear dynamics of processes of the type A+B−C→A−B+C.
Journal ArticleDOI
On reaction rate constants and rate kernels
Scott H. Northrup,James T. Hynes +1 more
TL;DR: In this paper, a simple model for a reversible isomerization reaction A ⇋ B is used to show how rate constants and their time-dependent generalizations can be related to microscopic reactive steps and nonreactive internal dynamics (e.g., vibrational relaxation).
Journal ArticleDOI
Microscopic theory of condensed phase chemical reactions. II. Configuration space equations
TL;DR: In this article, configuration space equations for the description of reactive pair dynamics are derived from the pair phase space kinetic equations derived in the preceding paper, which are generalizations of the conventional Smoluchowski equations.