Transition state theory and the dynamics of hard disks

The dynamics of two and five disk systems confined in a square has been studied using molecular dynamics simulations and compared with the predictions of transition state theory. We determine the partition functions Z and Z^\ddagger of transition state theory using a procedure first used by Salsburg and Wood for the pressure. Our simulations show this procedure and transition state theory are in excellent agreement with the simulations. A generalization of the transition state theory to the case of a large number of disks N is made and shown to be in full agreement with simulations of disks moving in a narrow channel. The same procedure for hard spheres in three dimensions leads to the Vogel-Fulcher-Tammann formula for their alpha relaxation time.Comment: 1 new author, new simulations and figures, less speculation. Now 6 pages, 6 figures, 1 animation. Animation may be viewed at http://www.theory.physics.manchester.ac.uk/~godfrey/supplement/activated_dynamics2.htm

Femtosecond transition-state dynamics

This article presents the progress made in probing femtosecond transition–state dynamics of elementary reactions. Experiments demonstrating the dynamics in systems characterized by a transition region and by a saddle-point transition state are reported, and comparison with theory is made

Automated transition state theory calculations for high-throughput kinetics

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.Comment: 29 pages, 8 figure

The Transition State in a Noisy Environment

Transition State Theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a time-dependent dividing surface free of such recrossings in the presence of noise. The no-recrossing limit of Transition State Theory thus becomes generally available for the description of reactions in a fluctuating environment

Chaotic Dynamics in Multidimensional Transition States

The crossing of a transition state in a multidimensional reactive system is mediated by invariant geometric objects in phase space: An invariant hyper-sphere that represents the transition state itself and invariant hyper-cylinders that channel the system towards and away from the transition state. The existence of these structures can only be guaranteed if the invariant hyper-sphere is normally hyperbolic, i.e., the dynamics within the transition state is not too strongly chaotic. We study the dynamics within the transition state for the hydrogen exchange reaction in three degrees of freedom. As the energy increases, the dynamics within the transition state becomes increasingly chaotic. We find that the transition state first looses and then, surprisingly, regains its normal hyperbolicity. The important phase space structures of transition state theory will therefore exist at most energies above the threshold