The most commonly used theoretical models for describing chemical kinetics are accurate in two limits. When relaxation is fast with respect to reaction time scales, thermal transition state theory (TST) is the theoretical tool of choice. In the limit of slow relaxation, an energy resolved description like RRKM theory is more appropriate. For intermediate relaxation regimes, where much of the chemistry in nature occurs, theoretical approaches are somewhat less well established. However, in recent years master equation approaches have been successfully used to analyze and predict nonequilibrium chemical kinetics across a range of intermediate relaxation regimes spanning atmospheric, combustion, and (very recently) solution phase organic chemistry. In this article, we describe a Master Equation Solver for Multi-Energy Well Reactions (MESMER), a user-friendly, object-oriented, open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where energy transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user options specified via keywords and also includes some unique statistical mechanics approaches like contracted basis set methods and nonadiabatic RRKM theory for modeling spin-hopping. It is our hope that the design principles implemented in MESMER will facilitate its development and usage by workers across a range of fields concerned with chemical kinetics. As accurate thermodynamics data become more widely available, electronic structure theory is increasingly reliable, and as our fundamental understanding of energy transfer improves, we envision that tools like MESMER will eventually enable routine and reliable prediction of nonequilibrium kinetics in arbitrary systems.

Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ( 15 N, 13 C, 2 H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for "promoting motions" in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate.kinetics | computational chemistry | biological chemistry | biophysics | quantum biology

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

4079 2.4.3. Modeling Pressure-Dependent Reactions 4080 2.5. Dynamics 4083 2.6. Product Energy Distributions 4085 2.7. State of the Art 4085 3. Thermodynamics 4086 4. Reactions of OH Radicals 4087 4.1. OH + H 2 , CH 4 4.2. OH + CO 4.3. OH + C 2 H 4 4.4. OH + (CH 3 ) 2 CO, CH 3 OH 4.5.

The oxidation of aromatic compounds in the troposphere substantially contributes to the formation of O(3) and secondary aerosol on a regional scale. Nevertheless, the initial stages of aromatic oxidation remain poorly understood. In this work, we present a quantitative analysis of previous experimental measurements relevant to atmospheric benzene oxidation. Using results from G3X(MP2), G3X(MP2)-RAD, CASSCF, and CASPT2 electronic structure theory, we have performed master equation (ME) calculations examining the kinetics of the benzene-OH adduct in the presence of O(2). Our results show the system to be complicated, with four isomers that may be formed following O(2) addition giving rise to multiple decay time scales of the benzene-OH adduct. We have examined the available experimental data in line with our findings and performed a sensitivity analysis of the agreement between the experimental and calculated kinetics with respect to uncertainties in the calculated stationary point energies. Our mechanism gives a phenol yield of 0.55 to 0.65, with the remainder giving a cis bridged bicyclic peroxy radical. Under atmospheric conditions, the epoxide yield is small. Distinct from the TST approaches and free energy surfaces available in previous studies, analysis of our ME results shows that several of the reactions occurring in this system are not at the high-pressure limit in the atmosphere.