MESMER: An Open-Source Master Equation Solver for Multi-Energy Well Reactions

Abstract

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.

Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling

“…where k and k d are the same constants as described in equation 1 and k dm is the first order loss of for Multi Energy-well Reactions) [30]. Microcanonical rate coefficients for the barrierless association of OH and methanol to form the complex C were calculated using an inverse Laplace transform method [31] and microcanonical rate coefficients for the hydrogen abstraction processes occurring via either TS-H or TS-M (see Figure 1) were calculated using Rice, Ramsperger, Kassel and Marcus (RRKM) theory.…”

Communication: Thermal unimolecular decomposition of syn-CH3CHOO: A kinetic study

“…Using the calculated PES properties, anharmonic constants, and rovibrational parameters obtained with mHEAT (see above), a simplified two-dimensional-(E,J)-grained master equation was solved using an eigenvalue-eigenvector matrix technique [51][52][53][54][55][56][57][58][59][60][61] to obtain the time evolution of various intermediates as well as phenomenological rate constants as functions of pressure (P = 10 −3 to 10 4 Torr) and temperature (T = 200-400 K) that cover atmospheric conditions. Figure 2 displays the time evolution of various species as a function of pressure at 300 K, while Figure 3 shows the time evolution of various species as a function of temperature at 1 atm.…”

Analysis of the Kinetics and Yields of OH Radical Production from the CH3OCH2 + O2 Reaction in the Temperature Range 195–650 K: An Experimental and Computational study

“…Within our formulation of the ME, products are represented using the infinite sink approximation. 35 There are three chemically significant eigenvalues, closely related in magnitude to the In the ME analysis of the available experimental data, the calculated total loss rate coefficients (k2) and the theoretical OH yields, obtained from fits to the time resolved species profiles at 1 ms, were fitted to the corresponding experimental quantities. The eigenvalues and yields can be obtained directly from solution of the chemical master equation.…”