Systematic Determination of Complex Reaction Mechanisms

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John Ross of Stanford University is supported by the Theoretical and Computational Chemistry Program to develop further approaches to the determination of reaction pathways and mechanisms of complex reaction systems. The effort emphasizes the need for methods with small numbers of measurements, possibly of limited accuracy. Four new methods will be explored. In the first, a pulse perturbation approach will be examined using theory, model reaction calculations, and experiments, in order to elucidate the causal connectivities of species in the reaction pathways. A variant of this approach, a delayed response method, will be studied using theory and calculations with the goal of providing information on the number of chemical species in the reaction pathways, on rate coefficients, and on the reaction mechanism. Genetic algorithm methods will be used on a model system to study the possibility that oscillatory chemical reactions may have evolved in biological systems as a result of regular periodic perturbations, focusing on evolutionary changes in a reaction mechanism due to external effects. Finally, the reaction mechanism and stochastic analysis of memory effects and oscillations in single-molecule reactions will be investigated. Establishing how chemical reactions occur is an important goal in all fields of chemistry, including biological chemistry. This task has been approached, for nearly the last hundred years, by determining the chemical species present, studying separately the rates of various elementary chemical reactions in the entire reaction system, and then guessing the reaction mechanism, which is the proper combination of elementary reaction steps that lead from reactions to products that reproduce observations. For complex chemical reaction systems, this is an arduous and often controversial task, since many different proposed reaction mechanisms frequently fit the available data. The research that will be carried out in this project approaches the solution of chemical reaction mechanism problems from an alternative viewpoint, and the outcomes may have substantial impact on the determination of the mechanisms of complex chemical and biochemical systems in vitro, and ultimately in vivo.