Chemistry

This part of TraX investigates the dynamics of chemical reactions in complex environments. This moniker encompasses a variety of important reactions, including reactions of biomolecules in living systems. The characterization of rates and pathways for chemical reactions in complex solvents remains a primary concern. They determine which design pathways can realistically be used to accelerate or suppress particular reactions. Transition state theory (TST) has been successful at providing approximate values within a framework that is easy to implement. However, it fails to provide exact rates or fully characterize complex environments. In its traditional form, it postulates the existence of a dividing surface (DS) between reactants and products that every reactive trajectory must cross once and only once. Such a surface is often difficult or impossible to find. Moreover, invariant manifolds can provide much more detailed information about the reaction dynamics.

In TraX we explore how to use these manifolds for the realistic description of reactions. In a driven system, these manifolds are time-dependent. We investigate how they guide trajectories across the DS, and use them to develop a geometric rate theory based on the moving DS. This rate formula can then be incorporated into standard algorithms for rate calculations, which thus can take advantage of the recrossing-free DS.

We investigate the role of the DS and of the invariant manifolds in a realistic all-atom model of a reaction in solution, namely, the lithium cyanide isomerization in a bath of noble gas atoms. This is a large step away from the model systems in which the TST geometry has so far been investigated, and an essential step towards making the geometric structures available as practical tools for rate calculation.