  We studied the reaction dynamics of a proposed prebiotic reaction
theoretically. The chemical process involves acetone cyanohydrin or
formalcyanohydrin reacting with hydrosulfide in an aqueous environment. Rate
constants and populations of reactant and product bimolecular geometric
orientations for the reactions were obtained by using density functional theory
for the energies, transition state theory for the rates and matrix
exponentiation as well as the hybrid tau-leaping algorithm for the population
dynamics. The role of including the solvent explicitly versus implicitly was
also investigated. We found that adding water or hydrogen sulfide molecules
explicitly lowers the activation energy barrier and leads to a more efficient
reaction pathway. In particular, hydrogen sulfide was a better proton donor.
Further, when adding the solvent explicitly a synchronous reaction mechanism
was observed while a concerted reaction mechanism was seen when using an
implicit solvent model. Finally, we studied the role of including more than one
reactant and product bimolecular orientation geometry in the dynamics.
Including all pathways, reactant to reactant, product to product, reactant to
product and product to reactant reduced the reaction half-time by two orders of
magnitude and was therefore determined to be fundamental for an accurate
description of the dynamics. Overall, we found that most reactions which
involve formalcyanohydrin occur more rapidly or at the same speed as reactions
which involve acetone cyanohydrin at room temperature.
