Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

ABSTRACT: Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to wh

SUBMITTER: Kazemi M 

PROVIDER: S-EPMC4458863 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature