Implicit and explicit solvent models have opposite effects on radiation damage rate constant for thymine

Abstract

Solvation can alter reaction mechanisms through hydrogen bonding, ion–dipole interactions, and van der Waals forces to mention a few. In the study of radiation damage to DNA, solvent effects should be included to model the aqueous biological system of cells adequately. In the present study, we have investigated the effects of different solvent models in calculations of Gibbs free energies and reaction rates for hydrogen abstraction of the methyl group of thymine by the hydroxyl radical at the ω B97X-D/6-311++G(2df,2pd) level of theory with the Eckart tunneling correction. The solvent, water, was included either through the implicit polarizable continuum model (PCM) or through explicit modeling of one or two water molecules at the site of reaction as well as a combination of both. Our investigation shows that the implicit solvent model increases the barrier height and decreases the rate constant for hydrogen abstraction, leading to a value in better agreement with experimental results, whereas solvation by explicit solvent modeling has the opposite effect. Hence, the PCM seems to provide a better description for radiation damage in thymine, which improves the understanding of the reaction mechanisms behind radiation damage to DNA.