TY - JOUR

T1 - Implicit and explicit solvent models have opposite effects on radiation damage rate constant for thymine

AU - Sørensen, Lea Northcote

AU - Sauer, Stephan P. A.

PY - 2022/9/21

Y1 - 2022/9/21

N2 - 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 ωB97X-D/6-311++G(2df,2pd) level of theory with the Eckart tunnelling correction. The solvent, water, was included through either the implicit polarizable continuum model (PCM) or through explicit modelling 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 heights and decreases the rate constant for hydrogen abstraction, leading to a value in better agreement with experimental results, whereas solvation by explicit solvent modelling has the opposite effect. Hence, the PCM model seems to provide a better description for radiation damage in thymine, which improves the understanding of the reaction mechanisms behind radiation damage to DNA.

AB - 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 ωB97X-D/6-311++G(2df,2pd) level of theory with the Eckart tunnelling correction. The solvent, water, was included through either the implicit polarizable continuum model (PCM) or through explicit modelling 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 heights and decreases the rate constant for hydrogen abstraction, leading to a value in better agreement with experimental results, whereas solvation by explicit solvent modelling has the opposite effect. Hence, the PCM model seems to provide a better description for radiation damage in thymine, which improves the understanding of the reaction mechanisms behind radiation damage to DNA.

KW - Faculty of Science

KW - solvation

KW - Density Functional Theory

KW - Radiation Damage

KW - Kinetics

KW - Thymine

KW - Hydroxyl radical

U2 - 10.1016/bs.aiq.2021.10.002

DO - 10.1016/bs.aiq.2021.10.002

M3 - Journal article

VL - 85

SP - 245

EP - 265

JO - Advances in Quantum Chemistry

JF - Advances in Quantum Chemistry

SN - 0065-3276

ER -