title: An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting.
abstract: In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5' and C6-C6' bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schrödinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6' bond is accompanied by both an increase in electron density on the C6 and C6' carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and nonequilibrium trajectories.
authors.affiliation: Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA. ali.hassanali@phys.chem.ethz.ch
authors.forename: Ali A
authors.initials: AA
authors.lastname: Hassanali
authors.forename: Dongping
authors.initials: D
authors.lastname: Zhong
authors.forename: Sherwin J
authors.initials: SJ
authors.lastname: Singer
mesh_terms: D000838:Anions / Q000737:chemistry; D004260:DNA Repair; D056004:Molecular Dynamics Simulation; D011740:Pyrimidine Dimers / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D000838:Anions; D011740:Pyrimidine Dimers; D012997:Solvents; D014867:Water