Molecular dynamics insights into electron-catalyzed dissociation repair of cyclobutane pyrimidine dimer

Abstract

Excess electrons are not only an important source of radiation damage, but also participate in the repair process of radiation damage such as cyclobutane pyrimidine dimer (CPD). Using ab initio molecular dynamics (AIMD) simulations, we reproduce the single excess electron stepwise catalytic CPD dissociation process in detail with an emphasis on the energy levels and molecular structure details associated with excess electrons. On the basis of the AIMD simulations on the CPD aqueous solution with two vertically added excess electrons, we exclude the early-proposed [2+2]-like concerted synchronous dissociation mechanism, and analyze the difference between the symmetry of the actual reaction and the symmetry of the frontier molecular orbitals which deeply impact the mechanism. Importantly, we propose a new model of the stepwise electron-catalyzed dissociation mechanism that conforms to the reality. This work not only provides dynamics insights into the excess electron catalyzed dissociation mechanism, but also reveals different roles of two excess electrons in two bond-cleavage steps (promoting versus inhibiting).