UV-induced formation of the thymine–thymine pyrimidine (6-4) pyrimidone photoproduct – a DFT study of the oxetane intermediate ring opening

Abstract

The mechanism by which the hypothetical oxetane/azetidine intermediate formed during the photochemical process leading to pyrimidine (6-4) pyrimidone photoproducts when DNA is submitted to UV radiation opens is investigated computationally by DFT using a 5′-TT-3′ dinucleoside monophosphate as a structural model. First, the feasibility of an intramolecular mechanism involving one proton transfer inducing opening of the oxetane ring is examined. It results in a very high Gibbs energy of activation (+166 kJ mol⁻¹) and quite a low Gibbs energy of reaction (−35 kJ mol⁻¹). The protonation state of the phosphate group is shown to have little effect while the bulk effect of an aqueous environment modeled by the Polarizable Continuum Model method lowers slightly the activation barrier (by about 10–20 kJ mol⁻¹), not enough to explain the fact that the oxetane intermediate is not observed experimentally. Then the catalytic effect of water molecules on the reaction pathway is studied by including either 1 or 2 assisting water molecules in the chemical system. The resulting activation barrier is considerably lowered and in the most favorable situation – a phosphate group deprotonated and 2 assisting water molecules – the Gibbs energy activation is as low as +44 kJ mol⁻¹ and the Gibbs energy of reaction is quite favorable: −79 kJ mol⁻¹, suggesting that in biological systems the oxetane ring opening process proceeds with explicit intervention of water molecules from the environment.