Steered molecular dynamic simulations of the tautomeric equilibria in solution of DNA bases

In this work a theoretical study of the tautomeric equilibria between the canonical and rare forms of the four nitrogenous DNA bases was performed. The study focused on the calculation of the reaction and activation energies of these processes, where proton transfer is described with a concerted and synchronous mechanism. The processes were studied in vacuum and in aqueous solution showing the influence that the aqueous environment has on these properties. The calculations were carried out with molecular simulations using the Steered Molecular Dynamic (SMD) technique and were compared with calculations by electronic methods at MP2/PCM/6-311 ++G(d,p) level, finding a similar response with both methodologies; hence this methodology can be considered as a good alternative for the study of processes with proton transfer. The study was extended to the process of double proton transfer through a mechanism assisted by a water molecule in an aqueous environment, finding a more favorable response with this assistance, especially at the kinetic level, since it decreases considerably the activation barriers of the processes. The microscopic description of the solvent also has a repercussion on the process energies, since some of the molecules of the medium can compete with the assistant molecule, decreasing the activation energy when the solvent is considered as a continuum.