DNA Triplet Energies by Free Energy Perturbation Theory.

Abstract

Determining the energetics of triplet electronic states of nucleobases in the biological macromolecular environment of nucleic acids is essential for an accurate description of the mechanism of photosensitization and the design of drugs for cancer treatment. In this work, we aim at developing a methodological approach to obtain accurate free energies of triplets in DNA beyond the state of the art, able to reproduce the decrease of triplet energies measured experimentally for T in DNA (270 kJ/mol) vs in the isolated nucleotide in aqueous solution (310 kJ/mol). For such purposes, we adapt the free energy perturbation method to compute the free energy related to the transformation of a pure singlet state into a pure triplet state via "alchemical" intermediates with mixed singlet-triplet nature. By this means, standard deviation errors are only a few kJ/mol, contrary to the large errors of tenths of kJ/mol obtained by averaging the singlet and triplet energies derived from molecular dynamics simulations. The reduced statistical errors obtained by the free energy perturbation approach allow us to rationalize with confidence the triplet stabilization observed experimentally when comparing the thymine nucleotide and thymine in DNA. Spin polarization rather than excimer interactions between the π-stacked nucleobases originates the lower values of the triplet energies in DNA. The developed approach implemented in QM³ shall be useful for determining free energies of triplets and other states like ionic or charge separation states in any other macromolecular system with impact in biomedicine and materials science.