American Chemical Society
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Calculations of pKa’s and Redox Potentials of Nucleobases with Explicit Waters and Polarizable Continuum Solvation

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posted on 2015-05-28, 00:00 authored by Bishnu Thapa, H. Bernhard Schlegel
The SMD implicit solvation model augmented with one and four explicit water molecules was used to calculate pKa’s and redox potentials of N-methyl-substituted nucleic acid bases guanine, adenine, cytosine, thymine, and uracil. Calculations were carried out with the B3LYP/6-31+G­(d,p) level of theory. The same numbers of water molecules were hydrogen bonded to the neutral, protonated, and deprotonated nucleobases in their unoxidized and oxidized forms. The improvement in pKa1 involving neutrals and cations was modest. By contrast, the improvement in pKa2 involving neutrals and anions was quite significant, reducing the mean absolute error from 4.6 pKa units with no waters, to 2.6 with one water and 1.7 with four waters. For the oxidation of nucleobases, adding explicit waters did little to improve E(X,H+/XH), possibly because both species in the redox couple are neutral molecules at pH 7.