title: Calculations of pKa's and redox potentials of nucleobases with explicit waters and polarizable continuum solvation.
abstract: 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.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.
authors.forename: Bishnu
authors.initials: B
authors.lastname: Thapa
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.
authors.forename: H Bernhard
authors.initials: HB
authors.lastname: Schlegel
mesh_terms: D000225:Adenine / Q000737:chemistry*; D002412:Cations / Q000737:chemistry; D003596:Cytosine / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008957:Models, Genetic; D015394:Molecular Structure; D010084:Oxidation-Reduction; D011522:Protons; D012997:Solvents / Q000737:chemistry; D013941:Thymine / Q000737:chemistry*; D014498:Uracil / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D002412:Cations; D011522:Protons; D012997:Solvents; D014867:Water; D014498:Uracil; D006147:Guanine; D003596:Cytosine; D000225:Adenine; D013941:Thymine