π- vs σ-Radical States of One-Electron-Oxidized DNA/RNA Bases: A Density Functional Theory Study

As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form pi- or pi-radicals. While most DNA base systems form pi-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauracil, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive sigma-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of pi- and a-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of pi- and sigma-radicals in C-s symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that sigma- and pi-radical it states in one bases of thymine, T(N3-H)(center dot), and uracil, U(N3-H)(center dot), are very close in energy; i.e., the pi-radical it is only ca. 4 kcal/mol more stable than the sigma-radical. For the one radicals of cytosine, C center dot+, C(N4-H)(center dot), adenine, A(center dot+), A(N6-H)(center dot), and guanine, G(center dot+), G(N2-H)(center dot), G(N1-H)(center dot), the pi-radicals are ca. 16-41 kcal/mol more stable than their corresponding sigma-radicals. Inclusion of solvent (PCM) is found to stabilize the pi- over sigma-radical of each of the systems. U(N3-H)(center dot) with three discrete water molecules in the gas phase is found to form a three electron sigma bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the it radical remains most stable.