Ab Initio Molecular Orbital Calculations of DNA Bases and Their Radical Ions in Various Protonation States: Evidence for Proton Transfer in GC Base Pair Radical Anions

Document Type


Publication Date



Ab initio molecular orbital calculations of various protonation states of DNA base and DNA base radical ions were performed to aid our understanding of primary radiation processes in DNA. Each of the structures was optimized at the STO-3G and 3-21G levels of theory, and single point calculations were performed at the 6-31G*//3-21G and 6-31+G(d)//3-21G levels. Each of the protonation states important to proton-transfer reactions in base pair radical ions found in irradiated DNA was considered. Calculations for three protonation states for the cytosine reduced radical were performed and the most stable is found to be the N-3 ring-protonated species. Calculations for the vertical ionization energies of the individual DNA bases yielded the following order T > C > A > G with the same order found for the adiabatic electron affinities of the bases. The best fit to experiment was found with Koopmans' theorem ionization potentials. The energy for proton transfer in the GC and AT base pair radical cation and radical anions were estimated from the energies of the individual species. All proton transfers were found to be energetically unfavorable except for the GC anion radical which is favored by 13 kcal. INDO calculations for ions of stacked four base DNA model system AT/GC predict the site of electron trapping in DNA model system is thymine, and the hole is found on guanine as predicted from ab initio energies for the individual bases. Both ab initio and INDO results for the AT/GC anion predict the site of the anion shifts from thymine to cytosine on the transfer of a proton from guanine to the cytosine anion. These results lead to a revised model for ion radical localization after irradiation of DNA.