Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.

Ionization energy thresholds have been calculated for the canonical DNA and RNA bases both in the gas phase and in aqueous solution at HF and MP2 levels of theory using standard 6-31++G(d,p) basis set. It is shown that the use of the spin projection procedure to correct the open-shell systems for contamination by higher spin states significantly improves the calculated ionization energies. This correction provides practically experimental accuracy to the calculated ionization energies in gas and in aqueous phase. The stabilization of the vertical and adiabatic radical cation energies by water solvation range from 2.15 to 2.58 eV, and from 2.12 to 2.79 eV, relative to the gas-phase results, respectively. The ab initio calculations show that longrange bulk polarization interactions have a significant role in the lowering of the first ionization energy of the DNA and RNA bases. Taking into account the stabilization of the free electron by the solvent, the adiabatic ionization energies in aqueous solution are estimated to be 5. 27, 5.05, 4.91, 4.81, and 4.42 eV for uracil, thymine, cytosine, adenine, and guanine, respectively.

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Projected MP2/6-31++G(d,p) ionization potential calculations have recently been performed on the DNA bases in the gas phase and in aqueous solution (J. Phys. Chem. A, 2004, 6373). The goal of the present work is to explore methods to perform these same calculations with density functional theory. New results for the vertical ionization potentials for the DNA bases at the B3LYP/6-31++G(d,p) level are close to the PMP2 results and also close to the experimental results. Vertical ionization potentials for the DNA bases in aqueous medium at the PCM/B3LYP/6-31++G(d,p) level are thymine 5.41, (5.36), cytosine 5.32, (5.24), adenine 5.05, (5.08), and guanine 4.71, (4.77) eV. The numbers in parentheses are the previous PCM/PMP2 results. Again, the DFT results are comparable to the PMP2 results. Results are also presented for the vertical ionization potential of 5-MeC in the gas phase and also in aqueous solution. This results in a cytosine base that has an IP more like a purine and may therefore have to be considered to be in competition with guanine as a hole trap.

Single crystals of 2'-deoxyguanosine 5'-monophosphate were X-irradiated at 10 K and at 65 K, receiving doses between 4.5 and 200 kGy, and studied using K-band EPR, ENDOR, and field-swept ENDOR (FSE) spectroscopy. Evidence for five base-centered and more than nine sugar-centered radicals was found at 10 K following high radiation doses. The base-centered radicals were the charged anion, the N10-deprotonated cation, the C8 H-addition radical, a C5 H-addition radical, and finally a stable radical so far unidentified but with parameters similar to those expected for the charged cation. The sugar-centered radicals were the H-abstraction radicals centered at C1', C2', C3', and C5', an alkoxy radical centered at O3', a C5'-centered radical in which the C5'-O5' phosphoester bond appears to be ruptured, a radical tentatively assigned to a C4'-centered radical involving a sugar-ring opening, as well as several additional unidentified sugar radicals. Most radicals were formed regardless of radiation doses. All radicals formed following low doses (4.5-9 kGy) were also observed subsequent to high doses (100-200 kGy). The relative amount of some of the radicals was dose dependent, with base radicals dominating at low doses, and a larger relative yield of sugar radicals at high doses. Above 200 K a transformation from a sugar radical into a base radical occurred. Few other radical transformations were observed. In the discussion of primary radicals fromed in DNA, the presence of sugar-centered radicals has been dismissed since they are not apparent in the EPR spectra. The present data illustrate how radicals barely traceable in the EPR spectra may be identified due to strong ENDOR resonances. Also, the observation of a stable radical with parameters similar to those expected for the charge guanine cation is interesting with regard to the nature of the primary radicals stabilized in X-irradiated DNA.