He I, UV photoelectron data and results from self-consistent-field (SCF) and post-SCF molecular orbital calculations were used to evaluate multiple gas-phase ionization potentials (IPs) of the phosphorylated dinucleotide (5')pGpAp both isolated and in a cluster with Na+ and H2O. SCF calculations with a split-valence basis set indicate that the ground-state valence orbital structure of (5')pGpAp is generally localized on the base, sugar, or phosphate groups and that: orbitals in the dinucleotide are similar to orbitals in the model compounds and anion, 1,9-dimethylguanine, 9-methyladenine, 3-hydroxytetrahydrofuran, and H2PO4-. This correlation parallels that Fn mononucleotides (Fernando, H.; Papadantonakis, G. A.; Kim, N. S.; LeBreton, P. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5550-5555; Kim, N. S.; LeBreton, P. R. J. Am. Chem. Sec. 1996, 118, 3694-3707) and permits the correction of SCF ionization potentials using experimental IPs for the model compounds and theoretical IPs from post-SCF calculations on H2PO4-. A comparison of IPs of (5')pGpAp, (5')pGpA, 2'-deoxyguanosine 5'-phosphate (5'-dGMP(-)), and 2'-deoxyadenosine 5'-phosphate (5'-dAMP(-)), both isolated and in gas-phase clusters with Na+ and H2O, indicates that the electrostatic influence of Na+ and the anionic phosphate groups is great. IPs decrease significantly as the number of phosphate groups increases. For 5'-dGMP(-), (5')pGpA, and 5'pGpAp, the lowest adiabatic guanine ionization potentials are 5.2, 3.1, and 1.6 eV, respectively; the lowest phosphate vertical IPs are 5.1, 3.1, and 1.9 eV. Gas-phase IPs were combined with hydration energies obtained with a Langevin dipole relaxation model to evaluate the 22 lowest aqueous ionization energies in (5')pGpAp as well as ionization energies in the other nucleotides with and without counterions. The electrostatic dependence of the gas-phase IPs on the number of phosphate groups is modulated in aqueous solution. For 5'-dGMP(-), (5')pGpA, and (5')pGpAp, the aqueous guanine and phosphate ionization energies lie in the ranges 4.2-4.9 eV and 5.5-6.1 eV, respectively. Solvent relaxation similarly modulates Na+ electrostatic effects. It also alters the relative energies of ionization events. In the gas phase, the first adiabatic base IP is equal to or larger than the lowest phosphate vertical IF. In water, the base ionization energies are 1.2-1.3 eV smaller than the phosphate ionization energies. Guanine gas-phase pi ionization energies in five different B-DNA oligomer models, each containing six stacked base pairs, were compared with site-specific reactivity data for methylation at the guanine N7 and O-6 atoms by the carcinogen, N-methyl-N-nitrosourea (MNU). O-6 methylation is associated with MNU carcinogenesis; N7 methylation is the principal DNA reaction pathway. At both guanine atoms, reactivity increases as the lowest guanine pi ionization potential decreases. This is consistent with a description of transition slates in which activation barriers are lowered as nucleotide base pi polarizability increases.