UV photoelectron spectroscopy and ab initio characterization of valence orbital structures and conformations of neutral phosphate esters

Conduction-band-edge ionization thresholds of DNA components in aqueous solution

Numerous investigations have focused on DNA damage induced by ionizing radiation; however, photoionization threshold energies of nucleic acid components in aqueous solution are not known. Herein, data from gas-phase photoelectron experiments have been combined with results from self-consistent field and post-self-consistent field molecular orbital calculations and with theoretical Gibbs free energies of hydration to describe aqueous ionization energies of 2'-deoxythymidine 5'-phosphate (5'-dTMP-) and 2'-deoxycytidine 5'-phosphate (5'-dCMP-). For the test molecules, indole and tryptophan, this approach yields aqueous ionization energies (4.46 and 4.58 eV, respectively) in agreement with experimental values (4. 35 and 4.45 eV). When uridine and 2'-deoxythymidine ionization energies are evaluated, the results agree with recent data from 193-nm laser measurements indicating that uridine ionization occurs via a one-photon event. For 5'-dCMP- and 5'-dTMP-, a comparison of aqueous ionization energies with gas-phase ionization potentials (IPs) indicates that hydration alters the relative energies of ionization events. In the gas phase, phosphate vertical IPs are approximately 1.3 eV smaller than base IPs. In aqueous solution, the base and phosphate ionization energies are more similar, and only differ by approximately 0.5 eV. For 5'-dCMP- and 5'-dTMP-, the increased favorableness of base ionization, which accompanies hydration, is consistent with experimental data indicating that, at 77 K in aqueous perchlorate glasses, the primary photoionization pathway involves base ionization followed by deprotonation.

UV photoelectron and theoretical characterization of 2'-deoxyguanosine-5'-phosphate valence electronic properties: changes in structure associated with the B to Z-DNA conformational transition

He(I) UV photoelectron spectroscopy and ab initio SCF molecular orbital calculations with the 4-31G basis set have been employed to characterize the valence electronic structures of 2'-deoxyguanosine-5'-phosphate (5'-dGMP-). In 5'-dGMP-, the electron distributions of the upper occupied orbitals are localized and similar to those appearing in 1,9-dimethylguanine (1), 3-hydroxytetrahydrofuran (2) and CH3HPO4- (3). Theoretical ionization potentials (IP's) of 5'-dGMP- (4) have been obtained by applying Koopmans' Theorem to the 4-31G SCF results. The IP's of seven orbitals in the base and sugar groups in 4, predicted from the 4-31G SCF calculations, have been individually corrected by comparison to results from 4-31G SCF calculations on neutral 5'-dGMP, and to Hel photoelectron spectra of the model compounds, 1 and 2. The IP's of six of the highest occupied orbitals of the phosphate group in 4 and in the model anion 3, predicted from 4-31G SCF calculations, have been corrected by comparing 4-31G SCF results for PO2- to theoretical IP's obtained from second-order Møller-Plesset perturbation calculations on PO2-. For 4 in the conformation occurring in B-DNA, the first IP's associated with the phosphate, base, and sugar groups occur at 5.1, 5.6 and 6.6 eV, respectively. A comparison of the valence electronic structures of 4 in geometries associated with the B and Z-DNA conformations indicates that in B-DNA the base and sugar orbitals have lower IP's than in Z-DNA, while the phosphate orbitals have higher IP's.

Evidence for nonintercalative complexes formed from the reversible binding of benzo[a]pyrene metabolites to closed-circular, single-stranded M13mp19 DNA

The fluorescence excitation spectrum of complexes formed from the reversible binding of the proximate carcinogen, trans-7,8-dihydroxy-7,8-dihydro-benzo[a]pyrene (BP78D) to closed-circular, single-stranded, viral M13mp19 DNA (SS M13 DNA) exhibits a red-shift of 5 nm compared to the spectrum of BP78D measured without DNA or with native, calf thymus DNA. In SS M13 DNA which is 0.10 mM in PO4-, the fluorescence intensity of BP78D is 2.3 times smaller than the intensity measured without DNA; however, the fluorescence lifetime (42.7 nsec) of BP78D with SS M13 DNA is 1.7-1.8 times larger than the lifetimes of BP78D measured without DNA or with calf thymus DNA. These results are consistent with the conclusion that, in addition to binding sites which cause fluorescence quenching, SS M13 DNA contains sites which permit formation of BP78D inclusion complexes that have weaker interactions with nucleotide bases than those occurring in intercalated complexes. The association constant (1.45 +/- 0.01 x 10(5) M-1) for the binding of BP78D to SS M13 DNA is more than 9.0 times larger than that for binding to calf thymus DNA. It is 7.1 times larger than that for the binding of the less genotoxic metabolite, trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene (BP45D) to SS M13 DNA. UV Photoelectron data and results from ab initio molecular orbital calculations suggest that a difference in polarizability contributes to the greater SS M13 DNA binding of BP78D compared to that of BP45D.