UV photoelectron and quantum mechanical characterization of DNA and RNA bases: valence electronic structures of adenine, 1,9-dimethyl-guanine, 1-methylcytosine, thymine and uracil

Abstract

HeI UV photoelectron spectra of adenine, 1,9-dimethylguanine, 1-methylcytosine, thymine and uracil have been interpreted with the aid of results from ab initio SCF-MO calculations employing a double zeta 4–31G basis set, and HAM/3 semiempirical calculations. Ionization potentials from results of the SCF-MO calculations have been obtained through the application of Koopmans' theorem. For cytosine and guanine, problems associated with the occurrence of more than one tautomeric form in the gas phase have been circumvented by examining methyl substituted derivatives of these bases. For adenine, 1,9-dimethylguanine, thymine and uracil the current assignments, based on the results of the 4–31G SCF and HAM/3 calculations, are essentially the same as those provided in earlier studies. For 1-methylcytosine, the results of the current calculations and recent findings concerning the tautomerism of cytosine in nonpolar environments has led to new assignments. The vertical ionization potentials of the first (π 1), second (π 2), third (π 3) and fourth (π 4) highest occupied π orbitals in adenine are 8.48, ≈9.6, ≈10.5, and 12.10 eV, respectively. The ionization potentials of the first through third (n 1-n 3) lone-pair orbitals are ≈9.6, ≈10.5, and 11.39 eV. In 1,9-dimethylguanine, the π 1, π 4 and π 5 orbitals have ionization potentials of 8.09, ≈11.0, and 12.31 eV, while the π 2 and π 3 orbitals have ionization potentials in the range between 9.3 and 10.2 eV. Values for the ionization potentials of the n 1 and n 2 orbitals lie in the range between 9.3 and 10.2 eV, and the value for the n 3 orbital is ≈11.0 eV. In 1-methylcytosine, the ionization potentials of the π 1 through π 4 orbitals are 8.65, ≈9.7, 11.53, and 12.40 eV; the values for the n 1 and n 2 orbitals lie in the range 9.5 to 10.0 eV. For uracil, the ordering of the ionization potentials is π 1 (9.59 eV), n 1 (10.11 eV), π 2 (10.56 eV), n 2 (11.16 eV), and π 3 (12.63 eV). In thymine, the energetic ordering of orbitals is the same as in uracil and the corresponding ionization potentials have values of 9.18, 10.03, 10.39, 10.82 and 12.27 eV. An examination of DNA and RNA alkylation patterns occurring in reactions with dimethyl-sulfate, methylmethanesulfonate and N-methyl- N-nitrosourea indicates that the reactivity of nucleotide bases towards methylating reagents increases as the base ionization potentials decrease.