Anionic and Neutral Complexes of Uracil and Water

Abstract

Several isomeric structures of the uracil−water complex and its covalent-bound anion were calculated ab initio with second-order, many-body, perturbation theory and the 6-311++G** basis set. In all neutral complexes, water forms two hydrogen bonds with uracil. In each of the conventional anionic forms, a single, but stronger and shorter, hydrogen bond is found. All complexes are nonplanar, but ring-puckering is less pronounced in neutrals than in anions. Several isomers of the anionic uracil−water complex have positive adiabatic electron-detachment energies. The existence of multiple anionic isomers with vertical electron-detachment energies between 0.30 and 0.90 eV accounts for the broad photoelectron spectrum. The lowest unoccupied molecular orbital of the neutral complex at the geometry of the anionic complex provides a simple explanation for the structural and energetic consequences of electron attachment.

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

“…The water binding energies of the first water molecule found for these systems in the present work are similar and very close to those of the protonated nucleotides obtained in another laboratory [21]. Interestingly, the water interaction energies for the protonated uracil and thymine are similar to those calculated [6,10] for corresponding valence-bound anions of these bases. Considering the relative stabilities of protonated tautomers and favorable sites for interactions with water molecules, possible structures for H-bonded complexes have been presented.…”

“…Interestingly, in the conventional anionic complex Ura Ϫ · H 2 O, the water binding is strongest at the uracil O 8 site [6] and, calculated at the UMBPT (2) . Although the differences between these values are within the range of the experimental uncertainty, the slightly lower binding strengths for ThyH ϩ · (H 2 O) n ϭ 1,2 than the corresponding UraH ϩ · (H 2 O) n ϭ 1,2 can be accounted for by the somewhat higher PA of Thy (210.5 kcal/mol) than that of Ura (208.6 kcal/mol).…”

“…The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment.…”

“…The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] and nucleosides [14] with water molecules have been performed theoretically. A few experimental studies have been carried out on hydration enthalpies [15], IR spectra [13], UV spectra [16], hydration dynamics [17] of DNA bases, ionization potentials [18], and metastable decay [19] of hydrated adenine and thymine cations.…”

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

“…And furthermore, the solvation of the uracil anionic state by one water molecule provides an extra stabilization of this state by ca. 0.4 eV [58,59]. Thus, the solvation of U − by the amino acid would have to provide an extra stabilization of 1.3 eV to be consistent with the maxima of the PES peaks at 1.8 eV, which is again improbable.…”