Theoretical Study of the Interaction between Thymine and Water. Protonation and Deprotonation Enthalpies and Comparison with Uracil

Abstract

The optimized geometries, harmonic vibrational frequencies, and energies of the three cyclic structures of the thymine−water complex are computed using density functional theory (B3LYP) combined with the 6-31++G(d,p) basis set. The proton affinity of the oxygen atoms and the deprotonation enthalpy of the NH bonds of thymine are computed at the same level and compared with recent data on uracil. In both uracil and thymine, the deprotonation enthalpies are lower (1391−1449 kJ mol-1) than those of the biological NH donors of the peptide links (1470−1485 kJ mol-1) (Mautner, M. J. Am. Chem. Soc. 1988, 110, 3075). Harmonic vibrational frequencies are also reported for the uracil−water complexes. In both uracil and thymine complexes, the most stable hydrogen bond is formed at the O site characterized by the smallest proton affinity and at the NH site characterized by the highest acidity. The intermolecular distances and the energies of the hydrogen bonds formed at the different sites of thymine and uracil depend on the proton affinity and the deprotonation enthalpy of these sites. New correlations between these parameters are presented and the cooperativity in the closed structures discussed.

The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications

“…The calculations and experimental data are in agreement, within experimental error. B3LYP/6-31ϩG* therefore appears to be a reasonable method and level at which to calculate gas-phase enthalpies of deprotonation of nucleobases [1,2,14,81,[83][84][85].…”

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

“…The most basic site in this structure is at the O 8 atom with a proton affinity (PA) of 205.5 kcal/mol for uracil and 207.0 kcal/mol for thymine, and is more basic by about 6.9 -8.4 kcal/mol than the O 7 atom [3,26]. Protonations at the N and C atoms in 1 are less favorable than at the O atoms.…”

“…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.…”

Effects of protonation and deprotonation on the reactivity of quinolone: A theoretical study

“…The molecular structures of the studied species were optimized using density functional theory (DFT) with the B3LYP hybrid exchange-correlation functional and the 6-311G** basis set [14][15][16][17][18][19][20]. The geometry optimization results suggested that there was a tendency to form interand intra-molecular hydrogen-bonds.…”