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. Chern. Sec. 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.