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The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.

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The effects of intermolecular hydrogen bonding on the vibrational frequencies of uracil are discussed on the basis of ab initio calculations. DFT methods are applied to calculated vibrational frequencies of various uracil dimers, namely six cyclic structures and four T-shaped arrangements, as well as eight uracil-water complexes. Frequency shifts experienced by some normal modes in the dimerisation are clearly correlated with acidity or basicity of the interaction sites. Interaction energies and frequency changes indicate that cooperativity plays a fundamental role in a self-association process. Moreover the cooperative effects increase their contribution with the strength of hydrogen bonding. The theoretical IR spectra of all the hydrogen bonded uracils considered here are compared with the FT-IR spectra of uracil and thymine measured in an N 2 matrix at different concentrations.

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