The effect of hydrogen bonding on the structures of uracil and some methyl derivatives studied by experiment and theory

The equilibrium structures of uracil, thymine (5-methyluracil), 1-methyluracil and 1,3-dimethyluracil have been determined from ab initio MO calculations at the HF, MP2 and DFT/6-31G(d) levels. Thymine has also been studied in the solid state by X-ray diffraction. A systematic investigation of the effects of intermolecular association on the structure of uracil and its methyl derivatives has then been carried out by theoretical calculations. Based on information from the solid state, a dimer for 1-methyluracil, a trimer for thymine and a hexamer for uracil are used as theoretical models (at HF and DFT levels) to simulate the neighboring intermolecular interactions found in the crystal. The geometrical perturbations observed in the uracilic moiety, on going from an isolated molecule to the crystal phase, are mainly due to self-association and confirm the fundamental role of conjugative stabilization of the intermolecular hydrogen bonding in such DNA bases.