Geometrical and vibrational properties of nucleic acid constituents interacting with explicit water molecules as analyzed by density functional theory calculation.: 1.: Uracil+nwH2O (nw=1,...,7)

To analyze the preferential sites of interaction of water molecules with uracil (RNA base) through the first hydration shell, we resorted to density functional theory (DFT) calculations by means of B3LYP exchange and correlation functionals. The effect of two different basis sets with and without diffuse orbitals, i.e., 6-31G* and 6-31++G*, respectively, has been studied on the energetics, as well as on the geometrical and vibrational properties, of the studied compounds. Water molecules have been gradually placed in an average plane containing uracil, and their number (n(w)) was varied from 1 to 7. For a given value of n(w), different possible interaction sites of water molecule(s) with respect to the base have been taken into consideration. The results obtained from this investigation allowed us to estimate the energy difference separating optimized configurations by taking into account both electronic and vibrational energies. The most energetically favorable configurations for a given n(w) value were then used in further calculations with higher n(w) values. It has been shown that the most energetically favorable supermolecular configurations found with large number of n(w) contain water dimers and water trimers. Geometrical parameters of uracil, water molecules, and hydrated uracil have been discussed in detail. Calculated vibrational modes for uracil and hydrated uracil (uracil + 7H(2)O) have been compared with those previously analyzed by optical spectroscopy.