Ab Initio Molecular Dynamics Study of Uracil in Aqueous Solution

Abstract

The hydrogen bonding of uracil in aqueous solution is investigated using density functional based ab initio molecular dynamics simulation (“Car−Parrinello”). During the 7 ps trajectory, the solute was observed to be coordinated by a first hydration shell composed of up to nine water molecules. Six water molecules are hydrogen-bonded to the amide and carbonyl groups and three further water molecules are located on either side of the uracil ring with a tendency to approach the ring through π-hydrogen bonding. The hydrogen bonding is characterized by the computation of a number of structural and dynamical correlation functions. To highlight the importance of the finite temperature bulk solvent, these results are compared to structures obtained by a number of previous structural studies of ground-state hydrated clusters. The analysis presented here is the structural complement to an ab initio molecular dynamics determination of the infrared absorption spectrum of aqueous uracil that has appeared as a separate publication (J. Phys. Chem. B 2003, 107, 10344).