Modeling of the “hydration shell” of uracil and thymine in small water clusters by DFT and MP2 methods

The hydration shell formation of uracil and thymine in complexes comprising 11 water molecules was studied using B3LYP/6-31 G(d), B3LYP/6-31+G(d) and MP2/6-31G(d). The most favorable structures from molecular mechanics calculations were used as starting configurations for the geometry optimizations. Structures showing a clustering of the water molecules were found to be preferred over structures with water distributed around uracil/thymine (obtained previously by Shishkin et al.) due to the increased attractive interaction between the water molecules in the clustered complexes. The results indicate that the hydration shell structure is determined by a competition between water-water and base-water interactions. (c) 2006 Elsevier B.V. All rights reserved.