Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

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 electronic structure methods (density functional theory -- DFT, and second-order Møller-Plesset perturbation theory -- MP2) (1). The most favorable structures from Molecular Mechanics (MM) calculations were used as starting configurations for the geometry optimizations. Structures showing a clustering of the water molecules (Figure 1A) were found to be preferred over structures with water distributed around uracil/thymine (Figure 1B). This is due to the increased attractive interaction between the water molecules in the clustered complexes (quantified by the larger water-water interaction in the clustered complexes, as shown in Table 1 for uracil-(H2O)11). This demonstrates that search procedures that overemphasize the base-water interaction, like the modified scheme of monosolvation (MSM) previously employed to create hydrated uracil and thymine complexes (2), cannot predict the preferred clustering of water molecules around the base. The results indicate that the hydration shell structure is determined by a competition between water-water and base-water interactions.

References and Footnotes
  1. V. I. Danilov, T. van Mourik, V. I. Poltev. Chem. Phys. Lett., 429, 255-260 (2006).
  2. O. V. Shishkin, L. Gorb, J. Leszczynski. Int. J. Mol. Sci. 1, 17-27 (2000).

Victor I. Danilov1
Tanja van Mourik2
Valery I. Poltev3

1Institute of Molecular Biology and Genetics
National Academy of Sciences of Ukraine
150 Zabolotny Str.
Kiev-143, 03143, Ukraine
Email: vid@ipnet.kiev.ua
2School of Chemistry
University of St Andrews
North Haugh, St. Andrews
Fife, KY16 9ST, Scotland, UK
Email: tanja.vanmourik@st-andrews.ac.uk
3Fac. Ciencias Físico-Matemáticas
BUAP, C.U., San Manuel
C.P. 72570, Puebla, México
Institute of Theoretical and Experimental Biophysics
Russian Academy of Sciences
Pushchino, Moscow Region 142290, Russia
Email: vipov@mail.ru