Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

A PM6 Study of the ?Hydration Shell? of Nucleic Acid Bases in Small Water Clusters

The hydration shell formation of uracil, thymine, cytosine, and adenine in small water clusters was studied using density functional theory (DFT) (1) and the new semiempirical PM6 method (2). The lowest energy structures from Molecular Mechanics (MM) calculations and structures obtained via the modified scheme of monosolvation [MSM (3)] were used as starting configurations for the geometry optimizations. The MM-derived structures, Figure 1, show a clustering of the water molecules, whereas in the MSM-derived structures the water molecules are distributed around the base in a chain-like formation. In good agreement with our previous DFT results, PM6 calculations predict the clustered structures to be energetically preferred, even though the water-base interaction is larger, Table I, in all complexes except A-(H2O)16. This indicates that methods that overemphasize the base-water interaction, like the MSM scheme, cannot predict the preferred clustering of water molecules around nucleic acid bases.

Figure 1: PM6-optimized structures of the different complexes studied. As starting structure the most favorable structure from MM calculations was employed.

References and Footnotes
  1. V. I. Danilov, T. van Mourik, V. I. Poltev. Chem Phys Lett 429, 255-260 (2006); T. van Mourik, V. I. Danilov, A. S. Deryabina, E. Gonzalez and V. I. Poltev. to be published.
  2. J. P. P. Stewart. MOPAC, Version 7.036W (2007).
  3. O. V. Shishkin, L. Gorb, J. Leszczynski. Int J Mol Sci 1 17-27 (2000); J Phys Chem B104, 5357-5361 (2000); O. S. Sukhanov, O. V. Shishkin, L. Gorb, Y. Podolyan, J. Leszczynski. J Phys Chem B 107, 2846-2852 (2003).

Victor I. Danilov1
James J. P. Stewart2
Tanja van Mourik3, *

1Institute of Molecular Biology and Genetics
National Academy of Sciences of Ukraine
150 Zabolotny Str.
Kiev-143, 03143, Ukraine
2Stewart Computational Chemistry
Colorado Springs, CO, 80921 USA
3School of Chemistry
University of St Andrews
North Haugh, St. Andrews
Fife, KY16 9ST, Scotland, UK

*Email: tanja.vanmourik@st-andrews.ac.uk