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Modeling of the Hydration Shell of Uracil and Thymine
Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Sciences of Ukraine, 60 Lenina Avenue., Kharkiv 310001, Ukraine
Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, MS 39217, USA
* Author to whom correspondence should be addressed.
Received: 4 January 2000; Accepted: 30 March 2000 / Published: 4 March 2000
Abstract: The molecular geometry of complexes of uracil and thymine with 11 water molecules was calculated using the density functional theory with the B3LYP functional. The standard 6-31G(d) basis set has been employed. It was found that the arrangement of water molecules forming a locked chain around the nucleobases significantly differs for uracil and thymine. The presence of a methyl group in thymine results in strong non-planarity of the hydrated shell. The existence of C-H...O hydrogen bonds between the water molecules and the hydrophobic part of the nucleobases is established. Interactions with water molecules cause some changes in the geometry of uracil and thymine which can be explained by the contribution of a zwitter-ionic dihydroxy resonance form into the total structure of the molecules.
Keywords: Uracil; Thymine; Hydration; Molecular structure; Hydrogen bonds; Density functional theory
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Shishkin, O.V.; Gorb, L.; Leszczynski, J. Modeling of the Hydration Shell of Uracil and Thymine. Int. J. Mol. Sci. 2000, 1, 17-27.
Shishkin OV, Gorb L, Leszczynski J. Modeling of the Hydration Shell of Uracil and Thymine. International Journal of Molecular Sciences. 2000; 1(2):17-27.
Shishkin, Oleg V.; Gorb, Leonid; Leszczynski, Jerzy. 2000. "Modeling of the Hydration Shell of Uracil and Thymine." Int. J. Mol. Sci. 1, no. 2: 17-27.