Hydrogen bonding of thymine and uracil with surface of dickite: An ab initio study

Abstract

The density functional theory (DFT) by means of the B3LYP functional and the 6-31G(d) basis set has been applied to analyze the hydrogen boding of selected nucleic acid bases (thymine and uracil) with the representative cluster models of the clay mineral, dickite. The results obtained from this investigation reveal that the formation of hydrogen bonds accounts for the stabilization of thymine and uracil on the mineral surface. The intermolecular distances and strength of the hydrogen bonds depend on the type of the surface (tetrahedral or octahedral) and on the hydration of the surface. Generally, thymine and uracil are less stable on the tetrahedral surface than on the octahedral surface. The most energetically favorable adsorption is predicted in the case of the system containing hydrated octahedral mineral fragment. The adsorption of thymine on the surface of dickite results in changes in geometry and polarization of thymine. These effects are more significant in the case of the octahedral adsorption than for the tetrahedral adsorption.