Simulation of the First Hydration Shell of Nucleosides D4T and Thymidine: Structures Obtained Using MP2 and DFT Methods

Abstract

A comparative theoretical analysis on the effect of the solvent on the molecular structure and energetics of the most stable conformers of the nucleoside analogue D4T (stavudine) and of the natural nucleoside thymidine (Thy) was carried out. Solvent effects were considered using the Tomasi's polarized continuum model (PCM) and including a variable number (1-13) of explicit water molecules surrounding the nucleoside in order to simulate the first hydration shell. More than 200 cluster structures with water were analyzed. B3LYP and MP2 quantum chemical methods were used. The CP-corrected interaction energies for D4T and water molecules were computed. For cases where literature data are available, the computed values were in good agreement with previous experimental and theoretical studies. In the isolated state, conformer I (anti-gg-gg) appears the most stable for D4T molecule and conformer II (anti-gg-gt) for Thy molecule. In D4T with eight water molecules, conformer II changes to conformer I. Thus, conformer I seems preferred when water molecules are situated in the first hydration shell. However, in hydrated thymidine conformer Ia (anti-gg-tg) is the more stable one, and the first hydration shell is more extended than in D4T molecule. The effect of the hydration on the total atomic charges and intermolecular distances were also discussed. Several general conclusions on hydrogen bonds network and involved interaction energies were underlined.