HYDRATION OF CYTIDINE, 2'-DEOXYCYTIDINE AND THEIR PHOSPHATE SALTS IN THE AQUEOUS-SOLUTIONS - A MOLECULAR-DYNAMICS COMPUTER-SIMULATION STUDY

To compare the hydration pattern of the cytidine (Cyd) and 2'-deoxycyt idine (dCyd) in the aqueous solutions at the level of microscopic inte ractions, Molecular Dynamics (MD) computer simulations have been under taken. The results indicate that the hydration of the heterocyclic bas e moiety in cytidine and 2'-deoxycytidine has a hydrophobic character. None of the three potential Watson - Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosid es in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the thr ee-dimensional networks of H-bonds involving all hydrophilic centres a re formed differently around the ribose and 2'-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been e valuated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have be en calculated. The changes in the pattern of hydration with the increa sed concentration of nucleosides and upon nucleoside protonation are d iscussed. The analysis of the pairwise interaction energies are also p resented.