[Study of the hydration characteristics of nucleic acid bases and their complementary pairs using the Monte-Carlo...

To elucidate the role of certain atomic groups in the formation of the nucleic acid hydrate shell, we simulated the systems involving a base or a complementary pair (the base molecules are methylated in N9 of purines and in N1 of pyrimidines) and 25 water molecules using the Monte-Carlo method. All hydrophilic centers, except for N1 purines and N3 pyrimidines in complementary pairs, form hydrogen bonds (H-bonds) with water molecules. The mean numbers of H-bonds formed by different centers, and distributions of the geometric characteristics of these bonds, which appeared similar to those in crystals, have been calculated. The formation of bridges of one, two of three water molecules between hydrophilic centers was shown. The probabilities of formation of these bridges have been calculated.