  DNA is the most important biological molecule, and its hydration contributes
essentially to the structure and functions of the double helix. We analyze the
microhydration of the individual bases of nucleic acids and their methyl
derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov
(PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM)
calculations at MP2/6-31G(d,p) level of theory. A comparison is made between
the calculated interaction energies and the experimental enthalpies of
microhydration of bases, obtained from mass spectrometry at low temperatures.
Each local water-base interaction energy minimum obtained with MM corresponds
to the minimum obtained with QM. General qualitative agreement was observed in
the geometrical characteristics of the local minima obtained via the two groups
of methods. MM minima correspond to slightly more coplanar structures than
those obtained via QM methods, and the absolute MM energy values overestimate
corresponding values obtained with QM. For Adenine and Thymine the QM local
minima energy values are closer to those obtained by the PM potential (average
of 0.72 kcal/mol) than by the AMBER force field (1.86 kcal/mol). The
differences in energy between MM and QM results are more pronounced for Guanine
and Cytosine, especially for minima with the water molecule forming H-bonds
with two proton-acceptor centers of the base. Such minima are the deepest ones
obtained via MM methods while QM calculations result in the global minima
corresponding to water molecule H-bonded to one acceptor and one donor site of
the base. Calculations for trimethylated bases with a water molecule
corroborate the MM results. The energy profiles were obtained with some degrees
of freedom of the water molecule being frozen. This data will contribute to the
improvement of the molecular mechanics force fields.
