A systematic comparative study has been carried out on the explicit hydration of the cytosine base (C),
cytosine−cytosine hydrogen-bonded (H-bonded) base pair (CC) and cytosine−cytosine stacked dimer (C/C).
An electrostatics-based model, electrostatic potential for intermolecular complexation (EPIC) has been used
to generate initial geometries of the hydrated complexes for ab initio calculations. For this purpose, first the
topography of the molecular electrostatic potential (MESP) for C, CC and C/C is explored. Several geometries
of the complexes, C...(H2O)
n
, CC...(H2O)
n
and C/C...(H2O)
n
(n = 1, 2 and 3) are investigated with EPIC
followed by constrained optimization at the HF/6-31G** level. Further, single point (SP) energy calculations
have been performed at the MP2/6-31G** level to assess the role of electron correlation contribution in the
hydration process. This study reveals that C/C stacked dimer hydrates better than the hydrogen-bonded (H-bonded) CC pair. Energetics of these systems show a clear-cut additional stability of 1 to 2.5 kcal/mol at the
HF/6-31G** level and more than 3 kcal/mol at the MP2/6-31G**//HF/6-31G** level for C/C...3H2O complex
as compared to CC...3H2O. The present study thus confirms that the stacked base pair hydrates better than
the corresponding H-bonded base pair.
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