Does a stacked DNA base pair hydrate better than a hydrogen-bonded one? An ab initio study

Sivanesan, D. ; Babu, K. ; Gadre, Shridhar R. ; Subramanian, V. ; Ramasami, T. (2000) Does a stacked DNA base pair hydrate better than a hydrogen-bonded one? An ab initio study Journal of Physical Chemistry A, 104 (46). pp. 10887-10894. ISSN 1089-5639

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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.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:10385
Deposited On:04 Nov 2010 05:50
Last Modified:31 May 2011 09:47

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