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Study of the Hydrogen Bond in Different Orientations of Adenine-Thymine Base Pairs: an ab initio Study

M. Monajjemi1*, B. Chahkandi1,2, K. Zare1, and A. Amiri3

1Science and Research Campus, Islamic Azad University, Hesarak, Poonak, P.O. Box 14515-775, Tehran, Iran; E-mail: m_monajjemi@yahoo.com

2Department of Chemistry, Shahrood Campus, Islamic Azad University, Shahrood, Iran

3Department of Chemistry, Central Tehran Campus, Islamic Azad University, Tehran, Iran

* To whom correspondence should be addressed.

Received May 15, 2004; Revision received September 13, 2004
In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G** basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 Å, respectively, at B3LYP/6-31G** level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 Å). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G** and HF/6-31G** levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G** and B3LYP/6-31++G** levels, respectively. The computed B3LYP/6-31G** bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol).
KEY WORDS: Watson-Crick base pairs, ab initio, B3LYP, hydrogen bonding