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1 Polish Journal of Chemistry

1 2008

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Quantum Chemical Study of the Nature of Stacking Interactions of 2-Oxo-adenine with Native B-DNA Purines

Czyżnikowska Ż., Zaleśny R., Cysewski P.

Polish Journal of Chemistry

2008

Vol. 82, nr 12

2269-2279

The scan of intermolecular interaction energy surfaces for stacked complexes of 2-oxoadenine (AA) with purine bases was performed using the density-fitting approach at the MP2 level of theory with correlation-consistent Dunning's basis sets. Moreover, the convergence of stabilization energy to the basis-set limit was analyzed using two-point extrapolation formula proposed by Halkier et al. Four different complexes in two different context alignments appearing in B-DNA were considered, namely 5c-A/A-3', 5'-A/AA-3', 5c-AA/A-3', 5c-G/A-3', 5'-G/AA-3', 5'-A/G-3' and 5'-AA/G-3'. The results of ab initio calculation allow to arrive at conclusion that oxidation of adenine at C2 position does not lead to significant changes in the structural parameters of stacked complexes. However, the modification of adenine by hydroxyl radical affects noticeably the stabilization energy only for 5'-G/AA-3' complex. In order to explain the source of this large stabilization effect, the intermolecular interaction energy decomposition was performed at the MP2/aug-cc-pVDZ level of theory for the minima on the interaction energy surfaces of adenine (2-oxo-ad e nine) with guanine. It was found that the observed larger stabilization energy for 5'-G/AA-3' compared to 5'-G/A-3' arises from the electrostatic interactions.