Ukr.Biochem.J. 2011; Volume 83, Issue 4, Jul-Aug, pp. 16-28

The 5′-deoxyadenylic acid molecule conformational capacity: quantum-mechanical investigation using density functional theory (DFT)

T. Yu. Nikolaienko1, L. A. Bulavin1, D. M. Hovorun1,2

1Taras Shevchenko Kyiv National University, Ukraine;
2Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;

Exhaustive conformational analysis of the 5′-deoxyadenylic acid molecule, has been carried out by the quantum-mechanical density functional theory method at the MP2/6-311++G(d,p) // DFT B3LYP/6-31G(d,p) theory level. As many as 726 of its conformations have been revealed with the relative gas phase Gibbs energies under standard­ conditions from 0 to 12.1 kcal/mole. It has been shown, that the energetically most favorable conformation has north sugar puckering and syn- orien­tation of the nitrogenous base and is stabilized by intramolecular OP1HP1∙∙∙N3 and O3′H∙∙∙OP hydrogen bonds. Four conformations have been shown to have their geometry similar to that of AI-DNA and four – of BI-DNA. One conformer of the 5′-deoxyadenylic acid molecule is similar to its sodium salt hexahydrate structure in crystalline state resolved by the X-ray diffraction method and taken from literature. It is shown that effective charges of C4′ and C5′ atoms are the most sensitive to the molecule conformation ones. The role of the intramolecular OH∙∙∙N hydrogen bonds in formation of the 5′-deoxyadenylic acid molecule structure has been demonstrated.

Keywords: , , , , ,

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