Biopolymers and Cell. 2011; 27 (1): 74-81
Analysis of 2-deoxy-D-ribofuranose molecule conformational capacity with the quantum-mechanical density functional method
T. Yu. Nikolaienko, L. A. Bulavin, D. M. Hovorun1,2
Taras Shevchenko National University of Kyiv
64, Volodymyrska St., Kyiv, Ukraine, 01033
1Institute of Molecular Biology and Genetics NAS of Ukraine
150, Akademika Zabolotnogo St., Kyiv, Ukraine, 03680
2Institute of High Technologies, Taras Shevchenko National University of Kyiv
2, korp.5, Pr. Akademika Hlushkova, Kyiv, Ukraine, 03022
Aim. To reveal the exhaustive conformational family for alpha- and beta-anomeric forms of the 2-deoxy-D-ribofuranose molecule and to elucidate whether this molecule can be considered as the representative DNA sugar model. Methods. The molecule conformations were described with four torsion angles (beta, gamma, epsilon and chi') and the sugar pseudorotation angle P. In 810 initial geometries for each of the anomeric forms all torsion angles (beta, gamma, epsilon and chi') were set to each of three values: +60, –60 and 180, while the furanose ring pseudorotation angle was set to each of 10 different values. The geometry optimization had been carried out with the quantum-mechanical density functional theory (DFT) method with the B3LYP exchange-correlation functional and standard 6-31G(d, p) basis set. Single point electron energies in the optimized geometries were calculated at the MP2/6-311++G (d, p) theory level while the MP2/cc-pVQZ theory level was used to calculate the electron energies of energetically most favorable conformations for alpha- and beta-anomeric forms. Normal vibrations anharmonicity was described by the spectroscopic second-order perturbation theory (PT2). Results. The exhaustive conformational families for both anomeric forms of the 2-deoxy-D- ribofuranose molecule were obtained. For alpha-anomer it consists of 89 structures and contains 107 structures for beta-anomer. It is shown, that in gas-phase mixture of alpha- and beta-anomers in thermodynamic equilibrium the former would dominate with the 82:18 % ratio. In each conformation the normal vibrations anharmonicity has been characterized. Conclusions. The presence of B- and AII-DNA-like conformations in conformational families of both anomeric forms is established. It is shown, that the anharmonic correction can lead to significant (more than kBT under standard conditions) changes in the vibrational part of the molecule’s Gibbs energy.
Keywords: 2-deoxy-D-ribofuranose, conformational analysis, ab initio calculations