ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

Calculation of electrostatic interactions in torsional potential of the internucleotide phosphodiesteric unit

J. Mlýnek, T. Bleha, and I. Tvaroška

Polymer Institute, Slovak Academy of Sciences, 809 34 Bratislava

Abstract: The effect of parametrization of the electrostatic term on the conformation energies of a phosphodiesteric unit was investigated by the method of potential functions (PFM). The charges found for the di-Me phosphate ion by different quantum chem. methods were used as parameters. It was revealed by using the CNDO/2 or ab initio charge distribution that the electrostatic term shows almost no contribution to the torsional potential around the P-O bond. In this case, PFM predicts energetically almost equiv. gauche and trans stable conformations for the rotation around the P-O bond. The inclusion of the lone electron pairs on O atoms in the electrostatic term does not result in the expected suppression of preference of the trans-trans conformation; rather, it considerably favors this conformation with respect to the others. A comparison of the torsional potentials obtained by CNDO/2 and PFM method revealed that the PFM does not involve those intramol. interactions the symmetry of which can be described by the terms V₁ and V₂ in the Fourier expansion of torsional potential. Attention was also paid to other approxns. inherent to PFM that may be the origin of differing predictions for oligo- and polynucleotides given by PFM on the one hand and MO calcns. and x-ray data on the other hand.

Full paper in Portable Document Format: 341a3.pdf

Chemical Papers 34 (1) 3–17 (1980)