Conformational studies on polynucleotide chains. IV. Backbone structure of ribonucleic acids

Abstract

AbstractIn preceding papers the energies associated with the internal rotations in the sugar–phosphate–sugar complex were described with an analytical potential consisting of a Lennard‐Jones 6–12 term and an intrinsic torsional term and representing the best fit to a large number of energies computed with a quantum mechanical ab initio technique. The complex considered there (of 37 atoms and with the chemical formula C10H18O8P) is repesentative of deoxyribonucleic acids. In this paper we apply our potential to evaluating the intramolecular energies of the 39‐atom complex C10H18O10P, representative of the ribonucleic acids. The potential energies for the internal rotations (considered independent from one another) and the energy maps for rotations about consecutive bonds of the backbone chain are critically compared, both with those obtained for the deoxy system and with those obtained from different theoretical approaches as available from literature. It is shown that, at least for certain combinations of the internal rotation angles, the choice of the starting geometry for the sugarphosphate–sugar molecule (bond lengths and valence angles) strongly affects the value of the computed energy. If a proper geometry is used, very low energies are predicted by our potential in correspondence of the sets of torsional angles found in various RNAs by x‐ray crystallography.