Conformational studies on polynucleotide chains. I. Hartree-Fock energies and description of nonbonded interactions with Lennard-Jones potentials.

Abstract

AbstractThe sugar–phosphate–sugar complex C10H18O8P, a unit of the polynucleotide chains, was analyzed, making use of 100 conformational energies computed in the Hartree‐Fock approximation with a small basis set of Gaussian type orbitals. The geometry of the conformations [which corresponds to the C(2′)‐endo deoxy system], the basis set, and the computed total energies are reported in this work. In addition, a number of attempts are presented where we searched for a computationally very simple analytical expression apt to fit, with reasonable accuracy, the computed energies. Lennard‐Jones type potential seems to offer an appropriate form capable of reproducing the positions of the maxima and the minima resulting from ab initio computations, but neither the 6‐12 nor other similar forms seem to be able to correctly reproduce the intensity of the barriers. Form a details analysis of the barriers to rotation about the bonds O(5′)—C(5′) and C(5′)—C(4′) in terms of nonboned interactions, we found that a substantial improvement in the fit of analytical to ab initio energies may be obtained by distinguishing between atoms characterized by the same atomic number but having different chemical characteristics, like the oxygen atoms of the phosphate group, on one hand, and the oxygen atoms of the sugar rings and the hydroxyl groups, on the other.