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Conformational studies on polynucleotide chains. II. Analysis of steric interactions and derivation of potential functions for internal rotations
Author(s) -
Tosi Camillo,
Clementi Enrico,
Matsuoka Osamu
Publication year - 1978
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1978.360170105
Subject(s) - chemistry , van der waals force , internal rotation , steric effects , ab initio , computational chemistry , potential energy , ab initio quantum chemistry methods , molecule , polynucleotide , thermodynamics , atomic physics , stereochemistry , physics , organic chemistry , mechanical engineering , engineering , biochemistry
In the first paper of this series we showed that the total electronic energy, computed ab initio in the Hartree‐Fock approximation for both independent and coupled rotations of the five torsional angles in the sugar–phosphate–sugar complex C 10 H 18 O 8 P, can be reproduced with reasonable accuracy by a Lennard‐Jones 6‐12 potential, with different attractive and repulsive parameters assigned to the four oxygens of the phosphate group, on one hand, and the four oxygens of the sugar rings and the hydroxyl groups, on the other. The conclusion was reached on the basis of some attempts at the derivation of analytical expressions capable of correctly describing the energies obtained with the quantum mechanical computations. An analysis of the barriers to internal rotation for the angles φ and ψ indicated the possibility of improving the description through addition of further terms, in particular of an intrinsic torsional potential. In order to obtain a fit based on all internal rotations of the sugar–phosphate–sugar molecules, and coupling numerical accuracy with physical significance, we made a study of the possible contributions to the conformational energy: intrinsic torsional energy, electrostatic interactions, London attractions, van der Waals repulsions. The results of this study show that the best description of ab initio energies is offered by a potential containing a Lennard‐Jones 6‐12 term and an intrinsic torsional term.