Biopolym. Cell. 1996; 12(5):5-12.
http://dx.doi.org/10.7124/bc.000441
On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases
1Hovorun D. M., 1Mishchuk Ya. R., 1Kondratyuk I. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

An interconversion of canonical nucleotide bases adenine, guanine and cytosine, exactly an inversion about a plane, and anisotropic inner rotation around exocyclic C-N bonds, and structural perturbations and the bases' profanation as well, have AMI and MNDO/H methods with an optimization of full structural parameters and agradient norm < 0.01.An mutually coordinated relaxational behaviour of essential structural parameters which describe valence bond configurations of amino group N atoms and neighbouring double C–N bonds were analysed. It was found that pπ-conjugation of an electron lone pair of an amino group nitrogen atom with a ring π-electron system is a main factor to determine structural-dynamical properties of exocyclic amino groups of canonical nucleotide bases, and moreover, of the bases themselves. Besides appreciable effects of other intramolecular interactions, namely intramolecular H-bonds (first of all of NH...N type), steric factors, and an electrostatic repulsion of electron lone pairs of neighbouring (endo- and exocyclic) nitrogen atoms as well, were estimated. They determine both nonequivalence of amino group NH bonds (as well as amino group ground-state orientation about a ring plane) and an anisotropy ofamino group inner rotation.
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