Abstract

Quantum mechanics ab initio computations are used to improve molecular mechanics force fields for nucleic acids. The most important phenomenon of nucleic acid structure, which cannot be properly reproduced by existing force fields of molecular mechanics, is phenomenon of nonplanarity and flexibility of base amino groups. This phenomenon is described by precise quantum mechanics ab initio calculations. As a first step in developing force field, based on both experimental and accurate quantum chemistry data, the calculations of the MP2/631G(d,p) ab initio level of theory were performed for extended sets of amino group torsion angles of cytosine, one of nucleic acid bases. Dependences of internal base energy and base geometry parameters on three amino group torsions were constructed and analyzed. Construction of two-dimensional maps for energy and geometry parameters as functions of amino hydrogen torsions enables to suggest trial analytical expressions for additional terms responsible for amino group flexibility. Exact values of coefficients in the formulae for the molecule energy and amino group geometry parameters will be obtained after the comparison of the results of quantum mechanics and molecular mechanics computations for base-base interactions in various mutual base arrangements. (c) 2005 Elsevier B.V. All rights reserved.