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. 2008 Jul 18;33(5-6):499–514. doi: 10.1007/s10867-008-9091-2

Electron Correlated Ab Initio Study of Amino Group Flexibility for Improvement of Molecular Mechanics Simulations on Nucleic Acid Conformations and Interactions

V I Poltev 1,✉, E Gonzalez 1, A Deriabina 1, A Martinez 1, A Furmanchuk 2, L Gorb 2, J Leszczynski 2
PMCID: PMC2565772  PMID: 19669535

Abstract

High level ab initio studies demonstrate substantial conformational flexibility of amino groups of nucleic acid bases. This flexibility is important for biological functions of DNA. Existing force field models of molecular mechanics do not describe this phenomenon due to a lack of quantitative experimental data necessary for an adjustment of empirical parameters. We have performed extensive calculations of nucleic acid bases at the MP2/6-31G(d,p) level of ab initio theory for broad set of amino group configurations. Two-dimensional maps of energy and geometrical characteristics as functions of two amino hydrogen torsions have been constructed. We approximate the maps by polynomial expressions, which can be used in molecular mechanics calculations. Detailed considerations of these maps enable us to propose a method for determination of numerical coefficients in the developed formulae using restricted sets of points obtained via higher-level calculations.

Keywords: Molecular mechanics, Correlated ab initio calculations, Nucleic acids, Amino group flexibility

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