Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

Aviane Flood; Curinetha Hubbard; Gareth Forde; Glake Hill; Leonid Gorb; Jerzy Leszczynski

doi:10.1080/07391102.2003.10506925

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

J Biomol Struct Dyn. 2003 Oct;21(2):297-302. doi: 10.1080/07391102.2003.10506925.

Authors

Aviane Flood¹, Curinetha Hubbard, Gareth Forde, Glake Hill, Leonid Gorb, Jerzy Leszczynski

Affiliation

¹ Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217, USA.

PMID: 12956613
DOI: 10.1080/07391102.2003.10506925

Abstract

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adenine / chemistry*
Base Pairing*
DNA Methylation*
Humans
Hydrogen Bonding
Models, Molecular
Models, Theoretical*
Thymine / chemistry*

Substances

Adenine
Thymine