Post hartree-fock studies of the canonical watson-crick dna base pairs: Molecular structure and the nature of stability

Victor I. Danilov, Victor M. Anisimov

Research output: Contribution to journalArticle

Abstract

Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6–31G(d) and 6-31G(d, p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases.

Original languageEnglish (US)
Pages (from-to)471-482
Number of pages12
JournalJournal of Biomolecular Structure and Dynamics
Volume22
Issue number4
DOIs
StatePublished - Feb 2005
Externally publishedYes

Keywords

  • Buckled geometry
  • Geometry optimization
  • Hartree-Fock
  • Morokuma-Kitaura analysis
  • Møller-Plesset
  • Propeller-twisted
  • Watson-Crick base pairs

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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