Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

The change in the electronic structure of a DNA duplex d(CGCGAATTCGCG)2 upon solvation was investigated by the ab initio fragment molecular orbital (FMO) method. The crystal structure of the duplex was immersed in a solvent box containing explicit water and Na+ ions, and the resultant solvated DNA was relaxed and annealed by the classical molecular dynamics method. From the annealed structure a series of solvated DNA configurations were constructed with varying solvent shell thicknesses (0-12Å). Each configuration was subjected to FMO calculation at the MP2/6-31G* level. Partial charge, internal energies, interaction energies between the bases and phosphate backbones, and fragment molecular orbitals within DNA were calculated and expressed as functions of the solvent thickness. Most of these physical properties within DNA converged at a shell thickness of 8Å, indicating the dominant effect of the first and second solvation layers. Ca. -7e charge, i.e. -0.6e per base pair, was transferred from DNA to the solvent. Upon solvation the Watson-Crick H-bonds became stabilized but the stacking interactions were destabilized. Based on the pair interaction energy decomposition analysis, these stability changes were attributed to modulation of the electrostatic interaction elicited by the rearrangement of the charge distribution due to the charge transfer to the solvent. Thus, this study revealed significant modulation of the electronic structure of the DNA upon solvation and its impact on molecular interactions, which can be described only through quantum-chemical calculations.

Original languageEnglish
Pages (from-to)29-37
Number of pages9
JournalComputational and Theoretical Chemistry
Volume1054
DOIs
Publication statusPublished - 2015 Feb 5
Externally publishedYes

Keywords

  • ABINIT-MP
  • DNA
  • Energy decomposition analysis
  • Fragment molecular orbital method
  • Interaction energy
  • Solvation

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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