The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA

Norio Yoshida, Yasuomi Kiyota, Fumio Hirata

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.

Original languageEnglish
Pages (from-to)83-92
Number of pages10
JournalJournal of Molecular Liquids
Volume159
Issue number1
DOIs
Publication statusPublished - Feb 15 2011
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Condensed Matter Physics
  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Materials Chemistry

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