Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra

Chewook Lee, Kwang Hee Park, Jin A. Kim, Seungsoo Hahn, Minhaeng Cho

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dGn: dC n and dAn: dTn double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG5C 5 and dA5T5 double helices in D2O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dGn: dCn double helix in D 2O solution are directly compared with closely related experimental results. The 2D IR spectra of dGn: dCn and dA n: dTn are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Original languageEnglish
Article number114510
JournalJournal of Chemical Physics
Volume125
Issue number11
DOIs
Publication statusPublished - 2006

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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