Simulation studies of amide I IR absorption and two-dimensional IR spectra of β hairpins in liquid water

Seungsoo Hahn, Sihyun Ham, Minhaeng Cho

Research output: Contribution to journalArticle

92 Citations (Scopus)

Abstract

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model β hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the β hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) β hairpin are directly compared with those of the realistic 16-residue (GB1) β hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A 17) β hairpin and the GB1 β hairpin are the same. The simulated IR spectrum of the GB1 β hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.

Original languageEnglish
Pages (from-to)11789-11801
Number of pages13
JournalJournal of Physical Chemistry B
Volume109
Issue number23
DOIs
Publication statusPublished - 2005 Jun 16

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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