Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides

Jun Ho Choi, Minhaeng Cho

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides.

Original languageEnglish
Pages (from-to)168-175
Number of pages8
JournalChemical Physics
Volume361
Issue number3
DOIs
Publication statusPublished - 2009 Jul 15

Keywords

  • Amide vibrations
  • Polypeptide
  • Vibrational spectroscopy

ASJC Scopus subject areas

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

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