Quantum-classical description of the amide I vibrational spectrum of trialanine

J Chem Phys. 2007 Feb 7;126(5):054509. doi: 10.1063/1.2431803.

Abstract

A quantum-classical description of the amide I vibrational spectrum of trialanine cation in D2O is given that combines (i) a classical molecular dynamics simulation of the conformational distribution of the system, (ii) comprehensive density functional theory calculations of the conformation-dependent and solvent-induced frequency fluctuations, and (iii) a semiclassical description of the vibrational line shapes which includes nonadiabatic transitions between vibrational eigenstates. Various assumptions that are usually employed in the calculation of condensed-phase vibrational spectra are tested, including the adiabatic, the Franck-Condon, and the second-order cumulant approximations, respectively. All three parts of the theoretical formulation are shown to have a significant impact on the simulated spectrum, suggesting that the interpretation of peptide amide I spectra may require substantial theoretical support.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry*
  • Computer Simulation*
  • Oligopeptides / chemistry*
  • Protein Conformation
  • Protein Structure, Secondary
  • Quantum Theory*
  • Spectrum Analysis*

Substances

  • Amides
  • Oligopeptides
  • alanyl-alanyl-alanine