Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

Phys Chem Chem Phys. 2009 Oct 28;11(40):9149-59. doi: 10.1039/b910269h. Epub 2009 Aug 5.

Abstract

A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetamides / chemistry
  • Amides / chemistry*
  • Dimethyl Sulfoxide / chemistry
  • Dipeptides / chemistry*
  • Molecular Dynamics Simulation
  • Oligopeptides / chemistry*
  • Protein Conformation
  • Solutions
  • Solvents / chemistry
  • Spectroscopy, Fourier Transform Infrared

Substances

  • Acetamides
  • Amides
  • Dipeptides
  • Oligopeptides
  • Solutions
  • Solvents
  • alanylalanine
  • alanyl-alanyl-alanine
  • N-methylacetamide
  • Dimethyl Sulfoxide