IR spectra of N -methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations

Seongeun Yang, Minhaeng Cho

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47 Citations (Scopus)

Abstract

We applied the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulation method in assessing IR spectra of N -methylacetamide and its deuterated form in aqueous solutions. The model peptide is treated at the Austin Model 1 (AM1) level and the induced dipole effects by the solvent are incorporated in fluctuating solute dipole moments, which are calculated using partial charges from Mulliken population analyses without resorting to any available high-level ab initio dipole moment data. Fourier transform of the solute dipole autocorrelation function produces in silico IR spectra, in which the relative peak intensities and bandwidths of major amide bands are quantitatively compatible with experimental results only when both geometric and electronic polarizations of the peptide by the solvent are dealt with at the same quantum-mechanical level. We cast light on the importance of addressing dynamic charge fluctuations of the solute in calculating IR spectra by comparing classical and QM/MM MD simulation results. We propose the adjustable scaling factors for each amide mode to be directly compared with experimental data.

Original languageEnglish
Article number134503
JournalJournal of Chemical Physics
Volume123
Issue number13
DOIs
Publication statusPublished - 2005 Oct 3

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Dipole moment
Amides
Molecular dynamics
solutes
molecular dynamics
Peptides
amides
peptides
Water
Computer simulation
dipole moments
Autocorrelation
water
dipoles
Fourier transforms
simulation
Polarization
Bandwidth
autocorrelation
casts

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

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