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

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.

Conformational Flexibility of l-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands

“…Particularly, for the Raman signal, the broader relative widths of peaks corresponding to normal mode nos. [4][5][6]8, and 24-26 can be explained by the molecular flexibility (cf., Figures 5 and 6). Overall, the experimental line widths, however, are still slightly wider, which can be attributed to a dynamical influence of the solvent, not included in the static CPCM model.…”

“…It is generally accepted that the inhomogeneous line width broadening of spectral lines is caused by equilibria of many conformations and solvent interactions. [8][9][10][11][12] In the past many studies were dedicated to resolution of conformational mixtures by vibrational spectroscopy. [13][14][15][16] Yet the movement of the CH 3 , NH 3 , and CO 2 groups has been traditionally considered only as a side-product of solvent clustering.…”

Molecular dynamics with restrictions derived from optical spectra

“…However, for many systems such a quasi-classical approach has been well-justified within the instantaneous mode approximations and other computational schemes. [18][19][20] Typically, the vibrational and electronic excitations observable in the spectra occur in a much faster time scale than common conformation motions and the coupling is minimized.…”

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

“…In addition, once validated, the simulations provide the opportunity for further in-depth analysis and understanding of the atomic and molecular motions which are responsible for the observed time scales. 29 Essentially two approaches have been pursued to perform such simulations: (a) running an MD simulation with a standard force field in order to sample the conformational space and then calculating instantaneous frequency shifts of the chromophore of interest, utilizing maps that have typically been pre-calculated on a higher ab-initio level of theory, [30][31][32][33] or (b) developing better, physics-based empirical force fields that are used for both the MD trajectory and the spectral calculation in a consistent manner. 29,34 For cyanide in water, a force field that correctly describes solvation free energies, vibrational relaxation and the 1-dimensional spectroscopy was found to closely match the experimentally measured spectral diffusion dynamics.…”