Biswas, Sohag and Mallik, Bhabani S.
(2020)
Solvent-mediated dynamics and stretching profile of amide modes: QM/MM simulations of N-methylacetamide in ionic and various molecular liquids.
Journal of Molecular Liquids, 317.
p. 114202.
ISSN 01677322
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Abstract
In this study, we performed QM/MM molecular dynamics simulations of a simple biomolecular model, N-methylacetamide molecule, in five different polar and non-polar solvents to understand the effects of solvents on structure, dynamics and vibrational spectral profiles of amide modes. The solvents considered for the study are water, methanol, chloroform, carbon tetrachloride, and an ionic liquid, 1-butyl-3-methylimidazolium chloride. The structural correlations are studied by calculating RDFs. The dynamic stability and hydrogen bond lifetimes of possible hydrogen-bonded pairs are analyzed by the hydrogen bond population correlation function approach. Weak hydrogen bonding interaction is found between amide and chloroform molecules via the C[dbnd]O group. Most substantial hydrogen bonding interaction is observed between N[sbnd]H of amide and Cl− of the ionic liquid. The calculations of vibrational stretching frequency were performed through wavelet transformation of obtained trajectories to understand the effects of solvents on spectral profiles of amide I and amide II bands. The vibrational stretching frequency distributions of amide I mode exhibit first peak very close to each other in the water, methanol, and ionic liquid. The maximum blue shift is observed in carbon tetrachloride, and the amide II mode also behaves similarly in the solvent. The maximum redshift is noticed in the ionic liquid medium for N[sbnd]H mode due to the strongest hydrogen bond interaction. We analyzed the stretching dynamics of both the modes in terms of their response towards the polarity and hydrogen bonding ability of the surrounding solvents
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