Differing preferential ion binding to the peptide bond in ionic environment from classical and first principles molecular dynamics simulations

Biswas, Sohag and Mallik, Bhabani S. (2020) Differing preferential ion binding to the peptide bond in ionic environment from classical and first principles molecular dynamics simulations. Journal of Molecular Liquids, 318. p. 114257. ISSN 01677322

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Abstract

The interactions of ions with N-methylacetamide (NMA) in hydrated ionic liquid (IL), methylammonium formate (MAF), with varying concentrations were studied by molecular dynamics simulations. As the interactions depend on the choice of potential, the current study aims to compare the preferential binding of cation and anion of MAF to peptide bond of NMA utilizing force field-based classical molecular dynamics (CMD) and first principles molecular dynamics (FPMD) simulations. NMA forms a stable hydrogen bonding network with anion. First principles molecular dynamics simulations predict hydrogen bonding interaction with both anion and cation in pure IL. In contrast, the classical molecular dynamics simulations provide evidence of the strong interaction of NMA with anion only. However, NMA interacts with cation in the presence of water as a co-solvent. Water molecules facilitate the more significant cation-anion distance, which decreases the electrostatic interaction between ions. In aqueous solutions, the self-diffusivity of the entities increases as compared to pure IL. The value of residence time rises with an increase in the concentration of IL. The analysis of hydrogen bond auto-correlation function reveals that with increasing IL concentration, the short-range force increases, and simultaneously, the lifetime of intermolecular hydrogen bonds increases. Between NMA-cation and NMA-anion, the strength of the NMA-anion hydrogen bond is stronger than the former. The preferential solvation is due to nature of predefined classical potential as compared to FPMD simulations.

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IITH Creators:
IITH CreatorsORCiD
Biswas, SohagUNSPECIFIED
Mallik, Bhabani Shankarhttp://orcid.org/0000-0001-9657-1497
Item Type: Article
Uncontrolled Keywords: Autocorrelation functions; Classical molecular dynamics; First principles molecular dynamics; Hydrogen bonding interactions; Hydrogen bonding network; Intermolecular hydrogen bonds; Molecular dynamics simulations; Preferential solvation
Subjects: Chemistry
Chemistry > Inorganic chemistry
Divisions: Department of Chemistry
Depositing User: . LibTrainee 2021
Date Deposited: 30 Jun 2021 09:35
Last Modified: 30 Jun 2021 09:35
URI: http://raiith.iith.ac.in/id/eprint/8066
Publisher URL: http://doi.org/10.1016/j.molliq.2020.114257
OA policy: https://v2.sherpa.ac.uk/id/publication/14013
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