Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell

Biswas, Aritri and Mallik, Bhabani S. (2020) Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell. RSC Advances, 10 (11). pp. 6658-6670. ISSN 2046-2069

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We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine. Structural aspects of the solvation shell are analyzed by calculating radial, spatial, and combined distribution functions. Wavelet analysis of trajectories computes the average vibrational stretch frequency of all the OD modes at ∼2416 cm-1. We observe our calculated average O-D vibrational stretch frequency in aqueous glycine, ∼2416 cm-1 matches with the earlier reported values. Computational tools enable the calculation of frequencies inside the solvation shell as well as the bulk OD modes. In the normalized frequency distribution, the average frequency inside the hydrophilic solvation shell of aminic nitrogen and carboxyl oxygen is found to be 2425 and 2423 cm-1, respectively. Contrary to the frequency range in hydrophilic solvation, the average frequency around hydrophobic methylene is ∼2550 cm-1, and the hydrogen bond and dangling lifetimes are 0.42 and 0.64 ps, respectively. These data confirm the presence of more non-hydrogen bonded (free OD) or "dangling" water molecules in the methylene solvation shell. Our results also show that the carboxylate-water hydrogen bonds are stronger than water molecules interacting with protons of the amine group. Two-dimensional infrared (2D-IR) spectroscopy probes femtosecond dynamics in chemical processes. The 2D-IR peak shapes in the respective ammonium and carboxylate hydrophilic solvation shells are found to be almost similar. However, a closer view reveals a slightly broader component of the diagonal line width for the OD stretch in the carboxylate hydration shell, which exhibits the differences in local environments surrounding the hydrophilic species. Our calculations of the frequency distribution, two-dimensional infrared (2D-IR) spectrum, the decay of frequency fluctuations, the lifetime of hydrogen bonds, and dangling modes unveil the distinct behavior of water molecules in solvation regions.

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IITH Creators:
IITH CreatorsORCiD
Mallik, Bhabani Shankarhttp://orcid.org/0000-0001-9657-1497
Item Type: Article
Uncontrolled Keywords: Femtosecond dynamics; First principles molecular dynamics; Frequency distributions; Frequency fluctuation; Hydrophilic species; Normalized frequencies; Two-dimensional infrared (2D IR); Vibrational dynamics;Amino acids; Calculations; Carboxylation; Dangling bonds; Distribution functions; Hydrophilicity; Molecular dynamics; Molecules; Shells (structures); Solvation
Subjects: Chemistry
Divisions: Department of Chemistry
Depositing User: . LibTrainee 2021
Date Deposited: 06 Jul 2021 06:35
Last Modified: 06 Jul 2021 06:35
URI: http://raiith.iith.ac.in/id/eprint/8130
Publisher URL: http://doi.org/10.1039/c9ra10521b
OA policy: https://v2.sherpa.ac.uk/id/publication/25266
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