A molecular dynamics simulations study on the behavior of liquid N-methylacetamide in presence of NaCl: Structure, dynamics and H-bond properties

Pattanayak, Subrat Kumar; Chowdhuri, Snehasis

doi:10.1016/j.molliq.2012.05.012

Cited by 27 publications

(11 citation statements)

References 63 publications

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“…In the presence of choline, a layer of water is accumulated around protein surface which leads to slowing down of their rotation, which has been reflected in the higher value of

τ_{2}

(∼25 times higher than

τ_{2}

in bulk water) (Figure a). The slowdown of the orientational correlation of the constituents in a mixture compared to their dynamics in the absence of their partner has been shown previously considering N‐methylacetamide and NaCl mixture in water . The spatial orientation of the three components in the ternary mixture creates a crowded layer around the protein.…”

Section: Resultsmentioning

confidence: 70%

“…The slowdown of the orientational correlation of the constituents in a mixture compared to their dynamics in the absence of their partner has been shown previously considering N-methylacetamide and NaCl mixture in water. [78] The spatial orientation of the three components in the ternary mixture creates a crowded layer around the protein. In that environment, rotational relaxation of water appears to be extremely slow as reflected in the high value of t 2 .…”

Section: Calculation Of Rotational Autocorrelation Functionsmentioning

confidence: 99%

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Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

et al. 2020

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Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all‐atom molecular dynamics simulations on a model protein, HP‐36. Based on our calculation of Kirkwood‐Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto‐correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano‐crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP‐36.

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“…In the presence of choline, a layer of water is accumulated around protein surface which leads to slowing down of their rotation, which has been reflected in the higher value of

τ_{2}

(∼25 times higher than

τ_{2}

Section: Resultsmentioning

confidence: 70%

Section: Calculation Of Rotational Autocorrelation Functionsmentioning

confidence: 99%

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

et al. 2020

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“…56 Therefore, the silver mercaptide aggregates that belong to complexes containing also metal ions interact with water molecules other than those that are in the unbound state, since functional groups coordinated by metal ions do not form hydrogen bonds with water. [57][58][59] We can conclude that the addition of salt leads to the coordination of some functional groups by metal ions on the surface of SM supramonomers. In turn, this process causes solubility depression of the supramonomers since the groups coordinated by metal ions do not form hydrogen bonds with water.…”

Section: Model Of Gelation In Cssmentioning

confidence: 78%

Mechanism of gelation in low-concentration aqueous solutions of silver nitrate with l-cysteine and its derivatives

et al. 2017

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We discuss the results of experimental studies of the processes of gelation in aqueous solutions of silver nitrate with l-cysteine and its derivatives. We focus on understanding what determines if these small molecules will self-assemble in water at their extremely low concentration to form a gel. A mechanism of gel formation in a cysteine-silver solution (CSS) is proposed. The analysis of the results indicates that filamentary aggregates of a gel network are formed via interaction of NH and C(O)O groups that belong to neighboring silver mercaptide (SM) aggregates. In turn, formation of sulphur-silver bonds between silver mercaptide molecules is responsible for self-assembling these molecules into SM aggregates which can be considered as supramonomers. Free polar groups located on the surfaces of the aggregates can form hydrogen bonds with water molecules, which explains the unique ability of CSS hydrogels to trap water at low concentrations of low-molecular-weight hydrogelators.

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“…It is defined as [35][36][37][38][39][40][41][42][43][44][45]52] where the correlation function C HB (t), clearly describes the probability that a hydrogen bond is intact at time t, given it was intact at time zero, independent of possible breaking in the interim time. Thus, the dynamics of C HB (t) describes the structural relaxation of hydrogen bonds, and the associated relaxation times τ R can be interpreted as the time scale of reorganization of NH 4 + -water or water-water hydrogen bonds.…”

Section: Hydrogen Bond Dynamics: Lifetime and Structural Relaxation Timementioning

confidence: 99%

Pressure and temperature dependence on the hydrogen bonding and dynamics of ammonium ion in liquid water: A molecular dynamics simulations study

Pattanayak

Chowdhuri

2013

Journal of Molecular Liquids

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A molecular dynamics simulations study on the behavior of liquid N-methylacetamide in presence of NaCl: Structure, dynamics and H-bond properties

Cited by 27 publications

References 63 publications

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

Mechanism of gelation in low-concentration aqueous solutions of silver nitrate with l-cysteine and its derivatives

Pressure and temperature dependence on the hydrogen bonding and dynamics of ammonium ion in liquid water: A molecular dynamics simulations study

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