Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Abstract

The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ∼1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation-O NMA radial distribution function decreases whereas the Cl − ৄH NMA radial distribution function increases with ion concentration. On the other hand, the cation-O water and Cl − ৄH water radial distribution function shows very negligible change with respect to ion concentration.We have also calculated NMA-water and water-water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O NMA ৄH water is comparatively slower than the H NMA ৄO water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.

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

“…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.…”

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study

“…Now we studied the dynamical properties [ [45] , [46] , [47] ]. We conducted molecular dynamics simulation analysis using the GROMACS software [ 48 ] CHARMM General force field (CGenFF) was used to perform ligand parameterization [ 49 ].…”

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

“…To calculate the hydrogen bond properties and dynamics of NMA-water, water-water and osmolyte-water hydrogen bonds, we use a set of geometric criteria [34][35][36][37][38][39][40][41][42][43][44], where it is assumed that a hydrogen bond between two species exists, if the following distance and angular criteria are satisfied, i.e., R (OX) < R c (OX) , R (OH) < R c (OH) and θ < θ c . In case of NMA-water and water-water hydrogen bond, the distance and angular criteria are taken from previous studies [36,37].…”

“…In case of NMA-water and water-water hydrogen bond, the distance and angular criteria are taken from previous studies [36,37]. For osmolyte (O t )-water (H W ) hydrogen bond, R (OX) and R (OH) denote the oxygen (osmolyte)-oxygen (water) and oxygen (osmolyte)-hydrogen (water) distances and the corresponding quantities with subscript 'c' denote the cut-off values.…”