scholarly journals Hydrophobicity of small alkane molecules (propane dimer) in solvents: a classical molecular dynamics study

BIBECHANA ◽  
2020 ◽  
Vol 17 ◽  
pp. 1-12
Author(s):  
Bikash Panthi ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Histogram Analysis ◽  
Analysis Method ◽  
Classical Molecular Dynamics ◽  
Solvent Environment ◽  
Weighted Histogram ◽  
Weighted Histogram Analysis

Molecular Dynamics (MD) simulations of propane dimer in different solvents (water, acetonitrile and methanol) were performed by using CHARMM platform for modeling the solute and solvents. A series of Umbrella sampling MD simulations were carried out in each solvent separately and potential of mean force (PMFs) were calculated by using Weighted Histogram Analysis Method. Results show that two minima (contact minima and solvent separated minima) characterize the PMF of propane dimer in all three solvent environments. The contact minima are deeper and less sensitive to solvent environment for its position. However, significant effect in the position of second minima, solvent separated minima, was observed. Our study reveals that the interaction between propane dimer is softer in methanol and acetonitrile than in water. BIBECHANA 17 (2020) 1-12  

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

1992 ◽  
Vol 13 (8) ◽  
pp. 1011-1021 ◽  
Author(s):  
Shankar Kumar ◽  
John M. Rosenberg ◽  
Djamal Bouzida ◽  
Robert H. Swendsen ◽  
Peter A. Kollman
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Histogram Analysis ◽  
Analysis Method ◽  
Energy Calculations ◽  
Weighted Histogram ◽  
Weighted Histogram Analysis

Hydrophobicity of an isobutane dimer in water, methanol and acetonitrile as solvents — A classical molecular dynamics study

2019 ◽  
Vol 33 (32) ◽  
pp. 1950391
Author(s):  
Sailesh Bataju ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Center Of Mass ◽  
Sampling Technique ◽  
Md Simulations ◽  
Solvation Shell ◽  
Umbrella Sampling ◽  
Water Model ◽  
Solvent Environment ◽  
Potential Of Mean Forces

The potential of mean forces (PMFs) has been determined for an isobutane dimer in various solvent environments such as water, methanol and acetonitrile at a temperature of 298 K and pressure of 1 bar using GROMACS software. All the molecular dynamics (MD) simulations are carried out using a TIP3P water model under a CHARMM36 forcefield. Following Umbrella Sampling technique, PMFs are calculated and analyzed using Weighted Histogram Analysis Method (WHAM) and coordination number of first solvation shell is extracted for all solvents using radial distribution function. The shape of PMFs contains contact minima, solvent-separated minima and desolvation maxima. The values of contact minima are not affected much by solvent environment and found to be at 0.5377, 0.5480 and 0.5495 nm for water, methanol and acetonitrile respectively. The corresponding energy depths are found −0.9134, −0.7080 and −0.5295 kcalmol[Formula: see text]. The variation observed at solvent-separated minima is noticeable and found at 0.9012, 0.9721 and 0.9151 nm for water, methanol and acetonitrile, respectively. The coordination number of the first solvation shell by taking an isobutane molecule as a reference from their center of mass is found to be 28.1, 16.9 and 14.8 for water, methanol and acetonitrile, respectively. There is a soft hydrophobic interaction between isobutane dimer and solvents like methanol and acetonitrile relative to water, might be due to the presence of competitive methyl group of methanol and acetonitrile in the solvent medium.

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