scholarly journals Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area

1995 ◽  
Vol 99 (9) ◽  
pp. 2885-2892 ◽  
Author(s):  
A. Wallqvist ◽  
B. J. Berne
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Surface Area ◽  
Solvation Free Energy

An Insight into Solubility of H2S in Choline Based Ionic Liquids from Molecular Dynamics Simulation

2020 ◽  
Vol 17 (2) ◽  
pp. 1422-1431
Author(s):  
Fitri Norizatie Mohd Salehin ◽  
Khairulazhar Jumbri ◽  
Anita Ramli ◽  
Shaari Daud
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Volume ◽  
Chemical Potential ◽  
Alkyl Chain ◽  
Solvation Free Energy ◽  
Volume Effect ◽  
Dynamics Simulation ◽  
Percentage Error ◽  
Molar Density

Solvation free energy of six choline based ILs were computed under molecular dynamics (MD) simulation using Bennet Acceptance Ratio (BAR) method. H2S removal from the natural gas can be accomplished by absorption process using a solvent. Degree elimination of gases in liquid can be estimated by excess chemical potential (μex), Henry’s law constant (kH), enthalpy (hex), and entropy (sex). The Optimised Potential Liquids Simulation (OPLS) force fields used for ILs were validated against experimental density in order to get valid results of solvation free energy. The percentage error of the predicted density of six choline based ILs were below than 2.0% which is a good agreement with the previous study. The highest value of kH was 109.23 atm gained by choline thiocyanate [Chl][tcy] and the lowest value of kH was 23.25 atm obtained by choline acetate [Chl][act]. There are many features that influence the solubility of H2S for example length of alkyl chain, free volume effect, molar density, type of anions and hydrogen bonding interaction. In order to understand the behaviour of H2S molecules in ILs system, the radial distribution function (RDF) of H2S-ILs and RDF for specific atom were analysed. Basically, the shorter the alkyl chain, increase in molar density of ILs, reduce the free volume thus provide less space for H2S to occupy and decrease insolubility.

Binding Free Energy and the structural changes determination in hGH protein with different concentrations of copper ions (A molecular dynamics simulation study)

2016 ◽  
Vol 15 (05) ◽  
pp. 1650045 ◽  
Author(s):  
Elham Tazikeh-Lemeski
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Surface Area ◽  
Structural Changes ◽  
Copper Ions ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area

In this study, we estimated the optimum concentration of copper ions that are effective in the stability and the structural changes of human growth hormone (hGH) protein in the combination of different concentrations of these ions at the molecular level using molecular dynamics simulation by Gromacs 4.6.5 software. Moreover, to estimate the binding affinity of copper ions to hGH protein, binding free energies is calculated by the molecular mechanics Poisson–Boltzmann Surface Area (MM-PBSA). The analysis of molecular dynamics (MD) trajectories as dictionary of the secondary structure of protein (DSSP), solvent accessible surface area (SASA) and binding free energy calculations show that hGH protein structure is more stabilized by increasing a limited concentration of copper ions. These findings align with our previous experimental studies.

Solvation free energy of solvation of biomass model cellobiose molecule: A molecular dynamics analysis

2017 ◽  
Vol 245 ◽  
pp. 97-102 ◽  
Author(s):  
I. Vyalov ◽  
Y. Vaksler ◽  
V. Koverga ◽  
F.A. Miannay ◽  
M. Kiselev ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Solvation Free Energy ◽  
Dynamics Analysis ◽  
Free Energy Of Solvation

Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mohammad Emamian ◽  
Hedayat Azizpour ◽  
Hojatollah Moradi ◽  
Kamran Keynejad ◽  
Hossein Bahmanyar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Solvation Free Energy ◽  
Summation Method ◽  
Dynamics Simulation ◽  
Experimental Result ◽  
Coefficient Of Determination ◽  
Solvation Model ◽  
The Difference

Abstract In this study, molecular dynamics simulation was applied for calculating solvation free energy of 16 solute molecules in methanol solvent. The thermodynamic integration method was used because it was possible to calculate the difference in free energy in any thermodynamic path. After comparing results for solvation free energy in different force fields, COMPASS force field was selected since it had the lowest error compared to experimental result. Group-based summation method was used to compute electrostatic and van der Waals forces at 298.15 K and 1 atm. The results of solvation free energy were obtained from molecular dynamics simulation and were compared to the results from Solvation Model Density (SMD) and Universal Continuum Solvation Model (denoted as SM8), which were obtained from other research works. Average square-root-error for molecular dynamics simulation, SMD and SM8 models were 0.096091, 0.595798, and 0.70649. Furthermore, the coefficient of determination (R 2) for molecular dynamics simulation was 0.9618, which shows higher accuracy of MD simulation for calculating solvation free energy comparing to two other models.

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