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.

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.

Assessing the ligand selectivity of sphingosine kinases using molecular dynamics and MM-PBSA binding free energy calculations

2016 ◽  
Vol 12 (4) ◽  
pp. 1174-1182 ◽  
Author(s):  
Liang Fang ◽  
Xiaojian Wang ◽  
Meiyang Xi ◽  
Tianqi Liu ◽  
Dali Yin
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Model Building ◽  
Binding Free Energy ◽  
Homology Model ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Ligand Selectivity ◽  
Sphingosine Kinases ◽  
Binding Free Energy Calculations

Three residues of SK1 were identified important for selective SK1 inhibitory activity via SK2 homology model building, molecular dynamics simulation, and MM-PBSA studies.

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile

scholarly journals Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

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