scholarly journals Choline-Based Ionic Liquids-Incorporated IRMOF-1 for H2S/CH4 Capture: Insight from Molecular Dynamics Simulation

Processes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 412
Author(s):  
Mohamad Adil Iman Ishak ◽  
Mohd Faisal Taha ◽  
Mohd Dzul Hakim Wirzal ◽  
Muhammad Najib Nordin ◽  
Muslim Abdurrahman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Md Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Crowding Effect ◽  
Metal Organic ◽  
The Stability ◽  
Stable Incorporation

The removal of H2S and CH4 from natural gas is crucial as H2S causes environmental contamination, corrodes the gas stream pipelines, and decreases the feedstock for industrial productions. Many scientific researches have shown that the metal-organic framework (MOF)/ionic liquids (ILs) have great potential as alternative adsorbents to capture H2S. In this work, molecular dynamics (MD) simulation was carried out to determine the stability of ILs/IRMOF-1 as well as to study the solubility of H2S and CH4 gases in this ILs/IRMOF-1 hybrid material. Three choline-based ILs were incorporated into IRMOF-1 with different ratios of 0.4, 0.8, and 1.2% w/w, respectively, in which the most stable choline-based ILs/IRMOF-1 composite was analysed for H2S/CH4 solubility selectivity. Among the three choline-based ILs/IRMOF-1, [Chl] [SCN]/IRMOF-1 shows the most stable incorporation. However, the increment of ILs loaded in the IRMOF-1 significantly reduced the stability of the hybrid due to the crowding effect. Solvation free energy was then computed to determine the solubility of H2S and CH4 in the [Chl] [SCN]/IRMOF-1. H2S showed higher solubility compared to CH4, where its solubility declined with the increase of choline-based IL loading.

scholarly journals Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach

2021 ◽  
Vol 11 ◽  
Author(s):  
Prem Prakash Kushwaha ◽  
Atul Kumar Singh ◽  
Tanya Bansal ◽  
Akansha Yadav ◽  
Kumari Sunita Prajapati ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Docking ◽  
Active Site ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Kcal Mole ◽  
Hydrogen Bond Formation ◽  
Docking Score

The present study explores the SARS-CoV-2 drugable target inhibition efficacy of phytochemicals from Indian medicinal plants using molecular docking, molecular dynamics (MD) simulation, and MM-PBSA analysis. A total of 130 phytochemicals were screened against SARS-CoV-2 Spike (S)-protein, RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro). Result of molecular docking showed that Isoquercetin potentially binds with the active site/protein binding site of the Spike, RdRP, and Mpro targets with a docking score of -8.22, -6.86, and -9.73 kcal/mole, respectively. Further, MS 3, 7-Hydroxyaloin B, 10-Hydroxyaloin A, showed -9.57, -7.07, -8.57 kcal/mole docking score against Spike, RdRP, and Mpro targets respectively. The MD simulation was performed to study the favorable confirmation and energetically stable complex formation ability of Isoquercetin and 10-Hydroxyaloin A phytochemicals in Mpro-unbound/ligand bound/standard inhibitor bound system. The parameters such as RMSD, RMSF, Rg, SASA, Hydrogen-bond formation, energy landscape, principal component analysis showed that the lead phytochemicals form stable and energetically stabilized complex with the target protein. Further, MM-PBSA analysis was performed to compare the Gibbs free energy of the Mpro-ligand bound and standard inhibitor bound complexes. The analysis revealed that the His-41, Cys145, Met49, and Leu27 amino acid residues were majorly responsible for the lower free energy of the complex. Drug likeness and physiochemical properties of the test compounds showed satisfactory results. Taken together, the study concludes that that the Isoquercetin and 10-Hydroxyaloin A phytochemical possess significant efficacy to bind SARS-Cov-2 Mpro active site. The study necessitates further in vitro and in vivo experimental validation of these lead phytochemicals to assess their anti-SARS-CoV-2 potential.

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

scholarly journals Interaction of Coumarin Phytoestrogens with ERα and ERβ: A Molecular Dynamics Simulation Study

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1165 ◽  
Author(s):  
Ting Wang ◽  
Yunfei Wang ◽  
Xuming Zhuang ◽  
Feng Luan ◽  
Chunyan Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Human Life ◽  
Simulation Method ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Molecular Dynamics Methods ◽  
17Β Estradiol ◽  
The Stability

Coumarin phytoestrogens, as one of the important classes of phytoestrogens, have been proved to play an important role in various fields of human life. In this study, molecular simulation method including molecular docking and molecular dynamics methods were performed to explore the various effects between four classical coumarin phytoestrogens (coumestrol, 4-methoxycoumestrol, psoralen and isopsoralen), and estrogen receptors (ERα, ERβ), respectively. The calculated results not only proved that the four coumarin phytoestrogens have weaker affinity than 17β-estradiol to both ERα, and ERβ, but also pointed out that the selective affinity for ERβ is greater than ERα. In addition, the binding mode indicated that the formation of hydrogen bond and hydrophobic interaction have an important effect on the stability of the complexes. Further, the calculation and decomposition of binding free energy explored the main contribution interactions to the total free energy.

ReaxFF molecular dynamics simulation of thermal stability of a Cu3(BTC)2 metal–organic framework

2012 ◽  
Vol 14 (32) ◽  
pp. 11327 ◽  
Author(s):  
Liangliang Huang ◽  
Kaushik L. Joshi ◽  
Adri C. T. van Duin ◽  
Teresa J. Bandosz ◽  
Keith E. Gubbins
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Metal Organic ◽  
Thermal Stability Of ◽  
Organic Framework

Molecular dynamics simulation of the structure and interfacial free energy barriers of mixtures of ionic liquids and divalent salts near a graphene wall

2017 ◽  
Vol 19 (1) ◽  
pp. 846-853 ◽  
Author(s):  
Víctor Gómez-González ◽  
Borja Docampo-Álvarez ◽  
Trinidad Méndez-Morales ◽  
Oscar Cabeza ◽  
Vladislav B. Ivaništšev ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Interfacial Free Energy ◽  
Dynamics Simulation ◽  
Energy Barriers ◽  
Divalent Salts

A molecular dynamics study of graphene-confined mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]) with Mg[BF4]2 is reported.

Molecular Dynamic Simulation on the Stability of Corporated Metal Organic Framework and Choline Based Ionic Liquids

2020 ◽  
Vol 17 (2) ◽  
pp. 1547-1556
Author(s):  
Mohamad Adil Iman Ishak ◽  
Khairulazhar Jumbri ◽  
Mohamad Azmi Bustam@Khalil ◽  
Shaari Daud
Keyword(s):  
Ionic Liquids ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Metal Organic Framework ◽  
Radius Of Gyration ◽  
Stable Conformation ◽  
Metal Organic ◽  
The Stability ◽  
Organic Framework

A compatibility and stability of Isoreticular Metal Organic Framework (IRMOF-1) impregnated with choline based ionic liquids (ILs) are studied by molecular dynamic simulation. Among three proposed IL/IRMOF-1 hybrid composites, cholinium formate, ([Chl][Fm]) is nominated as the best IL to be incorporated with IRMOF-1 since it shows the lowest RMSD value (0.502 nm, 0.637 nm, 0.923 nm) at three IL/IRMOF-1 w/w ratio (0.4%, 0.8% and 1.2%) respectively and become representative to all three ILs. Oxygen atom in the bridging carboxyl group shows the most flexible atom through RMSF analysis since it shows the highest fluctuation (1.001 nm) at WIL/IRMOF-1 = 0.4%. The RDF shows that the interaction between [Chl]+ and [Fm]− is higher in composite phase compare to bulky phase due to confinement effect of IRMOF-1. Both [Chl]+ and [Fm]− seem to be preferred to locate around carboxylate group inside the IRMOF-1 whereby [Fm]− shows the dominant interaction and strongly interacts with IRMOF-1 compared to [Chl]+. In terms of mobility, the cation shows high mobility with SDF value of 0.0419 nm2 in which mobility is expected to be increased with increasing of ILs ratio (0.4%, 0.8% and 1.2%) respectively. Intensity of the ions population around IRMOF-1 is interpreted by density map which is in agreement with the RDF analysis. Finally, the stability of the IRMOF-1 is confirmed by the radius of gyration (Rg) analysis in which 0.4% ILs shows the most stable conformation with the lowest Rg value = 1.667 nm that is in consistent with the RMSD analysis. Overall, the structural stability of IRMOF-1 is well interpreted and impregnation of ILs literally increase the stability of framework at lower IL/IRMOF-1 w/w ratio.

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