scholarly journals Effective Fragment Potential Version 2 - Molecular Dynamics (EFP2-MD) Simulation for Investigating Solution Structures of Ionic Liquids

2016 ◽  
Vol 45 (8) ◽  
pp. 1009-1011 ◽  
Author(s):  
Nahoko Kuroki ◽  
Hirotoshi Mori
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Md Simulation ◽  
Solution Structures ◽  
Effective Fragment Potential

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.

Molecular dynamics simulation of amino acid ionic liquids near a graphene electrode: effects of alkyl side-chain length

2016 ◽  
Vol 18 (48) ◽  
pp. 33053-33067 ◽  
Author(s):  
Behnoosh Sadeghi Moghadam ◽  
Mohammad Razmkhah ◽  
Mohammad Taghi Hamed Mosavian ◽  
Fatemeh Moosavi
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Amino Acid ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Alkyl Side Chain ◽  
Graphene Surface ◽  
Nanoscopic Structure

The nanoscopic structure of amino acid ionic liquids (AAILs) as biodegradable electrolytes near a neutral graphene surface was studied by molecular dynamics (MD) simulation.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

Prediction of Ionic Liquids Properties through Molecular Dynamics Simulations

2014 ◽  
Vol 4 (2) ◽  
pp. 151-172 ◽  
Author(s):  
Marta L.S. Batista ◽  
Joao A.P. Coutinho ◽  
Jose R.B. Gomes
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

Molecular Dynamics Study of the Gold/Ionic Liquids Interface

2015 ◽  
Vol 119 (30) ◽  
pp. 9883-9892 ◽  
Author(s):  
Elisabete S. C. Ferreira ◽  
Carlos M. Pereira ◽  
M. Natália D. S. Cordeiro ◽  
Daniel J. V. A. dos Santos
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids

scholarly journals Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

2021 ◽  
Vol 121 (4) ◽  
pp. 2292-2324
Author(s):  
Jovan Damjanovic ◽  
Jiayuan Miao ◽  
He Huang ◽  
Yu-Shan Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cyclic Peptides ◽  
Solution Structures ◽  
Dynamics Simulations
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