Molecular dynamics simulation studies on ethane and acetylene mixture in CuBTC metal organic framework

2014 ◽  
Author(s):  
S. A. Prabhudesai ◽  
V. K. Sharma ◽  
S. Mitra ◽  
R. Mukhopadhyay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Metal Organic ◽  
Organic Framework

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

scholarly journals Metal–Organic Framework (MOF) through the Lens of Molecular Dynamics Simulation: Current Status and Future Perspective

2020 ◽  
Vol 4 (2) ◽  
pp. 75 ◽  
Author(s):  
Amin Hamed Mashhadzadeh ◽  
Ali Taghizadeh ◽  
Mohsen Taghizadeh ◽  
Muhammad Tajammal Munir ◽  
Sajjad Habibzadeh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Metal Organic Framework ◽  
Theoretical Perspective ◽  
Industrial Applications ◽  
Dynamics Simulation ◽  
Current Status ◽  
Future Perspective ◽  
Short Period ◽  
Metal Organic

As hybrid porous structures with outstanding properties, metal–organic frameworks (MOFs) have entered into a large variety of industrial applications in recent years. As a result of their specific structure, that includes metal ions and organic linkers, MOFs have remarkable and tunable properties, such as a high specific surface area, excellent storage capacity, and surface modification possibility, making them appropriate for many industries like sensors, pharmacies, water treatment, energy storage, and ion transportation. Although the volume of experimental research on the properties and performance of MOFs has multiplied over a short period of time, exploring these structures from a theoretical perspective such as via molecular dynamics simulation (MD) requires a more in-depth focus. The ability to identify and demonstrate molecular interactions between MOFs and host materials in which they are incorporates is of prime importance in developing next generations of these hybrid structures. Therefore, in the present article, we have presented a brief overview of the different MOFs’ properties and applications from the most recent MD-based studies and have provided a perspective on the future developments of MOFs from the MD viewpoint.

scholarly journals Thermal and Guest-Assisted Structural Transition in the NH2-MIL-53(Al) Metal Organic Framework: A Molecular Dynamics Simulation Investigation

Nanomaterials ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 531 ◽  
Author(s):  
Roald Boulé ◽  
Claire Roland ◽  
Laurent Le Pollés ◽  
Nathalie Audebrand ◽  
Aziz Ghoufi
Keyword(s):  
Molecular Dynamics ◽  
Structural Transition ◽  
Physical Mechanism ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Reversible Transition ◽  
Metal Organic ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen ◽  
Organic Framework

Reversible structural transition between the Large (LP) and Narrow Pore (NP) forms (breathing phenomena) of the MIL-53(X, X = Al, Cr, Fe, Ga) Metal Organic Framework (MOF) is probably one of the most amazing physical properties of this class of soft-porous materials. Whereas great attention has been paid to the elucidation of the physical mechanism ruling this reversible transition, the effect of the functionalization on the flexibility has been less explored. Among functionalized MIL-53(Al) materials, the case of NH2-MIL-53(Al) is undoubtedly a very intriguing structural transition rarely observed, and the steadier phase corresponds to the narrow pore form. In this work, the flexibility of the NH2-MIL-53(Al) metal organic framework was investigated by means of molecular dynamics simulations. Guest (methanol) and thermal breathing of the NH2-MIL-53(Al) was thus explored. We show that it is possible to trigger a reversible transition between NP and LP forms upon adsorption, and we highlight the existence of stable intermediate forms and a very large pore phase. Furthermore, the NP form is found thermodynamically stable from 240 to 400 K, which is the result of strong intramolecular hydrogen bonds.

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

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