A Molecular Dynamics and Computational Study of Ligand Docking and Electron Transfer in Ferritins

2012 ◽  
Vol 116 (31) ◽  
pp. 9287-9302 ◽  
Author(s):  
Vijaya Subramanian ◽  
Deborah G. Evans
Keyword(s):  
Molecular Dynamics ◽  
Electron Transfer ◽  
Computational Study ◽  
Ligand Docking

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Liquid dibromomethane under pressure: a computational study

2021 ◽  
Vol 23 (4) ◽  
pp. 2964-2971
Author(s):  
Bernadeta Jasiok ◽  
Mirosław Chorążewski ◽  
Eugene B. Postnikov ◽  
Claude Millot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Computational Study ◽  
Thermal Expansivity ◽  
Dynamics Simulations ◽  
Isobaric Thermal Expansivity

Thermophysical properties of liquid dibromomethane are investigated by molecular dynamics simulations between 268 and 328 K at pressures up to 3000 bar. Notably, the isotherms of the isobaric thermal expansivity cross around 800 bar.

scholarly journals Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 709
Author(s):  
Dakshinamurthy Sivakumar ◽  
Sathish-Kumar Mudedla ◽  
Seonghun Jang ◽  
Hyunjun Kim ◽  
Hyunjin Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Erectile Dysfunction ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Cardiovascular Diseases ◽  
Neurodegenerative Disorders ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Interaction Patterns

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were generated by molecular docking followed by molecular dynamics simulation for 100 ns in triplicate for each system to understand the interactions’ stability. The results were carefully analyzed, focusing on the ligands’ non-bonded interactions with PDE9 in different metal systems.

Computational Study for Molecular Properties of Some of the Isolated Chemicals from Leaves Extract of Guiera Senegalensis as Aluminium Corrosion Inhibitor

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
A. M. Ayuba ◽  
◽  
M. Abubakar ◽  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Energy Gap ◽  
Computational Study ◽  
Physical Adsorption ◽  
Chemical Constituents ◽  
Molecular Size ◽  
Structural Features ◽  
Inhibitor Molecule ◽  
Fukui Indices

The present work describes the computational methods for the corrosion inhibition of aluminium using three selected chemical constituents (5-methyldihydroflavasperone, 5-methylflavasperone and methoxylated naphthyl butanone) reportedly obtained from the leaves extract of Guirea senegalensis. Quantum chemical calculations including EHOMO, ELUMO, energy gap (ΔE), electronegativity (χ), global hardness (η) and fraction of electrons transfer from the inhibitor molecule to the aluminium surface (ΔN) were calculated. The local reactive sites through Fukui indices which explain the effect of structural features of these components in relation to electrophilic and nucleophilic point of attack were evaluated. The similarities in quantum chemical parameters for the compounds obtained revealed that the adsorption strengths of the molecules will be mostly determined by molecular size rather than electronic structure parameters. Fukui indices showed that the point of interaction of inhibitor molecule with the Al(l10) surface were through aromatic carbon atom rich in pi-electrons and oxygen atom of the alkanone functional group in the inhibitor molecules. Molecular dynamics simulations describing the adsorption behavior of the inhibitor molecule on Al(110) surface through Forcite quench molecular dynamics were carried out. The compounds were found to all obey the mechanism of physical adsorption because of their relatively low adsorption energies.

The Computational Study of Microchannel Thickness Effects on H2O/CuO Nanofluid Flow with Molecular Dynamics Simulations

2021 ◽  
pp. 118240
Author(s):  
Yanpeng Shang ◽  
Reza Balali Dehkordi ◽  
Supat Chupradit ◽  
Davood Toghraie ◽  
Andrei Sevbitov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Study ◽  
Nanofluid Flow ◽  
Dynamics Simulations

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis

2009 ◽  
Vol 14 (2) ◽  
pp. 257-276 ◽  
Author(s):  
Serdar Durdagi ◽  
Manthos G. Papadopoulos ◽  
Panagiotis G. Zoumpoulakis ◽  
Catherine Koukoulitsa ◽  
Thomas Mavromoustakos
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Homology Modeling ◽  
Cannabinoid Receptors ◽  
De Novo ◽  
Computational Study ◽  
Dynamics Analysis ◽  
De Novo Drug Design
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