Au–Fe nanoparticles visited by MD simulation: structural and thermodynamic properties affected by chemical composition

2018 ◽  
Vol 42 (12) ◽  
pp. 9666-9675 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Esmat Mehrjouei ◽  
Amir Nasser Shamkhali ◽  
Mohsen Abbaspour ◽  
Sirous Salemi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Chemical Composition ◽  
Molecular Dynamics Simulation ◽  
Thermodynamic Properties ◽  
Thermodynamic Stability ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Core Shell ◽  
Fe Nanoparticles ◽  
Melting Mechanism

In this work, Fe–Au nanoalloys and Fe@Au core–shell nanoclusters are investigated via classical molecular dynamics simulation to determine the effect of their composition on their thermodynamic stability and melting mechanism.

Molecular Dynamics Simulation of Thermodynamic Properties for CO2/Ionic Liquid Systems

2009 ◽  
Vol 25 (11) ◽  
pp. 2291-2295
Author(s):  
WANG Wei-Bin ◽  
◽  
◽  
YIN Jian-Zhong ◽  
SUN Li-Hua ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulation ◽  
Thermodynamic Properties ◽  
Dynamics Simulation ◽  
Liquid Systems

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

scholarly journals High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1

2019 ◽  
Vol 20 (4) ◽  
pp. 819 ◽  
Author(s):  
Md Rehman ◽  
Mohamed AlAjmi ◽  
Afzal Hussain ◽  
Gulam Rather ◽  
Meraj Khan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Virtual Screening ◽  
Enzyme Kinetics ◽  
High Throughput ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Multi Drug Resistance ◽  
Stable Complex ◽  
High Throughput Virtual Screening

The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates.

Molecular dynamics simulation of the local concentration and structure in multicomponent aerosol nanoparticles under atmospheric conditions

2017 ◽  
Vol 19 (25) ◽  
pp. 16681-16692 ◽  
Author(s):  
Katerina S. Karadima ◽  
Vlasis G. Mavrantzas ◽  
Spyros N. Pandis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Organic Compound ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Core Shell ◽  
Local Concentration ◽  
Atmospheric Conditions ◽  
Aerosol Nanoparticles

MD simulations predicted core–shell or partially engulfed morphologies (depending on the type of the organic compound present) in multicomponent aerosol nanoparticles.

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