scholarly journals Theoretical Insights into the Electron Capture Behavior of H2SO4···N2O Complex: A DFT and Molecular Dynamics Study

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2349 ◽  
Author(s):  
Wei-Hua Wang ◽  
Wen-Ling Feng ◽  
Wen-Liang Wang ◽  
Ping Li
Keyword(s):  
Molecular Dynamics ◽  
Electron Capture ◽  
Atmospheric Chemistry ◽  
Density Functional ◽  
Molecular Complexes ◽  
Dft Method ◽  
Dynamics Simulation ◽  
Oh Radical ◽  
Before And After ◽  
Reduced Density

Both sulfuric acid (H2SO4) and nitrous oxide (N2O) play a central role in the atmospheric chemistry in regulating the global environment and climate changes. In this study, the interaction behavior between H2SO4 and N2O before and after electron capture has been explored using the density functional theory (DFT) method as well as molecular dynamics simulation. The intermolecular interactions have been characterized by atoms in molecules (AIM), natural bond orbital (NBO), and reduced density gradient (RDG) analyses, respectively. It was found that H2SO4 and N2O can form two transient molecular complexes via intermolecular H-bonds within a certain timescale. However, two molecular complexes can be transformed into OH radical, N2, and HSO4− species upon electron capture, providing an alternative formation source of OH radical in the atmosphere. Expectedly, the present findings not only can provide new insights into the transformation behavior of H2SO4 and N2O, but also can enable us to better understand the potential role of the free electron in driving the proceeding of the relevant reactions in the atmosphere.

scholarly journals Croweacin and Ammi visnaga (L.) Lam Essential Oil derivatives as green corrosion inhibitors for brass in 3% NaCl medium: Quantum Mechanics investigation and Molecular Dynamics Simulation Approaches

2020 ◽  
Vol 10 (4) ◽  
pp. 378 ◽  
Author(s):  
Anas Chraka ◽  
Ihssane Raissouni ◽  
Nordin Ben Seddik ◽  
Said Khayar ◽  
Soukaina El Amrani ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Metal Surface ◽  
Electrostatic Potential ◽  
Active Sites ◽  
Density Functional ◽  
Corrosion Inhibitors ◽  
Dft Method ◽  
Dynamics Simulation ◽  
Ammi Visnaga

<p class="Mabstract"><span lang="EN-US">The computational study was carried out to understand the anti-corrosion properties of Croweacin, a major chemical component of two essential oils of <em>Ammi visnaga</em> (L.) Lam collected from northern Morocco in 2016 (EO16) and 2018 (EO18) against brass corrosion in a 3% NaCl medium. The study, moreover, considers the inhibitory effect of some minor compounds of EO18 such as Eugenol, Trans-Anethole, α-Isophorone, and Thymol. In this context, the quantum mechanics modelling using the density functional theory (DFT) method with B3LYP /6-31G (d, p) were conducted in the aqueous medium by the use of the IEFPCM model and SCRF theory. The DFT method was adopted to identify, analyze and interpret several elements such as the electronic features, the Frontier Molecular Orbitals (FMO) diagram, Molecular Electrostatic Potential (MEP), contours maps of the electrostatic potential (ESP), and the Mulliken population analysis. The DFT demonstrated that the studied compounds are excellent corrosion inhibitors.</span></p><p class="Mabstract"><span lang="EN-US">Furthermore, the Monte Carlo (MC) type simulation of molecular dynamics (MD) was carried out to provide information on the adsorption mechanism of the studied inhibitors through the active sites on the metal surface. This method informed us that the studied inhibitors have high adsorption energy when interacting with the metal surface, especially for Croweacin (-68.63 kcal/mol). The results obtained from DFT and the MC type simulations are in good agreement.</span></p>

Bayesian active learning of interatomic force field for molecular dynamics simulation of Pt/Ag(111)

2021 ◽  
Author(s):  
Kai Xu ◽  
Lei Yan ◽  
Bingran You
Keyword(s):  
Molecular Dynamics ◽  
Active Learning ◽  
Force Field ◽  
Density Functional ◽  
Process Model ◽  
Large Scale ◽  
Computational Cost ◽  
Dynamics Simulation ◽  
Potential Energy Landscape ◽  
Three Body

Force field is a central requirement in molecular dynamics (MD) simulation for accurate description of the potential energy landscape and the time evolution of individual atomic motions. Most energy models are limited by a fundamental tradeoff between accuracy and speed. Although ab initio MD based on density functional theory (DFT) has high accuracy, its high computational cost prevents its use for large-scale and long-timescale simulations. Here, we use Bayesian active learning to construct a Gaussian process model of interatomic forces to describe Pt deposited on Ag(111). An accurate model is obtained within one day of wall time after selecting only 126 atomic environments based on two- and three-body interactions, providing mean absolute errors of 52 and 142 meV/Å for Ag and Pt, respectively. Our work highlights automated and minimalistic training of machine-learning force fields with high fidelity to DFT, which would enable large-scale and long-timescale simulations of alloy surfaces at first-principles accuracy.

In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

2021 ◽  
Vol 24 ◽  
Author(s):  
Ashis Kumar Goswami ◽  
Hemanta Kumar Sharma ◽  
Neelutpal Gogoi ◽  
Ankita Kashyap ◽  
Bhaskar Jyoti Gogoi
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Discovery Studio ◽  
North East ◽  
Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

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