Experimental, quantum chemical calculations, and molecular dynamic simulations insight into the corrosion inhibition properties of 2-(6-methylpyridin-2-yl)oxazolo[5,4-f][1,10]phenanthroline on mild steel

2012 ◽  
Vol 39 (5) ◽  
pp. 1927-1948 ◽  
Author(s):  
I. B. Obot ◽  
N. O. Obi-Egbedi ◽  
E. E. Ebenso ◽  
A. S. Afolabi ◽  
E. E Oguzie
Keyword(s):  
Mild Steel ◽  
Molecular Dynamic ◽  
Quantum Chemical Calculations ◽  
Corrosion Inhibition ◽  
Quantum Chemical ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Insight Into

Molecular dynamic simulations and quantum chemical calculations of adsorption process using amino-functionalized silica

2021 ◽  
Vol 330 ◽  
pp. 115544
Author(s):  
Yan Cao ◽  
Rahime Eshaghi Malekshah ◽  
Zahra Heidari ◽  
Rasool Pelalak ◽  
Azam Marjani ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Adsorption Process ◽  
Molecular Dynamic Simulations ◽  
Functionalized Silica ◽  
Dynamic Simulations

Molecular dynamic simulations of the tubulin–human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol

2013 ◽  
Vol 9 (6) ◽  
pp. 1470 ◽  
Author(s):  
Manivel Panneerselvam ◽  
Kannan Muthu ◽  
Muthukumaran Jayaraman ◽  
Upasana Sridharan ◽  
Pranitha Jenardhanan ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Regulatory Mechanism ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Structural Insight ◽  
Complex Structural ◽  
Insight Into ◽  
Inducing Resistance

scholarly journals The Theoretical Investigations and Molecular Dynamic Stimulation of Isoniazid as a Corrosion Inhibitor

2021 ◽  
pp. 24-31
Author(s):  
O. E. Obolo ◽  
D. T. Oloruntoba ◽  
J. O. Borode
Keyword(s):  
Corrosion Inhibitor ◽  
Molecular Dynamic ◽  
Quantum Chemical ◽  
Inhibition Mechanism ◽  
Molecular Dynamic Simulations ◽  
Chemical Parameters ◽  
Dynamic Simulations ◽  
Quantum Chemical Parameters ◽  
Theoretical Investigations ◽  
Expired Drug

API5L Steel is known as one of the most useful materials on earth which is also subject to corrosion in certain environments. Many methods have been used to minimize its corrosion, but the use of inhibitors is widely accepted. The use of green inhibitors has gained wide usage because of their environmental friendliness. The theoretical investigations of isoniazid as corrosion inhibitor was carried out using Fourier transform infrared spectroscopy (FTIR), whereas theoretically, quantum chemical parameters and molecular dynamic simulations of the inhibitor were studied. The analyses of the experimental results showed that the expired drug (isoniazid) decreased the corrosion rate of API5L steel in a 0.5M H2SO4 medium. The inhibition efficiency decreased with a decrease in inhibitor concentration. FTIR results showed that the inhibition mechanism is physical through the functional groups present in the expired drug. Relying on quantum chemical parameters and molecular dynamic simulations results, the adsorption/binding strength of the concerned inhibitor molecule on API5L steel surface follows a good order. The computed adsorption/binding energy values (Eads) for the various isolated concentrations from the inhibitor indicate the adsorption process to be non-covalent (physiosorption) which is in good agreement with the literature.

scholarly journals Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2

2021 ◽  
pp. 66-67
Author(s):  
P.V. Artyushenko ◽  
◽  
V.A. Mironov ◽  
D.I. Morozov ◽  
I.A. Shchugoreva ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Molecular Dynamic ◽  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Computational Approach ◽  
Receptor Binding Domain ◽  
Dynamic Simulations ◽  
X Ray ◽  
X Ray Scattering

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifi cations in order to increase the binding with the RBD. Th us, a new aptamer Apt25 was designed. Th e procedure of 1) aptamer structure modeling/modifi cation, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed several times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. Th e proposed computational approach to selection and refi nement of aptamers is universal and can be used for wide range of molecular ligands and targets

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