Advances in Density-functional-based Modeling Techniques - Recent Extensions of the Car-Parrinello Approach

The Binding mechanism of Ivermectin and levosalbutamol with spike protein of SARS-CoV-2

10.21203/rs.3.rs-160254/v1 ◽

2021 ◽

Author(s):

Joyanta Kumar Saha ◽

Md. Jahir Raihan

Keyword(s):

Density Functional ◽

Binding Energies ◽

Spike Protein ◽

Binding Mechanism ◽

Functional Theory ◽

Modeling Techniques ◽

Charge Analysis ◽

The Stability ◽

Approved Drugs ◽

Fda Approved Drugs

Abstract In this study, we have investigated the binding mechanism of two FDA approved drugs (ivermectin and levosalbutamol) with the spike protein of SARs-CoV-2 using three different computational modeling techniques. Molecular docking results predict that ivermectin shows a large binding affinity for spike protein (-9.0 kcal/mol) compared to levosalbutamol (-4.1 kcal/mol). Ivermectin binds with GLN492, GLN493, GLY496 and TRY505 residues in the spike protein through hydrogen bonds and levosalbutamol binds with TYR453 and TYR505 residues. Using density functional theory (DFT) studies, we have calculated the binding energies between ivermectin and levosalbutamol with residues in spike protein which favor their binding are − 17.8 kcal/mol and − 20.08 kcal/mol, respectively. The natural bond orbital (NBO) charge analysis has been performed to estimate the amount of charge transfer that occurred by two drugs during interaction with residues. Molecular dynamics (MD) study confirms the stability of spike protein bound with ivermectin through RMSD and RMSF analyses. Three different computer modeling techniques reveal that ivermectin is more stable than levosalbutamol in the active site of spike protein where hACE2 binds. Therefore, ivermectin can be a suitable inhibitor for SARS-CoV-2 to enter into the human cell through hACE2.

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Case Study in a Conceptual DFT Investigation of New Corrosion Inhibitor

Letters in Applied NanoBioScience ◽

10.33263/lianbs114.40074015 ◽

2021 ◽

Vol 11 (4) ◽

pp. 4007-4015

Keyword(s):

Molecular Orbital ◽

Density Functional ◽

Basis Set ◽

Functional Theory ◽

Dft Modeling ◽

Highest Occupied Molecular Orbital ◽

The Density Functional Theory ◽

Modeling Techniques ◽

Lowest Unoccupied Molecular Orbital

Inhibition efficiency of thiosemicarbazide derivative, namely 4-ethyl-1-(4-oxo-4-phenylbutanoyl)thiosemicarbazide (EOPT) on corrosion of mild steel, was investigated utilizing the density functional theory (DFT) modeling techniques in the aqueous phase. Chemical parameters at the quantum level, such as energies of highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), dipole moment (µ), absolute electronegativity (χ), global hardness (η), softness (σ), and the fraction of electrons transferred (∆N) have been determined at the B3LYP level of theory with 6-31G (d, p) basis set.

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Doping effects on the geometric and electronic structure of tin clusters

Physical Chemistry Chemical Physics ◽

10.1039/c9cp05124d ◽

2019 ◽

Vol 21 (44) ◽

pp. 24478-24488 ◽

Cited By ~ 1

Author(s):

Martin Gleditzsch ◽

Marc Jäger ◽

Lukáš F. Pašteka ◽

Armin Shayeghi ◽

Rolf Schäfer

Keyword(s):

Density Functional Theory ◽

Electronic Structure ◽

Density Functional ◽

Beam Deflection ◽

Functional Theory ◽

Doping Effects ◽

Depth Analysis ◽

Trajectory Simulations

In depth analysis of doping effects on the geometric and electronic structure of tin clusters via electric beam deflection, numerical trajectory simulations and density functional theory.

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