scholarly journals Ascorbic Acid as an Inhibitor for SARS-CoV-2 Virus Reproduction: A Theoretical Approach

2021 ◽  
Vol 53 (03) ◽  
pp. 181-185
Author(s):  
Mohammed Abed Jawad ◽  
Keyword(s):  
Ascorbic Acid ◽  
Active Sites ◽  
Docking Study ◽  
Basis Set ◽  
Sufficient Time ◽  
Ligand Efficiency ◽  
Total Electron Density ◽  
Total Electron ◽  
Virus Reproduction

In the present study, ascorbic acid’s or Vitamin C’s influence (VC) in inhibition of SARS-CoV-2 virus reproduction was investigated. Gaussian 09 with a basis set of 6-311G (d, p), MGL tools, DSV, and LigPlus software were used. According to the Total Electron Density (TED) and Millikan charges, the active sites for adsorption were determined. Further, the docking study had clearly revealed the role of VC in inhibition of the virus reproduction in accordance with binding energy (Eb) and ligand efficiency (LE). The vitamin’s interaction with the virus’s spikes may limit its replication or provide the immune system sufficient time to recognize the infection, which enhances the possibility of producing appropriate antibodies.

On the role of lysine in the active site Ser-X-X-Lys region of penicillin-recognizing enzymes

2010 ◽  
Vol 88 (1) ◽  
pp. 1-4
Author(s):  
Saul Wolfe ◽  
Kiyull Yang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Penicillin G ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
One Step ◽  
Optimized Geometries

Using Autodock, docking of penicillin G to the crystal structures of penicillin-recognizing enzymes leads to an alignment in the active site Ser-X-X-Lys region consisting of the serine hydroxyl group, the terminal amino group of lysine, a second hydroxyl group, and the N–C=O of the β-lactam. This alignment is consistent with the notion that acylation of the serine hydroxyl group proceeds by a one-step cooperative mechanism in which C–O bond formation and proton transfer to the β-lactam nitrogen take place through a heteroatom bridge. For the cooperative ring opening of penam by two molecules of methanol and one molecule of methylamine or one molecule of water, density functional theory with the B3LYP DFT gradient-corrected functional and the 6–31G(d) basis set reproduces the alignment seen in the docked structures. Methylamine lowers the barrier calculated at MP2/6–31G(d) from the DFT-optimized geometries by 3 kcal/mol; water increases the barrier by 4 kcal/mol. The function of the conserved lysine in the active sites of penicillin-recognizing enzymes is therefore to catalyze the formation of an acyl enzyme by a cooperative mechanism.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

2014 ◽  
Vol 70 (3) ◽  
pp. 568-579 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Direct Methods ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Total Electron Density ◽  
Total Electron

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

scholarly journals Optimized Atomic Partial Charges and Radii Defined by Radical Voronoi Tessellation of Bulk Phase Simulations

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1875
Author(s):  
Martin Brehm ◽  
Martin Thomas
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Voronoi Tessellation ◽  
Software Tool ◽  
Bulk Phase ◽  
Basis Set ◽  
Total Electron Density ◽  
Total Electron ◽  
Partial Charges ◽  
Atomic Radii

We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Voronoi integration. The approach is particularly well suited for the calculation of partial charges in periodic bulk phase systems. We apply the method to five exemplary liquid phase simulations and show how the optimized charges can help to understand the interactions in the systems. Well-known effects such as reduced ion charges below unity in ionic liquid systems are correctly predicted without any tuning, empiricism, or rescaling. We show that the basis set dependence of our method is very small. Only the total electron density is evaluated, and thus, the approach can be combined with any electronic structure method that provides volumetric total electron densities—it is not limited to Hartree–Fock or density functional theory (DFT). We have implemented the method into our open-source software tool TRAVIS.

scholarly journals Estimation of the Efficiency of Corrosion Inhibition by Zn-Dithiocarbamate Complexes: a Theoretical Study

2021 ◽  
pp. 3323-3335
Author(s):  
Mustafa M. Kadhim ◽  
Layla A. Al. Juber ◽  
Ahmed S. M. Al-Janabi
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Room Temperature ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Total Electron Density ◽  
Functional Theory ◽  
Total Electron ◽  
Homo Lumo

    Seven Zn-dithiocarbamate complexes were suggested as corrosion inhibitors. Density functional theory (DFT) was used to predict the ability of inhibition. Room temperature conditions were applied to suggest the optimization of complexes, physical properties, and corrosion parameters. In addition, the HOMO, LUMO, dipole moment, energy gap, and other parameters were used to compare the inhibitors efficiency. Gaussian 09 software with LanL2DZ basis set was used. Total electron density (TED) and electrostatic surface potential (ESP) were utilized to show the sites of adsorption according to electron density.

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