scholarly journals Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study

2021 ◽  
Vol 11 (14) ◽  
pp. 6291
Author(s):  
Andrea Madabeni ◽  
Pablo Andrei Nogara ◽  
Folorunsho Bright Omage ◽  
João Batista Teixeira Rocha ◽  
Laura Orian
Keyword(s):  
Density Functional ◽  
Rational Drug Design ◽  
Functional Theory ◽  
Main Protease ◽  
Rational Drug ◽  
Mechanistic Investigation ◽  
Pharmacologically Active ◽  
First Time ◽  
Insight Into

The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.

Molecular Modelling of Ground- and Excited-States Vibrations in Organic Conducting Devices: Hexakis(n-hexyloxy)triphenylene (HAT6) as Case Study

2010 ◽  
Vol 63 (3) ◽  
pp. 388 ◽  
Author(s):  
M. Zbiri ◽  
M. R. Johnson ◽  
L. Haverkate ◽  
F. M. Mulder ◽  
G. J. Kearley
Keyword(s):  
Excited State ◽  
Electronic State ◽  
Ground State ◽  
Density Functional ◽  
Excited Electronic State ◽  
Molecular Vibrations ◽  
Functional Theory ◽  
Model Calculations ◽  
Insight Into

In order to gain insight into fundamental aspects of organic photocell materials, we have calculated ground and excited electronic-state structures and molecular vibrations for an isolated HAT6 molecule (hexakis(n-hexyloxy)triphenylene). Excited-state calculations are carried out using time-dependent density functional theory and frequencies are evaluated analytically using coupled perturbed Kohn–Sham equations. These model calculations have been validated against new infrared and ultraviolet data on HAT6 in solution. The main allowed valence excitation, having the largest oscillator strength, is chosen for the structural and vibrational investigations. Comparison with the ground-state vibrational dynamics reveals surprisingly large spectral differences. In addition, the alkoxy tails, which are usually considered to play only a structural role, are clearly involved in the molecular vibrations and the structural distortion of the excited electronic state compared with the ground state. The tails may play a more important role in charge separation, transport and excited-state relaxation than was previously thought. In this case, chemical modification of the tails would allow vibrational and related properties of organic photocell materials to be tailored.

scholarly journals A theoretical study of structure, bonding and property of platinum(II)-8-hydroxyquinolines complexes with carbene and heavier homologues

2020 ◽  
Vol 129 (1B) ◽  
Author(s):  
Huynh Thi Phuong Loan ◽  
Hoang Van Duc ◽  
Nguyen Thi Ai Nhung
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Significant Contribution ◽  
Theoretical Study ◽  
Energy Gap ◽  
Functional Theory ◽  
Dissociation Energies ◽  
First Time ◽  
Equilibrium Geometries ◽  
Insight Into

<p>In this work, a theoretical study for platinum(II)-8-hydroxyquinolines-tetrylene complexes [{PtCl-C<sub>9</sub>H<sub>6</sub>NO}-NHE<sub>Ph</sub>] (<strong>Pt-EPh</strong>)<strong> </strong>are investigated for the first time using density functional theory (DFT). Quantum chemical calculations using DFT and charge methods at the BP86 level with basic sets SVP, TZVPP have been carried out to get insight into the structures and property for <strong>Pt-EPh</strong>. The optimization of equilibrium geometries of the ligands<strong> EPh</strong> in <strong>Pt-EPh</strong> are bonded in distorted end-on way to <strong>Pt</strong> fragment with the bending angle, a, slightly decreases from carbene <strong>Pt-CPh</strong> to germylene <strong>Pt-GePh</strong>. Quantum chemical parameters such as <em>E</em><sub>HOMO</sub>, <em>E</em><sub>LUMO</sub>, the energy gap (<em>E</em><sub>LUMO </sub>– <em>E</em><sub>HOMO</sub>), electronegativity (χ), global hardness (η), and global softness (<em>S</em>) in the neutral molecules have been calculated and discussed. Bond dissociation energies (BDEs), D<sub>e </sub>(kcal.mol<sup>-1</sup>), decrease from the slighter to the heavier homologues. The hybridization of atoms E have large p characters while the hybridization of atom Pt has greater d character which lead to the Pt-E bond possesses not only NHE<sub>Ph</sub>→{ PtCl-C<sub>9</sub>H<sub>6</sub>NO} strong σ-donation but also a significant contribution π-donation NHE<sub>Ph</sub>→{PtCl-C<sub>9</sub>H<sub>6</sub>NO} and a weak π-backdonation metal-ligand NHE<sub>Ph</sub>←{PtCl-C<sub>9</sub>H<sub>6</sub>NO} in complexes <strong>Pt-Eph </strong>was also considered.</p>

scholarly journals A theoretical study of structure, bonding and property of platinum(II)-8-hydroxyquinolines complexes with carbene and heavier homologues

2020 ◽  
Vol 129 (1B) ◽  
pp. 41-48
Author(s):  
Huynh Thi Phuong Loan ◽  
Hoang Van Duc ◽  
Nguyen Thi Ai Nhung
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Theoretical Study ◽  
Energy Gap ◽  
Functional Theory ◽  
Dissociation Energies ◽  
The Density Functional Theory ◽  
First Time ◽  
Equilibrium Geometries ◽  
Insight Into

In this work, a theoretical study for platinum(II)-8-hydroxyquinoline-tetrylene complexes [{PtCl–C9H6NO}–NHEPh] (Pt–EPh) is carried out for the first time by using the density functional theory (DFT). Quantum chemical calculations with DFT and charge methods at the BP86 level with basic sets SVP and TZVPP have been perfomed to get insight into the structures and property of Pt–EPh. The optimization of equilibrium geometries of the ligands EPh in Pt–EPh, bonded in the distorted end-on way to the Pt fragment is studied, in which the bending angle slightly decreases from carbene Pt–CPh to germylene Pt–GePh. Quantum chemical parameters such as EHOMO, ELUMO, the energy gap (ELUMO – EHOMO), electronegativity, global hardness, and global softness in the neutral molecules have been calculated and discussed. Bond dissociation energies decrease from the slighter to the heavier homologues. The hybridization of atoms E has large p characters, while the hybridization of atom Pt has a greater d character. Thus, the Pt–E bond possesses not only NHEPh→{PtCl–C9H6NO} strong -donation but also a significant contribution of π-donation NHEPh→{PtCl–C9H6NO}, and a weak π-backdonation metal-ligand NHEPh←{PtCl-C9H6NO} in complexes Pt-EPh is also considered.

scholarly journals Single-crystalline epitaxial TiO film: A metal and superconductor, similar to Ti metal

2021 ◽  
Vol 7 (2) ◽  
pp. eabd4248
Author(s):  
Fengmiao Li ◽  
Yuting Zou ◽  
Myung-Geun Han ◽  
Kateryna Foyevtsova ◽  
Hyungki Shin ◽  
...  
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Tight Binding ◽  
Crystal Form ◽  
Titanium Monoxide ◽  
Binding Model ◽  
Functional Theory ◽  
Single Crystalline ◽  
First Time ◽  
Lattice Matched

Titanium monoxide (TiO), an important member of the rock salt 3d transition-metal monoxides, has not been studied in the stoichiometric single-crystal form. It has been challenging to prepare stoichiometric TiO due to the highly reactive Ti2+. We adapt a closely lattice-matched MgO(001) substrate and report the successful growth of single-crystalline TiO(001) film using molecular beam epitaxy. This enables a first-time study of stoichiometric TiO thin films, showing that TiO is metal but in proximity to Mott insulating state. We observe a transition to the superconducting phase below 0.5 K close to that of Ti metal. Density functional theory (DFT) and a DFT-based tight-binding model demonstrate the extreme importance of direct Ti–Ti bonding in TiO, suggesting that similar superconductivity exists in TiO and Ti metal. Our work introduces the new concept that TiO behaves more similar to its metal counterpart, distinguishing it from other 3d transition-metal monoxides.

scholarly journals Ab Initio Study of Ferroelectric Critical Size of SnTe Low-Dimensional Nanostructures

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 732 ◽  
Author(s):  
Takahiro Shimada ◽  
Koichiro Minaguro ◽  
Tao Xu ◽  
Jie Wang ◽  
Takayuki Kitamura
Keyword(s):  
Density Functional ◽  
Critical Size ◽  
Density Functional Theory Calculations ◽  
Cell Width ◽  
Functional Theory ◽  
Unit Cells ◽  
Principle Density Functional Theory ◽  
Low Dimensional ◽  
Insight Into ◽  
Ferroelectric Perovskite

Beyond a ferroelectric critical thickness of several nanometers existed in conventional ferroelectric perovskite oxides, ferroelectricity in ultimately thin dimensions was recently discovered in SnTe monolayers. This discovery suggests the possibility that SnTe can sustain ferroelectricity during further low-dimensional miniaturization. Here, we investigate a ferroelectric critical size of low-dimensional SnTe nanostructures such as nanoribbons (1D) and nanoflakes (0D) using first-principle density-functional theory calculations. We demonstrate that the smallest (one-unit-cell width) SnTe nanoribbon can sustain ferroelectricity and there is no ferroelectric critical size in the SnTe nanoribbons. On the other hand, the SnTe nanoflakes form a vortex of polarization and lose their toroidal ferroelectricity below the surface area of 4 × 4 unit cells (about 25 Å on one side). We also reveal the atomic and electronic mechanism of the absence or presence of critical size in SnTe low-dimensional nanostructures. Our result provides an insight into intrinsic ferroelectric critical size for low-dimensional chalcogenide layered materials.

A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine

2016 ◽  
Vol 39 (3-4) ◽  
Author(s):  
Sandeep Pokharia ◽  
Rachana Joshi ◽  
Mamta Pokharia ◽  
Swatantra Kumar Yadav ◽  
Hirdyesh Mishra
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Functional Theory ◽  
Insight Into

AbstractThe quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H

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