scholarly journals Interrelated Mechanism by Which the Methide Quinone Celastrol, Obtained from the Roots of Tripterygium wilfordii, Inhibits Main Protease 3CLpro of COVID-19 and Acts as Superoxide Radical Scavenger

2020 ◽  
Vol 21 (23) ◽  
pp. 9266
Author(s):  
Francesco Caruso ◽  
Manrose Singh ◽  
Stuart Belli ◽  
Molly Berinato ◽  
Miriam Rossi
Keyword(s):  
Density Functional ◽  
Superoxide Radical ◽  
Covalent Bond ◽  
Radical Scavenger ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
Functional Theory ◽  
Redox Biology ◽  
Proton Transfers ◽  
Main Protease

We describe the potential anti coronavirus disease 2019 (COVID-19) action of the methide quinone inhibitor, celastrol. The related methide quinone dexamethasone is, so far, among COVID-19 medications perhaps the most effective drug for patients with severe symptoms. We observe a parallel redox biology behavior between the antioxidant action of celastrol when scavenging the superoxide radical, and the adduct formation of celastrol with the main COVID-19 protease. The related molecular mechanism is envisioned using molecular mechanics and dynamics calculations. It proposes a covalent bond between the S(Cys145) amino acid thiolate and the celastrol A ring, assisted by proton transfers by His164 and His41 amino acids, and a π interaction from Met49 to the celastrol B ring. Specifically, celastrol possesses two moieties that are able to independently scavenge the superoxide radical: the carboxylic framework located at ring E, and the methide-quinone ring A. The latter captures the superoxide electron, releasing molecular oxygen, and is the feature of interest that correlates with the mechanism of COVID-19 inhibition. This unusual scavenging of the superoxide radical is described using density functional theory (DFT) methods, and is supported experimentally by cyclic voltammetry and X-ray diffraction.

scholarly journals 2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

2015 ◽  
Vol 11 ◽  
pp. 2179-2188 ◽  
Author(s):  
Yury A Sayapin ◽  
Inna O Tupaeva ◽  
Alexandra A Kolodina ◽  
Eugeny A Gusakov ◽  
Vitaly N Komissarov ◽  
...  
Keyword(s):  
Density Functional ◽  
Acetic Acid Solution ◽  
Intramolecular Proton Transfer ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
Derivatives Of

A series of derivatives of 2-hetaryl-1,3-tropolone (β-tropolone) was prepared by the acid-catalyzed reaction of 2-methylbenzoxazoles, 2-methylbenzothiazoles and 2,3,3-trimethylindoline with 3,4,5,6-tetrachloro-1,2-benzoquinone. The molecular structures of the three representative compounds were determined by X-ray crystallography. In crystal and (as shown by the DFT PBE0/6-311+G** calculations) in solution, 2-hetaryl-4,5,6,7-tetrachloro- and 2-hetaryl-5,6,7-trichloro-1,3-tropolones exist in the NH-tautomeric form with a strong resonance-assisted intramolecular N–H···O hydrogen bond. The mechanism of the formation of 1,3-tropolones in the reaction of methylene-active five-membered heterocycles with o-chloranil in acetic acid solution has been studied using density functional theory (DFT) methods. The reaction of 2-(2-benzoxa(thia)zolyl)-5,6,7-trichloro(4,5,6,7-tetrachloro)-1,3-tropolones with alcohols leads to the contraction of the seven-membered tropone ring with the formation of 2-(2-benzoxa(thia)zolyl)-6-alkoxycarbonylphenols. The molecular structure of 2-(2-ethoxycarbonyl-6-hydroxy-3,4,5-trichlorophenyl)benzoxazole has been determined by X-ray diffraction. 2-(2-Benzoxa(thia)zolyl)-6-alkoxycarbonylphenols display intense green fluorescence with anomalous Stokes shifts caused by the excited state intramolecular proton transfer (ESIPT) effects.

scholarly journals Effective and Novel Application of Hydrodynamic Voltammetry to the Study of Superoxide Radical Scavenging by Natural Phenolic Antioxidants

Antioxidants ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 14 ◽  
Author(s):  
Stuart Belli ◽  
Miriam Rossi ◽  
Nora Molasky ◽  
Lauren Middleton ◽  
Charles Caldwell ◽  
...  
Keyword(s):  
Density Functional ◽  
Superoxide Radical ◽  
Structural Information ◽  
Radical Scavenging ◽  
Phenolic Antioxidants ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Quantitative Manner ◽  
Hydrodynamic Voltammetry ◽  
Insight Into

The reactions of antioxidants with superoxide radical were studied by cyclic voltammetry (CV)—and hydrodynamic voltammetry at a rotating ring-disk electrode (RRDE). In both methods, the superoxide is generated in solution from dissolved oxygen and then measured after being allowed to react with the antioxidant being studied. Both methods detected and measured the radical scavenging but the RRDE was able to give detailed insight into the antioxidant behavior. Three flavonoids, chrysin, quercetin and eriodictyol, were studied, their scavenging activity of superoxide was assessed and the molecular structure of each flavonoid was related to its scavenging capability. From our improved and novel RRDE method, we determine the ability of these 3 antioxidants to react with superoxide radical in a more quantitative manner than the classical CV. Density Functional Theory (DFT) and single crystal X-ray diffraction data provide structural information that assists in clarifying the scavenging molecular mechanism. Hydroxyls associated with the A ring, as found in chrysin, scavenge superoxide in a different manner than those found in the B ring of flavonoids, as those in quercetin and eriodictyol.

scholarly journals Tetranuclear Oxo-Titanium Clusters with Different Carboxylate Aromatic Ligands: Optical Properties, DFT Calculations, and Photoactivity

Materials ◽  
2018 ◽  
Vol 11 (9) ◽  
pp. 1661 ◽  
Author(s):  
Maciej Janek ◽  
Aleksandra Radtke ◽  
Tadeusz Muzioł ◽  
Maria Jerzykiewicz ◽  
Piotr Piszczek
Keyword(s):  
Band Gap ◽  
Density Functional ◽  
Uv Light ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
Functional Theory ◽  
Carboxylate Ligands ◽  
Oxo Complexes ◽  
Spin Resonance ◽  
Infrared And Raman Spectroscopy

Titanium(IV) oxo-clusters of the general formula (Ti4O2(OiBu)10(O2CR’)2) (R’ = C13H9 (1), PhCl (2), PhNO2 (3)) were studied in order to estimate their potential photoactivity. The structure of the resulting tetranuclear Ti(IV) oxo-complexes was then determined via single crystal X-ray diffraction, infrared and Raman spectroscopy, and electron spin resonance (ESR). An analysis of diffuse reflectance spectra (DRS) allowed for the assessment of band gap values of (1)–(3) microcrystalline samples complexes. The use of different carboxylate ligands allowed the band gap of tetranuclear Ti(IV) oxo-clusters to be modulated in the range of 3.6 eV–2.5 eV. Density functional theory (DFT) methods were used to explain the influence of substitutes on band gap and optical activity. Dispersion of (1)–(3) microcrystals in the poly(methyl methacrylate) (PMMA) matrixes enabled the formation of composite materials for which the potential photocatalytic activity was estimated through the study on methylene blue (MB) photodegradation processes in the presence of UV light. The results obtained revealed a significant influence of carboxylate ligands functionalization on the photoactivity of synthesized tetranuclear Ti(IV) oxo-complexes.

scholarly journals Exo⇔Endo Isomerism, MEP/DFT, XRD/HSA-Interactions of 2,5-Dimethoxybenzaldehyde: Thermal, 1BNA-Docking, Optical, and TD-DFT Studies

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5970
Author(s):  
Nabil Al-Zaqri ◽  
Mohammed Suleiman ◽  
Anas Al-Ali ◽  
Khaled Alkanad ◽  
Karthik Kumara ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Structural Parameters ◽  
Population Analysis ◽  
Xrd Analysis ◽  
X Ray Diffraction ◽  
Optical Energy Gap ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Td Dft

The exo⇔endo isomerization of 2,5-dimethoxybenzaldehyde was theoretically studied by density functional theory (DFT) to examine its favored conformers via sp2–sp2 single rotation. Both isomers were docked against 1BNA DNA to elucidate their binding ability, and the DFT-computed structural parameters results were matched with the X-ray diffraction (XRD) crystallographic parameters. XRD analysis showed that the exo-isomer was structurally favored and was also considered as the kinetically preferred isomer, while several hydrogen-bonding interactions detected in the crystal lattice by XRD were in good agreement with the Hirshfeld surface analysis calculations. The molecular electrostatic potential, Mulliken and natural population analysis charges, frontier molecular orbitals (HOMO/LUMO), and global reactivity descriptors quantum parameters were also determined at the B3LYP/6-311G(d,p) level of theory. The computed electronic calculations, i.e., TD-SCF/DFT, B3LYP-IR, NMR-DB, and GIAO-NMR, were compared to the experimental UV–Vis., optical energy gap, FTIR, and 1H-NMR, respectively. The thermal behavior of 2,5-dimethoxybenzaldehyde was also evaluated in an open atmosphere by a thermogravimetric–derivative thermogravimetric analysis, indicating its stability up to 95 °C.

Site preference and atomic ordering in the ternary Rh5Ga2As: first-principles calculations

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Nilanjan Roy ◽  
Sucharita Giri ◽  
Harshit ◽  
Partha P. Jana
Keyword(s):  
Total Energy ◽  
First Principles ◽  
Density Functional ◽  
Structure Type ◽  
Site Preference ◽  
X Ray Diffraction ◽  
Atomic Ordering ◽  
Functional Theory ◽  
The Stability ◽  
Bonding Characteristics

Abstract The site preference and atomic ordering of the ternary Rh5Ga2As have been investigated using first-principles density functional theory (DFT). An interesting atomic ordering of two neighboring elements Ga and As reported in the structure of Rh5Ga2As by X-ray diffraction data only is confirmed by first-principles total-energy calculations. The previously reported experimental model with Ga/As ordering is indeed the most stable in the structure of Rh5Ga2As. The calculation detected that there is an obvious trend concerning the influence of the heteroatomic Rh–Ga/As contacts on the calculated total energy. Interestingly, the orderly distribution of As and Ga that is found in the binary GaAs (Zinc-blende structure type), retained to ternary Rh5Ga2As. The density of states (DOS) and Crystal Orbital Hamiltonian Population (COHP) are calculated to enlighten the stability and bonding characteristics in the structure of Rh5Ga2As. The bonding analysis also confirms that Rh–Ga/As short contacts are the major driving force towards the overall stability of the compound.

scholarly journals Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Lütgert ◽  
J. Vorberger ◽  
N. J. Hartley ◽  
K. Voigt ◽  
M. Rödel ◽  
...  
Keyword(s):  
Equation Of State ◽  
Polyethylene Terephthalate ◽  
Density Functional ◽  
Equations Of State ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Shock Hugoniot ◽  
Highly Correlated

AbstractWe present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, $$({\hbox {C}}_{10} {\hbox {H}}_8 {\hbox {O}}_4)_n$$ ( C 10 H 8 O 4 ) n , also called mylar) shock-compressed to ($$155 \pm 20$$ 155 ± 20 ) GPa and ($$6000 \pm 1000$$ 6000 ± 1000 ) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

scholarly journals Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1032
Author(s):  
Anirban Naskar ◽  
Rabi Khanal ◽  
Samrat Choudhury
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Covalent Bond ◽  
Density Functional Theory Calculations ◽  
Antisite Defect ◽  
Defect States ◽  
Functional Theory ◽  
Electronic Defect ◽  
Constituent Elements

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

scholarly journals A machine learning platform for the discovery of materials

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Carl E. Belle ◽  
Vural Aksakalli ◽  
Salvy P. Russo
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Gw Approximation ◽  
Dft Methods ◽  
Functional Theory ◽  
Unit Cell Size ◽  
Learning Platform ◽  
Photovoltaic Materials ◽  
Wide Range ◽  
Quantum Espresso

AbstractFor photovoltaic materials, properties such as band gap $$E_{g}$$ E g are critical indicators of the material’s suitability to perform a desired function. Calculating $$E_{g}$$ E g is often performed using Density Functional Theory (DFT) methods, although more accurate calculation are performed using methods such as the GW approximation. DFT software often used to compute electronic properties includes applications such as VASP, CRYSTAL, CASTEP or Quantum Espresso. Depending on the unit cell size and symmetry of the material, these calculations can be computationally expensive. In this study, we present a new machine learning platform for the accurate prediction of properties such as $$E_{g}$$ E g of a wide range of materials.

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