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 Structural basis for the transformation pathways of the sodium naproxen anhydrate–hydrate system

IUCrJ ◽  
2014 ◽  
Vol 1 (5) ◽  
pp. 328-337 ◽  
Author(s):  
Andrew D. Bond ◽  
Claus Cornett ◽  
Flemming H. Larsen ◽  
Haiyan Qu ◽  
Dhara Raijada ◽  
...  
Keyword(s):  
Solid State ◽  
Density Functional ◽  
Structural Information ◽  
Structural Similarity ◽  
Structural Basis ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Face To Face ◽  
Transformation Pathways ◽  
Dehydration Processes

Crystal structures are presented for two dihydrate polymorphs (DH-I and DH-II) of the non-steroidal anti-inflammatory drug sodium (S)-naproxen. The structure of DH-I is determined from twinned single crystals obtained by solution crystallization. DH-II is obtained by solid-state routes, and its structure is derived using powder X-ray diffraction, solid-state13C and23Na MAS NMR, and molecular modelling. The validity of both structures is supported by dispersion-corrected density functional theory (DFT-D) calculations. The structures of DH-I and DH-II, and in particular their relationships to the monohydrate (MH) and anhydrate (AH) structures, provide a basis to rationalize the observed transformation pathways in the sodium (S)-naproxen anhydrate–hydrate system. All structures contain Na+/carboxylate/H2O sections, alternating with sections containing the naproxen molecules. The structure of DH-I is essentially identical to MH in the naproxen region, containing face-to-face arrangements of the naphthalene rings, whereas the structure of DH-II is comparable to AH in the naproxen region, containing edge-to-face arrangements of the naphthalene rings. This structural similarity permits topotactic transformation between AH and DH-II, and between MH and DH-I, but requires re-organization of the naproxen molecules for transformation between any other pair of structures. The topotactic pathways dominate at room temperature or below, while the non-topotactic pathways become active at higher temperatures. Thermochemical data for the dehydration processes are rationalized in the light of this new structural information.

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 X-ray Diffraction and Density Functional Theory Provide Insight into Vanadate Binding to Homohexameric Bromoperoxidase II and the Mechanism of Bromide Oxidation

2018 ◽  
Vol 13 (5) ◽  
pp. 1243-1259 ◽  
Author(s):  
Madlen Radlow ◽  
Mirjam Czjzek ◽  
Alexandra Jeudy ◽  
Jerome Dabin ◽  
Ludovic Delage ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Insight Into

scholarly journals Molecular Structure Studies on Allyl Sulfonamides: Synthesis, Theoretical Treatment and Evaluation of Biological Activity

2021 ◽  
Author(s):  
Anderson Rabello ◽  
Mayura Rubinger ◽  
Rafael Souza ◽  
Silvana Guilardi ◽  
Guilherme de Lima ◽  
...  
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Hirshfeld Surface ◽  
Theoretical Treatment ◽  
X Ray Diffraction ◽  
Frontier Orbitals ◽  
Functional Theory ◽  
X Ray ◽  
Lowest Unoccupied Molecular Orbitals ◽  
Insight Into

Two series of allyl sulfonamides, prepared from Morita-Baylis-Hillman adducts and primary aromatic sulfonamides, were fully characterized. The Z configuration for the products derived from 2-[hydroxy(phenyl)methyl]acrylonitrile (1) and E configuration for those derived from methyl 2-[hydroxy(phenyl)methyl]acrylate (2) were confirmed by X-ray diffraction for one compound of each series (1e, 2f). Density functional theory calculations for all allyl sulfonamides agreed with the X-ray crystallographic data. X-ray diffraction studies indicate that these compounds form dimers in their crystal structures. Fingerprint plots show that compound 1e is stabilized by H⋯H, C⋯H/H⋯C, O⋯H/H⋯O and N⋯H/H⋯N interactions, while the compound 2f has no N⋯H/H⋯N contacts. Hirshfeld surface analyses were performed to gain insight into the behavior of these interactions. Calculated frontier orbitals showed that their highest occupied and lowest unoccupied molecular orbitals are antibonding orbitals. The allyl sulfonamides 1e and 2f are among the most active compounds in each series, inhibiting approximately 60% of the mycelial growth of Botrytis cinerea at 3 mmol L-1.

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.

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.

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