A threefold approach including quantum chemical, molecular docking and molecular dynamic studies to explore the natural compounds from Centaurea jacea as the potential inhibitors for COVID-19

In the current report, we studied the possible inhibitors of COVID-19 from bioactive constituents of Centaurea jacea using a threefold approach consisting of quantum chemical, molecular docking and molecular dynamic techniques. Centaurea jacea is a perennial herb often used in folk medicines of dermatological complaints and fever. Moreover, anticancer, antioxidant, antibacterial and antiviral properties of its bioactive compounds are also reported. The Mpro (Main proteases) was docked with different compounds of Centaurea jacea through molecular docking. All the studied compounds including apigenin, axillarin, Centaureidin, Cirsiliol, Eupatorin and Isokaempferide, show suitable binding affinities to the binding site of SARS-CoV-2 main protease with their binding energies -6.7 kcal/mol, -7.4 kcal/mol, -7.0 kcal/mol, -5.8 kcal/mol, -6.2 kcal/mol and -6.8 kcal/mol, respectively. Among all studied compounds, axillarin was found to have maximum inhibitor efficiency followed by Centaureidin, Isokaempferide, Apigenin, Eupatorin and Cirsiliol. Our results suggested that axillarin binds with the most crucial catalytic residues CYS145 and HIS41 of the Mpro, moreover axillarin shows 5 hydrogen bond interactions and 5 hydrophobic interactions with various residues of Mpro. Furthermore, the molecular dynamic calculations over 60 ns (6×106 femtosecond) time scale also shown significant insights into the binding effects of axillarin with Mpro of SARS-CoV-2 by imitating protein like aqueous environment. From molecular dynamic calculations, the RMSD and RMSF computations indicate the stability and dynamics of the best docked complex in aqueous environment. The ADME properties and toxicity prediction analysis of axillarin also recommended it as safe drug candidate. Further, in vivo and in vitro investigations are essential to ensure the anti SARS-CoV-2 activity of all bioactive compounds particularly axillarin to encourage preventive use of Centaurea jacea against COVID-19 infections.

First-Principles Calculations of Y-Si-O Nanoclusters and Effect of Si on Microstructure and Mechanical Properties of 12Cr ODS Steel in Vacuum Sintering System

High density of thermally stable Y-Si-O nanoparticles dispersed in the Fe matrix play a primary role in oxide dispersion strengthened (ODS) steel. In this study, the binding energies of solutes Y, O and Si with vacancies have been calculated in the framework of first-principles density functional theory. According to the calculations, any two solutes of Y, O and Si bound with each other strongly in the second nearest neighboring (NN) sites while not in 1NN. A vacancy (v) bounds strongly with Y and O in 1NN site. The binding sequence of solutes with v followed O-v → Y-v → Si-v, and the affinity of Y, Si and v with O followed O-Y → O-v → O-Si. The nucleation mechanism of Y-O-Si nanoclusters was determined, which gave the feasibility of adding Si to ODS steels. The core (consisting of Si and O)-shell (enriched Fe and Cr) structure of the microparticles was found in ODS steels containing Si, fabricated by mechanical alloying (MA) and vacuum sintering. Moreover the nanoparticles of monoclinic cubic Y2O3, Y2SiO5 and Y2Si2O7 with sizes of 5 ~ 12 nm were observed in ODS steel. Si reduced the sintering temperature by maximizing densities and mechanical properties at a lower sintering temperature. The steel with 3 wt% Si was sintered at 1280 °C, exhibiting the best comprehensive mechanical properties. The tensile strength, hardness and relative density were 1025 MPa, 442.44 HV and 95.3%, respectively.

Mott–Hubbard insulating state for the layered van der Waals $$\hbox {FePX}_3$$ (X: S, Se) as revealed by NEXAFS and resonant photoelectron spectroscopy

A broad family of the nowadays studied low-dimensional systems, including 2D materials, demonstrate many fascinating properties, which however depend on the atomic composition as well as on the system dimensionality. Therefore, the studies of the electronic correlation effects in the new 2D materials is of paramount importance for the understanding of their transport, optical and catalytic properties. Here, by means of electron spectroscopy methods in combination with density functional theory calculations we investigate the electronic structure of a new layered van der Waals $$\hbox {FePX}_3$$ FePX 3 (X: S, Se) materials. Using systematic resonant photoelectron spectroscopy studies we observed strong resonant behavior for the peaks associated with the $$3d^{n-1}$$ 3 d n - 1 final state at low binding energies for these materials. Such observations clearly assign $$\hbox {FePX}_3$$ FePX 3 to the class of Mott–Hubbard type insulators for which the top of the valence band is formed by the hybrid Fe-S/Se electronic states. These observations are important for the deep understanding of this new class of materials and draw perspectives for their further applications in different application areas, like (opto)spintronics and catalysis.

Synthesis Factors Dependence of Magnetic Properties of CoFe2O4 and CoFe2-xGdxO4 Semicrystalline Nanoparticles with desired Morphology through Hydrothermal Procedure

In the present study, CoFe2O4 and CoFe2-xGdxO4 nanoparticles were synthesized by the hydrothermal process. The CoFe2O4 nanoparticles were synthesized at different temperatures (70oC, 100oC, 150oC, and 200oC), molar ratio of CoCl2/ FeCl3 (0/2, 0.75/2, 1/2, 1.5/2, and 2/2). Gadolinium-doped cobalt ferrite (CoFe2-xGdxO4) nanoparticles have also been synthesized with Gd/Fe molar ratios of 0.18 and 0.53. The XRD patterns indicate that cobalt ferrite and Gadolinium-doped cobalt ferrite nanoparticles have been successfully synthesized without impurities with a medium degree of crystallinity. The XRD patterns show that by increasing the synthesis temperature from 70oC to 200oC, the size of the nanoparticles decreased from 50.49nm to 32.45nm while the morphology of the nanoparticles also changed from a shapeless and agglomerated state to a spherical shape. The XPS curve illustrated several peaks corresponding to Fe+3, Co+2, and O 1s. The binding energies for Co and Fe were consistent with Fe 2p and Co 2p binding energies for cobalt ferrite nanoparticles. The magnetic saturation value (Ms) increased from 17.253 emu/g to 54.438 emu/g with a rise in the synthesis temperature. The effects of FeCl3/CoCl2 molar ratio on the magnetic properties showed the highest value of Ms (54.438 emu/g) and the coercivity (HC) of 744.56 Oe for a 2/1 molar ratio. The addition of gadolinium to the composition resulted in a reducing of the magnetic properties of nanoparticles; accordingly, the amount of saturated magnetization was reduced to 22.469 emu/g. Another effect of gadolinium dopant in the composition was a change in nanoparticle morphology from spherical to rod shape. The final aim of this study was to investigate the possible utilization of CoFe2O4 and CoFe2-xGdxO4 nanoparticles in medical treatment in the near future.

Phloroglucinol as a Potential Candidate against Trypanosoma congolense Infection: Insights from In Vivo, In Vitro, Molecular Docking and Molecular Dynamic Simulation Analyses

Sub-Saharan Africa is profoundly challenged with African Animal Trypanosomiasis and the available trypanocides are faced with drawbacks, necessitating the search for novel agents. Herein, the chemotherapeutic potential of phloroglucinol on T. congolense infection and its inhibitory effects on the partially purified T. congolense sialidase and phospholipase A2 (PLA2) were investigated. Treatment with phloroglucinol for 14 days significantly (p < 0.05) suppressed T. congolense proliferation, increased animal survival and ameliorated anemia induced by the parasite. Using biochemical and histopathological analyses, phloroglucinol was found to prevent renal damages and splenomegaly, besides its protection against T. congolense-associated increase in free serum sialic acids in infected animals. Moreover, the compound inhibited bloodstream T. congolense sialidase via mixed inhibition pattern with inhibition binding constant (Ki) of 0.181 µM, but a very low uncompetitive inhibitory effects against PLA2 (Ki > 9000 µM) was recorded. Molecular docking studies revealed binding energies of −4.9 and −5.3 kcal/mol between phloroglucinol with modeled sialidase and PLA2 respectively, while a 50 ns molecular dynamics simulation using GROMACS revealed the sialidase-phloroglucinol complex to be more compact and stable with higher free binding energy (−67.84 ± 0.50 kJ/mol) than PLA2-phloroglucinol complex (−77.17 ± 0.52 kJ/mol), based on MM-PBSA analysis. The sialidase-phloroglucinol complex had a single hydrogen bond interaction with Ser453 while none was observed for the PLA2-phloroglucinol complex. In conclusion, phloroglucinol showed moderate trypanostatic activity with great potential in ameliorating some of the parasite-induced pathologies and its anti-anemic effects might be linked to inhibition of sialidase rather than PLA2.

Encapsulating Metal-Organic-Foam Derived Nanocages into a Microcapsule for Shuttle Effect-Suppressive Lithium-Sulfur Batteries

Long-term stable secondary batteries are highly required. Here, we report a unique microcapsule encapsulated with metal organic foams (MOFs)-derived Co3O4 nanocages for a Li-S battery, which displays good lithium-storage properties. ZIF-67 dodecahedra are prepared at room temperature then converted to porous Co3O4 nanocages, which are infilled into microcapsules through a microfluidic technique. After loading sulfur, the Co3O4/S-infilled microcapsules are obtained, which display a specific capacity of 935 mAh g−1 after 200 cycles at 0.5C in Li-S batteries. A Coulombic efficiency of about 100% is achieved. The constructed Li-S battery possesses a high rate-performance during three rounds of cycling. Moreover, stable performance is verified under both high and low temperatures of 50 °C and −10 °C. Density functional theory calculations show that the Co3O4 dodecahedra display large binding energies with polysulfides, which are able to suppress shuttle effect of polysulfides and enable a stable electrochemical performance.

A Comparison of Structure, Stability of Neutral and Cationic Vanadium-doped Germanium Clusters GenV0/+ (n = 2 - 8) by using Density Function Theorym clusters GenV0/+ (n = 2 - 8) by using density function theory

The geometries, stabilities and electronic properties of vanadium-doped germanium clusters GenV0/+ (n=2-8) were systematically investigated by using density functional theory (DFT) at the PBE level and the 6-311+G(d) basis set. The results show that the geometries of lowest-energy structures of the cationic clusters are only significant different from those of the neutral at n = 6 or 7. The ground state of neutral clusters is a doublet, except Ge2V which is a quartet while that of cationic clusters is a triplet, except Ge8V+, which is a singlet. The average binding energy values generally increase with increasing cluster size. The results from average binding energies showed that it is more stable for the cationic than neutral clusters at the same size. Furthermore, the calculated values of fragmentation energy, second-order energy difference, HOMO-LUMO gap and adiabatic ionization potential suggest that the neutral clusters possess higher stability when n = 2, 5, 8 and the cations are more stable when n = 2, 3, 5 and 6.

Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides

An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.

Water Interaction with Fe2NiP Schreibersite (110) Surface: a Quantum Mechanical Atomistic Perspective

Phosphorus is an element of primary importance for all living creatures, being present in many biological activities in the form of phosphate (PO43-). However, there are still open questions about the origin of this specific element and on the transformation which allowed it to be incorporated in biological systems. The most probable source of prebiotic phosphorus is the intense meteoritic bombardment during the Archean era, few million years after the solar system formation, which brought tons of iron-phosphide materials (schreibersite) on the early Earth crust. It was recently demonstrated that by simple wetting/corrosion processes from this material various oxygenated phosphorus compounds are produced. In the present work, the wetting process of schreibersite (Fe2NiP) was studied by computer simulations using density functional theory, with the PBE functional supplemented with dispersive interactions through a posteriori empirical correction. To start disentangling the complexity of the system, only the most stable (110) surface of Fe2NiP was used simulating different water coverages, from which structures, water binding energies and vibrational spectra have been predicted. The computed (ana-)harmonic infrared spectra have been compared with the experimental ones, thus confirming the validity of the adopted methodology and models.