CONTEXT: While Au-based catalysts recently have shown tremendous potential in glucose oxidation to gluconic acid, the detailed reaction mechanism is still unclear, which impedes the development of direct glucose fuel cell (DGFC). METHODS: Using density functional theory (DFT), we exhibit some new adsorption configurations and oxidation mechanisms by considering both the open chain form and the ring form of glucose on Au(111) surface in the presence of OH. The strong interactions between glucose and the OH adsorbed surface are obtained. Moreover, form the calculated energy pathways, the oxidation of glucose in the open chain involves the dissociation of the formyl C - H bond by the adsorbed OH, while the ring form glucose oxidation is initiated by O - H bond rupture rather than C - H bond scission and preferentially undergoes the ring-open process to generate the open chain form glucose. Meanwhile, the results demonstrate that the adsorbed OH assists in reducing the activation energy of reaction process.

CONTEXT: NLRP9 is a member of nucleotide-binding domain leucine-rich repeat-containing receptors and is found to be associated with many inflammatory diseases. In the current scenario, the identification of promising anti-inflammatory compounds from natural sources by repurposing approach is still relevant for the early prevention and effective management of the disease. METHODS: In the present study, we docked bioactives of Ashwagandha (Withanoside IV, Withanoside V, Withanolide A, Withanolide B, and Sitoindoside IX) and two control drugs against bovine NLRP9 protein. ADME/T analysis was used to determine the physiochemical properties of compounds and standard drugs. Molecular modeling was used to evaluate the correctness and quality of protein structures. In silico docking analysis revealed Withanolide B had the highest binding affinity score of -10.5 kcal/mol, whereas, among control drugs, doxycycline hydrochloride was most effective (-10.3 kcal/mol). The results of this study revealed that bioactives of Withania somnifera could be promising inhibitors against bovine NLRP9. In the present study, molecular simulation was used to measure protein conformational changes over time. The Rg value was found to be 34.77A°. RMSD and B-factor were also estimated to provide insights into the flexibility and mobile regions of protein structure. A functional protein network interaction was constructed from information collected from non-curative sources as protein-protein interactions (PPI) that play an important role in determining the function of the target protein and the ability of the drug molecule. Thus, in the present situation, it is important to identify bioactives with the potential to combat inflammatory diseases and provide strength and immunity to the host. However, there is still a need to study in vitro and in vivo to further support these findings.

CONTEXT: Langmuir adsorption of gas molecules of NO, NO2, and NH3 on the graphitic GaN and GaP sheets has been accomplished using density functional theory. The changes of charge density have shown a more important charge transfer for GaN compared to GaP which acts both as the electron donor while gas molecules act as the stronger electron acceptors through adsorption on the graphitic-like GaN surface. The adsorption of NO and NO2 molecules introduced spin polarization in the PL-GaN sheet, indicating that it can be employed as a magnetic gas sensor for NO and NO2 sensing. METHODS: The partial electron density states based on "PDOS" graphs have explained that the NO and NO2 states in both of GaN and GaP nanosheets, respectively, have more of the conduction band between - 5 and - 10 eV, while expanded contribution of phosphorus states is close to gallium states, but nitrogen and oxygen states have minor contributions. GaN and GaP nanosheets represent having enough capability for adsorbing gases of NO, NO2, and NH3 through charge transfer from nitrogen atom and oxygen atom to the gallium element owing to intra-atomic and interatomic interactions. Ga sites in GaN and GaP nanosheets have higher interaction energy from Van der Waals' forces with gas molecules.

CONTEXT: 3,4-Bisnitrofurazanfuroxan (DNTF) is a typical high energy density compound (HEDC), it has high crystal density and detonation parameters, but also high mechanical sensitivity. To decrease its mechanical sensitivity, the DNTF based polymer bonded explosives (PBXs) was designed. The pure DNTF crystal and PBXs models were established. The stability, sensitivity, detonation performance and mechanical properties of DNTF crystal and PBXs models were predicted. Results show that PBXs models containing fluorine rubber (F2311) and fluorine resin (F2314) have higher binding energy, meaning that DNTF/F2311 and DNTF/F2314 is relatively more stable. PBXs models have higher value of cohesive energy density (CED) than pure DNTF crystal, DNTF/F2311 and DNTF/F2314 have the highest value of CED, implying that the sensitivity of PBXs is effectively decreased, DNTF/F2311 and DNTF/F2314 is more insensitive. PBXs have lower crystal density and detonation parameters than DNTF, the energy density is declined, DNTF/F2314 has higher energetic performance than other PBXs. Compared with pure DNTF crystal, engineering moduli (tensile modulus, shear modulus, bulk modulus) of PBXs models are obviously decreased, but Cauchy pressure is increased, implying that the mechanical properties of PBXs is superior to pure DNTF component, the PBXs containing F2311 or F2314 have more preferable mechanical properties. Consequently, DNTF/F2311 and DNTF/F2314 have the best comprehensive properties and is more attractive among the designed PBXs, indicating that F2311 and F2314 are more advantageous and promising in ameliorating properties of DNTF. METHODS: The properties of DNTF crystal and PBXs models were predicted through molecular dynamics (MD) method under Materials Studio 7.0 package. The MD simulation was performed with isothermal-constant volume (NVT) ensemble, and the force field was chosen as COMPASS force field. The temperature was set as 295 K, the time step was 1 fs and the total MD simulation time was 2 ns.

In this work, we have investigated the electrochemical characteristics of armchair silicon carbide nanoribbon (ASiCNR) for its potential deployment as 2D lithium-ion battery anode material. Density functional theory approach is used to calculate the adsorption energy, storage capacity, and open circuit voltage of ASiCNR for LIB. Adsorption of Li atoms introduces the new energy bands which cross the Fermi level; this results in semiconductor to metallic transition of ASiCNR. It indicates the strong interaction of Li atoms towards the ASiCNR. When adsorption of Li atoms increases one by one, the adsorption energy (E[Formula: see text]) per Li atoms increases gradually. When all favourable sites are adsorbed by Li atoms E[Formula: see text] reached its maximum value and it results in maximum storage capacity of 818 mAhg[Formula: see text] and open circuit voltage of 1.15 V. Diffusion barrier of Li atoms for the substrate is 0.42 eV. Our computational results suggest that ASiCNR can be used as an anode material for Li-ion batteries, and it provides the theoretical background for the future study on ASiCNR and other Li storage structures.

CONTEXT: Explosives have a wide range of applications in many fields due to their high energy and high density. Recently, a new synthesized co-crystal explosive DAF:ADNP presents high detonation performance and low sensitivity. This work is aimed to understand how the structure and intermolecular interactions affect the performance of the DAF:ADNP co-crystal. The results indicate that the formed π-π interactions and stronger hydrogen bonds in the co-crystal enhance its stability and its impact sensitivity is reduced. The strong intralayer H···N and H···O interactions and interlayer π-π stacking are the main driving force for the formation of the co-crystal. Compared with the pure crystals, the detonation performance of the co-crystal slightly decreases, while its sensitivity reduces. METHODS: All calculations were used the DFT-PBE-D method with Vanderbilt-type ultrasoft pseudopotentials and plane wave (340.0 eV) in the CASTEP package. Radial distribution function were calculated by NVT-MD simulations for 100 ps with a time step of 1 fs at 298 K. Hirshfeld surfaces were generated by CrystalExplorer 3.0 and reduced density gradient analyses were performed by Multiwfn 3.0.

BACKGROUND: Inflammation-provoked disorders including cancer are arbitrated by cyclooxygenase-2 (COX-2). Celecoxib and niflumic acid are among the potent and selective inhibitors of this enzyme while aspirin (acetylsalicylic acid) and sodium salicylate are its non-selective and lesser potent inhibitors. Despite these proven studies, the comparative structural study of these selective and non-selective molecules at atomistic scale in complex state with COX-2 that may answer this differential inhibitory behavior has not been accomplished spotlighting the imperative need of additional research in this area. Thus, this study was framed to provide a strong explanation for the enigma of higher inhibitory activity of celecoxib-niflumic acid duo in comparison to aspirin and sodium salicylate towards COX-2. METHODS: A contemporary approach including advanced molecular docking against COX2, molecular dynamics of receptor-ligand complexes, simulation-trajectory-backed MMGBSA for different time points, radius of gyration (Rg) calculations, and e-pharmacophores approach was employed to attain a rational conclusion. RESULTS: Our findings demonstrated the higher binding affinity of celecoxib and niflumic acid over aspirin and sodium salicylate against COX-2. Although both selective and non-selective COX-2 inhibitors manifested nearly the same stability in the active site of this enzyme but the e-pharmocophoric features found in the case of selective inhibitors scored over non-selective ones. Thus, our findings excluded the differential stability to be the cause of stronger potency of selective inhibitors but attributed their potency to greater number of complementary features present in these inhibitors against the active site of inflammation engendering COX-2.

CONTEXT: The rationalization of acid rain formation steps is fundamental for mitigating its effects. It is believed the hydroxysulfinyl radical is an intermediate species for the production of atmospheric sulfuric acid. Two stable configurations HOSO and HSO2 have been reported for such a radical in the gas phase. This work aims at studying these isomers in the aqueous medium. The electrical and reactivity quantities - electronic chemical potential ([Formula: see text]), chemical hardness ([Formula: see text]), and electrophilicity ([Formula: see text]) - are here calculated and compared. Considering first solvation shells (15 H2O for HSO2 and 23 H2O for HOSO), an increase of 25% in the dipole moment of HSO2 was obtained, while the dipole moment of HOSO decreases in 11%. Both solvated isomers grow softer ([Formula: see text] decreases) contrasted to the gas phase. METHODS: HOSO and HSO2 are studied through a sequential Monte Carlo/quantum mechanics approach. Lennard-Jones plus the Coulomb potentials were used to represent intermolecular potential interaction in the frame of the DICE package. Molecular structure calculations were performed at CASPT2/aug - cc - pV(T + d)Z level of theory using the MOLPRO suite of programs.

CONTEXT AND RESULTS: This work aims to study the influence of the absence and presence of permanent charges on the electronic and dynamical properties of the non-covalent bound diatomic systems involving He and Li, Be as neutral and ionic partners. The charge displacement results suggest that in the formation of HeLi[Formula: see text], HeBe[Formula: see text], and HeBe[Formula: see text], the neutral He atom undergoes, in the electric field of the ion, a pronounced electronic polarization, and the natural bond order theoretical approach indicates that in the formation of the molecular orbital He acts as a weak electron donor. The energy decomposition analysis provides the dispersion and induction components as the attractive leading terms controlling the stability of all systems, confirming that the formed bond substantially maintains a non-covalent nature which is also supported by the Quantum Theory of Atoms in Molecules (QTAIM) analysis. Finally, it was found that the HeLi and HeBe neutral systems are unstable under any condition, HeLi[Formula: see text] and HeBe[Formula: see text] ionic systems are stable below 317K and 138K, respectively, while the HeBe[Formula: see text] system becomes unstable only after 3045K. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The potential energy curves and interactions in all systems were studied theoretically based on coupled-cluster singles and doubles method with perturbative inclusion of triples CCSD(T) method with an aug-cc-pV5Z basis set. More precisely, it was determined the potential energy curves describing the stability of the HeLi, HeLi[Formula: see text], HeBe, HeBe[Formula: see text], and HeBe[Formula: see text] systems, the charge displacement within the formed adducts, the decomposition of their total interaction energy, the topological analysis of their bonds, their rovibrational energies, their spectroscopic constants and lifetimes.

Diketene (4-methylideneoxetan-2-one) is a precursor to the formation of either two molecules of ketene, or allene and CO2 using pyrolysis techniques. It is not known experimentally which of these pathways is followed, or indeed if both are, during the dissociation process. We use computational methods to show that the formation of ketene has a lower barrier than formation of allene and CO2 under standard conditions (by 12 kJ/mol). According to CCSD(T)/CBS, CBS-QB3 and M06-2X/cc-pVTZ calculations the formation of allene and CO2 is favoured thermodynamically under standard conditions of temperature and pressure; however, kinetically the formation of ketene is favoured from transition state theory calculations at standard and elevated temperatures.

CONTEXT: Acinetobacter baumannii, one of the critical ESKAPE pathogens, is a highly resilient, multi-drug-resistant, Gramnegative, rod-shaped, highly pathogenic bacteria. It is responsible for almost 1-2% of all hospital-borne infections in immunocompromised patients and causes community outbreaks. Because of its resilience and MDR characteristics, looking for new strategies to check the infections related to this pathogen becomes paramount. The enzymes involved in the peptidoglycan biosynthetic pathway are attractive and the most promising drug targets. They contribute to the formation of the bacterial envelope and help to maintain the rigidity and integrity of the cell. The MurI (glutamate racemase) is one of the crucial enzymes that aid in the formation of the pentapeptide responsible for the interlinkage of peptidoglycan chains. It converts L-glutamate to D-glutamate, which is required to synthesise the pentapeptide chain. METHODS: In this study, the MurI protein of A. baumannii (strain AYE) was modelled and subjected to high-throughput virtual screening against the enamine-HTSC library, taking UDP-MurNAc-Ala binding site as the targeted site. Four ligand molecules, Z1156941329 (N-(1-methyl-2-oxo-3,4-dihydroquinolin-6-yl)-1-phenyl-3,4-dihydro-1H-isoquinoline-2-carboxamide), Z1726360919 (1-[2-[3-(benzimidazol-1-ylmethyl)piperidin-1-yl]-2-oxo-1-phenylethyl]piperidin-2-one), Z1920314754 (N-[[3-(3-methylphenyl)phenyl]methyl]-8-oxo-2,7-diazaspiro[4.4]nonane-2-carboxamide) and Z3240755352 (4R)-4-(2,5-difluorophenyl)-1-(4-fluorophenyl)-1,3a,4,5,7,7a-hexahydro-6H-pyrazolo[3,4-b]pyridin-6-one), were identified to be the lead candidates based on Lipinski's rule of five, toxicity, ADME properties, estimated binding affinity and intermolecular interactions. The complexes of these ligands with the protein molecule were then subjected to MD simulations to scrutinise their dynamic behaviour, structural stability and effects on protein dynamics. The molecular mechanics/Poisson-Boltzmann surface area-based binding free energy analysis was also performed to compute the binding free energy of protein-ligand complexes, which offered the following values -23.32 ± 3.04 kcal/mol, -20.67 ± 2.91kcal/mol, -8.93 ± 2.90 kcal/mol and -26.73 ± 2.95 kcal/mol for MurI-Z1726360919, MurI-Z1156941329, MurI-Z3240755352 and MurI-Z3240755354 complexes respectively. Together, the results from various computational analyses utilised in this study proposed that Z1726360919, Z1920314754 and Z3240755352 could act as potential lead molecules to suppress the function of MurI protein from Acinetobacter baumannii.

CONTEXT: The use of Molecular Dynamics (MD) simulations to examine the mechanical characteristics of polymer composites reinforced with calcium carbonate (CaCO3) and graphene (GR) is represented in this work. The effects of CaCO3 and GR nanoadditives in polylactic acid (PLA) matrix in different concentrations were evaluated using the results of MD simulations. Experimental analyses have been conducted to validate the results of MD based on the mechanical properties of fabricated nanocomposites, including modulus of elasticity, shear modulus, and Poisson's ratio. The modeling, computation, and analysis of several simulations on the improved mechanical characteristics of PLA/CaCO3 and PLA/GR nanocomposites are introduced and discussed. The results revealed that the addition of GR nanoparticles were more effective in enhancing the mechanical properties of PLA components as compared with that of CaCO3 nanoparticles, as the modulus of elasticity, shear modulus and Poisson's ratio increased by approximately 21%, 17%, and 16% for addition of 3 wt% GR nanoparticles in the PLA matrix, respectively. METHODS: The mechanical behavior of PLA/CaCO3 and PLA/GR nanocomposites have been simulated based on the molecular dynamic technique using material studio (MS) that enabled the analyses of synergy between the polymer molecules and the nanoparticles. Molecular models for a system of nanocomposites were built by embedding the nano-clusters into an amorphous PLA matrix. Nanoparticles have been modeled as spherical nanoclusters of graphite and calcite unit cells. Molecular models of the pure PLA matrix were also developed for comparison. The relaxed systems of MD simulations have been carried out to calculate the mechanical properties of nanocomposites containing 1, 3 and 5 wt% nanofiller contents. To validate the results of the simulations, the PLA/CaCO3 and PLA/GR nanocomposite granules, containing different weight ratios of the nanofillers in the matrix, have been synthesized by melt-blending technique. These granules have been used to produce tensile test samples by injection molding technique, with different fractions of nanoparticles in the matrix, to study the effects of such nanoadditives on the mechanical properties of the PLA nanocomposites.

CONTEXT: The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)8-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm2), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm2) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector. METHODS: The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.

CONTEXT: Hydrogenation is an effective way to open a band gap of the metallic ψ-graphene, expanding its application in electronics. Evaluating the mechanical properties of hydrogenated ψ-graphene, especially the effect of hydrogen coverage, is also crucial to the application of ψ-graphene. Here, we demonstrate the mechanical properties of ψ-graphene depend closely on the hydrogen coverage and arrangement. Upon hydrogenation, Young's modulus and intrinsic strength of ψ-graphene decrease due to breaking of sp2 carbon networks. Both the ψ-graphene and hydrogenated ψ-graphene exhibit mechanical anisotropy. During changing the hydrogen coverage, the variation of mechanical strength of the hydrogenated ψ-graphene relies on the tensile direction. In addition, the arrangement of hydrogen also contributes to the mechanical strength and fracture behavior of hydrogenated ψ-graphene. Our results not only present a comprehensive understanding of the mechanical properties of hydrogenated ψ-graphene, but also provide a reference to tailor the mechanical properties of other graphene allotropes, which are of potential interest in materials science. METHODS: Vienna ab initio simulation package based on the plane-wave pseudopotential technique was employed for the calculations. The exchange-correlation interaction was described by the Perdew-Burke-Ernzerhof functional within the general gradient approximation and the ion-electron interaction was treated with the projected augmented wave pseudopotential.

CONTEXT: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. METHODS: The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.

CONTEXT: A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (- 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of - 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals. METHODS: Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski's rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.

CONTEXT: Ferroelectric ceramic polymer composites have become the preferred electrocaloric materials due to their light weight and high polarization strength. But the mechanical properties were desired to be improved. In this study, the polyvinylidene fluoride trifluoro ethylene chloride (PVTC) and barium titanate (BT) composites were prepared, and the microstructure and mechanical properties were investigated by molecular dynamics simulations and experiments. It was found that with the increase of BT ceramic content in the composites, the yield stress is significantly reduced, which can be reduced by 16.07%. By comparing with the experimental data, the agglomeration and stress mechanism of the composites were proposed. METHOD: The microstructure of the composite was analyzed using radial distribution function, self-diffusion coefficient, and glass transition temperature. The agglomeration mechanism of the composite was revealed from the microscopic point of view, and the rationality of the agglomeration behavior was verified by experiments. The calculations were performed by Material Studio 2019 software and the COMPASS force field was adopted.

CONTEXT: 3,4-bis(3-nitrofurazan-4-yl)furoxan (DNTF) is a new energetic compound with high energy and high density, and it is an important component of propellant and melt cast explosive. In order to study the effect of solvent on the growth morphology of DNTF, the growth plane of DNTF in vacuum is predicted by attachment energy (AE) model, and then the modified attachment energy of each growth plane in different solvents is calculated by molecular dynamics simulation. The morphology of crystal in solvent is predicted by modified attachment energy (MAE) model. The factors affecting crystal growth in solvent environment are analyzed by mass density distribution, radial distribution function and diffusion coefficient. The results show that the growth morphology of crystal in solvent is not only related to the adsorption strength of solvent to crystal plane, but affected by the attraction of crystal plane to solute. The hydrogen bond plays an important role in the adsorption strength between solvent and crystal plane. The polarity of solvent has a great influence on the crystal morphology, and the interaction between the solvent with stronger polarity and the crystal plane is stronger. The morphology of DNTF in n-butanol solvent is closer to spherical, which can effectively reduce the sensitivity of DNTF. METHODS: The molecular dynamics simulation is carried out under the COMPASS force field of Materials Studio software. Gaussian software is used to calculate the electrostatic potential of DNTF at B3LYP-D3/6-311 + G (d, p) theoretical level.

CONTEXT: Quinoxaline 1,4-di-N-oxide is a scaffold with a wide array of biological activities, particularly its use to develop new antiparasitic agents. Recently, these compounds have been described as trypanothione reductase (TR), triosephosphate isomerase (TIM), and cathepsin-L (CatL) inhibitors from Trypanosoma cruzi, Trichomonas vaginalis, and Fasciola hepatica, respectively. METHODS: Therefore, the main objective of this work was to analyze quinoxaline 1,4-di-N-oxide derivatives of two databases (ZINC15 and PubChem) and literature by molecular docking, dynamic simulation and complemented by MMPBSA, and contact analysis of molecular dynamics' trajectory on the active site of the enzymes to know their potential effect inhibitory. Interestingly, compounds Lit_C777 and Zn_C38 show preference as potential TcTR inhibitors over HsGR, with favorable energy contributions from residues including Pro398 and Leu399 from Z-site, Glu467 from γ-Glu site, and His461, part of the catalytic triad. Compound Lit_C208 shows potential selective inhibition against TvTIM over HsTIM, with favorable energy contributions toward TvTIM catalytic dyad, but away from HsTIM catalytic dyad. Compound Lit_C388 was most stable in FhCatL with a higher calculated binding energy by MMPBSA analysis than HsCatL, though not interacting with catalytic dyad, holding favorable energy contribution from residues oriented at FhCatL catalytic dyad. Therefore, these kinds of compounds are good candidates to continue researching and confirming their activity through in vitro studies as new selective antiparasitic agents.

CONTEXT: In this study, we predict the stability, elastic, electronic and optical properties of double perovskite (DP) Cs2CuIrF6. The detailed investigation of electronic structure and optical properties to find the suitability of DP Cs2CuIrF6 for device applications. From the structural optimization results, the stability of DP (Cs2CuIrF6) is in cubic order and belongs to the Fm-3 m space group (#225) with a nonmagnetic (NM) state. Additionally, the elastic results show that this DP is mechanically stable in a cubic and ductile manner. Further, we explain in detail the semiconducting nature of the proposed DP with the help of electronic structure and density of states (DOS). The electronic band gap of DP Cs2CuIrF6 is 0.72 eV (LV-XC). The optical part discussion, like the dielectric function ε, reflectivity R, refractive index n, absorption coefficient α and optical conductivity σ up to 13.00 eV. The studied compound is explored as a potential candidate for optoelectronic applications. METHODS: The density functional theory (DFT) within generalized gradient approximation (GGA) scheme of Perdew, Burke and Ernzerhof (PBE) as implemented in Wien2k computational code is utilized to achieve stable structure, elastic, electronic and optical properties of this material. The dynamic stability of this material was studied using the finite displacement method implemented in the CASTEP computational code. The elastic results have been computed by the IRelast package implemented in the Wien2k computational code.

CONTEXT: The synthesis of azobenzene materials is an important aspect of the research in the field of photo-switch materials. It is currently thought that azobenzene molecules exist in the cis and trans form of molecular structure configuration. However, the reaction process allowing for reversible energy switches from trans to cis form is still challenging. Therefore, it is crucial to understand the molecular properties of the azobenzene compounds in order to provide reference for future synthesis and application. Affirmation supporting this perspective has been substantially derived from theoretical results in the isomerization process and whether these molecular structures may affect the electronic properties entirely needs to be confirmed. In this study, I give my effort to understand the molecular structure properties of the cis and trans form of azobenzene molecule from 2-hydroxy-5-methyl-2'-nitroazobenzene (HMNA). Their chemistry phenomena are investigated using the density functional theory (DFT) method. This study shows that the trans-HMNA has a molecular size of 9.0 Å and the cis-HMNA has a molecular size of 6.6 Å. The trans-HMNA exhibits an electronic transition of π → π* type driven by an azo bond, whereas the cis-HMNA exhibits an electronic transition of n → π* type with respect to the non-bonding electrons of oxygen and nitrogen atoms. Therefore, the HMNA mechanism pathway from trans to cis form is feasible to undergo at the inversion pathway in the ground state. METHODS: All DFT calculations were performed using the Gaussian Software Packages (Gaussian 09 Revision-A.02 and GaussView 5.0.8). Gaussum 3.0 software was selected to visualize the molecular orbital levels in the density of states diagram. The optimized molecular geometrical parameter was calculated using B3LYP/cc-pVTZ level in the gas phase. TD-DFT with M06-2X/cc-pVTZ level was used as a method for the precise interpretation of excited states in molecular systems.

CONTEXT: The design and synthesis of new high energy density materials is an important part of the research in the field of high energy materials. However, the synthesis of high-energy materials is very difficult and dangerous. Therefore, it is necessary to design the compounds in advance and evaluate the performance of the designed compounds, so as to screen the high-energy candidate compounds with excellent performance and provide reference for future synthesis and application. 1,2,5-oxadiazole (furazan) and 1,2,4-oxadiazole are five-membered nitrogen-oxygen heterocycles. Because their structures contain high-energy N-O, C=N bonds, they can effectively improve the energy density and oxygen balance of compounds, which has attracted widespread attention. In this paper, 42 kinds of oxadiazole-bifurazan energetic derivatives were designed by inserting different functional groups and changing the parent bridging groups with 1,2,4-oxadiazole and furazan as the basic structural units. Their electronic structures, aromaticity, heats of formation (HOFs), detonation properties, thermodynamic properties and electrostatic potential were systematically studied by density functional than theory (DFT). The results show that -C (NO2)3 has the greatest improvement effect on HOFs among all the substituent groups. The detonation performance of -N=N- bridged oxadiazole-bifurazan derivatives is better than that of -NH-NH- bridged derivatives. And -C(NO2)3 is the most effective group to improve the detonation performance and density of compounds. Compared with the parent compounds, when a -C(NO2)3 was introduced, the density increased by about 5.5%. A6 (D = 10.30 km·s-1, P = 48.86 GPa) and D6 (D = 9.57 km·s-1, P = 42.31 GPa) are the compounds with the best D and P among the designed compounds, which are higher than RDX and HMX, and are potential candidates for new high-energy materials. METHODS: With the help of Gaussian16 software and Multiwfn 3.8 package, the B3LYP method in density functional theory was selected. The 6-311G (d, p) basis set was used to optimize the structure of the 42 derivatives, and the high-precision def2-TZVPP basis set was used to calculate the energy.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) is an unprecedented pandemic, threatening human health worldwide. The need to produce novel small-molecule inhibitors against the ongoing pandemic has resulted in the use of drugs such as chloroquine, azithromycin, dexamethasone, favipiravir, ribavirin, remdesivir and azithromycin. Moreover, the reports of the clinical trials of these drugs proved to produce detrimental effects on patients with side effects like nephrotoxicity, retinopathy, cardiotoxicity and cardiomyopathy. Recognizing the need for effective and non-harmful therapeutic candidates to combat COVID-19, we aimed to develop promising drugs against SARS-COV-2. DISCUSSION: In the current investigation, high-throughput virtual screening was performed using the Comprehensive Marine Natural Products Database against five non-structural proteins: Nsp3, Nsp5, Nsp12, Nsp13 and Nsp15. Furthermore, standard precision (SP) docking, extra precision (XP) docking, binding free energy calculation and absorption, distribution, metabolism, excretion and toxicity studies were performed using the Schrӧdinger suite. The top-ranked 5 hits obtained by computational studies exhibited to possess a greater binding affinity with the selected non-structural proteins. Amongst the five hits, CMNPD5804, CMNPD20924 and CMNPD1598 hits were utilized to design a novel molecule (D) that has the capability of interacting with all the key residues in the pocket of the selected non-structural proteins. Furthermore, 200 ns of molecular dynamics simulation studies provided insight into the binding modes of D within the catalytic pocket of selected proteins. CONCLUSION: Hence, it is concluded that compound D could be a promising inhibitor against these non-structural proteins. Nevertheless, there is still a need to conduct in vitro and in vivo studies to support our findings.

CONTEXT: We present a periodic hybrid DFT investigation of the structural and electronic properties of both stoichiometric and oxygen-defective TiO2 anatase bulk and (101) surface, in singlet and triplet spin states. In all cases, an excellent agreement with available photoelectron spectroscopy data has been obtained, reproducing the offsets of the deep defect levels positions from the conduction band minimum of TiO2 created upon oxygen vacancy (VO) formation. For the bulk, different local structural polaronic distortions around the VO site have been evidenced depending on the spin state considered. Although a similar conclusion has been drawn for the defective surface for the nine different vacancy positions which have been considered, large migration of the twofold coordinated surface O atom has also been evidenced, up to the initial vacancy site in some cases. The very good agreement obtained with available experimental data regarding the offsets from the conduction band minimum of the deep defect levels positions both for the bulk and the (101) surface of TiO2 anatase is encouraging for the application of the proposed hybrid-based computational strategy to TiO2 surface-related processes such as TiO2-based photocatalysis in which oxygen vacancies are known to play a key role. METHODS: All calculations have been performed with Crystal17, considering different hybrid functionals with both effective core pseudopotentials and all-electron atom-centered basis sets, as well as additional empirical dispersion effects with the D2 and D3 models.

CONTEXT: Nanoporous metals (NPMs) have a three-dimensional bicontinuous porous network structure that consists of interconnected nanoligaments. NPMs have the potential to effectively attenuate and dissipate the effects of impacts and blasts. Previous studies do not provide data on the possible effects of porosity at the nanoscale. METHODS: Molecular dynamics simulations based on the embedded-atom method potential were performed using the open-source code LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). RESULTS: Nanoporous gold (NPG) absorbs shock energy first through the elastic-plastic deformation of ligaments and then through the collapse of ligaments. After the shock loading is relaxed, NPG with lower porosity has a higher amount of springback, and new voids tend to nucleate and grow at collapsed ligaments where the packing is looser. NPG with higher porosity has a better ability to resist the propagation of a shock wave and is subjected to a smaller stress effect.

Iron is one of the essential metals required by almost all living organisms. However, nature has certain constraints in distributing this element among tissues. Since polymeric oxide-bridged Fe (III) is the prominent source of Fe (III) ions, the insolubility of Fe (III) ions in aqueous systems reduces the direct uptake by cells. Secondly, the free-Fe entities which generate .OH radicals pave the way to the destruction of the cells. Hence, a protective coordination environment via sophisticated chemical systems is required for the acquisition of Fe, its successive transport, storage, and effective utilization in various tissues. Siderophores are polydentate ligands used by bacterial cells for Fe acquisition, with a relatively high affinity for Fe (III) ions. Secreted from the bacterial cells into the external aqueous medium, they sequester Fe to give a soluble complex which re-enters the organism at a specific receptor. Once it gets inside the cell, the Fe is released from the complex and utilized for essential biochemical reactions. The medicinal applications of these natural ligands, developing progressively in various research groups, necessitate the theoretical aspects of their coordination chemistry. This research paper deals with the coordination chemistry of one of the siderophores, cepabactin (Cep). The chemical computations confirm that the FeIII(Cep)3 complex is octahedral and high spin. The oxygen atoms of Cep, which are hard and negatively charged, thus act as electron donors in the FeIII(Cep)3 complex formation. This in turn makes the siderophores relatively less attractive towards Fe (II) ions.