An efficient edge based data structure for the compressible Reynolds-averaged Navier–Stokes equations on hybrid unstructured meshes

An efficient edge based data structure has been developed in order to implement an unstructured vertex based finite volume algorithm for the Reynolds-averaged Navier–Stokes equations on hybrid meshes. In the present approach, the data structure is tailored to meet the requirements of the vertex based algorithm by considering data access patterns and cache efficiency. The required data are packed and allocated in a way that they are close to each other in the physical memory. Therefore, the proposed data structure increases cache performance and improves computation time. As a result, the explicit flow solver indicates a significant speed up compared to other open-source solvers in terms of CPU time. A fully implicit version has also been implemented based on the PETSc library in order to improve the robustness of the algorithm. The resulting algebraic equations due to the compressible Navier–Stokes and the one equation Spalart–Allmaras turbulence equations are solved in a monolithic manner using the restricted additive Schwarz preconditioner combined with the FGMRES Krylov subspace algorithm. In order to further improve the computational accuracy, the multiscale metric based anisotropic mesh refinement library PyAMG is used for mesh adaptation. The numerical algorithm is validated for the classical benchmark problems such as the transonic turbulent flow around a supercritical RAE2822 airfoil and DLR-F6 wing-body-nacelle-pylon configuration. The efficiency of the data structure is demonstrated by achieving up to an order of magnitude speed up in CPU times.     

12β-Acetyloxyperforatin,a New Limonoid from Harrisonia Perforata

A new A, D-seco limonoid, named 12-acetyloxyperforatin (1), along with three known ones, were isolated from the leaves of Harrisonia perforata. Their structures were elucidated on the basis of spectroscopic analysis, including extensive NMR techniques and computational modelling. These compounds showed no inhibitory activity against the 11β-HSD1 enzyme.     

Unravelling the Enigma of Nonoxidative Conversion of Methane on Iron Single-Atom Catalysts

The direct, nonoxidative conversion of methane on a silica-confined single-atom iron catalyst is a landmark discovery in catalysis, but the proposed gas-phase reaction mechanism is still open to discussion. Here, we report a surface reaction mechanism by computational modeling and simulations. The activation of methane occurs at the single iron site, whereas the dissociated methyl disfavors desorption into gas phase under the reactive conditions. In contrast, the dissociated methyl prefers transferring to adjacent carbon sites of the active center (Fe₁©SiC₂), followed by C−C coupling and hydrogen transfer to produce the main product (ethylene) via a key −CH−CH₂ intermediate. We find a quasi Mars–van Krevelen (quasi-MvK) surface reaction mechanism involving extracting and refilling the surface carbon atoms for the nonoxidative conversion of methane on Fe₁©SiO₂ and this surface process is identified to be more plausible than the alternative gas-phase reaction mechanism.     

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.     

Synthesis,molecular modeling,TD-DFT,antimicrobial, and in vitro therapeutic activity of new spherical nano-sized sulfonamide imine ligands and their zinc (II) and copper (II) complexes

A series of nanometer-sized spherical sulfonamide imine ligands HL ¹ -HL ⁵ and their copper and zinc complexes were synthesized and fully characterized based on elemental analyses, spectroscopic (UV/vis, FT-IR, NMR, EPR, SEM) studies, molar conductance and thermal analyses. Furthermore, computational studies of HL ¹ -HL ⁵ were carried out by the DFT/B3LYP method. TD-DFT, HOMO and LUMO energy values, chemical hardness, electronegativity, electrophilic index, softness, and other parameters were calculated. Screening against several pathogenic microorganisms indicated that HL ¹ exhibited high activity against the tested Gram-negative bacteria relative to other analogues and the inhibition activity is greater than the standard Gentamicin. Analogously, HL ² exhibited high potent activity against the tested Gram-positive bacteria. Copper complexes exhibited a higher potent activity than zinc analogues. Noteworthy, inhibition activity of [Cu ( L ³ )(OAc)] complex is higher than that of the standard Ampicillin. [Cu ( L ² )(OAc)] complex displayed a similar activity of the standard bactericides and fungicides in use. The complexes showed appreciated values of MIC against bacterial strains: B. subtilis (MIC = 0.4 μg / mL), E. coli and S. pneumonia (MIC = 1.95 μg / mL) and P. aeruginosa (MIC = 7.81 μg / mL). in vitro cytotoxic activities study proved that [Cu ( L ³ )(OAc)] complex exhibited appreciable activity versus (HEPG-2); IC₅₀ = 4.8 μg/ml, while [Cu( L ² )(OAc)] complex showed a high activity against (MCF-7); IC₅₀ = 6.2 μg/ml. These results could be considered as new findings of promising antitumor candidates for experimental chemotherapy.     

Non‐enzymatic Ribonucleotide Reduction in the Prebiotic Context

Model studies of prebiotic chemistry have revealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynucleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide reductases, which are radical enzymes. This study considers potential non‐enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a putative H₂S/HS^. environment, are characterized using computational chemistry. A bio‐inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be potentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic requirements. Non‐cyclical pathways, in which HSS^. is generated in the final step instead of HS^., show a markedly increased thermodynamic driving force (ca. 70 kJ mol^?1) and thus warrant serious consideration in the context of the prebiotic ribonucleotide reduction.     

Ligands Based on Phosphine-Stabilized Aluminum(I), Boron(I), and Carbon(0)

A systematic quantum chemical study of the bonding in d⁶-transition-metal complexes, containing phosphine-stabilized, main-group-element fragments, (R₃P)₂E, as ligands (E=AlH, BH, CH⁺, C), is reported. By using energy decomposition analysis, it is demonstrated that a strong M−E bond is accompanied by weak P−E bonds, and vice versa. Although the Al−M bond is, for example, found to be very strong, the weak Al−P bond suggests that the corresponding metal complexes will not be stable towards phosphine dissociation. The interaction energies for the boron(I)-based ligand are lower, but still higher than those for two-carbon-based ligands. For neutral ligands, electrostatic interactions are the dominating contributions to metal–ligand bonding, whereas for the cationic ligand a significant destabilization, with weak orbital and even weaker electrostatic metal–ligand interactions, is observed. Finally, for iron(II) complexes, it is demonstrated that different reactivity patterns are expected for the four donor groups: the experimentally observed reversible E−H reductive elimination of the borylene-based ligand (E=BH) exhibits significantly higher barriers for the protonated carbodiphosphorane (CDP) ligand (E=CH) and would proceed through different intermediates and transition states. For aluminum, such reaction pathways are not feasible (E=AlH). Moreover, it is demonstrated that the metal hydrido complexes with CDP ligands might not be stable towards reduction and isomerization to a protonated CDP ligand and a reduced metal center.     

Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

Influence of Polarity and Activation Energy in Microwave–Assisted Organic Synthesis (MAOS)

The aim of this work was to determine the parameters that have decisive roles in microwave-assisted reactions and to develop a model, using computational chemistry, to predict a priori the type of reactions that can be improved under microwaves. For this purpose, a computational study was carried out on a variety of reactions, which have been reported to be improved under microwave irradiation. This comprises six types of reactions. The outcomes obtained in this study indicate that the most influential parameters are activation energy, enthalpy, and the polarity of all the species that participate. In addition to this, in most cases, slower reacting systems observe a much greater improvement under microwave irradiation. Furthermore, for these reactions, the presence of a polar component in the reaction (solvent, reagent, susceptor, etc.) is necessary for strong coupling with the electromagnetic radiation. We also quantified that an activation energy of 20–30 kcal mol⁻¹ and a polarity (μ) between 7–20 D of the species involved in the process is required to obtain significant improvements under microwave irradiation.