The intrinsic twinning and enigmatic twisting of aragonite crystals.

It is generally accepted that aragonite crystals of biogenic origin are characterized by significantly higher twin densities compared to samples formed during geological processes. Based on our single crystal X-ray diffraction (SCXRD) and transmission electron microscopy (TEM) study of aragonite crystals from various localities, we show that in geological aragonites, the twin densities are comparable to those of the samples from crossed lamellar zones of molluscs shells. The high twin density is consistent with performed calculations, according to which the Gibbs free energy of twin-free aragonite is close to that of periodically twinned aragonite structure. In some cases, high twin densities result in the appearance of diffuse scattering in SCXRD patterns. The obtained TEM and optical micrographs show that besides the twin boundaries (TBs) of growth origin, there are also TBs and especially stacking faults that were likely formed as the result of local strain compensation. SCXRD patterns of the samples from Tazouta, in addition to diffuse scattering lines, show Debye arcs in the [Formula: see text] plane. These Debye arcs are present only on one side of the Bragg reflections and have an azimuthal extent of nearly 30°, making the whole symmetry of the diffraction pattern distinctly chiral, which has not yet been reported for aragonite. By analogy with biogenic calcite crystals, we associate these arcs with the presence of misoriented subgrains formed as a result of crystal twisting during growth.

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism.

3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O2-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O2-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [1H Mims electron nuclear double resonance spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.

Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations.

Biomass-derived degraded lignin and cellulose serve as possible alternatives to fossil fuels for energy and chemical resources. Fast pyrolysis of lignocellulosic biomass generates bio-oil that needs further refinement. However, as pyrolysis causes massive degradation to lignin and cellulose, this process produces very complex mixtures. The same applies to degradation methods other than fast pyrolysis. The ability to identify the degradation products of lignocellulosic biomass is of great importance to be able to optimize methodologies for the conversion of these mixtures to transportation fuels and valuable chemicals. Studies utilizing tandem mass spectrometry have provided invaluable, molecular-level information regarding the identities of compounds in degraded biomass. This review focuses on the molecular-level characterization of fast pyrolysis and other degradation products of lignin and cellulose via tandem mass spectrometry based on collision-activated dissociation (CAD). Many studies discussed here used model compounds to better understand both the ionization chemistry of the degradation products of lignin and cellulose and their ions' CAD reactions in mass spectrometers to develop methods for the structural characterization of the degradation products of lignocellulosic biomass. Further, model compound studies were also carried out to delineate the mechanisms of the fast pyrolysis reactions of lignocellulosic biomass. The above knowledge was used to assign likely structures to many degradation products of lignocellulosic biomass.

Bodipy-based quinoline derivative as a highly Hg2+-selective fluorescent chemosensor and its potential applications.

A highly efficient sensor has been successfully developed using quinoline-based BODIPY compounds (8-quinoline-4,4-difluoro-4-boro-3a, 4a-diazaindacene (C1) and 7-hydroxy-8-quinoline-4,4-difluoro-4-boro-3a, 4a-diazindacene (C2) to detect Hg2+ ions. The sensor C1 exhibits remarkable selectivity in detecting Hg2+ with a limit of detection 3.06 × 10-8 mol/L. The developed chemical sensors have shown stability, cost-effectiveness, ease of preparation, and remarkable selectivity towards Hg2+ ions compared to other commonly occurring metal ions. The total recovery of the sensor C1 can be achieved by using a 0.1 mol/L solution of KI. The proposed sensor C1 has been applied to determine Hg2+ in tap and distilled water, yielding excellent results. In addition, the binding mode of C1-Hg2+ and C2-Hg2+ complexes was a 1:1 ratio confirmed by mass spectra, Job's plot, and DFT study. Moreover, the sensor C1 successfully applied for the biological studies results in negligible cytotoxicity, which demonstrates it can be used to determine Hg2+ in HT22 cells.

Chromene-chromene Schiff base as a fluorescent chemosensor for Th4+ and its application in bioimaging of Caenorhabditis elegans.

The manuscript presents the synthesis of a new di-chromene Schiff base (COM-CH) by combining 7-(diethylamino)-2-oxo-2H-chromene-3-carbohydrazide and 4-oxo-4H-chromene-3-carbaldehyde, and its characterization using various analytical techniques. The probe COM-CH functional group contains a hard donor atom that selectively complexes with Th4+ ions. This report investigated COM-CH's sensing ability towards Th4+ chromogenic and fluorogenic methods in ACN: H2O (8:2, v/v) with Th4+ ions. The COM-CH-Th4+ complex was excited at 430 nm, resulting in a bright emission band at 475 nm with a 45 nm Stokes shift. The COM-CH probe demonstrated the highest performance at pH 4.0 to 8.0, with a sensitivity of 18.7 nM. The complex formation of COM-CH with Th4+ was investigated using NMR, FTIR spectrometry, and density functional theory calculations. The COM-CH and Th4+ are bound with 2:1 stoichiometry and an association constant of 1.92 × 108 M-2. The probe's performance enabled the analysis of monazite sand and water samples for Th4+ content. The probe successfully detected Th4+ content in Caenorhabditis elegans, marking the first Th4+ detection in animal models.

Probing Correlation of Optical Emission and Defect Sites in Hexagonal Boron Nitride by High-Resolution STEM-EELS.

Optically bright emitters in hexagonal boron nitride (hBN) often acting as a source of a single-photon are mostly attributed to point-defect centers, featuring localized intra-bandgap electronic states. Although vacancies, anti-sites, and impurities have been proposed as candidates, the exact physical and chemical nature of most hBN single-photon emitters (SPEs) within the visible region are still up for debate. Combining site-specific high-angle annular dark-field imaging (HAADF) with electron energy loss spectroscopy (EELS), we resolve and identify a few carbon substitutions among neighboring hBN hexagons, all within the same sample region, from which typical defect emission is observed. Our experimental results are further supported by first-principles calculations, through which the stability and possible optical transitions of the proposed carbon-defect complex are assessed. The presented correlation between optical emission and defects provides valuable information toward the controlled creation of emitters in hBN, highlighting carbon complexes as another probable cause of its visible SPEs.

Emergent Dirac Fermions in Epitaxial Planar Silicene Heterostructure.

Silicene, a single layer of Si atoms, shares many remarkable electronic properties with graphene. So far, silicene has been synthesized in its epitaxial form on a few surfaces of solids. Thus, the problem of silicene-substrate interaction appears, which usually depresses the original electronic behavior but may trigger properties superior to those of bare components. We report the direct observation of robust Dirac-dispersed bands in epitaxial silicene grown on Au(111) films deposited on Si(111). By performing in-depth angle-resolved photoemission spectroscopy measurements, we reveal three pairs of one-dimensional bands with linear dispersion running in three different directions of an otherwise two-dimensional system. By combining these results with first-principles calculations, we explore the nature of these bands and point to strong interaction between subsystems forming a complex Si-Au heterostructure. These findings emphasize the essential role of interfacial coupling and open a unique materials platform for exploring exotic quantum phenomena and applications in future-generation nanoelectronics.

Theoretical Insights into the Selectivity of Nitrite Reduction to NH2OH on Single-Atom Catalysts.

Electroreduction of nitrate/nitrite to high-value-added products, including NH2OH, is an important way to achieve sustainable production of green energy. However, this electrosynthesis of NH2OH still suffers from poor selectivity due to the various competing reactions. Here, we screen out Ni-N4 and Cu-N4 catalysts for highly efficient nitrite electroreduction to NH2OH by adopting density functional theory (DFT) calculations. DFT calculations reveal that the high selectivity of Ni-N4 and Cu-N4 is ascribed to their weak adsorption of *NH2OH and *NH intermediates, thereby preventing the further reduction of NH2OH. Moreover, using *NO as a model intermediate, we studied the relationship between the 3d orbital occupancy and adsorption strength of the intermediate. It is found that Ni-N4 and Cu-N4 with fully occupied dxz, dyz, and dz2 orbitals have poor adsorption of *NO intermediate. This work provides a new route for NH2OH synthesis and offers perspectives on the crucial factors in determining the catalytic selectivity.

Lifshitz Transition in a Single-Atom-Thick GdxYb1-xPb3 Kagome Compound on Si(111).

Lanthanide (Ln) elements Gd and Yb alloyed with a Pb monolayer on the Si(111) substrate form LnPb3 compounds having the same crystal structure. They comprise a single-atom-thick Pb layer arranged in a slightly distorted kagome lattice with Ln atoms filling the hexagonal voids. They have similar electronic band structures except for the Fermi level position, which varies between the divalent Yb- and trivalent Gd-containing compounds by ∼0.47 eV. The ability to create a 2D solid solution with the unified continuous Pb layer and hexagonal voids randomly filled with either Gd or Yb atoms allows precise control of the Fermi level position. Small alteration of the Fermi level triggers drastic changes in the Fermi surface topology due to the Lifshitz transition, hence in the physical properties. In particular, the sheet resistance of the GdxYb1-xPb3/Si(111) system can be controllably varied over an order of magnitude range.

Thiacalix[4]arene-Protected Silver Nanoclusters Encapsulating Different Two-Electron Superatom Oligomers.

The subvalent silver kernel represents the nascent state of silver cluster formation, yet the growth mechanism has long been elusive. Herein, two silver nanoclusters (Ag30 and Ag34) coprotected by TC4A4- (H4TC4A = p-tert-butylthiacalix[4]arene) and TBPMT- (TBPMTH = 4-tert-butylbenzenemethanethiol) containing 6e and 4e silver kernels are synthesized and characterized. The trimer of the 2e superatom Ag14 kernel in Ag30 is built from a central Ag6 octahedron sandwiched by two orthogonally oriented Ag5 trigonal bipyramids through sharing vertexes, whereas a double-octahedral Ag10 kernel in Ag34 is a dimer of 2e superatoms. They manifest disparate polyhedron fusion growth patterns at the beginning of the silver cluster formation. Their excellent solution stabilities are contributed by the multisite and multidentate coordination fashion of TC4A4- and the special valence electron structures. This work demonstrates the precise control of silver kernel growth by the solvent strategy and lays a foundation for silver nanocluster application in photothermal conversion.

Unveiling the Morphology of Carbon-Supported Ru Nanoparticles by Multiscale Modeling.

Simulating the behavior of metal nanoparticles on supports is crucial for boosting their catalytic performance and various nanotechnology applications; however, such simulations are limited by the conflicts between accuracy and efficiency. Herein, we introduce a multiscale modeling strategy to unveil the morphology of Ru supported on pristine and N-doped graphene. Our multiscale modeling started with the electronic structures of a supported Ru single atom, revealing the strong metal-support interaction around pyridinic nitrogen sites. To determine the stable configurations of Ru2-13 clusters on three different graphene supports, global energy minimum searches were performed. The sintering of the global minimum Ru13 clusters on supports was further simulated by ab initio molecular dynamics (AIMD). The AIMD data set was then collected for deep potential molecular dynamics to study the melting of Ru nanoparticles. This study presents comprehensive descriptions of carbon-supported Ru and develops modeling approaches that bridge different scales and can be applied to various supported nanoparticle systems.

Vacancy-Enhanced Sb-N4 Sites for the Oxygen Reduction Reaction and Zn-Air Battery.

With the advantages of a Fenton-inactive characteristic and unique p electrons that can hybridize with O2 molecules, p-block metal-based single-atom catalysts (SACs) for the oxygen reduction reaction (ORR) have tremendous potential. Nevertheless, their undesirable intrinsic activity caused by the closed d10 electronic configuration remains a major challenge. Herein, an Sb-based SAC featuring carbon vacancy-enhanced Sb-N4 active centers, corroborated by the results of high-angle annular dark-field scanning transmission electron microscopy and X-ray absorption fine structure, has been developed for an incredibly effective ORR. The obtained SbSA-N-C demonstrates a positive half-wave potential of 0.905 V and excellent structural stability in alkaline environments. Density functional theory calculations reveal that the carbon vacancies weaken the adsorption between Sb atoms and the OH* intermediate, thus promoting the ORR performance. Practically, the SbSA-N-C-based Zn-air batteries achieve impressive outcomes, such as a high power density of 181 mW cm-2, showing great potential in real-world applications.

Multiscale Regulation of Ordered PtCu Intermetallic Electrocatalyst for Highly Durable Oxygen Reduction Reaction.

Transforming the Pt-M alloy into an ordered intermetallic is an effective strategy to improve the electrocatalytic activity and stability toward the oxygen reduction reaction (ORR). However, the synthesis of nanosized intermetallics remains challenging. Herein, we report an efficient ORR electrocatalyst, consisting of a monodisperse nanosized PtCu intermetallic on hollow mesoporous carbon spheres (HMCS). As predicted by theoretical calculations, PtCu intermetallics exhibit beneficial electronic structure, with a low theoretical overpotential of 0.33 V and enhanced Cu stability. Resulting from the multiscale modulation of catalyst structure, the O-PtCu/HMCS catalyst delivers a high mass activity of 2.73 A cm-2Pt at 0.9 V and remarkable stability. Identical location transmission electron microscopy (IL-TEM) investigations demonstrate that the rate of carbon corrosion is alleviated on HMCS, which contributes to the long-term durability. This work provides a promising design strategy for an ORR electrocatalyst, and the IL-TEM investigations offer new perspectives for the performance enhancement mechanism.

Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives.

This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound 3 h, followed closely by 6 h, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. In vivo oral toxicity studies were conducted for the most active compound 3 h, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of 3 h, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.

Identification of Helicobacter pylori-carcinogenic TNF-alpha-inducing protein inhibitors via daidzein derivatives through computational approaches.

Gastric cancer is considered a class 1 carcinogen that is closely linked to infection with Helicobacter pylori (H. pylori), which affects over 1 million people each year. However, the major challenge to fight against H. pylori and its associated gastric cancer due to drug resistance. This research gap had led our research team to investigate a potential drug candidate targeting the Helicobacter pylori-carcinogenic TNF-alpha-inducing protein. In this study, a total of 45 daidzein derivatives were investigated and the best 10 molecules were comprehensively investigated using in silico approaches for drug development, namely pass prediction, quantum calculations, molecular docking, molecular dynamics simulations, Lipinski rule evaluation, and prediction of pharmacokinetics. The molecular docking study was performed to evaluate the binding affinity between the target protein and the ligands. In addition, the stability of ligand-protein complexes was investigated by molecular dynamics simulations. Various parameters were analysed, including root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), hydrogen bond analysis, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM). The results has confirmed that the ligand-protein complex CID: 129661094 (07) and 129664277 (08) formed stable interactions with the target protein. It was also found that CID: 129661094 (07) has greater hydrogen bond occupancy and stability, while the ligand-protein complex CID 129664277 (08) has greater conformational flexibility. Principal component analysis revealed that the ligand-protein complex CID: 129661094 (07) is more compact and stable. Hydrogen bond analysis revealed favourable interactions with the reported amino acid residues. Overall, this study suggests that daidzein derivatives in particular show promise as potential inhibitors of H. pylori.

In silico analysis of potential inhibitors for breast cancer targeting 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyses.

Breast cancer (BC) is still one of the major issues in world health, especially for women, which necessitates innovative therapeutic strategies. In this study, we investigated the efficacy of retinoic acid derivatives as inhibitors of 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), which plays a crucial role in the biosynthesis and metabolism of oestrogen and thereby influences the progression of BC and, the main objective of this investigation is to identify the possible drug candidate against BC through computational drug design approach including PASS prediction, molecular docking, ADMET profiling, molecular dynamics simulations (MD) and density functional theory (DFT) calculations. The result has reported that total eight derivatives with high binding affinity and promising pharmacokinetic properties among 115 derivatives. In particular, ligands 04 and 07 exhibited a higher binding affinity with values of -9.9 kcal/mol and -9.1 kcal/mol, respectively, than the standard drug epirubicin hydrochloride, which had a binding affinity of -8.2 kcal/mol. The stability of the ligand-protein complexes was further confirmed by MD simulations over a 100-ns trajectory, which included assessments of hydrogen bonds, root mean square deviation (RMSD), root mean square Fluctuation (RMSF), dynamic cross-correlation matric (DCCM) and principal component analysis. The study emphasizes the need for experimental validation to confirm the therapeutic utility of these compounds. This study enhances the computational search for new BC drugs and establishes a solid foundation for subsequent experimental and clinical research.

Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism.

Arsenic contamination of groundwater is among one of the biggest health threats affecting millions of people in the world. There is an urgent need for efficient arsenic biosensors where the use of arsenic metabolizing enzymes can be explored. In this work, we have solved four crystal structures of arsenite oxidase (Aio) in complex with arsenic and antimony oxyanions and the structures determined correspond to intermediate states of the enzymatic mechanism. These structural data were complemented with density-functional theory calculations providing a unique view of the molybdenum active site at different time points that, together with mutagenesis data, enabled to clarify the enzymatic mechanism and the molecular determinants for the oxidation of As(III) to the less toxic As(V) species.

Water and Cu+ Synergy in Selective CO2 Hydrogenation to Methanol over Cu-MgO-Al2O3 Catalysts.

The CO2 hydrogenation reaction to produce methanol holds great significance as it contributes to achieving a CO2-neutral economy. Previous research identified isolated Cu+ species doping the oxide surface of a Cu-MgO-Al2O3-mixed oxide derived from a hydrotalcite precursor as the active site in CO2 hydrogenation, stabilizing monodentate formate species as a crucial intermediate in methanol synthesis. In this work, we present a molecular-level understanding of how surface water and hydroxyl groups play a crucial role in facilitating spontaneous CO2 activation at Cu+ sites and the formation of monodentate formate species. Computational evidence has been experimentally validated by comparing the catalytic performance of the Cu-MgO-Al2O3 catalyst with hydroxyl groups against that of its hydrophobic counterpart, where hydroxyl groups are blocked using an esterification method. Our work highlights the synergistic effect between doped Cu+ ions and adjacent hydroxyl groups, both of which serve as key parameters in regulating methanol production via CO2 hydrogenation. By elucidating the specific roles of these components, we contribute to advancing our understanding of the underlying mechanisms and provide valuable insights for optimizing methanol synthesis processes.

Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns.

Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.

Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study.

Acetonitrile, a polar molecule that cannot form hydrogen bonds on its own, interacts with solvent molecules mainly through the lone pair of its nitrogen atom and the π electrons of its CN triple bond [Correction added on 17 July 2024, after first online publication: Acetole has been changed to Acetonitrile in the preceeding sentence.]. Interestingly, acetonitrile exhibits an unexpected strengthening of the triple bond's force constant in an aqueous environment, leading to an upshift (blueshift) in the corresponding stretching vibration: this effect contrasts with the usual consequence of hydrogen bonding on the vibrational frequencies of the acceptor groups, that is, frequency redshift. This investigation elucidates this phenomenon using Raman spectroscopy to examine the behavior of acetonitrile in organic solvent, water, and silver ion aqueous solutions, where an even more pronounced upshift is observed. Raman spectroscopy is particularly well suited for analyzing aqueous solutions due to the minimal scattering effect of water molecules across most of the vibrational spectrum. Computational approaches, both static and dynamical, based on Density Functional Theory and hybrid functionals, are employed here to interpret these findings, and accurately reproduce the vibrational frequencies of acetonitrile in different environments. Our calculations also allow an explanation for this unique behavior in terms of electric charge displacements. On the other hand, the study of the interaction of acetonitrile with water molecules and metal ions is relevant for the use of this molecule as a solvent in both chemical and pharmaceutical applications.