Search Results (558)

Crystalline chlorobenzofuroxan (ClBF) exhibits persistent positional isomeric disorder, with 5-ClBF and 6-ClBF sharing the same crystallographic sites. Periodic density functional theory was used to investigate the associated configurational energetics and solid-state interconversion pathways. All 256 starting arrangements constructed from four local models—5-ClBF, 6-ClBF, and two atom-mapped representations of the same open-dinitroso structural model—over four molecular sites were optimized at fixed experimental lattice parameters. Among the 254 structures retaining the predefined molecular connectivity, the fully 5-ClBF configuration had the lowest electronic energy. Mixed cyclic configurations remained comparatively low in energy and showed non-additive, arrangement-dependent energy penalties. Ring-opened configurations and an alternative ordered model containing four-membered N–O–N–O rings were substantially less favorable. Eight representative one-site transformations yielded non-spin-polarized electronic barrier estimates of 170.1–217.7 kJ mol⁻¹, compared with 745.5 kJ mol⁻¹ for the investigated four-molecule transformation, for the complete four-molecule crystallographic unit cell. Three sequential branches differed in their intermediate barrier estimates but reached the same maximum electronic-energy level within the investigated model. The separation between modest configurational energy differences and substantially larger barrier estimates is consistent with kinetically hindered redistribution after a mixed isomeric population has been incorporated into the crystal, without quantitatively predicting the experimental populations or their origin. Full article

Nanoscale Al₃Sc precipitates strongly influence dislocation transport and heterogeneous plastic deformation in Al-Sc alloys. Here, the environment-dependent evolution of precipitate–dislocation interactions in an Al–0.3 wt.% Sc alloy was investigated by in-situ TEM tensile testing, assisted by EBSD, TEM, EDS, and atomic-resolution HAADF-STEM. The ordered Al₃Sc precipitates exhibit an average equivalent diameter of 27.0 ± 6.3 nm, an areal number density of ~27.5 μm⁻², and an average center-to-center spacing of ~102 nm, corresponding to an effective obstacle spacing of ~75 nm. The modified Orowan model gives a critical shear-stress increment of ~67 MPa and a macroscopic strengthening contribution of ~205 MPa. During intragranular deformation, dislocations undergo repeated bowing, pinning, depinning, and renewed glide. Near grain boundaries, precipitate arrangements promote directional dislocation transport and heterogeneous strain accommodation. At the crack tip, selective pinning redistributes plastic flow, promotes crack-tip blunting, and activates alternative slip paths, contributing to crack-path deflection. These observations establish a continuous mechanistic link between nanoscale precipitate characteristics, dislocation transport, heterogeneous plasticity, and crack propagation in Al-Sc alloys. Full article

Single-atom–nanocluster (SA–NC) architectures combine atomically dispersed metal sites and nanoscale ensembles, leveraging high utilization, defined coordination, cooperative adsorption, and tunable electronics to generate synergy via spatial, electronic, and intermediate-transfer pathways. Metal–organic framework (MOF)-derived materials with ordered metal nodes and structural diversity enable regulating these active centers from atomic to nanometer scales. This review systematically summarizes recent advances in MOF-derived electrocatalysts for the hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and oxygen reduction reaction (ORR) from the perspectives of material classification, controllable synthesis, and active-site engineering. We highlight the coordination and electronic structure modulation of single-atom sites, the nuclearity control and interfacial effects of nanoclusters, and the synergistic mechanisms in SA–NC, which are categorized into adjacent, discrete, and core–shell configurations. We further discuss how spatial arrangement, electronic communication, and intermediate spillover collectively govern catalytic performance. Despite significant advances, a major challenge remains in correlating dynamically evolving active species under operating conditions with their intrinsic catalytic behavior. Future progress requires the integration of operando characterization and theoretical modeling to establish quantitative structure–activity relationships, thereby shifting catalyst design from composition-based optimization toward interaction engineering among multiscale active centers. Full article

Alkaline agricultural soils pose a significant challenge for N₂O mitigation. Iron−modified biochar (FBC) holds potential for greenhouse gas reduction, yet its mechanisms in alkaline soils remain poorly understood. This study focused on alkaline loess in Yan’an, Shaanxi, and established three treatments (CK, BC1%, FBC1%), each with three replicates. Through a 90-day indoor cultivation experiment, combined with Raman spectroscopy and high-throughput sequencing, the study investigated the mechanism by which FBC suppresses N₂O emissions. Results showed that the specific surface area of FBC increased by 46.2%, the I_D/I_G ratio decreased, the arrangement of carbon atoms became more ordered, and the carbon-based microcrystalline structure was stabilized. After 90 days of cultivation, the pH of the FBC-treated sample was 0.17 lower than that of the CK-treated sample, the total nitrogen content decreased by 11.90%, and the cumulative N₂O emissions were reduced by 23.20%. High-throughput sequencing revealed microbial mechanisms underlying N₂O mitigation: Proteobacteria relative abundance significantly increased by 5.52%, while nitrogen cycling functional genes (amoA, nirK, etc.) showed selective relative abundance responses. These findings demonstrate that under alkaline loess conditions, the core mechanism of FBC emission reduction lies in the synergy of physical retention and biochemical regulation, where optimized pore structures hinder nitrogen oxide diffusion into anaerobic microenvironments. This study elucidates the dual efficacy of iron-modified biochar in nitrogen retention and gaseous emission reduction in alkaline soils, offering a promising material strategy for agricultural N₂O reduction. Full article

Reduction of [Tc(CO)₅Br] with sodium amalgam, sodium naphthalenide, or potassium graphite in THF and subsequent addition of bis(triphenylphosphine)iminium chloride, (PPN)Cl, gave mixtures of the orange-yellow Tc(0) compound (PPN)[Tc(CO)₉Cl], (PPN)[1], and the colorless Tc(I) complex (PPN)₂[Tc(CO)₃Cl₃], (PPN)₂[2]. The products have been studied by X-ray diffraction and NMR spectroscopy. The dimeric compound [1]⁻ represents the first example of an anionic technetium(0) complex with only one halide ligand in its coordination sphere. The equatorial carbonyl (and chlorido) ligands at the two technetium atoms show the expected staggered conformation around the (CO)Tc–Tc(CO) axis. The Tc–Tc bond is 3.0269(7) Å. The different nature of the two technetium atoms in compound [1]⁻ is reflected by the appearance of two different ⁹⁹Tc NMR signals in CD₂Cl₂ at −1770 and −2487 ppm, while the corresponding signal of the technetium(I) anion [2]²⁻ appears at −953 ppm in the same solvent. Anion [2]²⁻ shows the expected facial arrangement of the carbonyl and chlorido ligands. The use of the bulky PPN⁺ cation allowed the first determination of the [Tc(CO)₃Cl₃]²⁻ structure by X-ray diffraction without significant interference due to disorder effects in the coordination sphere of the transition metal. Full article

Nickel(II) offers an appealing base for metallodrug design as it is abundant, inexpensive and forms well-defined complexes with N,O-donor ligands. Therefore, five Ni(II) complexes containing two tridentate 2-imine-8-hydroxyquinoline Schiff base ligands, derived from morpholine, piperidine, imidazole or 2-methyl-1H-limidazole, were synthesized and characterized in solution and solid state via analytical and spectroscopic techniques. Single crystals were solved using X-ray diffraction for the complex derived from 4-(2-aminopropyl)morpholine (1). This Ni(II) complex exhibits a distorted octahedrally coordinated Ni(II) center bound to two monodeprotonated NNO-tridentate ligands, adopting a meridional coordination mode, with the two oxygen atoms arranged cis to each other. The stability of the complexes in aqueous media buffered at pH 7.4 was evaluated with UV–Vis spectroscopy and their binding to bovine serum albumin (BSA) was assessed with fluorescence titrations. All complexes show strong reversible binding to BSA (K_SV ~10⁵), which stabilizes the lipophilic complexes in aqueous media. The antiproliferative activity of the complexes was screened against colon cancer cell lines (Colo205 and Colo320). They exhibit moderate anticancer activity (IC₅₀ = 15.1–92.5 μM), with structure–activity relationships favoring imidazole derivatives and maintaining activity against the doxorubicin-resistant cell line (Colo320) with resistance indices (1.3–3.1) comparable to or lower than doxorubicin. Overall, the complexes represent a platform to develop new anticancer Ni-based drugs. Full article

Re₃Zr has recently been proposed in the cubic Pm-3n structure. Its alternative atomic arrangements and thermodynamic position within the Re–Zr system have not been systematically resolved. In this work, CALYPSO particle-swarm structure searches combined with density functional theory identify five Re₃Zr polymorphs with Cmcm, Fmmm, Immm, P4/mmm, and Fm-3m symmetries and compare them consistently with the reported Pm-3n phase. Formation enthalpies, a selected-phase partial convex hull, phonon dispersions, elastic properties, sound velocities, elastic Debye temperatures, electronic structures, and bonding characteristics are evaluated. All five CALYPSO structures lie below Pm-3n in fixed-composition energy, with Cmcm being the lowest. The Cmcm phase has a formation enthalpy of −0.257 eV atom⁻¹ and lies approximately 0.042 eV atom⁻¹ above the selected-phase partial hull, identifying it as a low-lying off-hull metastable candidate at 0 K. AIMD simulations at 300 and 1000 K show no obvious structural reconstruction of the Cmcm framework over the simulated time scales. All six structures exhibit no imaginary phonon frequencies and satisfy the corresponding mechanical-stability criteria. Their elastic responses are strongly structure dependent: P4/mmm has the largest Chen–Tian hardness estimates and elastic Debye temperature, whereas Fm-3m shows the weakest elastic anisotropy. All six polymorphs are metallic, with Fermi-level states dominated by Re-5d orbitals and predominantly delocalized bonding. These results provide a thermodynamically constrained 0 K reference for future synthesis, phase identification, and finite-temperature or kinetic investigations of hypothetical Re₃Zr polymorphs. Full article

Microtubule organization during cell division requires coordinated regulation by microtubule-associated proteins and protein kinase signaling pathways. In animals, TPX2 (Targeting Protein for Xklp2) regulates spindle assembly by binding to and activating Aurora A kinase. In Arabidopsis, individual TPX2-like (TPXL) proteins have been implicated in Aurora-associated functions, but whether the TPXL family members share common microtubule-associated properties and how TPXL-Aurora interactions differ across the family remain incompletely understood. Here, we investigated the structural and cellular relationships among the eight Arabidopsis TPX2-like proteins (TPXL1–TPXL8), microtubules, and Aurora kinases. AlphaFold3-based structural prediction indicated that specific interaction sites between TPXL proteins and tubulins were revealed at the three-dimensional structure and atomic level, suggesting that all TPXL proteins contain a conserved TPX2 domain contributing to their predicted tubulin association. Transient expression analyses showed that TPXL1–TPXL8 localized to microtubule arrays during both interphase and cell division. Although microtubule-associated domain is predicted to be conserved across the family, individual TPXL members exhibit distinct localization patterns on spindles and phragmoplasts, suggesting potential functional specialization. Further structural prediction and experimental validation revealed that only TPXL2, TPXL3, TPXL4, and TPXL8 interacted with AUR1 (Aurora 1) and AUR2, whereas no detectable interactions were observed for the other TPXL members or for any TPXL protein with AUR3. Structural prediction of TPXL–AUR1–tubulin complexes were consistent with a possible arrangement in which TPXL proteins contact both AUR1 and tubulin. Together, our findings suggest that Arabidopsis TPXL proteins have broad microtubule association and are coupled with selective Aurora kinase interaction to coordinate microtubule organization, providing a framework for future functional analysis of TPXL–Aurora–microtubule association during plant cell division. Full article

Structural analysis using X-rays and electron beams has long provided the average arrangement of atoms and molecules—that is, “structural information”—with high precision. By contrast, static measurements cannot directly yield dynamic information on how a material changes over time; instead, information on motion is convolved into a single numerical value such as the B-factor (atomic displacement parameter). Taking this limitation as its starting point, this review surveys the recent trend of introducing a time axis into measurements to observe material dynamics directly. First, we outline the technological foundations that have made the transition from static to time-resolved measurement possible. It rests on the dramatic shortening of exposure times, enabled by the increased brilliance of X-ray and electron sources and by advances in detection technology such as direct photon-counting detectors. Next, we survey dynamic measurement techniques, including time-resolved X-ray crystallography, coherent X-ray scattering, neutron scattering, and time-resolved electron microscopy. We also point out the essential limitation that most of them still return ensemble or volume averages. Building on this, we systematically describe diffracted X-ray tracking (DXT), diffracted X-ray blinking (DXB), small-angle X-ray blinking (SAXB), transmitted X-ray blinking (TXB), and electron-beam molecular dynamics (EBMD), which use gold nanocrystals and gold nanoparticles as motion probes. We distinguish throughout between methods that follow individual objects—DXT and EBMD, which yield trajectories of single labeled molecules or single particles—and methods that analyze intensity fluctuations arising from many contributors within one pixel or illuminated volume—DXB, SAXB and TXB. The latter are not single-molecule measurements; rather, they replace a global ensemble average by a spatially localized statistical one, retaining local heterogeneity that a bulk measurement would average away. Finally, we discuss the implementation and prospects of the large-volume data analysis—principal component analysis, Bayesian inference, machine learning, and autonomous measurement—needed to handle the explosively increasing amount of information that the time axis introduces. We close with the outlook that time-resolved measurement incorporating AI and big-data analysis will become established as a new measurement platform that complements and extends conventional static structural analysis. Full article

Recently we could demonstrate that the reaction of the bissilylated metalloid cluster K₂[Ge₉(Hyp)₂] (Hyp = Si(SiMe₃)₃) with phosphine-stabilized silver chlorides gives the intermetalloid cluster Ag₁₂[Ge₉(Hyp)₂]₆, featuring a silver core of twelve silver atoms surrounded by six [Ge₉(Hyp)₂] units. Thereby, the silver atoms in the core appear to have an oxidation state of less than +I, indicating that a redox chemistry also takes place during the formation. We now present a possible precursor or intermediate to the intermetalloid cluster in this reaction system with the formula Ag₈(PEt₃)₆[Ge₉(Hyp)₂]₄. In this compound only four [Ge₉(Hyp)₂] units are arranged in a plane and connected via eight silver atoms. This compound seems to contain only silver cations, shedding further light on the complex solution and coordination chemistry of [Ge₉(Hyp)₂]²⁻ with transition metal cations. As the intermetalloid cluster Ag₁₂[Ge₉(Hyp)₂]₆ can be obtained from dissolved crystals of Ag₈(PEt₃)₆[Ge₉(Hyp)₂]₄, this indicated that the Ag₈ compound might be an intermediate (kinetic product) on the way to the Ag₁₂ compound (thermodynamic product). Full article

Ilmenite is the core carrier of titanium resources in China. Conventional flotation systems generally have the problems of insufficient collector adsorption efficiency and limited separation index. Microwave pretreatment can strengthen the flotation process by activating the surface of minerals, but its regulation mechanism on the interface properties of ilmenite and the adsorption behavior of collectors remains to be systematically elucidated. Based on the previous research on the flotation separation effect of the ‘OHA + HDPA composite collector + microwave pretreatment (power of 800 W and irradiation time of 180s)’ system, this paper uses the OHA + HDPA (mass ratio 3:1) composite system as the collector and uses surface tension, contact angle, Zeta potential, infrared spectroscopy and X-ray photoelectron spectroscopy, and other multi-scale complementary characterization methods to systematically study the effect of microwave activation on the wettability of ilmenite surface and the adsorption of collector interface. The results show that the wettability of ilmenite surface by microwaves presents a two-way regulation characteristic. In a pure water system, microwave activation increases the surface polar active sites, the water contact angle decreases from 48.44° to 46.65°, and the hydrophilicity is slightly enhanced. Under the action of the collector, microwaves promoted the directional adsorption and orderly arrangement of reagents, the contact angle of minerals increased to 85.24°, the adhesion work reached 0.560 J/m², and the surface hydrophobicity and solid–gas adhesion ability were significantly improved. Interfacial electrokinetic analysis showed that microwave activation enhanced the positive surface charge of ilmenite, and the isoelectric point shifted from pH 5.1 to alkaline to pH 6.3. In the range of pH 2–10, the Zeta potential of the sample after microwave treatment shifted more negatively, which was due to the synergistic enhancement of electrostatic attraction and chemical chelation sites. Microscopic characterization confirmed that the collector was attached to the surface of ilmenite in the form of chemical adsorption. Microwaves did not change the essential properties of adsorption but increased the adsorption capacity of the collector by 10.9%, and the adsorption layer was more compact and orderly. A mechanism analysis reveals that microwave irradiation induces the oxidation of surface Fe²⁺ to Fe³⁺, and its atomic proportion increases from 23.91% to 38.64%, which significantly enhances the chelation between the collector and the iron site and the stability of the chemical bond. At the same time, combined with the change of XPS coordination environment, it is speculated that microwaves can induce lattice distortion, change the coordination environment of titanium atoms, increase the proportion of Ti-O-Fe bridge oxygen structure, increase the unsaturated titanium active site, and strengthen the coordination between the collector and the titanium site. The synergistic activation of iron–titanium multi-sites together enhances the adsorption strength and adsorption capacity of the collector. This study can provide theoretical support at the interface chemical level for the development of high-efficiency ilmenite flotation process. Full article

4H-SiC substrate is widely employed in semiconductor device fabrication owing to its unique crystal structure and excellent physicochemical properties. However, its deformation behavior during substrate processing remains complex and not fully understood. In this study, molecular dynamics (MD) simulations were performed to systematically investigate the deformation mechanism of single-crystal 4H-SiC during nanoindentation, serving as an atomic-scale analogue of the workpiece–abrasive interaction during substrate processing. Specifically, the relationship between the fluctuations of the load–depth curve and slip were revealed, with particular emphasis on the basal slip (BS) and prismatic slip (PS) behaviors. The results indicate that the fluctuations in the load–depth curve are primarily associated with the nucleation and propagation of dislocations. The initiation of BS is predominantly influenced by the atomic arrangement and stress distribution, while PS initiates at the terminus of BS as the indentation depth increases. Finally, nanoindentation experiments were conducted to validate the reliability of the MD simulations. These findings provide valuable insights into the deformation mechanism and mechanical behavior of 4H-SiC during practical substrate processing. Full article

The effect of the chlorine atom in the sixth position and methyl group in the third position of the uracil ring on the structural parameters, NBO charge distribution, and molecular properties of the 6-chloro-3-methyluracil (M6CU) biomolecule was analyzed in the isolated state, solid-state arrangement and within a double-stranded RNA microhelix. This effect, which was also compared to those with uracil and several uracil derivatives, leads to higher reactivity and the special properties of this pharmaceutical compound. Several correlations were established using MP2 and several DFT methods. The structural characterization of M6CU and a detailed analysis of the experimental FT-IR and FT-Raman spectra in the solid state was another aim studied in detail. For an accurate assignment, a simple approximation to a crystalline unit cell was optimized using a trimer form and the wavenumbers were subsequently corrected using several scaling procedures. The modified nucleobase M6CU forms base pairs with the complementary adenine and, therefore, it could replace uracil in the helix; based on our calculations, it leads to a noticeable helix deformation. This computational finding suggests its possible potential effect by binding to cancer-related or viral RNA helices. Molecular docking also revealed that M6CU could act as an active ligand within the 1JPW active site of the target β-catenin/Tcf4 protein complex. Full article

Background: The computation of DNA is a field of growing interest, primarily focused on studying its individual constituents, but a few authors have gone further by analyzing standard microhelices with DFT methods. Objective: Because these studies did not consider that, at the atomic level, other possible DNA and RNA helices with the WC-type arrangement are also stable, this is the main objective here. Methods: Therefore, forty microhelices were optimized in a simple model with three WC base pairs composed of nucleosides using the M06-2X DFT method. Results: Based on the spatial arrangement of the intramolecular H-bond with the 2′-OH group, five types of RNA:RNA double microhelices were obtained; by this arrangement, they were related to the corresponding DNA:DNA ones. In addition to A-type and B-type microhelices, two new types were found, conveniently named B1-type and C-type. The structural geometric parameters of all these optimized microhelices in an isolated state were compared and analyzed in detail. The total counterpoise-corrected interaction energies were determined in these microhelices. RNA microhelices with different types of intramolecular H-bond arrangements involving the 2′-OH group in each single strand were also optimized, as well as their corresponding DNA helices having the same spatial arrangement. Different DNA:RNA hybrid microhelices were also considered, and their structural geometric parameters were compared to those of other microhelices. Conclusions: the identification and detailed characterization, for the first time, of ten main stable spatial geometric shapes with different exocyclic and endocyclic torsional angles. Several relationships among the structural geometric parameters of these microhelices were also established. Although the new DNA/RNA helix types containing theoretically obtained WC pairs have not been found in biological helices, they could be synthesized and they may open the possibility of being used for other purposes. Full article

This year marks the tenth anniversary of the experimental discovery and structural identification of carbon honeycomb (CH) structures. One of the most prominent properties of CHs is their unique high sorption capacity, which may play an important role in numerous applications, such as Li/Na batteries, hydrogen storage and carbon dioxide capture, as well as in the production of unique composites. In this paper we examine how atoms captured in CHs can be distributed inside CH channels using argon as a neutral probing material. Through a comprehensive structural analysis of the high-energy electron diffraction data, we demonstrate that argon atoms are not randomly positioned, but are rather arranged in specific clusters within the CH nanochannels. In the paper we propose two different original approaches to the structural analysis of pure and argon-filled CHs. We have also revealed that not all CH channels of various sizes are filled with argon, considering the spatial confinement in the thinnest channels to be one of the reasons for such a behavior. It was also found that external conditions may play an important role in filling CHs with gases, particularly at growing temperatures, when atoms gradually desorb, first from the channels of the largest sizes. Full article