Crystallographic Structure Research Articles

Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence

Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.

Tuning Magnetic and Semiconducting Properties of Cr-Doped CaTiO3 Perovskites for Advanced Spintronic Applications

The physical properties of perovskite-type materials are sensitive to their chemical composition and crystallographic structure, which makes them highly versatile for various advanced technological applications. In this theoretical study, density functional theory (DFT) is employed to investigate the electronic properties of the perovskite-like material CaTiO3, focusing on the substitution of Ti4+ with the magnetic transition metal Cr4+. The results reveal a systematic increase in the effective magnetic moment and a gradual decrease in the bandgap with increasing Cr4+ content in the CaTi1−xCrxO3 system (x = 0.0, 0.25, 0.5, 0.75, 1.0). The interactions between electronic orbitals associated with Ti-O-Cr inter-octahedral bonds modify the magnetic response of the material, leading to hybridizations between valence and conduction states that alter its semiconductor character. This tunability in electronic and magnetic properties underscores the potential of these materials for applications in spintronics. This study offers novel insights into the design of new magnetic semiconductor materials with tailored functionalities, contributing to the development of next-generation spintronic devices.

On the supramolecular interactions into a pH- and Metal-Actuated Molecular Shuttle: some insights from QTAIM modeling.

Supramolecular contacts responsible for chemical interaction of cucurbit[7]uril (CB[7]) macrocycle on a Tolyl-Viologen-Phenylene-Imidazole (T-VPI) molecular thread, at acid pH (T-VPI-H+) or after Ag+ cation addition (T-VPI-Ag+), are analytically addressed in a computational framework combining Quantum Theory of Atoms in Molecules (QTAIM) with Density Functional Theory (DFT). In this respect, the crystallographic structure (CCDC number 2217466) is taken as reference condition for addressing the nature of the chemical interactions driving the shuttling of the CB[7] between T and P stations recently observed in dilute water solutions. Beside the host(CB[7]) vs guest(T-VPI-H+ or T-VPI-Ag+) complexation, the coordination sphere of the Ag+ cation is also investigated by means of local electronic energy density - H(r) - descriptors. The derived non-covalent interaction patterns are found to support diagnostic 1H NMR signals used for detecting the mutual position of the CB[7] along the axle. This work highlights the potentialities of a QTAIM based approach in the characterization of supramolecular and metal-complexation effects in molecular aggregates such as not-interlocked synthetic molecular shuttles.

Crystal structure of dihydroneopterin aldolase from Mycobacterium tuberculosis associated with 8-mercaptoguanine, and development of novel S8-functionalized analogues as inhibitors: Synthesis, enzyme inhibition, in vitro toxicity and antitubercular activity

The crystallographic structure of the FolB enzyme from Mycobacterium tuberculosis (MtFolB), complexed with its inhibitor 8-mercaptoguanine (8-MG), was elucidated at a resolution of 1.95 Å. A novel series of S8-functionalized 8-MG derivatives were synthesised and evaluated as in vitro inhibitors of dihydroneopterin aldolase (DHNA, EC 4.1.2.25) activity of MtFolB. These compounds exhibited IC50 values in the submicromolar range. Evaluation of the activity for five compounds indicated their inhibition mode and inhibition constants. Molecular docking analyses were performed to determine the enzyme-inhibitor intermolecular interactions and ligand conformations upon complex formation. The inhibitory activities of all compounds against the M. tuberculosis H37Rv strain were evaluated. Compound 3e exhibited a minimum inhibitory concentration in the micromolar range. Finally, Compound 3e showed no apparent toxicity in both HepG2 and Vero cells. The findings presented herein will advance the quest for novel, specific inhibitors targeting MtFolB, an attractive molecular target for TB drug development.

Unveiling the potential of novel 5α-reductase inhibitors via ligand based drug design, molecular docking and ADME predictions to manage BPH

Benign prostatic hyperplasia (BPH), a prevalent condition among elderly males characterized by the non-cancerous enlargement of the prostate gland is due to the increased stromal and epithelial cell numbers. The enlargement is driven by an active dihydrotestosterone (DHT), synthesized from its prohormone testosterone under the catalytic effect of 5α-reductase Type-II (5-AR2) enzyme. To reduce the increased DHT levels and ultimately to control prostate growth, inhibition of the 5-AR represent an interesting therapeutic target. The 3D crystallography structure 5-AR2, a member of the steroid 5-AR family belonging to the class of oxidoreductase has been resolved recently and opened the door to develop selective novel inhibitors of 5-AR Type-II isoform using molecular modeling techniques. The Force field and Gaussian-field three-dimensional quantitative structure–activity relationship (3D-QSAR) models have been developed using 42 selective 5-AR2 inhibitors belonging to chemical class of steroidal androstene. Partial least squares analysis produced statistically significant model with R2training = 0.9367, 0.9459 and predictability Q2test = 0.7233, 0.8595. Developed 3D-QSAR model include steric, electrostatic, hydrophobic, and hydrogen bond acceptor and donor field indicators, whereas the potential field contributions indicated the importance of steric feature in governing their biological activity. Protein-ligand interaction pattern analysis revealed that amino acid residues GLU57, ARG114, TYR91 present in the active site of 5-AR2 are crucial for lower energy complexes with good binding affinity. Identified hits were finally adjudged for their druggability by determining in-silico pharmacokinetic parameters. Further, RMSD, binding free energy calculations and post MD analysis demonstrated the enhanced binding affinity with better ΔGbind value (-79.6 ± 3.9 kcal/mol) of identified ligand A-10 than the reference molecule finasteride (-69.13 ± 4.69 kcal/mol). Combined approach of ligand-based and structure-based models have provided an improved understanding of the structural properties of androstene class that may be further used to develop novel 5-AR2 inhibitors to be useful in BPH.

Broadband spectral cyan emission phosphor for full-spectrum LED caused by interstitial site occupation

The phosphor with a highly condensed, rigid framework structure and a single crystallographic site often exhibit symmetrical narrow-band emission. It is challenging to achieve broadband emission by doping Eu2+ ions in similar structures. Here, we propose to control the occupation and quenching concentration of Eu2+ ions in a single-site matrix Sc2Si2O7 to increase efficiency and precise regulation of luminescence spectra substantially. The analysis of photoluminescence spectroscopy through steady-state, transient-state, and Gaussian fitting techniques has discovered two emission centers despite the presence of a single rare-earth substitution site. The theoretical calculations and bond valence sum subsequently prove that Eu2+ ions prefer substituting the Sc3+ and interval sites to emit intense cyan light. Under 340 nm excitation, broad cyan-emission (FWHM = 115 nm) is exhibited with a high quantum yield of 60.67 %. The present phosphor exhibits pronounced thermal stability, and the emission intensity can still keep 68.3 % at 170 °C compared to that at atmospheric temperature. The Sc2Si2O7: Eu2+ phosphor boasts exceptional potential as a highly efficient cyan component in full-spectrum WLEDs. By replacing the blue light component commonly found in WLEDs, the intelligent and healthy alternative Sc2Si2O7: Eu2+ phosphor can effectively decrease the harmful blue light. This work also highlights the critical need to analyze local phosphor distortions upon rare-earth substitution, especially in single crystallographic site structures.

Transformational faulting in Mn2GeO4 from olivine to wadsleyite structure: Implications for physical mechanism of deep-focus earthquakes

High-pressure and temperature deformation experiments interfaced with acoustic emission (AE) monitoring have been conducted to study transformational faulting in Mn2GeO4 olivine, which transforms to the β phase, isostructural to wadsleyite. Metastable Mn2GeO4 olivine exhibits a marked embrittlement behavior at temperatures between 800 and 1100 K, emitting numerous AEs. At each temperature, brittle deformation is characterized by a two-stage process: (1) a “preparation” stage with numerous diffusedly located low-magnitude AEs and large b values (>2), and (2) a failure stage where larger-magnitude AEs form a planar distribution with b values about 1. Microstructure analysis reveals extensive kink band development in olivine grains in the recovered samples. Kink band boundaries (KBBs), with a typical thickness of ∼100 nm, are filled with a nanometric β-Mn2GeO4 “gouge”. A dense array of secondary shear localizations is often present within the kink bands, suggesting significant shear deformation therein. The combined observations suggest that faulting in metastable Mn2GeO4 olivine is a self-similar process, from grain-scale to the sample-scale. Both observed embrittlement behavior and the microstructure of metastable Mn2GeO4 olivine are essentially identical to those in Mg2GeO4 olivine we have reported previously, indicating that the physical mechanism of faulting in metastable olivine is insensitive to the specific crystallographic structure of the high-pressure phase. The low b values (about 1) observed in the faulting process in our experiments are similar to those of deep focus earthquakes in cold subduction zones. Our observed mechanism explains deep focus seismicity in cold metastable mantle wedges, provided that the self-similarity assumption holds to geological scales.

Simulation of the THF hydrate-water interfacial free energy from computer simulation.

In this work, the tetrahydrofuran (THF) hydrate-water interfacial free energy is determined at 500 bar, at one point of the univariant two-phase coexistence line of the THF hydrate, by molecular dynamics simulation. The mold integration-host methodology, an extension of the original mold integration technique to deal with hydrate-fluid interfaces, is used to calculate the interfacial energy. Water is described using the well-known TIP4P/Ice model, and THF is described using a rigid version of the TraPPE model. We have recently used the combination of these two models to accurately describe the univariant two-phase dissociation line of the THF hydrate in a wide range of pressures from computer simulation [Algaba et al., J. Chem. Phys. 160, 164718 (2024)]. The THF hydrate-water interfacial free energy predicted in this work is compared with the only experimental data available in the literature. The value obtained, 27(2) mJ/m2, is in excellent agreement with the experimental data taken from the literature, 24(8) mJ/m2. To the best of our knowledge, this is the first time that the THF hydrate-water interfacial free energy is predicted from computer simulation. This work confirms that the mold integration technique can be used with confidence to predict the solid-fluid interfaces of complex structures, including hydrates that exhibit sI and sII crystallographic structures.

Surface Defects, Ni3+ Species, Charge Transfer Resistance, and Surface Area dictate the Oxygen Evolution Reaction Activity of Mesoporous NiCo2O4 Thin Films

NiCo2O4 has been proven to show high electrocatalytic activity, however facile and inexpensive techniques for preparation of this compound as mesostructured thin film is lacking. In this study, the sol‐gel synthesis of nanocrystalline mesoporous spinel NiCo2O4 thin films by dip‐coating and soft‐templating using the evaporation‐induced self‐assembly approach is reported. The morphology and crystallographic structure were thoroughly probed by various physicochemical characterization techniques collectively validating the development of uniform mesoporous NiCo2O4 architectures crystallizing exclusively in the cubic spinel phase after calcination in air. The surface area of the thin films depended on the calcination temperature. XPS investigations showed that the amount of Ni3+ and defective oxygen species increased for decreasing calcination temperatures. The overall electrochemical surface area, Ni3+ content, charge transfer resistance, and amount of defective oxygen sites were found to collectively control the oxygen evolution reaction performance. After an optimized annealing procedure at 300°C and chronopotentiometric analysis at 10 mA/cm2 for 1.5 h, a low overpotential of 330 mV vs. RHE at 10 mA/cm2 in alkaline solution was achieved. The results highlight the necessity of precise selection of the appropriate calcination temperature and electrochemical pre‐treatment conditions for adjusting the concentration of electrocatalytically active reaction sites of sol‐gel‐derived NiCo2O4 thin films.

Dissociation line and driving force for nucleation of the nitrogen hydrate from computer simulation. II. Effect of multiple occupancy.

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation.

Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ.

The mitochondrial single-stranded DNA (ssDNA)binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.

Unveiling the kinetic versatility of aryl-alcohol oxidases with different electron acceptors.

Introduction: Aryl-alcohol oxidase (AAO) shows a pronounced duality as oxidase and dehydrogenase similar to that described for other glucose-methanol-choline (GMC) oxidase/dehydrogenase superfamily proteins involved in lignocellulose decomposition. In this work, we detail the overall mechanism of AAOs from Pleurotus eryngii and Bjerkandera adusta for catalyzing the oxidation of natural aryl-alcohol substrates using either oxygen or quinones as electron acceptors and describe the crystallographic structure of AAO from B. adusta in complex with a product analogue. Methods: Kinetic studies with 4-methoxybenzyl and 3-chloro-4- methoxybenzyl alcohols, including both transient-state and steady-state analyses, along with interaction studies, provide insight into the oxidase and dehydrogenase mechanisms of these enzymes. Moreover, the resolution of the crystal structure of AAO from B. adusta allowed us to compare their overall folding and the structure of the active sites of both AAOs in relation to their activities. Results and Discussion: Although both enzymes show similar mechanistic properties, notable differences are highlighted in this study. In B. adusta, the AAO oxidase activity is limited by the reoxidation of the flavin, while in P. eryngii the slower step takes place during the reductive half-reaction, which determines the overall reaction rate. By contrast, dehydrogenase activity in both enzymes, irrespective of the alcohol participating in the reaction, is limited by the hydroquinone release from the active site. Despite these differences, both AAOs are more efficient as dehydrogenases, supporting the physiological role of this activity in lignocellulosic decay. This dual activity would allow these enzymes to adapt to different environments based on the available electron acceptors.

Modified nanomagnetite silica core shell with new Cu (II) N,N‐ chelating complex as an efficient and reusable catalyst in the C‐N bond formation

In this article, initially, the TCTCl (DiPrAEA)2 ligand was synthesized and characterized by Fourier transform infrared (FT‐IR), X‐ray crystallography, 1H‐ and 13C‐NMR spectroscopy, and elemental analysis. The crystallographic structure data for the ligand has been deposited at the Cambridge Crystallographic Data Centre (CCDC No. 2282732). Then, using of this novel multidentate ligand, a novel and stable copper (II) nanocatalyst complex was synthesized by anchoring copper (II) acetate onto the core‐shell surface (Fe3O4@SiO2) via the novel multidentate ligand TCTCl (DiPrAEA)2. The successful synthesis of the Fe3O4@SiO2‐NH‐TCT (DiPrAEA)2‐Cu (II) nanocatalyst was confirmed by employing physicochemical techniques such as FT‐IR, X‐ray diffraction, ultraviolet‐visible, thermogravimetric analysis, X‐ray photoelectron spectroscopy, Brunauer–Emmett–Teller, energy‐dispersive X‐ray, dynamic light scattering, inductively coupled plasma, transmission electron microscopy, field emission scanning electron microscopy, and vibrating sample magnetometer. Subsequently, this novel copper (II) nanomagnetic complex was evaluated as an efficient, reusable, and novel catalyst for the formation of C‐N bonds via the Ullmann coupling reaction of aryl halides and nitrogen‐containing compounds. The influence of this novel TCTCl (DiPrAEA)2 ligand on the reactivity and stability of the nanomagnetic copper complex was visible in the Ullmann reaction, which resulted in rapid reaction times and excellent yields, and seven times reusability.

A comparative study on the structure and properties of TiAlSiN coatings deposited by FCVA and HiPIMS

The TiAlSiN coating has garnered significant interest due to its exceptional hardness, high oxidation resistance temperature, robust film-substrate bond strength, excellent wear resistance, and superior thermal stability. The energetic ion beam technology has emerged as a potent method for fabricating thin films. In this study, TiAlSiN films were deposited utilizing magnetic filtered cathode vacuum arc (FCVA) and high power pulsed magnetron sputtering (HiPIMS), and their respective structures and properties were meticulously investigated and contrasted. Upon comparative analysis, it was observed that the elemental composition of the FCVA films underwent a pronounced change with the same. Depending on the desired film thickness, the deposition rate of the FCVA system was found to be superior over the same duration. The crystallographic structure of the films fabricated by both systems predominantly featured an fcc-(Ti,Al)N phase. Notably, at an N2 flow rate of 40 sccm, the film deposited via HiPIMS demonstrated remarkable hardness (27.04 GPa), an elevated H/E* ratio (0.103), and superior wear resistance (7.24×10−6 mm3/N∙m). The films produced by these two deposition methods exhibited discernible differences and clear trends in hardness, adhesion strength, and tribological properties. This research provides a valuable reference for selecting the most appropriate deposition process and parameters based on the desired attributes of the coatings.

Understanding protein adsorption on silica mesoporous materials through thermodynamic simulations

This work presents a molecular thermodynamic theory to study protein interactions within a charge-regulating silica-like nanopore structure. The theory accounts for electrostatic interactions, steric repulsions, finite-size entropic effects, and protonation equilibrium of silanol groups on silica and protein residue side-chains. Coarse-grained representations of proteins based on their 3D crystallographic structures are employed. We evaluate the influence of pH, salt concentration, and pore size on the adsorption of selected proteins (cytochrome c, lysozyme, and myoglobin) in both single- and binary-protein solutions. The surface charge density on the nanopore walls is less negative than on the adjacent planar surface, primarily influenced by pH and salt concentration. Adsorption within the nanopore from single protein solutions exhibits a non-monotonic behavior with pH, increasing with decreasing salt concentration and diminishing pore size. Analysis of the effective interactions between proteins and silica surfaces indicates that adsorption is enhanced when the protein size matches that of the nanopore. Evaluation of various adsorption pathways indicates minimized free energy when the protein enters the nanopore through its edge and contacts its cylindrical walls. In binary solutions, the presence of another protein significantly alters the affinity of a protein for the silica surfaces, potentially preventing its adsorption, and affects its organization on these surfaces upon adsorption.

Bifunctional properties of Ag/α-Fe2O3/rGO nanocomposite for supercapacitor and electrochemical nitrate sensing using tetradodecyl ammonium nitrate as ion-selective membrane.

Noble metal nanoparticles incorporated in hybrid nanocomposites are considered as promising candidates for electrochemical applications owing to their physicochemical properties. In this work, we demonstrated the preparation of Fe2O3/rGO nanocomposite by hydrothermal method, followed by in situ Ag binding synthesis for the fabrication of hybrid nanocomposite (Ag/α-Fe2O3/rGO). The crystallographic structure of the hybrid nanocomposite is examined by X-ray diffraction (XRD) analysis which confirms the characteristics of Ag, Fe2O3, and rGO. The microscopic studies and energy-dispersive X-ray analysis (EDS) spectra confirmed the presence and formation of hybrid nanostructures. Raman analysis results further corroborate the formation of composite with significant D and G bands in Fe2O3/rGO and Ag/α-Fe2O3/rGO samples, which follow XRD results. Cyclic voltammetry (CV) and galvanostatic charge-discharge (GCD) studies were carried out to analyze the faradaic capacitor behavior. A specific capacitance of 209.09 F/g was observed by GCD studies for Ag/α-Fe2O3/rGO composites at a current density of 1 A/g, which exhibited good capacitance retention of 94% for 5000 cycles at 7 A/g. Furthermore, the Ag/α-Fe2O3/rGO electrode was used for the electrochemical detection of nitrate ions in soil by utilizing an ion-selective membrane over the surface of the Ag/α-Fe2O3/rGO electrode. The fabricated nanocomposite electrode showed a significant change in the peak current values with the concentration of nitrate in a linear range from 10 to 450μM with the sensitivity to be calculated 1.426 μA μM-1cm-2 and limit of detection (LOD) calculated to be 0.18μM. The reproducibility and interference studies showed a promising result to be utilized for detecting nitrate ions in soil and in real-time applications.

Titanium: A systematic review of the relationship between crystallographic profile and cell adhesion.

Dental implant surface properties such as roughness, wettability, and porosity ensure cell interaction and tissue integration. The clinical performance of dental implants depends on the crystallographic texture and protein and cell bonds to the substrates, where grain size, orientation, and inclination are parameters responsible for favoring osteoblast adhesion and limiting bacterial adhesion. The lack of consensus on the best crystallographic plan for cell adhesion prompted this systematic review, which aims to answer the following question: "What is the influence of the crystallographic plane on titanium surfaces on cell adhesion?" by evaluating the literature on the crystallographic characteristics of titanium and how these dictate topographical parameters and influence the cell adhesion of devices made from this material. It followed the Preferred Reporting Standards for Systematic Reviews and Meta-Analyses (PRISMA 2020) registered with the Open Science Framework (OSF) (osf.io/xq6kv). The search strategy was based on the PICOS method. It chose in vitro articles that analyzed crystallographic structure correlated with cell adhesion and investigated the microstructure and its effects on cell culture, different crystal orientation distributions, and the influence of crystallinity. The search strategies were applied to the different electronic databases: PubMed, Scopus, Science Direct, Embase, and Google Scholar, and the articles found were attached to the Rayyan digital platform and assessed blindly. The Joanna Bringgs Institute (JBI) tool assessed the risk of bias. A total of 248 articles were found. After removing duplicates, 192 were analyzed by title and abstract. Of these, 18 were selected for detailed reading in their entirety, 9 of which met the eligibility criteria. The included studies presented a low risk of bias. The role of the crystallographic orientation of the exposed faces in a multicrystalline material is little discussed in the scientific literature and its impact is recognized as dictating the topographical characteristics of the material that facilitate cell adhesion.

Validation of Age Estimation Using the Compositional Variation of Dental Hard Tissue: An X-ray Diffraction Analysis.

Introduction X-rays and X-ray diffraction (XRD) are two non-destructive techniques that determine a material's crystallographic structure, chemical composition, and physical properties. They can also be used to estimate a person's age when it is unknown, assess the need for orthodontic treatment, or predict the likelihood of tooth decay. This research aims to validate the accuracy of age estimation through X-ray diffraction analysis of tooth hard tissue with compositional changes. Methodology Four tooth samples were analyzed using the Pan Analytical XRD (Malvern Panalytical Ltd., UK) unique d8 family platform, which uses Cu Kα radiation (0.154 nm) and a 0.02° scan rate from 0 to 80°. Results The angle of incidence (ω) is established between the sample and the X-ray source. The angle of diffraction, 2θ, is established between the detector and the incident beam. The detector angle 2θ and the incident angle ω always equal half. Inter-atomic distance, or d-spacing (D = 10^-8 cm in Angstrom units), is measured. A greater crystal size or a greater degree of crystallinity may be indicated by a higher peak intensity, which translates to an increased amount of atoms in the crystal. Conclusion The study's findings suggest that XRD is a promising new technique for age determination, as it has an advanced and dynamic approach to finding the crystallographic characteristics of the provided sample.

Modulated crystallographic shear structure in titanium–chromium oxides: their structure and phonon-transport properties

Advancements in phonon engineering have propelled the study of heat conduction within nanostructures, focusing on the wave nature of phonons for thermal conductivity manipulation. This work investigates the annealing-induced structural transformation of titanium–chromium oxide crystals, highlighting a role in modulating thermal conductivity through the regularization of crystallographic shear (CS) plane spacing. Utilizing high-angle annular dark-field scanning transmission electron microscopy and selected-area electron diffraction, a transformation from disordered to ordered arrangements of CS planes was observed through annealing at high temperatures. The thermal conductivity increased following annealing. The variability observed in the spacing of CS planes before annealing implies that phonon Anderson localization might play a role in the changes in thermal conductivity.

Taming the storm: potential anti-inflammatory compounds targeting SARS-CoV-2 MPro.

In severe COVID-19 cases, an exacerbated inflammatory response triggers a cytokine storm that can worsen the prognosis. Compounds with both antiviral and anti-inflammatory activities show promise as candidates for COVID-19 therapy, as they potentially act against the SARS-CoV-2 infection regardless of the disease stage. One of the most attractive drug targets among coronaviruses is the main protease (MPro). This enzyme is crucial for cleaving polyproteins into non-structural proteins required for viral replication. The aim of this review was to identify SARS-CoV-2 MPro inhibitors with both antiviral and anti-inflammatory properties. The interactions of the compounds within the SARS-CoV-2 MPro binding site were analyzed through molecular docking when data from crystallographic structures were unavailable. 18 compounds were selected and classified into five different superclasses. Five of them exhibit high potency against MPro: GC-376, baicalein, naringenin, heparin, and carmofur, with IC50 values below 0.2μM. The MPro inhibitors selected have the potential to alleviate lung edema and decrease cytokine release. These molecules mainly target three critical inflammatory pathways: NF-κB, JAK/STAT, and MAPK, all previously associated with COVID-19 pathogenesis. The structures of the compounds occupy the S1/S2 substrate binding subsite of the MPro. They interact with residues from the catalytic dyad (His41 and Cys145) and/or with the oxyanion hole (Gly143, Ser144, and Cys145), which are pivotal for substrate recognition. The MPro SARS-CoV-2 inhibitors with potential anti-inflammatory activities present here could be optimized for maximum efficacy and safety and be explored as potential treatment of both mild and severe COVID-19.