Search Results (28)

The mechanical response of high-entropy alloys (HEAs), specifically the FeNiCrCoAl HEA, was studied at both bulk and nanoparticle scales using molecular dynamics simulations. These simulations were performed using the LAMMPS software with an Embedded Atom Method (EAM) potential. The results show that Bulk HEAs exhibited enhanced hardening and plasticity, while in nanoparticles, distinct deformation patterns were observed, including nanotwin formation, V-shaped stacking fault planes, and intermittent dislocation activity due to free surface effects. The crystallographic orientation with respect to the compression significantly affected the deformation mechanisms, with the [100] direction favoring progressive hardening, while the [110] and [111] directions exhibited different stacking fault and dislocation dynamics. A detailed analysis using von Mises stress and dislocation analysis provided insights into the effects of scale on mechanical properties. Full article

We studied specially designed InAs/GaSb/AlSb/GaSb M-structures, a type-II superlattice (T2SL), that can serve as active materials for short-wavelength infrared (SWIR) applications. To obtain the dispersion relation of the investigated M-structures, k·p perturbation theory based on the eight-band model implemented in the nextnano++ v1.18.1 (nextnano GmbH, Munich, Germany) software was used. Numerical band-gap engineering and dispersion calculations for the investigated M-structures (composed of 6/1/5/1 monolayers, with InSb interfaces included) revealed the presence of an additional energy level within the energy gap. This energy level originates from the InSb-like interfaces and does not appear in structures with different layer or interface thicknesses. Its properties strongly depend on interface thickness, temperature, and strain. Numerical calculations of the probability density function ${|\Psi |}^2$, absorption coefficients, and optical absorption spectra at varying temperatures demonstrate that, under specific conditions, such as an optimised interface thickness and temperature, optical absorption increases significantly. These theoretical results are based on structures fabricated using molecular-beam epitaxy (MBE) technology. High-resolution X-ray diffraction (HRXRD) measurements confirm the high crystallographic quality of these M-structures. Full article

In a broad project designed to examine uranium transport by surface water from Sierra Peña Blanca to Laguna del Cuervo in the Chihuahuan Desert, sediments from intermittent streams and the lagoon have been extracted and studied. Two samples were sediments from the high area of the Sierra, close to the uranium deposit “El Nopal.” Moreover, 23 core segments extracted for dating sediments were analyzed to consider changes in the fine component concentrations. The techniques of scanning electron microscopy–energy dispersive X-ray spectroscopy, XRD in a conventional diffractometer, and high-resolution synchrotron XRD analysis were applied. The crystallographic objective of the present work was to evaluate the functionality of various methodologies when applied to cases of a detailed analysis of many polyphase samples with cryptocrystals. The methods for processing the experimental data were the Rietveld method in the current multi-pattern variant of the Fullprof program and the degree of crystallinity method for the rapid estimation of the proportion of cryptocrystals in a mixture. This last technique was developed with an ad hoc software package deposited in the GitLab public repository. Full article

Nanocrystalline (NC) materials have widespread industrial usage. X-ray and neutron diffraction techniques are primary tools for studying the structural and microstructural features of NC materials. Selected area electron diffraction (SAED) patterns collected using a transmission electron microscope (TEM) on polycrystalline nanostructured materials, featuring nested rings, that are analogous to Debye–Scherrer patterns, possess similar potentials to aid materials characterisation. The utility of SAED patterns is further enhanced by the possibility of applying crystallographic approaches, like full pattern fitting procedures, based on Rietveld refinement algorithms, enabling the evaluation of material features, such as crystallite size, lattice distortions, defect structures, and the presence of secondary phases even from very small volume scale. In this paper, we have discussed the possibilities afforded by a Rietveld code applied to SAED patterns of NC materials, including the mathematical implementation of the two-beam dynamical correction model in MAUD software (version 2.9995), and a critical discussion of the results obtained on different NC materials. Full article

Naphthoquinones eleutherin and isoeleutherin have demonstrated promising antibacterial activity, probably due to their quinone structure, which can generate reactive oxygen species. The study examines the activities of pathogens, such as Staphylococcus aureus and Escherichia coli, associated with antimicrobial resistance and explores their potential mechanisms of action. The MIC, IC₅₀, and MBC were determined. PharmMapper 2017 server and GOLD 2020.1 software were utilized for molecular docking to identify protein targets and interaction mechanisms. The docking predictions were verified by redocking, focusing on structures with RMSD below 2 Å. The molecular docking revealed a significant affinity of eleutherin for the peptide, transcriptional regulator QacR, and regulatory protein BlaR1 with better interactions with BlaR1 than the crystallographic ligand (benzylpenicillin). Isoeleutherin demonstrated specific interactions with methionine aminopeptidase, indicating specificity and affinity. In summary, the difference in naphthoquinones activities may be related to structural differences. Eleutherin exhibits potential as a therapeutic adjuvant to reverse bacterial resistance in S. aureus, suggesting this molecule interferes with the antibiotic resistance mechanism. The absence of homologous proteins or variations in the structure of the target proteins could be the cause of the inactivity against E. coli. Full article

Structures of some hydrogenated products and intermediates, prepared by a heterogeneous Pd/C or Ru/C catalyst starting from 4-pyridinecarbonitrile (4PN), in water and in the presence of an acidic additive (HCl or H₂SO₄), were confirmed in various salt forms of 4-piperidylmethylamine (4PIPA) and 4-pyridylmethylamine (4PA). Crystallographic unit cell structure of the completely hydrogenated product salts (4PIPA·H₂SO₄ and 4PIPA·2HCl) showed a common double-protonated [4PIPA+2H]²⁺ divalent cation structure, also proved by FT-IR, and that of the 4PA·H₂SO₄ intermediate salt was also indexed and modeled by means of powder X-ray diffraction, applying the DASH 4.0 software package and crystal coordinates coming from former single-crystal X-ray structure determination. Formations of the anhydrous and hydrated forms of 4PA·0.5H₂SO₄·xH₂O (x = 0 or x = 0.5, hemisulfates) were also studied by powder XRD and FT-IR spectroscopy for comparing these crystal structures. Full article

Protein three-dimensional (3D) structure prediction is one of the most challenging issues in the field of computational biochemistry, which has overwhelmed scientists for almost half a century. A significant breakthrough in structural biology has been established by developing the artificial intelligence (AI) system AlphaFold2 (AF2). The AF2 system provides a state-of-the-art prediction of protein structures from nearly all known protein sequences with high accuracy. This study examined the reliability of AF2 models compared to the experimental structures in drug discovery, focusing on one of the most common protein drug-targeted classes known as G protein-coupled receptors (GPCRs) class A. A total of 32 representative protein targets were selected, including experimental structures of X-ray crystallographic and Cryo-EM structures and their corresponding AF2 models. The quality of AF2 models was assessed using different structure validation tools, including the pLDDT score, RMSD value, MolProbity score, percentage of Ramachandran favored, QMEAN Z-score, and QMEANDisCo Global. The molecular docking was performed using the Genetic Optimization for Ligand Docking (GOLD) software. The AF2 models’ reliability in virtual drug screening was determined by their ability to predict the ligand binding poses closest to the native binding pose by assessing the Root Mean Square Deviation (RMSD) metric and docking scoring function. The quality of the docking and scoring function was evaluated using the enrichment factor (EF). Furthermore, the capability of using AF2 models in molecular docking to identify hits with key protein–ligand interactions was analyzed. The posing power results showed that the AF2 models successfully predicted ligand binding poses (RMSD < 2 Å). However, they exhibited lower screening power, with average EF values of 2.24, 2.42, and 1.82 for X-ray, Cryo-EM, and AF2 structures, respectively. Moreover, our study revealed that molecular docking using AF2 models can identify competitive inhibitors. In conclusion, this study found that AF2 models provided docking results comparable to experimental structures, particularly for certain GPCR targets, and could potentially significantly impact drug discovery. Full article

Octreotide is the first synthetic peptide hormone, consisting of eight amino acids, that mimics the activity of somatostatin, a natural hormone in the body. During the past decades, advanced instrumentation and crystallographic software have established X-Ray Powder Diffraction (XRPD) as a valuable tool for extracting structural information from biological macromolecules. The latter was demonstrated by the successful structural determination of octreotide at a remarkably high d-spacing resolution (1.87 Å) (PDB code: 6vc1). This study focuses on the response of octreotide to different humidity levels and temperatures, with a particular focus on the stability of the polycrystalline sample. XRPD measurements were accomplished employing an Anton Paar MHC-trans humidity-temperature chamber installed within a laboratory X’Pert Pro diffractometer (Malvern Panalytical). The chamber is employed to control and maintain precise humidity and temperature levels of samples during XRPD data collection. Pawley analysis of the collected data sets revealed that the octreotide polycrystalline sample is remarkably stable, and no structural transitions were observed. The compound retains its orthorhombic symmetry (space group: P2₁2₁2₁, a = 18.57744(4) Å, b = 30.17338(6) Å, c = 39.70590(9) Å, d ~ 2.35 Å). However, a characteristic structural evolution in terms of lattice parameters and volume of the unit cell is reported mainly upon controlled relative humidity variation. In addition, an improvement in the signal-to-noise ratio in the XRPD data under a cycle of dehydration/rehydration is reported. These results underline the importance of considering the impact of environmental factors, such as humidity and temperature, in the context of structure-based drug design, thereby contributing to the development of more effective and stable pharmaceutical products. Full article

With this report, the space group of $\left[Zn\left(Nal\right){\left(DACH\right)}_2\right]Cl$ is corrected ($Nal$: nalidixic acid mono-anion; $DACH$: diaminocyclohexane) from its wrong description in the literature. In the correct, non-centrosymmetric space group $P1$, the crystal structure is well ordered and the stereochemistry is correct. Crystallographic tools to recognize the correct symmetry are described. This work encourages experienced and inexperienced scientists to remain critical about the output of automatic, black-box crystallographic software. Full article

The identification of new psychoactive substances (compounds that mimic the effects of outlawed substances) poses a significant challenge due to their rapid emergence and continuous modifications. This phenomenon results in these molecules escaping legal regulation, allowing them to circumvent legislation. The phenethylamine class has garnered attention because its molecules replicate the effects of LSD and are associated with numerous cases of intoxication. In this study, we focused on three phenethylamines—2C-H, 25H-NBOH, and 25I-NBOMe—with crystallographic structures available in the Cambridge Crystallographic Data Center (CCDC) database. We conducted a systematic conformational analysis and compared the structural information obtained. Subsequently, we compared the spectra derived from this analysis with experimental details from the ENFSI database. Structural comparisons were made based on the RMSDs between the lower energy conformations and experimental crystallographic structures. Additionally, structures obtained from direct optimization were compared. We then simulated the spectra based on the X-ray structures and compared them with those in the experimental database. Interpretation was carried out using heat maps and PCA in Pirouette software. Combining in silico methods with experimental approaches provides a more comprehensive understanding of the characterization process of new psychoactive substances (NPSs). Full article

For the duplex stainless steel X2CrNiMoN22-5-3, phase-specific strain pole figures (strain PFs) for the phases ferrite (bcc) and austenite (fcc) were analysed under uniaxial tensile loading for various loading states in purely elastic and elasto-plastic regimes. Experimentally, strain PFs were determined by means of in situ neutron diffraction strain measurements under defined uniaxial loading. These experimental results were compared with strain PFs calculated using elasto-plastic self-consistent (EPSC) modelling. The comparison was performed for two different {hkl} planes per phase. While classic load stress and load partitioning analyses for multi-phase materials are often limited to the load direction and a selected direction transverse to it, the results illustrate the added value of determining a strain PF, especially when a phase-specific texture is present. The comparison with experimental data shows how well the load partitioning behaviour can be predicted using common EPSC models, using the example of a duplex stainless steel. The EPSC model used was validated with the software ISODEC in its elastic range. Based on the results of the EPSC model, and taking into account the local phase-specific crystallographic texture, a prediction can be made as to what extent intergranular stresses and phase-specific textures could affect the results of a (residual) stress analysis by means of the diffraction method. This makes it possible to assess whether, for technical applications, meaningful residual stress results can be expected in certain component directions. Full article

Comprehensive information on in situ microstructural and crystallographic changes during the preparation/manufacturing processes of various materials is highly necessary to precisely control the microstructural morphology and the preferred orientation (or texture) characteristics for achieving an excellent strength–ductility–toughness balance in advanced engineering materials. In this study, in situ isothermal annealing experiments with cold-rolled 17Ni-0.2C (mass%) martensitic steel sheets were carried out by using the TAKUMI and ENGIN-X time-of-flight neutron diffractometers. The inverse pole figures based on full-profile refinement were extracted to roughly evaluate the preferred orientation features along three principal sample directions of the investigated steel sheets, using the General Structure Analysis System (GSAS) software with built-in generalized spherical harmonic functions. The consistent rolling direction (RD) inverse pole figures from TAKUMI and ENGIN-X confirmed that the time-of-flight neutron diffraction has high repeatability and statistical reliability, revealing that the principal preferred orientation evaluation of steel materials can be realized through 90° TD ➜ ND (transverse direction ➜ normal direction) rotation of the investigated specimen on the sample stage during two neutron diffraction experiments. Moreover, these RD, TD, and ND inverse pole figures before and after the in situ experiments were compared with the corresponding inverse pole figures recalculated from the MUSASI-L complete pole figure measurement and the HIPPO in situ microstructure evaluation, respectively. The similar orientation distribution characteristics suggested that the principal preferred orientation evaluation method can be applied to the in situ microstructural evolution of bulk orthorhombic materials and spatially resolved principal preferred orientation mappings of large engineering structure parts. Full article

ENA transporters are a group of P-type ATPases that are characterized by actively moving Na⁺ or K⁺ out of the cell against their concentration gradient. The existence of these transporters was initially attributed to some fungi, although more recently they have also been identified in mosses, liverworts, and some protozoa. Given the current increase in the number of organisms whose genomes are completely sequenced, we set out to expand our knowledge about the existence of ENA in organisms belonging to other phylogenetic groups. For that, a hidden Markov model profile was constructed to identify homologous sequences to ENA proteins in protein databases. This analysis allowed us to identify the existence of ENA-type ATPases in the most primitive groups of fungi, as well as in other eukaryotic organisms not described so far. In addition, this study has allowed the identification of a possible new group of P-ATPases, initially proposed as ENA but which maintain phylogenetic distances with these proteins. Finally, this work has also addressed this study of the structure of ENA proteins, which remained unknown due to the lack of crystallographic data. For this purpose, a 3D structure prediction of the NcENA1 protein of the fungus Neurospora crassa was performed using AlphaFold2 software v2.3.1. From this structure, the electrostatic potential of the protein was analyzed. With all these data, the protein regions and the amino acids involved in the transport of Na⁺ or K⁺ ions across the membrane were proposed for the first time. Targeted mutagenesis of some of these residues has confirmed their relevant participation in the transport function of ENA proteins. Full article

The effect of deformation on the evolution of crystallographic texture in a Ti-15V-3Cr-3Sn-3Al (Ti-15333) alloy after unidirectional cold rolling was studied experimentally and numerically in the present investigation. An optical microscope (OM) and scanning electron microscope (SEM) were used to study the microstructures, while the crystallographic texture after cold rolling was studied with X-ray diffraction. The rolling process (deformation) was simulated with PRISMS-plasticity, open-source crystal plasticity software. Micro-indentations were performed on the initial solution-annealed sample with an equiaxed grain structure. The experimentally obtained load–displacement curve for a particular grain (orientation-φ₁, Φ, φ₂ = 325.2°, 18.0°, 66.2° (Bunge notation)) was compared with the crystal plasticity finite element method (FEM)-simulated load–displacement curve to obtain the calibration parameters. The obtained parameters, along with the experimental stress–strain curve, were used to recalibrate the PRISMS-plasticity software for the rolling simulations of the Ti-15333 alloy. It was observed that the γ-(normal direction, ND//<111>) and α-(rolling direction, RD//<110>) fibers strengthened with cold rolling, experimentally as well as numerically. The simulated orientation distribution functions (ODFs) matched reasonably well with those obtained from the experiments. The average values of von Mises stress and von Mises strain increased with an increase in deformation. Full article

The manuscript describes the phase composition, microstructure, some physical and mechanical properties of the Ti-Al system with addition of 2 at. % Dy (TAD) and Ho (TAH) obtained by “hydride technology”. Phase diagrams for Ti-Al-Dy and Ti-Al-Ho at a temperature of 1150 °C and basic properties for ternary phases Dy₆Ti₄Al₄₃ and Ho₆Ti₄Al₄₃ were calculated. A crystallographic database of stable and quasistable structures of the known elemental composition was created in the USPEX-SIESTA software by means of an evolutionary code. The calculations show that adding REM leads to a significant stabilizing effect in each Ti-Al-Me (Me = Dy, Ho) system without exception. It has been established that the lattice energies of AlTi₃Ho and AlTi₃Dy are, respectively, equal to: EAl₄Ti₁₂Dy₃ = −32,877.825 eV and EAl₄Ti₁₂Dy₃ = −31,227.561 eV. In the synthesized Ti₄₉Al₄₉Ho₂ compound, the main phases include Al-Ti, Al₃Ti₃ and Al₄Ti₁₂Ho₃ and the contributions to the theoretical intensity are equal to 44.83, 44.43 and 5.55%, respectively. Ti₄₉Al₄₉Dy₂ is dominated by the Al-Ti, Al₃Ti₃ and Al₄Ti₁₂Dy phases, whose contributions are equal to 65.04, 16.88 and 11.2%, respectively. The microhardness of TAD and TAN specimens is 1.61 ± 0.08 and 1.47 ± 0.07 GPa, respectively. Full article