Data of crystal structure of the monomeric red fluorescent protein DsRed.

The monomeric red fluorescent protein DsRed (mDsRed) is an optical probe widely used in multicolor applications in flow cytometry and fluorescence microscopy. Although the crystal structure of monomeric DsRed has been determined, its molecular dynamics have not been fully elucidated. To better understand its molecular flexibility, the crystal structure of mDsRed was recently determined, and its structure and temperature factors were analyzed. Solvent-accessible hole connected with the mDsRed chromophore was observed on the mDsRed surface structure. Electron density map analysis showed the tyrosine-ring group of the mDsRed chromophore in a cis-conformation, exhibiting flexibility with a nonplanar configuration between the tyrosine and imidazoline rings of the chromophore. Temperature factor analysis indicated that the top and bottom of the ß-barrel are relatively flexible. These structural findings extended our understanding of the molecular flexibility of mDsRed. The detailed data collection and structure determination reported in this study can be used for future structural analyses.

Affecting Charges and Structures of {Bi6} Architectures by 12-Electron Transition Metal Fragments.

Molecules based on polyatomic bismuth substructures are currently attracting a lot of attention owing to this heavy and essentially non-toxic element's uncommon chemical and physical properties, which include unprecedented bonding properties. Hexaatomic {Bi6} substructures that underly more complex cluster structures were recently reported to adopt different structures or exhibit different structural details as a consequence of the charge of the {Bi6} unit. This leads to either crown-shaped cycles for a nominal Bi66- or differently distorted trigonal prisms for compositions close to Bi62-. It was predicted by quantum chemistry that Bi64- should adopt a distinctly distorted boat-like shape, yet a corresponding compound has remained elusive. Here, we report a proof of this assumption by the synthesis and isolation of [K(crypt-222)]2[Bi6{Zn(hmds)}2]∙1.5THF (1), comprising a bimetallic [Bi6{Zn(hmds)}2]2- cluster that fulfils the prediction for the geometric and electronic structure of the missing link (crypt-222 = 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo-[8.8.8]hexa-cosane, hmds = hexamethyldisilazanid). A detailed quantum chemical study shows how the nature of Lewis-acidic transition metal complexes - in particular, 12-electron fragments - control and fine-tune the resulting {Bi6} architectures in accordance with the degree of electron-withdrawal from the polybismuthide core.

The Electron-Density Distribution of UCl4 and Its Topology from X-ray Diffraction.

The chemistry of $5f$ electrons in actinide complexes and materials is still poorly understood and represents a serious challenge and opportunity for experiment and theory. The study of the electron density distribution of the ground state of such systems through X-ray diffraction represents a unique opportunity to quantitatively investigate different chemical bonding interactions at once, but was considered ``almost impossible'' on heavy-atom systems, until very recently. Here, we present a combined experimental and theoretical investigation of the electron density distribution in UCl$_4$ crystals and comparison with the previously reported spin density distribution from polarized neutron diffraction. All approaches provide a consistent picture in terms of electron and spin density distribution, and chemical bond characterization. More importantly, the synergy between experiments and quantum-mechanical calculations allows to highlight the remarkable sensitivity of X-ray diffraction to $5f$ electrons in materials.

On the heterogeneous microstructure and strengthening mechanisms in a laser welding AZ80 magnesium alloy.

This study investigates the microstructural characteristics and mechanical properties of a laser welded AZ80 magnesium alloy. The welding process led to the formation of coarse-grained fusion zone (FZ), where a secondary phase formed continuous network. Mg17Al12 precipitation and coarsening of grain boundaries occurred in the heat affected zone. The welded joint exhibited excellent mechanical properties with a yield strength of 202 MPa and a joint efficiency of 92%. The microstructure analysis via EPMA and EBSD in conjunction with synchrotron X-ray diffraction analysis reveals that precipitates and increased dislocation density in the fusion zone are primary strengthening mechanisms for the laser welded AZ80 Mg alloy.

Antibacterial profile and antiproliferative activities over human tumor cells of new silver(I) complexes containing two distinct trifluoromethyl uracil isomers.

New silver(I) complexes of 5-(trifluoromethyl)uracil (5TFMU) and 6-(trifluoromethyl)uracil (6TFMU) isomers were synthesized, characterized, and evaluated as antibacterial and antiproliferative agents. Based on elemental and thermogravimetric analyses, the Ag-5TFMU and Ag-6TFMU species are formulated as AgC5H2F3N2O2 and Ag2C5HF3N2O2, respectively. Infrared and 13C solid-state nuclear magnetic resonance spectroscopies suggest coordination of the trifluoromethyluracil isomers to silver by both nitrogen and oxygen atoms. Confirmation of their structure and connectivity was achieved, in the absence of single crystals of suitable quality, by state-of-the-art structural powder diffraction methods. In Ag-5TFMU, the organic ligand is tridentate and two distinct metal coordination environments are found (linear AgN2 as well as C2v AgO4 geometries), whereas Ag-6TFMU contains a complex polymeric structure with tetradentate dianionic 6TFMU moieties and five distinct AgX2 (X = N, O) fragments, further stabilized by ancillary (longer) Ag…O contacts. These species presented modest activity over Gram-positive and Gram-negative bacterial strains, whereas Ag-6TFMU was active over a set of tumor cells, with the best activity over prostate (PC-3) and kidney cell lines and selectivity indices of 4.6 and 1.3, respectively. On the other hand, Ag-5TFMU was active over all considered tumor cells except MCF-7 (breast cancer). The best activity was found for PC-3 cells, but no selectivity was observed. The Ag-5TFMU and Ag-6TFMU species also reduced the proliferation of tongue squamous cell carcinoma cell lines SCC - 4 and SCC-15. Preliminary biophysical assays by circular dichroism suggest that the Ag-5TFMU complex interacts with DNA by intercalation, an effect not seen in Ag-6TFMU.

The Changing Phases of Bromopentafluorobenzene.

As part of a much larger study on non-covalent interactions in binary adducts, we have explored the solid-state structures of bromopentafluorobenzene (C6F5Br) using differential scanning calorimetry (DSC), variable-temperature powder X-ray diffraction (VT-PXRD), and single-crystal X-ray diffraction (SXD). DSC data initially indicated a single solid-state phase below the freezing point, but revealed additional weak transitions upon heating. The crystal structures of three solid-state phases have been solved. The SXD data showed that phases I and IV are centrosymmetric, whilst phase II is polar. However, the structure of phase III remains elusive due to the changing phase behaviour of C6F5Br that is determined as much as by kinetics as thermodynamics. The results underline the need for multiple analytical techniques to study non-covalent interactions and offer valuable data for refining computational models in crystal structure prediction and machine learning. A comparison with the iodinated counterpart is also made.

Large-Angle Rocking Beam Electron Diffraction of Large Unit Cell Crystals Using Direct Electron Detector.

We report a large-angle rocking beam electron diffraction (LARBED) technique for electron diffraction analysis. Diffraction patterns are recorded in a scanning transmission electron microscope (STEM) using a direct electron detector with large dynamical range and fast readout. We use a nanobeam for diffraction and perform the beam double rocking by synchronizing the detector with the STEM scan coils for the recording. Using this approach, large-angle convergent beam electron diffraction (LACBED) patterns of different reflections are obtained simultaneously. By using a nanobeam, instead of a focused beam, the LARBED technique can be applied to beam-sensitive crystals as well as crystals with large unit cells. This paper describes the implementation of LARBED and evaluates the performance using silicon and gadolinium gallium garnet crystals as test samples. We demonstrate that our method provides an effective and robust way for recording LARBED patterns and paves the way for quantitative electron diffraction of large unit cell and beam-sensitive crystals.

Data of crystal structure of the large Stokes shift fluorescent protein tKeima.

Large Stokes shift (LSS) fluorescent proteins (FPs) are important for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. tKeima is a tetrameric LSS FP from the stony coral Montipora sp. Analyzing the tetrameric interface of tKeima is necessary to understand the oligomeric state of the Keima family and to provide insights into engineering oligomeric FPs to generate monomeric FPs, which are useful for FP-based molecular and cell biology studies. Here, detailed experimental procedures for tKeima were reported, including spontaneous crystal growth, data collection for X-ray diffraction, and structure determination. This information can be used for future experiments to obtain the high-resolution structure of tKeima, providing accurate structural information to comprehensively understand the molecular function of tKeima and the protein engineering of tetrameric FPs.

Investigating the deposition of fibrous zeolite particles on leaf surfaces: A novel low-cost method for detecting the presence of airborne hazardous mineral fibers.

Naturally occurring fibrous minerals, such as erionite, can pose a significant threat to human health when disturbed and subsequently respired. Understanding the spatial abundance and characteristics of these hazardous fibrous minerals in ambient air is crucial for minimizing human exposure and assessing risk. Conventional detection methods for airborne hazardous mineral fibers, such as those developed for asbestos, are of limited utility in environmental settings where fiber concentrations are low and different fiber types may be present and can be costly especially when monitoring large areas over long periods of time. This study presents an innovative methodology for detecting and identifying the presence of airborne naturally occurring fibrous zeolites, using leaf surface deposition sampling, SEM-EDX analysis for the detection and assessment of elemental composition, and TEM-SAED with continuous rotation diffraction (MicroED) to determine their crystallographic unit cell parameters. In total, 309 fibrous zeolite particles (FZPs) were identified on a range of tree leaf surfaces across 80 % of the sampling sites located close to both active and disused zeolite quarries in the Taupo Volcanic Region, New Zealand. The FZPs displayed various morphologies including aggregates, bundles, and fibril-like structures. Of the FZPs detected, 92.2 % were < 5 µm in length. Tetrahedral Si:(Si+Al) ratio results indicated that 40 % of the FZPs were in the reference range for zeolite mordenite. TEM-SAED plus MicroED analysis resulted in 61 % of tested FZPs indexed to unit cell parameters that matched with mordenite. This research demonstrates the potential of leaf sampling as a cost-effective method for detecting airborne FZPs while the MicroED data can be utilized for distinguishing between different types of airborne fibrous zeolites in ambient air.

Application of a novel local and automatic PCA algorithm for diffraction pattern denoising in TEM-ASTAR analysis in microelectronics.

This paper introduces a novel denoising method for TEM-ASTAR™ Diffraction Pattern (DP) datasets, termed LAT-PCA (Local Automatic Thresholding - Principal Component Analysis). This approach enhances the established PCA algorithm by partitioning the 4D dataset (a 2D map of 2D DPs) into localized windows. Within these windows, PCA identifies a basis where the physical signal predominantly resides in the higher-order principal components. By thresholding lower-order components, the method effectively reduces noise while retaining the essential features of the DPs. The locality of the approach, focusing on small windows, enhances computational efficiency and aligns with the localized nature of the crystallographic grain signals in ASTAR. The automatic aspect of the method employs a theoretical pure noise distribution, i.e. a Marchenko-Pastur Distribution, to set a threshold, beyond which the components are mostly noise. The LAT-PCA method offers significant reductions in acquisition and post-processing times. With denoised data, selecting the correct parameters for accurate phase maps and grain orientations becomes more straightforward, facilitating robust quantitative grain analysis. Experiments performed on a silicon-germanium-carbon sample validate the method's efficacy. The sample was analyzed with varying acquisition times to produce a high signal-to-noise ratio reference dataset and a lower ratio test dataset. The LAT-PCA algorithm's denoising results on the test dataset were benchmarked against the reference, demonstrating considerable improvements and reliability. In summary, LAT-PCA is an effective, automatic solution for denoising TEM DP datasets. Its adaptability to different noise levels and local processing capability makes it a valuable tool for enhancing dataset quality and reducing the time required for data acquisition and analysis. This method can minimize acquisition time, conserve microscope usage, and reduce sample drift and deterioration, leading to more accurate characterizations with fewer deformation artifacts.

A hybrid simulation method towards the gamma ray phase contrast imaging for metallic material.

A high efficiency simulation method for propagation-based phase-contrast imaging, called directional macro-wavefront (DMWF), is developed with the aim of simulating high-energy phase-contrast imaging. This method takes both Monte Carlo and wave optical propagation into consideration. Traditional wave-optics-based simulation methods for phase-contrast imaging encounter unacceptable computational complexity when high-energy radiation is used. In contrast, this method effectively addresses this issue by using macro-wavefront integration. Several simulation examples using typical parameters of inverse Compton scattering sources are presented to illustrate the excellent energy adaptability and efficiency of the DMWF method. This method provides a more efficient approach for phase-contrast imaging simulations, which will drive the advancement of high-energy phase-contrast imaging.

A Quantitative Phase Analysis by Neutron Diffraction of Conventional and Advanced Aluminum Alloys Thermally Conditioned for Elevated-Temperature Applications.

As the issue of climate change becomes more prevalent, engineers have focused on developing lightweight Al alloys capable of increasing the power density of powertrains. The characterization of these alloys has been focused on mechanical properties and less on the fundamental response of microstructures to achieve these properties. Therefore, this study assesses the quality of the microstructure of two high-temperature Al alloys (A356 + 3.5RE and Al-8Ce-10Mg), comparing them to T6 A356. These alloys underwent thermal conditioning at 250 and 300 °C for 200 h. Time-of-flight neutron diffraction experiments were performed before and after conditioning. The phase evolution was quantified using Rietveld refinement. It was found that the Si phase grows significantly (13-24%) in T6 A356, A356 + 3.5RE, and T6 A356 + 3.5RE alloys, which is typically correlated with a reduction in mechanical properties. Subjecting the A356 3.5RE alloy to a T6 heat treatment stabilizes the orthorhombic Al4Ce3Si6 and monoclinic ß-Al5FeSi phases, making them resistant to thermal conditioning. These two phases are known for enhancing mechanical properties. Additionally, the T6 treatment reduced the vol.% of the cubic Al20CeTi2 and hexagonal á´¨-Al9FeSi3Mg5 phases by 13% and 23%, respectively. These phases have detrimental mechanical properties. The Al-8Ce-10Mg alloy cubic ß-Al3Mg2 phase showed significant growth (82-101%) in response to conditioning, while the orthorhombic Al11Ce3 phase remained stable. The growth of the beta phase is known to decrease the mechanical properties of this alloy. These efforts give valuable insight into how these alloys will perform and evolve in demanding high-temperature environments.

Texture of Hot-Compressed Metastable ß-Titanium Alloy Ti5321 Studied by Neutron Diffraction.

The textures of the ß- and α-phases of the metastable ß-titanium alloy Ti5321 after hot deformation were investigated by neutron diffraction. A hot-rolled bar was solutionized in the ß-phase field and then hot compressed above and below the ß-transus temperature. The initial texture after full recrystallization and grain growth in the ß-phase field exhibits a weak cube component {001}<100> and minor {112}<110> and {111}<110> components. After hot compression, a <100> fiber texture is observed, increasing in intensity with compression temperature. Below the ß-transus temperature, dynamic recrystallization of the ß-phase and dynamic spheroidization of the α-phase interact strongly. The texture of the α-phase is a <11-20> fiber texture, increasing in intensity with decreasing compression temperature. The mechanisms of texture formation during hot compression are discussed.

Physicochemical Characterization and Antimicrobial Properties of Lanthanide Nitrates in Dilute Aqueous Solutions.

This work presents the results of studying dilute aqueous solutions of commercial Ln(NO3)3 · xH2O salts with Ln = Ce-Lu using X-ray diffraction (XRD), IR spectroscopy, X-ray absorption spectroscopy (XAS: EXAFS/XANES), and pH measurements. As a reference point, XRD and XAS measurements for characterized Ln(NO3)3 · xH2O microcrystalline powder samples were performed. The local structure of Ln-nitrate complexes in 20 mM Ln(NO3)3 · xH2O aqueous solution was studied under total external reflection conditions and EXAFS geometry was applied to obtain high-quality EXAFS data for solutions with low concentrations of Ln3+ ions. Results obtained by EXAFS spectroscopy showed significant contraction of the first coordination sphere during the dissolution process for metal ions located in the middle of the lanthanide series. It was established that in Ln(NO3)3 · xH2O solutions with Ln = Ce, Sm, Gd, Yb (c = 134, 100, 50 and 20 mM) there are coordinated and, to a greater extent, non-coordinated nitrate groups with bidentate and predominantly monodentate bonds with Ln ions, the number of which increases upon transition from cerium to ytterbium. For the first time, the antibacterial and antifungal activity of Ln(NO3)3 · xH2O Ln = Ce, Sm, Gd, Tb, Yb solutions with different concentrations and pH was presented. Cross-relationships between the concentration of solutions and antimicrobial activity with the type of Ln = Ce, Sm, Gd, Tb, Yb were established, as well as the absence of biocidal properties of solutions with a concentration of 20 mM, except for Ln = Yb. The important role of experimental conditions in obtaining and interpreting the results was noted.

The influence of different radiotherapy doses on the mechanical properties and microstructure of the enamel and dentin of human premolar teeth.

OBJECTIVE: Radiation therapy is applied in the treatment of head and neck cancer patients. However, oral-health-related side effects like hyposalivation and a higher prevalence of caries have been shown. This study aims to assess the influence of different radiotherapy doses on the mechanical properties, roughness, superficial microstructure, and crystallinity of the enamel and dentin of human premolar teeth. METHODS: Specimens (n = 25) were categorized into five groups based on the radiation dose received (0, 10, 30, 50, and 70 Gy). The enamel and dentin of these specimens were subjected to a microhardness tester, profilometer, atomic force microscopy (AFM), scanning electron microscopy (SEM), and X­ray diffraction (XRD) before and after different irradiation doses and compared to hydroxylapatite in each group. The data were analyzed using repeated-measures analysis of variance (ANOVA). RESULTS: Therapeutic radiation doses of 30, 50, and 70 Gy led to a decrease in the microhardness and an increase in the average roughness of the enamel, and rougher surfaces were observed in the mixed three-dimensional images. Moreover, in the dentin, a similar outcome could be observed for more than 10 Gy. The main crystalline phase structure remained hydroxylapatite, but the crystallinity decreased and the crystalline size increased above 10 Gy. The superficial micromorphology revealed granulation, fissures, and cracks in a dose-dependent manner. Radiation below 70 Gy had little effect on the hydroxylapatite concentration during the whole experiment. CONCLUSION: Above a radiation dose of 30 Gy, the micromorphology of the tooth enamel changed. This occurred for dentin above 10 Gy, which indicates that dentin is more sensitive to radiotherapy than enamel. The radiation dose had an effect on the micromorphology of the hard tissues of the teeth. These results illustrate the possible mechanism of radiation-related caries and have guiding significance for clinical radiotherapy.

Label-Free Biosensor Based on Particle Plasmon Resonance Coupled with Diffraction Grating Waveguide.

Particle plasmon resonance (PPR), or localized surface plasmon resonance (LSPR), utilizes intrinsic resonance in metal nanoparticles for sensor fabrication. While diffraction grating waveguides monitor bioaffinity adsorption with out-of-plane illumination, integrating them with PPR for biomolecular detection schemes remains underexplored. This study introduces a label-free biosensing platform integrating PPR with a diffraction grating waveguide. Gold nanoparticles are immobilized on a glass slide in contact with a sample, while a UV-assisted embossed diffraction grating is positioned opposite. The setup utilizes diffraction in reflection to detect changes in the environment's refractive index, indicating biomolecular binding at the gold nanoparticle surface. The positional shift of the diffracted beam, measured with varying refractive indices of sucrose solutions, shows a sensitivity of 0.97 mm/RIU at 8 cm from a position-sensitive detector, highlighting enhanced sensitivity due to PPR-diffraction coupling near the gold nanoparticle surface. Furthermore, the sensor achieved a resolution of 3.1 × 10-4 refractive index unit and a detection limit of 4.4 pM for detection of anti-DNP. The sensitivity of the diffracted spot was confirmed using finite element method (FEM) simulations in COMSOL Multiphysics. This study presents a significant advancement in biosensing technology, offering practical solutions for sensitive, rapid, and label-free biomolecule detection.

Fresnel Diffraction Model for Laser Dazzling Spots of Complementary Metal Oxide Semiconductor Cameras.

Laser dazzling on complementary metal oxide semiconductor (CMOS) image sensors is an effective method in optoelectronic countermeasures. However, previous research mainly focused on the laser dazzling under far fields, with limited studies on situations that the far-field conditions were not satisfied. In this paper, we established a Fresnel diffraction model of laser dazzling on a CMOS by combining experiments and simulations. We calculated that the laser power density and the area of saturated pixels on the detector exhibit a linear relationship with a slope of 0.64 in a log-log plot. In the experiment, we found that the back side illumination (BSI-CMOS) matched the simulations, with an error margin of 3%, while the front side illumination (FSI-CMOS) slightly mismatched the simulations, with an error margin of 14%. We also found that the full-screen saturation threshold for the BSI-CMOS was 25% higher than the FSI-CMOS. Our work demonstrates the applicability of the Fresnel diffraction model for BSI-CMOS, which provides a valuable reference for studying laser dazzling.

Determination of five-parameter grain boundary characteristics in nanocrystalline Ni-W by scanning precession electron diffraction tomography.

Determining the full five-parameter grain boundary characteristics from experiments is essential for understanding grain boundaries impact on material properties, improving related models, and designing advanced alloys. However, achieving this is generally challenging, in particular at nanoscale, due to their 3D nature. In our study, we successfully determined the grain boundary characteristics of an annealed nickel-tungsten alloy (NiW) nanocrystalline needle-shaped specimen (tip) containing twins using Scanning Precession Electron Diffraction (SPED) Tomography. The presence of annealing twins in this face-centered cubic (fcc) material gives rise to common reflections in the SPED diffraction patterns, which challenges the reconstruction of orientation-specific virtual dark field (VDF) images required for tomographic reconstruction of the 3D grain shapes. To address this, an automated post-processing step identifies and deselects these shared reflections prior to the reconstruction of the VDF images. Combined with appropriate intensity normalization and projection alignment procedures, this approach enables high-fidelity 3D reconstruction of the individual grains contained in the needle-shaped sample volume. To probe the accuracy of the resulting boundary characteristics, the twin boundary surface normal directions were extracted from the 3D voxelated grain boundary map using a 3D Hough transform. For the sub-set of coherent Σ3 boundaries, the expected {111} grain boundary plane normals were obtained with an angular error of <3° for boundary sizes down to 400 nm². This work advances our ability to precisely characterize and understand the complex grain boundaries that govern material properties.

Clustering characteristic diffraction vectors in 4-D STEM data sets from overlapping structures in nanocrystalline and amorphous materials.

We describe a method for identifying and clustering diffraction vectors in four-dimensional (4-D) scanning transmission electron microscopy data to determine characteristic diffraction patterns from overlapping structures in projection. First, the data is convolved with a 4-D kernel, then diffraction vectors are identified and clustered using both density-based clustering and a metric that emphasizes rotational symmetries. The method works well for both crystalline and amorphous samples and in high- and low-dose experiments. A simulated dataset of overlapping aluminum nanocrystals provides performance metrics as a function of Poisson noise and the number of overlapping structures. Experimental data from an aluminum nanocrystal sample shows similar performance. For an amorphous Pd77.5Cu6Si16.5 thin film, experiments measuring glassy structure show strong evidence of 4- and 6-fold symmetry structures. A significant background arises from the diffraction of overlapping structures. Quantifying this background helps to separate contributions from single, rotationally symmetric structures vs. apparent symmetries arising from overlapping structures in projection.