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.

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.

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.

An Updated Structure of Oxybutynin Hydrochloride.

Oxybutynin (Ditropan), a widely distributed muscarinic antagonist for treating the overactive bladder, has been awaiting a definitive crystal structure for ≈50 years due to the sample and technique limitations. Past reports used powder X-ray diffraction (PXRD) to shed light on the possible packing of the molecule however their model showed some inconsistencies when compared with the 2D chemical structure. These are largely attributed to X-ray-induced photoreduction. Here microcrystal electron diffraction (MicroED) is used to successfully unveil the experimental 3D structure of oxybutynin hydrochloride showing marked improvement over the reported PXRD structure. Using the improved model, molecular docking is applied to investigate the binding mechanism between M3 muscarinic receptor (M3R) and (R)-oxybutynin, revealing essential contacts/residues and conformational changes within the protein pocket. A possible universal conformation is proposed for M3R antagonists, which is valuable for future drug development and optimization. This study underscores the immense potential of MicroED as a complementary technique for elucidating unknown pharmaceutical structures, as well as for protein-drug interactions.

Atomic Structure and 3D Shape of a Multibranched Plasmonic Nanostar from a Single Spatially Resolved Electron Diffraction Map.

Despite the interest in improving the sensitivity of optical sensors using plasmonic nanoparticles (NPs) (rods, wires, and stars), the full structural characterization of complex shape nanostructures is challenging. Here, we derive from a single scanning transmission electron microscope diffraction map (4D-STEM) a detailed determination of both the 3D shape and atomic arrangement of an individual 6-branched AuAg nanostar (NS) with high-aspect-ratio legs. The NS core displays an icosahedral structure, and legs are decahedral rods attached along the 5-fold axes at the core apexes. The NS legs show an anomalous anisotropic spatial distribution (all close to a plane) due to an interplay between the icosahedral symmetry and the unzipping of the surfactant layer on the core. The results significantly improve our understanding of the star growth mechanism. This low dose diffraction mapping is promising for the atomic structure study of individual multidomain, multibranched, or multiphase NPs, even when constituted of beam-sensitive materials.

3D electron diffraction studies of synthetic rhabdophane (DyPO4·nH2O).

In this study, we report the results of continuous rotation electron diffraction studies of single DyPO4·nH2O (rhabdophane) nanocrystals. The diffraction patterns can be fit to a trigonal lattice (P3121) with lattice parameters a = 7.019 (5) and c = 6.417 (5) Å. However, there is also a set of diffuse background scattering features present that are associated with a disordered superstructure that is double these lattice parameters and fits with an arrangement of water molecules present in the structure pore. Pair distribution function (PDF) maps based on the diffuse background allowed the extent of the water correlation to be estimated, with 2-3 nm correlation along the c axis and ∼5 nm along the a/b axis.

Impact of Gd doping on structural and magnetic characteristics of SrFeO3perovskite nanomaterial.

The SrFeO3nanoparticles doped with 5% and 10% Gd were synthesized using the solution combustion method. The phase formation of the synthesized nanoparticles was confirmed by powder x-ray diffraction analysis. Field emission scanning electron microscope and HRTEM were employed to examine the morphology of the samples, revealing well-ordered, agglomerated nanoparticles. Energy dispersive x-ray spectroscopy analysis was conducted on all samples, confirming the presence of the desired elements. X-ray photoelectron spectroscopy confirmed the presence of mixed oxidation states of Fe3+and Fe4+. Magnetization studies, performed using a SQUID magnetometer, showed ferromagnetic behaviour in all samples, with a significant increase in magnetic moment observed with higher Gd doping. The enhanced magnetic moments and reduced coercivity in Gd-doped SrFeO3suggest that these materials could be suitable for spintronic applications.

Pt12H24-: a Cuboctahedral Platinum Hydride Cluster Cage.

The platinum hydride cluster Pt12H24- is studied in gas phase by a combination of trapped ion electron diffraction and density functional theory computations. We find a cuboctahedral platinum cage with bridge bound hydrogen atoms. This unusual structure is stabilized by Pt-H-Pt multicenter bonds and shows characteristics of spherical aromaticity.

An orbital strategy for regulating the Jahn-Teller effect.

The Jahn-Teller effect (JTE) arising from lattice-electron coupling is a fascinating phenomenon that profoundly affects important physical properties in a number of transition-metal compounds. Controlling JT distortions and their corresponding electronic structures is highly desirable to tailor the functionalities of materials. Here, we propose a local coordinate strategy to regulate the JTE through quantifying occupancy in the [Formula: see text] and [Formula: see text] orbitals of Mn and scrutinizing the symmetries of the ligand oxygen atoms in MnO6 octahedra in LiMn2O4 and Li0.5Mn2O4. The effectiveness of such a strategy has been demonstrated by constructing P2-type NaLi x Mn1 - x O2 oxides with different Li/Mn ordering schemes. In addition, this strategy is also tenable for most 3d transition-metal compounds in spinel and perovskite frameworks, indicating the universality of local coordinate strategy and the tunability of the lattice-orbital coupling in transition-metal oxides. This work demonstrates a useful strategy to regulate JT distortion and provides useful guidelines for future design of functional materials with specific physical properties.

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II): discovery of the first ruthenium tetrapyrrole cis-dicarbonyl complex by X-ray and electron diffraction.

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II), [Ru(C33H16F10N4)(CO)2] or Ru(CO)2[DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetrapyrrole complex. The neutral complex sports two carbonyls and an oligotetrapyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO)2[DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetrapyrrole ligand, but also the first metal biladiene complex in which the tetrapyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO)2[DMBil1] is weakly luminescent, displaying λem = 552 nm upon excitation at λex = 500 nm, supports two reversible 1 e- reductions at -1.45 and -1.73 V (versus Fc+/Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photocatalytic and photosensitization applications. While the structure of Ru(CO)2[DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. An independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.

Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches.

The TIR (Toll/interleukin-1 receptor) domain represents a vital structural element shared by proteins with roles in immunity signalling pathways across phyla (from humans and plants to bacteria). Decades of research have finally led to identifying the key features of the molecular basis of signalling by these domains, including the formation of open-ended (filamentous) assemblies (responsible for the signalling by cooperative assembly formation mechanism, SCAF) and enzymatic activities involving the cleavage of nucleotides. We present a historical perspective of the research that led to this understanding, highlighting the roles that different structural methods played in this process: X-ray crystallography (including serial crystallography), microED (micro-crystal electron diffraction), NMR (nuclear magnetic resonance) spectroscopy and cryo-EM (cryogenic electron microscopy) involving helical reconstruction and single-particle analysis. This perspective emphasizes the complementarity of different structural approaches.

The effect of the acceleration voltage on the quality of structure determination by 3D-electron diffraction.

Nowadays, 3D Electron Diffraction (3DED) is widely used for the structure determination of sub-micron-sized particles. In this work, we investigate the influence of the acceleration voltage on the quality of 3DED datasets acquired on BaTiO3 nanoparticles. Datasets were acquired using a wide range of beam energies, from common, high acceleration voltages (300 kV and 200 kV) to medium (120 kV and 80 kV) and low acceleration voltages (60 kV and 30 kV). It was observed that, in the integration process, Rint increases as the beam energy is reduced, which is mainly due to the increased dynamical scattering. Nevertheless, the structure was solved successfully in all cases. The structure refinement was comparable for all beam energies with small deficiencies such as negative atomic displacements for the heaviest atom in the structure, barium. Including extinction correction in the refinement noticeably improved the model for low acceleration voltages, probably due to higher beam absorption in these cases. Dynamical refinement, however, shows superior results for higher acceleration voltages, since the dynamical refinement calculations currently ignore inelastic scattering effects.

Autoencoder latent space sensitivity to material structure in convergent-beam low energy electron diffraction.

The convergent-beam low energy electron diffraction technique has been proposed as a novel method to gather local structural and electronic information from crystalline surfaces during low-energy electron microscopy. However, the approach suffers from high complexity of the resulting diffraction patterns. We show that Convolutional Autoencoders trained on CBLEED patterns achieve a highly structured latent space. The latent space is then used to estimate structural parameters with sub-angstrom accuracy. The low complexity of the neural networks enables real time application of the approach during experiments with low latency.

A simple protocol for determining the zone axis direction from selected-area electron diffraction spot patterns of cubic materials.

Using the well known Rn ratio method, a protocol has been elaborated for determining the lattice direction for the 15 most common cubic zone axis spot patterns. The method makes use of the lengths of the three shortest reciprocal-lattice vectors in each pattern and the angles between them. No prior pattern calibration is required for the method to work, as the Rn ratio method is based entirely on geometric relationships. In the first step the pattern is assigned to one of three possible pattern types according to the angles that are measured between the three reciprocal-lattice vectors. The lattice direction [uvw] and possible Bravais type(s) and Laue indices of the corresponding reflections can then be determined by using lookup tables. In addition to determining the lattice direction, this simple geometric analysis allows one to distinguish between the P, I and F Bravais lattices for spot patterns aligned along [013], [112], [114] and [233]. Moreover, the F lattice can always be uniquely identified from the [011] and [123] patterns.

Optimization of three-dimensional electron diffuse scattering data acquisition.

The diffraction patterns of crystalline materials with local order contain sharp Bragg reflections as well as highly structured diffuse scattering. In this study, we quantitatively show how the diffuse scattering in three-dimensional electron diffraction (3D ED) data is influenced by various parameters, including the data acquisition mode, the detector type and the use of an energy filter. We found that diffuse scattering data used for quantitative analysis are preferably acquired in selected area electron diffraction (SAED) mode using a CCD and an energy filter. In this study, we also show that the diffuse scattering in 3D ED data can be obtained with a quality comparable to that from single-crystal X-ray diffraction. As electron diffraction requires much smaller crystal sizes than X-ray diffraction, this opens up the possibility to investigate the local structure of many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.

MicroED structure of the C11 cysteine protease clostripain.

Clostripain secreted from Clostridium histolyticum is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of C. histolyticum clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/ß/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.

Orthorhombic Polar Phase in Sodium Niobate Nanoribbons.

Ferroelectric materials exhibit switchable spontaneous polarization below Curie's temperature, driven by octahedral distortions and rotations, as well as ionic displacements. The ability to manipulate polarization coupled with persistent remanence, drives diverse applications, including piezoelectric devices. In the last two decades, nanoscale exploration has unveiled unique material properties influenced by morphology, including the capability to manipulate polarization, patterns, and domains. This paper focuses on the characterization of nanometric sodium niobate (SN) synthesized from metallic niobium through alkali hydrothermal treatment, utilizing electron microscopy techniques, including high-resolution differential phase contrast (DPC) in scanning transmission electron microscopy (STEM). The material exhibits a nanoribbon structure forming a tree root-like network. The study identifies crystallographic phase, atomic columns displacement directions, and surface features, such as exposed planes and the absence of particular atomic columns. The high sensitivity of integrated DPC images proves crucial in overcoming observational challenges in other STEM modes. These observations are essential for potential applications in electronic, photocatalytic, and chemical reaction contexts.

On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors.

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.

From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion.

3D electron diffraction (3DED) is increasingly employed to determine molecular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using dichloromethane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations.