Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (microED), is an emerging method for determining structures from submicron-sized crystals. With the development of rapid and convenient data collection protocols, acquiring dozens of datasets in a single 3D ED/microED session has become routine. A fast and automated workflow for processing, scaling and merging a large number of 3D ED/microED datasets can significantly accelerate the structure determination process. Herein, we present an XDS-based pipeline with a graphical user interface for automated real-time and offline batch 3D ED/microED data processing (AutoLEI). We demonstrate the functionality and applications of the pipeline through four examples, using both offline and real-time data processing capabilities. The samples include small organic molecules, metal–organic frameworks (MOFs) and proteins, showcasing the versatility and efficiency of AutoLEI in various applications.

3D electron diffraction (3D ED) has undergone impressive development in the last decade. However, its accuracy and reproducibility have never been tested, up to now, in different laboratories on the same batch of samples. This paper reports a round robin on three test structures, two inorganic and one organic, solved and refined with 3D ED in seven different laboratories employing different transmission electron microscopes, with different acceleration voltages, different methodologies and different detectors. The results of the round robin show a remarkable accuracy of the technique that, in the case of kinematical refinement, is around 0.05 Å error on atomic positions for the inorganic samples and 0.15 Å for the beam-sensitive organic crystal. Dynamical refinement further improves the accuracy. The analysis of diverse samples and numerous data sets again confirms that dynamical refinement is a well established procedure, significantly reducing the refinement R factors, improving the accuracy of the structure models in most cases, and providing fine structural details, such as hydrogen-atom positions and the absolute structure, for both inorganic and organic samples.

Microcrystal electron diffraction (MicroED), also known as three-dimensional electron diffraction (3D ED), allows the collection of diffraction data from submicrometre-sized crystals under low electron-dose conditions. Despite having several advantages over conventional X-ray crystallographic techniques, susceptibility to radiation damage is a great challenge that remains to be solved in MicroED. Similar to X-ray crystallography, radiation damage to the macromolecular crystal structures in MicroED manifests in two forms: global damage that affects the overall order of the crystal lattice and site-specific damage that affects highly sensitive residues and moieties in macromolecules. Traditionally, the unit e⁻ Å⁻² has been used for electron-dose estimations, which does not consider the interaction between the incident electron beam and the sample. In this study, we clarify the terminology for describing `dose' in electron crystallography, including the procedure for converting values from e⁻ Å⁻² to grays (Gy). Furthermore, we investigated data-processing strategies that could be used to limit the effects of radiation damage to the crystal. During MicroED data collection, radiation damage increases with the number of acquired ED frames because the accumulated electron dose increases. Data collected from several crystals and processed in this way can be merged to increase the completeness and subsequently be used for structure refinement. According to our results, this approach improves the resolution of the data, the data statistics, the structure determination and the quality of the final structure.

Prussian blue analogues (PBA) are a large family of functional materials with diverse applications such as in electrochemical fields. However, their use in the emerging two-electron oxygen reduction reaction for clean production of hydrogen peroxide (H₂O₂) is lagging. Herein, a general solvent exchange induced reconstruction strategy is demonstrated, through which an abnormal NiNi-PBA superstructure is synthesized as a high-performance electrocatalyst for H₂O₂ generation. The resultant NiNi-PBA superstructure has a stoichiometric composition with saturated lattice water, and a leaf-like morphology composed of interconnected small-size nanosheets with identical orientation and predominate {210} side surface exposure. Our studies show that the Ni−N centers on {210} facets are the active sites, and the saturated lattice H₂O favors a six-coordinated environment that results in high selectivity. The “perfect” structure including stoichiometric composition and ideal facet exposure leads to a high selectivity of ~100 % and H₂O₂ yield of 5.7 mol g⁻¹ h⁻¹, superior to the reported MOF-based electrocatalysts and most other electrocatalysts.

Understanding the structure of an active pharmaceutical ingredient is essential for gaining insights into its physicochemical properties. Sodium valproate, one of the most effective antiepileptic drugs, was first approved for medical use in 1967. However, the structure of its anhydrous form has remained unresolved. This is because it was difficult to grow crystals of sufficient size for single-crystal X-ray diffraction (SCXRD). Although 3D electron diffraction (3D ED) can be used for studying crystals that are too small for SCXRD, the crystals of anhydrous sodium valproate are extremely sensitive to both humidity and electron beams. They degrade quickly both in air and under an electron beam at room temperature. In this study, we developed a glovebox-assisted cryo-transfer workflow for the preparation of EM grids in a protected atmosphere to overcome the current challenges for studying air- and beam-sensitive samples using 3D ED. Using this technique, we successfully determined the structure of anhydrous sodium valproate, revealing the formation of Na-valproate polyhedral chains. Our results provide a robust framework for the 3D ED analysis of air-sensitive crystals, greatly enhancing its utility across various scientific disciplines.

Zeolites are crystalline microporous materials constructed by corner-sharing tetrahedra (SiO₄ and AlO₄), with many industrial applications as ion exchangers, adsorbents and heterogeneous catalysts. However, the presence of micropores impedes the use of zeolites in areas dealing with bulky substrates. Introducing extrinsic mesopores, that is, intercrystal/intracrystal mesopores, in zeolites is a solution to overcome the diffusion barrier. Still, those extrinsic mesopores are generally disordered and non-uniform; moreover, acidity and crystallinity are always, to some extent, impaired. Thus, synthesizing thermally stable zeolites with intrinsic mesopores that are of uniform size and crystallographically connected with micropores, denoted here as intrinsic mesoporous zeolite, is highly desired but still not achieved. Here we report ZMQ-1 (Zeolitic Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, no. 1), an aluminosilicate zeolite with an intersecting intrinsic meso-microporous channel system delimited by 28 × 10 × 10-rings, in which the 28-ring has a free diameter of 22.76 Å × 11.83 Å, which reaches the mesopore domain. ZMQ-1 has high thermal and hydrothermal stability with tunable framework Si/Al molar ratios. ZMQ-1 is the first aluminosilicate zeolite with an intrinsic meso-microporous channel system. The Brønsted acidity of ZMQ-1 imparts high activity and unique selectivity in the catalytic cracking of heavy oil. The position of the organic structure-directing agent (OSDA) used for ZMQ-1 synthesis was determined from three-dimensional electron diffraction (3D ED) data, which shows the unique structure-directing role of the OSDA in the formation of the intrinsic meso-microporous zeolite. This provides an incentive for preparing other stable mesopore-containing zeolites.

Layered conducting polymers have drawn widespread interest in electrochemical energy systems with capacitive ion storage. However, the semi-infinite ion diffusion through the lengthy path within their lamellar structures restricts the power performance, especially in high mass loading electrodes (>10 mg cm^–2). Herein, we improve the ion diffusion in layered conducting polymers by constructing ion-penetrable defects through mechanical modulation of hydrogen bonding, i.e., ball milling. The ball-milled layered conducting polymers endow the fabrication of high mass loading (up to 30 mg cm^–2) electrodes for electrochemical capacitors (ECs) with a remarkable areal capacitance of 1.71 F cm^–2 and volumetric capacitance of 148.2 F cm^–3 at 150 mA cm^–2. Asymmetric ECs are further prototyped, delivering a high areal energy of 0.916 mWh cm^–2 and a volumetric energy of 28.68 Wh L^–1 at 12.5 mW cm^–2. These findings represent a critical step forward to the practical application of layered conducting polymers for high-power devices with miniaturized configuration.

3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product. 

Two new polymorphs (forms VIII and IX) of piroxicam were discovered through poly(ethylene glycol) (PEG)-assisted melt crystallization, and their structures were revealed by 3D electron diffraction (3D ED). This discovery provides insight into the potential of PEG in pharmaceutical polymorph discovery and verifies the significance of 3D ED as an essential technique for structural determination of pharmaceuticals. Furthermore, the direct contribution of intermolecular hydrogen bonding to melting points was discussed based on the structural divergency between the newly solved form VIII and the previously reported form IV. Combining PEG-assisted melt crystallization and 3D ED not only accelerated the discovery of new polymorphs but also provided unique opportunities for understanding structure-property relationships in pharmaceutical crystals.

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 (microcrystal 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.