InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction

STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.

Applications of Transmission Electron Microscopy in Phase Engineering of Nanomaterials

Phase engineering of nanomaterials (PEN) is an emerging field that aims to tailor the physicochemical properties of nanomaterials by precisely manipulating their crystal phases. To advance PEN effectively, it is vital to possess the capability of characterizing the structures and compositions of nanomaterials with precision. Transmission electron microscopy (TEM) is a versatile tool that combines reciprocal-space diffraction, real-space imaging, and spectroscopic techniques, allowing for comprehensive characterization with exceptional resolution in the domains of time, space, momentum, and, increasingly, even energy. In this Review, we first introduce the fundamental mechanisms behind various TEM-related techniques, along with their respective application scopes and limitations. Subsequently, we review notable applications of TEM in PEN research, including applications in fields such as metallic nanostructures, carbon allotropes, low-dimensional materials, and nanoporous materials. Specifically, we underscore its efficacy in phase identification, composition and chemical state analysis, in situ observations of phase evolution, as well as the challenges encountered when dealing with beam-sensitive materials. Furthermore, we discuss the potential generation of artifacts during TEM imaging, particularly in scanning modes, and propose methods to minimize their occurrence. Finally, we offer our insights into the present state and future trends of this field, discussing emerging technologies including four-dimensional scanning TEM, three-dimensional atomic-resolution imaging, and electron microscopy automation while highlighting the significance and feasibility of these advancements.

A robust ultra-microporous cationic aluminum-based metal-organic framework with a flexible tetra-carboxylate linker

Al-based cationic metal-organic frameworks (MOFs) are uncommon. Here, we report a cationic Al-MOF, MIP-213(Al) ([Al₁₈(μ₂-OH)₂₄(OH₂)₁₂(mdip)₆]6Cl·6H₂O) constructed from flexible tetra-carboxylate ligand (5,5'-Methylenediisophthalic acid; H₄mdip). Its crystal structure was determined by the combination of three-dimensional electron diffraction (3DED) and high-resolution powder X-ray diffraction. The structure is built from infinite corner-sharing chains of AlO₄(OH)₂ and AlO₂(OH)₃(H₂O) octahedra forming an 18-membered rings honeycomb lattice, similar to that of MIL-96(Al), a scarce Al-polycarboxylate defective MOF. Despite sharing these structural similarities, MIP-213(Al), unlike MIL-96(Al), lacks the isolated μ₃-oxo-bridged Al-clusters. This leads to an ordered defective cationic framework whose charge is balanced by Cl^- sandwiched between two Al-trimers at the corner of the honeycomb, showing strong interaction with terminal H₂O coordinated to the Al-trimers. The overall structure is endowed by a narrow quasi-1D channel of dimension ~4.7 Å. The Cl^- in the framework restrains the accessibility of the channels, while the MOF selectively adsorbs CO₂ over N₂ and possesses high hydrolytic stability.

Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data

Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds-ranging from small organic compounds to metal-organic frameworks to inorganic materials-are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.

Electron crystallography and dedicated electron-diffraction instrumentation

Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.

Electron Diffraction of 3D Molecular Crystals

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

Single-crystal structure determination of nanosized metal-organic frameworks by three-dimensional electron diffraction

Metal-organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.

Highly Effective Photocatalytic Radical Reactions Triggered by a Photoactive Metal-Organic Framework

On account of their inherent reactive properties, radical reactions play an important role in organic syntheses. The booming photochemistry provides a feasible approach to trigger the generation of radical intermediates in organic reaction processes. Thus, developing effective photocatalysts becomes the key step in radical reactions. In this work, the triphenylamine moiety with photoactivity is successfully embedded in a highly porous and stable metal-organic framework (MOF), and the obtained MOF, namely, Zr-TCA, naturally displays a photoactive property derived from the triphenylamine-based ligand. In photocatalytic studies, the triphenylamine-based Zr-TCA not only exhibits a high catalytic activity on the aerobic oxidation of sulfides via the generation of the superoxide radical anion (O2•-) under light irradiation but also shows good efficiency in the trifluoromethylation of arenes and heteroarenes by the formation of the trifluoromethyl radical (CF3•) as an intermediate. Moreover, the high performance of Zr-TCA can be well maintained over a wide range of substrates in these radical reactions, and the recycled Zr-TCA still retains its excellent photocatalytic activity. The high recyclability and catalytic efficiency to various substrates make the constructed triphenylamine-based Zr-TCA a promising photocatalyst in diverse radical reactions.

Structure Elucidation and Computationally Guided Synthesis of SSZ‐43: A One‐Dimensional 12‐Ring Zeolite with Unique Sinusoidal Channels

The structure of zeolite SSZ‐43 was determined by 3D electron diffraction, synchrotron X‐ray powder diffraction, and high‐resolution transmission electron microscopy. The SSZ‐43 framework forms one‐dimensional, sinusoidal 12‐ring channels from 5⁴6¹butterfly units commonly found in other zeolites, but with unique 6.5×6.5 Å apertures and 12‐ring 6.5×8.9 Å windows perpendicular to the channels. SSZ‐43 crystals are intergrowths of two polytypes: ≈90 % orthorhombic polytype A with ABAB stacking of the 12‐rings, and ≈10 % monoclinic polytype B with ABCABC stacking. Molecular modeling performed on the idealized Si‐SSZ‐43 structure along with empirical relationships for zeolite selectivity in boron‐ and aluminum‐containing synthesis gels were used in a combined approach to design new di‐quaternary ammonium organic structure‐directing agents (OSDAs). Experimental trials demonstrated that the new OSDAs produced SSZ‐43 over a broader range of compositions than previous mono‐quaternary OSDAs.

3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications

In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.

A simple pressure-assisted method for MicroED specimen preparation

Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.