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

Applying 3D ED/MicroED workflows toward the next frontiers

We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.

Structure solution and refinement of beam-sensitive nano-crystals

Radiation sensitive materials are among the most difficult materials to study, even more so if they exist only as nanometer-sized particles, where their size is either intentional because of enhanced properties at the nano-scale or it is unintentional because it is impossible to obtain bigger particles of the same structure. In both cases characterization methods need to be optimized to get the most information out of these particles before the radiation damages them to a point where their structure is altered. When the particles are crystallized, both characteristics, the small size and the beam sensitivity, call for electron diffraction as a privileged investigation tool. The strong interaction of electrons (as compared to X-rays) with matter allows single crystal diffraction experiments on nanometer-sized crystals and for the same amount of beam damage, electron diffraction yields more information than X-rays. These inherent advantages of electron diffraction are optimized in the recently developed low-dose electron diffraction tomography (LD-EDT) by minimizing the necessary dose for a complete data collection. In this contribution we show that in some cases even doses as low as 2 e-/Ų can induce damage in crystal structures that inhibit a correct structure refinement. However, by LD-EDT we can obtain data using extremely low doses that don't alter the structure which make it then possible not only to solve crystal structures but also to refine them using dynamical diffraction theory. Here a synthetic oxide containing volatile Na and a metal-organic framework are given as examples. A dynamical refinement of the structures is possible with data sets requiring a dose of less than 0.15 e-/Ų.

Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy

Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.

Visualizing Noncovalent Interactions and Property Prediction of Submicron-Sized Charge-Transfer Crystals from ab-initio Determined Structures

The charge-transfer (CT) interactions between organic compounds are reflected in the (opto)electronic properties. Determining and visualizing crystal structures of CT complexes are essential for the design of functional materials with desirable properties. Complexes of pyranine (PYR), methyl viologen (MV), and their derivatives are the most studied water-based CT complexes. Nevertheless, very few crystal structures of CT complexes have been reported so far. In this study, the structures of two PYRs-MVs CT crystals and a map of the noncovalent interactions using 3D electron diffraction (3DED) are reported. Physical properties, e.g., band structure, conductivity, and electronic spectra of the CT complexes and their crystals are investigated and compared with a range of methods, including solid and liquid state spectroscopies and highly accurate quantum chemical calculations based on density functional theory (DFT). The combination of 3DED, spectroscopy, and DFT calculation can provide important insight into the structure-property relationship of crystalline CT materials, especially for submicrometer-sized crystals.

Advances and applications of microcrystal electron diffraction (MicroED)

Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography.

Revolutionizing the structural design and determination of covalent-organic frameworks: principles, methods, and techniques

Covalent organic frameworks (COFs) represent an important class of crystalline porous materials with designable structures and functions. The interconnected organic monomers, featuring pre-designed symmetries and connectivities, dictate the structures of COFs, endowing them with high thermal and chemical stability, large surface area, and tunable micropores. Furthermore, by utilizing pre-functionalization or post-synthetic functionalization strategies, COFs can acquire multifunctionalities, leading to their versatile applications in gas separation/storage, catalysis, and optoelectronic devices. Our review provides a comprehensive account of the latest advancements in the principles, methods, and techniques for structural design and determination of COFs. These cutting-edge approaches enable the rational design and precise elucidation of COF structures, addressing fundamental physicochemical challenges associated with host-guest interactions, topological transformations, network interpenetration, and defect-mediated catalysis.

Wavy Two-Dimensional Conjugated Metal-Organic Framework with Metallic Charge Transport

Two-dimensional conjugated metal-organic frameworks (2D c-MOFs) have emerged as a new class of crystalline layered conducting materials that hold significant promise for applications in electronics and spintronics. However, current 2D c-MOFs are mainly made from organic planar ligands, whereas layered 2D c-MOFs constructed by curved or twisted ligands featuring novel orbital structures and electronic states remain less developed. Herein, we report a Cu-catecholate wavy 2D c-MOF (Cu3(HFcHBC)2) based on a fluorinated core-twisted contorted hexahydroxy-hexa-cata-hexabenzocoronene (HFcHBC) ligand. We show that the resulting film is composed of rod-like single crystals with lengths up to ∼4 μm. The crystal structure is resolved by high-resolution transmission electron microscopy (HRTEM) and continuous rotation electron diffraction (cRED), indicating a wavy honeycomb lattice with AA-eclipsed stacking. Cu3(HFcHBC)2 is predicted to be metallic based on theoretical calculation, while the crystalline film sample with numerous grain boundaries apparently exhibits semiconducting behavior at the macroscopic scale, characterized by obvious thermally activated conductivity. Temperature-dependent electrical conductivity measurements on the isolated single-crystal devices indeed demonstrate the metallic nature of Cu3(HFcHBC)2, with a very weak thermally activated transport behavior and a room-temperature conductivity of 5.2 S cm-1. Furthermore, the 2D c-MOFs can be utilized as potential electrode materials for energy storage, which display decent capacity (163.3 F g-1) and excellent cyclability in an aqueous 5 M LiCl electrolyte. Our work demonstrates that wavy 2D c-MOF using contorted ligands are capable of intrinsic metallic transport, marking the emergence of new conductive MOFs for electronic and energy applications.

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.

Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons

One-dimensional (1D) materials demonstrate anisotropic in-plane physical properties that enable a wide range of functionalities in electronics, photonics, valleytronics, optoelectronics, and catalysis. Here, we undertake an in-depth study of the growth mechanism for equimolar midentropy alloy of (NbTaTi)_0.33S₃ nanoribbons as a model system for 1D transition metal trichalcogenide structures. To understand the thermodynamic and kinetic effects in the growth process, the energetically preferred phases at different synthesis temperatures and times are investigated, and the phase evolution is inspected at a sequence of growth steps. It is uncovered that the dynamics of the growth process occurs at four different stages via preferential incorporation of chemical species at high-surface-energy facets. Also, a sequence of temperature and time dependent nonuniform to uniform phase evolutions has emerged in the composition and structure of (NbTaTi)_0.33S₃ which is described based on an anisotropic vapor-solid (V-S) mechanism. Furthermore, direct evidence for the 3D structure of the charge density wave (CDW) phase (width less than 100 nm) is provided by three-dimensional electron diffraction (3DED) in individual nanoribbons at cryogenic temperature, and detailed comparisons are made between the phases obtained before and after CDW transformation. This study provides important fundamental information for the design and synthesis of future 1D alloy structures.

Challenges in modelling dynamic processes in realistic nanostructured materials at operating conditions

The question is addressed in how far current modelling strategies are capable of modelling dynamic phenomena in realistic nanostructured materials at operating conditions. Nanostructured materials used in applications are far from perfect; they possess a broad range of heterogeneities in space and time extending over several orders of magnitude. Spatial heterogeneities from the subnanometre to the micrometre scale in crystal particles with a finite size and specific morphology, impact the material's dynamics. Furthermore, the material's functional behaviour is largely determined by the operating conditions. Currently, there exists a huge length-time scale gap between attainable theoretical length-time scales and experimentally relevant scales. Within this perspective, three key challenges are highlighted within the molecular modelling chain to bridge this length-time scale gap. Methods are needed that enable (i) building structural models for realistic crystal particles having mesoscale dimensions with isolated defects, correlated nanoregions, mesoporosity, internal and external surfaces; (ii) the evaluation of interatomic forces with quantum mechanical accuracy albeit at much lower computational cost than the currently used density functional theory methods and (iii) derivation of the kinetics of phenomena taking place in a multi-length-time scale window to obtain an overall view of the dynamics of the process. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Structure determination of a low-crystallinity covalent organic framework by three-dimensional electron diffraction

Covalent organic frameworks (COFs) have been attracting intense research due to their permanent porosity, designable architecture, and high stability. However, COFs are challenging to crystallize and their synthesis often results in tiny crystal sizes and low crystallinities, which hinders an unambiguous structure determination. Herein, we demonstrate that the structure of low-crystallinity COF Py-1P nanocrystals can be solved by coupling three-dimensional electron diffraction (3DED) with simulated annealing (SA). The resulting model is comparable to that obtained from high-crystallinity samples by dual-space method. Moreover, for low-resolution 3DED data, the model obtained by SA shows a better framework than those provided by classic direct method, dual-space method, and charge flipping. We further simulate data with different resolutions to understand the reliability of SA under different crystal quality conditions. The successful determination of Py-1P structure by SA compared to other methods provides new knowledge for using 3DED to analyze low-crystallinity and nanosized materials.

Research Progress on Metal-Organic Frameworks by Advanced Transmission Electron Microscopy

Metal-organic frameworks (MOFs), composed of metal nodes and inorganic linkers, are promising for a wide range of applications due to their unique periodic frameworks. Understanding structure-activity relationships can facilitate the development of new MOFs. Transmission electron microscopy (TEM) is a powerful technique to characterize the microstructures of MOFs at the atomic scale. In addition, it is possible to directly visualize the microstructural evolution of MOFs in real time under working conditions via in situ TEM setups. Although MOFs are sensitive to high-energy electron beams, much progress has been made due to the development of advanced TEM. In this review, we first introduce the main damage mechanisms for MOFs under electron-beam irradiation and two strategies to minimize these damages: low-dose TEM and cryo-TEM. Then we discuss three typical techniques to analyze the microstructure of MOFs, including three-dimensional electron diffraction, imaging using direct-detection electron-counting cameras, and iDPC-STEM. Groundbreaking milestones and research advances of MOFs structures obtained with these techniques are highlighted. In situ TEM studies are reviewed to provide insights into the dynamics of MOFs induced by various stimuli. Additionally, perspectives are analyzed for promising TEM techniques in the research of MOFs' structures.

From crystal phase mixture to pure metal-organic frameworks - Tuning pore and structure properties

In this study, a sonochemical route for the preparation of a new Hf-MIL-140A metal-organic framework from a mixture of UiO-66/MIL-140A is presented. The sonochemical synthesis route not only allows the phase-pure MIL-140A structure to be obtained but also induces structural defects in the MIL-140A structure. The synergic effect between the sonochemical irradiation and the presence of a highly acidic environment results in the generation of slit-like defects in the crystal structure, which increases specific surface area and pore volume. The BET-specific surface area in the case of sonochemically derived Zr-MIL-140A reaches 653.3 m2/g, which is 1.5 times higher than that obtained during conventional synthesis. The developed Hf-MIL-140A structure is isostructural to Zr-MIL-140A, which was confirmed by synchrotron X-ray powder diffraction (SR-XRD) and by continuous rotation electron diffraction (cRED) analysis. The obtained MOF materials have high thermal and chemical stability, which makes them promising candidates for applications such as gas adsorption, radioactive waste removal, catalysis, and drug delivery.

Unique Role of GeO2 as a Noninvasive Promoter of Nano-Sized Zeolite Crystals

The synthesis of zeolites with nano-sized dimensions is often limited to a narrow design space that conventionally relies upon the design of organics to direct hierarchical materials. Here, it is demonstrated that the addition of an inorganic modifier, germanium oxide (GeO₂ ), to a zeolite growth mixture directs the formation of crystals with ultrasmall dimensions. This effect is observed for zeolites ZSM-11 and ZSM-5 over a range of synthesis conditions wherein the role of GeO₂  in zeolite crystallization deviates from its typical function as a heteroatom. Notably, the final products contain trace amounts of Ge, which indicates the inorganic modifier does not compete for sites in the zeolite framework based on its formation of a discrete phase that enables GeO₂  recovery. Catalytic tests using the methanol-to-hydrocarbons reaction reveal significant enhancement in the performance of zeolite catalysts prepared with GeO₂  compared to reported examples of nano-sized zeolites. These findings highlight a potentially generalizable and commercially viable synthesis method to reduce mass-transport limitations in zeolites for diverse applications.

Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method

Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R ₁ values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.

Direct Location of Organic Molecules in Framework Materials by Three-Dimensional Electron Diffraction

In the study of framework materials, probing interactions between frameworks and organic molecules is one of the most important tasks, which offers us a fundamental understanding of host-guest interactions in gas sorption, separation, catalysis, and framework structure formation. Single-crystal X-ray diffraction (SCXRD) is a conventional method to locate organic species and study such interactions. However, SCXRD demands large crystals whose quality is often vulnerable to, e.g., cracking on the crystals by introducing organic molecules, and this is a major challenge to use SCXRD for structural analysis. With the development of three-dimensional electron diffraction (3D ED), single-crystal structural analysis can be performed on very tiny crystals with sizes on the nanometer scale. Here, we analyze two framework materials, SU-8 and SU-68, with organic molecules inside their inorganic crystal structures. By applying 3D ED, with fast data collection and an ultralow electron dose (0.8-2.6 e^- Å^-2), we demonstrate for the first time that each nonhydrogen atom from the organic molecules can be ab initio located from structure solution, and they are shown as distinct and well-separated peaks in the difference electrostatic potential maps showing high accuracy and reliability. As a result, two different spatial configurations are identified for the same guest molecule in SU-8. We find that the organic molecules interact with the framework through strong hydrogen bonding, which is the key to immobilizing them at well-defined positions. In addition, we demonstrate that host-guest systems can be studied at room temperature. Providing high accuracy and reliability, we believe that 3D ED can be used as a powerful tool to study host-guest interactions, especially for nanocrystals.