Three-dimensional Electron Diffraction Research Articles

Crystal structures of two new high-pressure oxynitrides with composition SnGe4N4O4, from single-crystal electron diffraction.

SnGe4N4O4 was synthesized at high pressure (16 and 20 GPa) and high temperature (1200 and 1500°C) in a large-volume press. Powder X-ray diffraction experiments using synchrotron radiation indicate that the derived samples are mixtures of known and unknown phases. However, the powder X-ray diffraction patterns are not sufficient for structural characterization. Transmission electron microscopy studies reveal crystals of several hundreds of nanometres in size with different chemical composition. Among them, crystals of a previously unknown phase with stoichiometry SnGe4N4O4 were detected and investigated using automated diffraction tomography (ADT), a three-dimensional electron diffraction method. Via ADT, the crystal structure could be determined from single nanocrystals in space group P63mc, exhibiting a nolanite-type structure. This was confirmed by density functional theory calculations and atomic resolution scanning transmission electron microscopy images. In one of the syntheses runs a rhombohedral 6R polytype of SnGe4N4O4 could be found together with the nolanite-type SnGe4N4O4. The structure of this polymorph was solved as well using ADT.

Modular Design of Highly Stable Semiconducting Porous Coordination Polymer for Efficient Electrosynthesis of Ammonia.

Developing highly stable porous coordination polymers (PCPs) with integrated electrical conductivity is crucial for advancing our understanding of electrocatalytic mechanisms and the structure-activity relationship of electrocatalysts. However, achieving this goal remains a formidable challenge because of the electrochemical instability observed in most PCPs. Herein, we develop a "modular design" strategy to construct electrochemically stable semiconducting PCP, namely, Fe-pyNDI, which incorporates a chain-type Fe-pyrazole metal cluster and π-stacking column with effective synergistic effects. The three-dimensional electron diffraction (3D ED) technique resolves the precise structure. Both theoretical and experimental investigation confirms that the π-stacking column in Fe-pyNDI can provide an efficient electron transport path and enhance the structural stability of the material. As a result, Fe-pyNDI can serve as an efficient model electrocatalyst for nitrate reduction reaction (NO3RR) to ammonia with a superior ammonia yield of 339.2 μmol h-1 cm-2 (14677 μg h-1 mgcat. -1) and a faradaic efficiency of 87 % at neutral electrolyte, which is comparable to state-of-the-art electrocatalysts. The in-situ X-ray absorption spectroscopy (XAS) reveals that during the reaction, the structure of Fe-pyNDI can be kept, while part of the Fe3+ in Fe-pyNDI was reduced in situ to Fe2+, which serves as the potential active species for NO3RR.

Unraveling a Stable 16-Ring Aluminophosphate DNL-11 through Three-Dimensional Electron Diffraction for Atmospheric Water Harvesting.

Sorption-based atmospheric water harvesting (AWH) is a promising solution for addressing water scarcity. Developing cost-effective and stable water adsorbents with high water uptake capacity and a low-temperature regeneration requirement is a crucially important procedure. In this Communication, we present a novel and stable aluminophosphate (AlPO) molecular sieve (MS) named DNL-11 with 16-ring channels synthesized by using an affordable and commercialized organic structure directing agent (OSDA), whose crystallographic structure is elucidated by three-dimensional electron diffraction (3D ED). DNL-11 exhibits a significant water uptake capacity (189 mg/g) at a very low vapor pressure (5% relative humidity at 30 °C). In addition, most of the adsorbed water can be effortlessly removed by purging N2 at 25 °C under ambient pressure conditions. This may expand the possibility of AWH under extreme drought conditions.

Mechanochemical Synthesis and Three-Dimensional Electron Diffraction Structure Solution of a Novel Cu-Based Protocatechuate Metal-Organic Framework.

Mechanochemical synthesis is a powerful approach to obtain new materials, limiting costs, and times. However, defected and submicrometrical-sized crystal products make critical their characterization through classical single-crystal X-ray diffraction. A valid alternative is represented by three-dimensional (3D) electron diffraction, in which a transmission electron microscope is used, like a diffractometer. This work matches a green water-based mechanochemical synthesis and 3D electron diffraction to obtain and characterize a Cu-based protocatechuate metal-organic framework (PC-MOF). Its structure has been fully refined through dynamical diffraction theory, and free water molecules could be detected in the channels of the framework. Thermal characterization, focused on the dehydration profile determination, leads to the formation of a novel high-temperature 2D coordination polymer, fully solved with 3D electron diffraction data. At last, the strong activity of the PC-MOF against cationic dyes like methylene blue has been reported.

High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34.

Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.

Three-dimensional electron diffraction on clinkers: the belite α'H incommensurate modulated structure.

Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure.

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds.

There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.

Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm.

Three-dimensional electron diffraction (3D-ED) is a powerful technique for crystallographic characterization of nanometre-sized crystals that are too small for X-ray diffraction. For accurate crystal structure refinement, however, it is important that the Bragg diffracted intensities are treated dynamically. Bloch wave simulations are often used in 3D-ED, but can be computationally expensive for large unit cell crystals due to the large number of diffracted beams. Proposed here is an alternative method, the `scattering cluster algorithm' (SCA), that replaces the eigen-decomposition operation in Bloch waves with a simpler matrix multiplication. The underlying principle of SCA is that the intensity of a given Bragg reflection is largely determined by intensity transfer (i.e. `scattering') from a cluster of neighbouring diffracted beams. However, the penalty for using matrix multiplication is that the sample must be divided into a series of thin slices and the diffracted beams calculated iteratively, similar to the multislice approach. Therefore, SCA is more suitable for thin specimens. The accuracy and speed of SCA are demonstrated on tri-isopropyl silane (TIPS) pentacene and rubrene, two exemplar organic materials with large unit cells.

Single-Crystal One-Dimensional Porous Ladder Covalent Polymers.

The synthesis of single-crystal, one-dimensional (1D) polymers is of great importance but a formidable challenge. Herein, we report the synthesis of single-crystal 1D ladder polymers in solution by dynamic covalent chemistry. The three-dimensional electron diffraction technique was used to rigorously solve the structure of the crystalline polymers, unveiling that each polymer chain is connected by double covalent bridges and all polymer chains are packed in a staggered and interlaced manner by π-π stacking and hydrogen bonding interactions, making the crystalline polymers highly robust in both thermal and chemical stability. The synthesized single-crystal polymers possess permanent micropores and can efficiently remove CO2 from the C2H2/CO2 mixture to obtain high-purity C2H2, validated by dynamic breakthrough experiments. This work demonstrates the first example of constructing single-crystal 1D porous ladder polymers with double covalent bridges in solution for efficient C2H2/CO2 separation.

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.

DNL-16: A new zeolitic layered silicate unraveled by three-dimensional electron diffraction

DNL-16: A new zeolitic layered silicate unraveled by three-dimensional electron diffraction

Reticular Synthesis of Highly Crystalline Three-Dimensional Mesoporous Covalent-Organic Frameworks for Lipase Inclusion.

The synthesis and application of three-dimensional (3D) mesoporous covalent-organic frameworks (COFs) are still to be developed. Herein, two mesoporous 3D COFs with an stp topology were synthesized in a highly crystalline form with aniline as the modulator. The chemical composition of these COFs was confirmed by Fourier transform infrared (FT-IR) and 13C cross-polarization magic angle spinning nuclear magnetic resonance (NMR) spectroscopies. These 3D mesoporous COFs were highly crystalline and exhibited permanent porosity and good chemical stability in both aqueous and organic media. The space group and unit cell parameters of COF HFPTP-TAE were verified by powder X-ray diffraction (PXRD), small-angle X-ray scattering, and three-dimensional electron diffraction (3D ED). The appropriate pore size of the COF HFPTP-TAE facilitated the inclusion of enzyme lipase PS with a loading amount of 0.28 g g-1. The lipase⊂HFPTP-TAE (⊂ refers to "include in") composite exhibited high catalytic activity, good thermal stability, and a wide range of solvent tolerance. Specifically, it could catalyze the alcoholysis of aspirin methyl ester (AME) with high catalytic efficiency. Oriented one-dimensional (1D) channel mesopores in HFPTP-TAE accommodated lipase, meanwhile preventing them from aggregation, while windows on the wall of the 1D channel favored molecular diffusion; thus, this COF-enzyme design outperformed its amorphous isomer, two-dimensional (2D) mesoporous COF, 3D mesoporous COF with limited crystallinity, and mesoporous silica as an enzyme host.

Quantitative three-dimensional local order analysis of nanomaterials through electron diffraction

Structure-property relationships in ordered materials have long been a core principle in materials design. However, the introduction of disorder into materials provides structural flexibility and thus access to material properties that are not attainable in conventional, ordered materials. To understand disorder-property relationships, the disorder – i.e., the local ordering principles – must be quantified. Local order can be probed experimentally by diffuse scattering. The analysis is notoriously difficult, especially if only powder samples are available. Here, we combine the advantages of three-dimensional electron diffraction – a method that allows single crystal diffraction measurements on sub-micron sized crystals – and three-dimensional difference pair distribution function analysis (3D-ΔPDF) to address this problem. In this work, we compare the 3D-ΔPDF from electron diffraction data with those obtained from neutron and x-ray experiments of yttria-stabilized zirconia (Zr0.82Y0.18O1.91) and demonstrate the reliability of the proposed approach.

Znucalite, the only known zinc uranyl carbonate: Its crystal structure and environmental implications

Abstract Znucalite is a zinc uranyl-carbonate mineral that was until recently only partially characterized with a formula originally given as Zn12Ca(UO2)(CO3)3(OH)22·4H2O, with an unknown crystal structure and ambiguous symmetry determinations. We have reinvestigated this mineral using three-dimensional electron diffraction (3D ED) and powder X-ray diffraction and revealed for the first time its structural details. Znucalite is unambiguously monoclinic, P21/m, with a = 10.722(2) Å, b = 6.259(1) Å, c = 25.355(1) Å, β = 101.13(1)°, and V = 1669.54(9) Å3. The structure refinement of the 3D ED data using the dynamical approach (Robs = 0.1594 for 3579 observed reflections and 244 parameters) provided the following structure model. Znucalite possesses a layered structure, with a [Zn10(OH)14(CO3)2] double sheet (with Zn2+ both in octahedra and tetrahedra), which is connected to a thick interlayer that hosts U 6+, Ca2+, and H2O molecules. The linkage between structural units and the interlayer occurs via the vertices of ZnO4 tetrahedra protruding from the sheet. In the interlayer, differences in ordering between U and Ca take place and likely cause the difficulties encountered during the attempts to solve the structure. The refined structural formula of znucalite, Zn10Ca0.828[UO2]0.828[CO3]4(OH)15.312(H2O)5.484, corresponds well to the composition obtained from the electron-microprobe analyses, (Zn9.84Al0.16)Σ10.00 Ca0.83(UO2)0.80[(CO3)3.96(SO4)0.04]Σ4.00(OH)15.42(H2O)5.48. Raman spectroscopy evidenced the presence of several non-equivalent CO3 groups, as well as OH and H2O. The U-O bond lengths obtained from the stretching frequencies of UO22+ vibrations are in line with the structural model. A discussion on the environmental importance of znucalite is appended, based on geochemical calculations with an estimate of the solubility product for this mineral.

Investigation of the milling characteristics of different focused ion beam sources assessed by three-dimensional electron diffraction from crystal lamellae

Investigation of the milling characteristics of different focused ion beam sources assessed by three-dimensional electron diffraction from crystal lamellae

Direct location of guest molecules in porous crystalline materials by three-dimensional electron diffraction

Direct location of guest molecules in porous crystalline materials by three-dimensional electron diffraction

Three-dimensional electron diffraction of pure sulfur: challenges and achievements

Three-dimensional electron diffraction of pure sulfur: challenges and achievements

Three-dimensional electron diffraction of small molecules on the MerlinEM detector

Three-dimensional electron diffraction of small molecules on the MerlinEM detector

Making the Most of 3D Electron Diffraction: Best Practices to Handle a New Tool

Along with the adoption of three-dimensional electron diffraction (3D ED/MicroED) as a mainstream tool for structure determination from sub-micron single crystals, questions about best practices regarding each step along the workflow, from data collection to structure solutions, arise. In this paper, we discuss three particular aspects of a 3D ED/MicroED experiment which, after hundreds of structures solved in Rigaku’s laboratories, we have found to be important to consider carefully. First, for a representative model system of a hydrated compound (trehalose dihydrate), we show that cryo-transfer of the sample into the diffractometer is an effective means to prevent dehydration, while cooling of the sample without cryo-transfer yields a marginal improvement only. Next, we demonstrate for a small (tyrosine) and a large (clarithromycin) organic compound, how a simplified and fast workflow for dynamical diffraction calculations can determine absolute crystal structures with high confidence. Finally, we discuss considerations and trade-offs for choosing an optimal effective crystal-to-detector distance; while a long distance is mandatory for a protein (thaumatin) example, even a small molecule with difficult diffraction behavior (cystine) yields superior results at longer distances than the one used by default.

Synthesis of (±)-zeapyranolactone, a noncanonical strigolactone isolated from maize, and determination of its overall relative configuration

Strigolactones are a class of apocarotenoids known as rhizosphere semiochemicals and plant hormones. They are classified as either canonical, with a tricyclic lactone (ABC ring) and a butenolide (D ring) comprising their basic skeleton, or noncanonical, deviating from the basic skeleton. Here, zeapyranolactone, a noncanonical strigolactone isolated from maize, was synthesized for the first time as a racemic and diastereomeric mixture, and its relative stereochemistry was determined by three-dimensional electron diffraction crystallography as 4S*,4aS*,2′R*. The synthetic route developed is straightforward and does not rely on the use of typical protective groups.