Three-dimensional Electron Diffraction Research Articles

Synthesis, crystal structure, and topology of a polycatenated bismuth coordination polymer

Abstract Solvothermal reaction of Bi(NO3)3·5H2O with the flexible ligand 1,3,5-tris[4-(carboxyphenyl)oxamethyl]-2,4,6-trimethylbenzene (H3TBTC) in methanol at 120 °C for 1 h led to the formation of a novel coordination polymer (CP) with the composition of Bi(TBTC). The structure of the microcrystalline material was determined through three-dimensional electron diffraction (3DED) measurements and phase purity was confirmed by a Pawley refinement, elemental analysis, and thermal analysis. The compound crystallizes in the triclinic space group P 1 ‾ $P\overline{1}$ with one Bi3+ cation and one TBTC3− trianion in the asymmetric unit. Edge-sharing of BiO7 polyhedra leads to the formation of dinuclear Bi2O12 units, which through coordination to six TBTC3− ions form a layered two-periodic structure. Upon heating the material in air, the unit cell volume contracts by 9%, which is attributed to a shift in the inter-layer arrangement and to the flexibility of the building units of the structure. The compound starts to decompose at ∼300 °C. Topological analysis revealed layers consisting of 3-c and 6-c nodes, consistent with the two-periodic kgd net – the dual of the Kagome net (kgm). However, due to the non-planar nature of the Bi(TBTC) layers, adjacent layers are interlaced by polycatenation.

SCM-25: A Zeolite with Ordered Meso-cavities Interconnected by 12×12×10-Ring Channels Determined by 3D Electron Diffraction.

Zeolites with large cavities that are accessible via wide pore windows are desirable but very rare. They have been dominantly used as catalysts in industry. Here we report a novel porous germanosilicate SCM-25, the zeolite structure containing ordered meso-cavities (29.9 × 7.6 × 6.0 Å3) interconnected by 10- and 12-ring channels. SCM-25 was synthesized as nanosized crystals by using a simple organic structure-directing agent (OSDA). Three-dimensional (3D) electron diffraction shows that SCM-25 crystallizes in the orthorhombic space group Cmmm with a = 14.62 Å, b = 51.82 Å, c = 13.11 Å, which is one of the zeolites with the largest unit cell dimensions. We demonstrate that 3D electron diffraction is a powerful technique for determining the complex structure of SCM-25, including the disorders and distributions of framework atoms silicon and germanium. SCM-25 has a high surface area (510 m2/g) and high thermal stability (700 °C). Furthermore, we propose a potential postsynthetic strategy for the preparation of zeolites with ordered meso-cavities by applying the ADOR (assembly–disassembly–organization–reassembly) approach.

Organic Cocrystals of TCNQ and TCNB Based on an Orthocetamol Backbone Solved by Three-Dimensional Electron Diffraction

Organic Cocrystals of TCNQ and TCNB Based on an Orthocetamol Backbone Solved by Three-Dimensional Electron Diffraction

Three-dimensional electron diffraction: a powerful structural characterization technique for crystal engineering

The recent advances in three-dimensional electron diffraction (3D ED) are highlighted with a focus on its applications for investigating nanocrystals.

An intriguing canting dipole configuration and its evolution under an electric field in La-doped Pb(Zr,Sn,Ti)O3 perovskites

Despite the fact that electric dipole ordering plays a key role in the unique physical properties of dielectric materials, electric dipole configurations mostly appear simply as either parallel or antiparallel. Here, we report a canting electric dipole configuration in La-doped Pb(Zr,Sn,Ti)O3 perovskites based on advanced neutron, synchrotron X-ray and three-dimensional electron diffraction techniques. It is revealed that, arising from the coupling between the atomic displacement and oxygen octahedral tilting, this unique electric dipole configuration displays a canting arrangement aligned in the (110)p plane that possesses an antiparallel component along the [110]P direction and a parallel component along the [001]P direction. Remarkably, under an in-situ electric field, the electric dipoles continuously rotate with a gradually reduced canting angle, as confirmed by phase-field simulations, and ultimately evolve into a ferroelectric ordering. Such an evolution gives rises to a small hysteresis and an equivalent lattice strain to the macroscopic strain. These findings enrich the current understanding of the types of electric dipole configurations in dielectric materials and are expected to aid the design of new dielectric materials with emergent properties.

Electron Microscopy of Nanoporous Crystals

ConspectusNanoporous crystals, such as silica mesoporous crystals (SMCs), zeolites, metal–organic frameworks (MOFs) and covalent organic frameworks (COFs), usually have unique geometrical features of periodically arranged pores from micro-, meso- to macro-scale. They have great potential to be structurally designed toward novel materials for various applications, such as storage, separation, and catalysis. In addition to the synthesis and applications of these materials, the structural analysis of nanoporous crystals is also critical for obtaining novel materials and unravelling their structure–property relationships. The crystal structure determines the pore size and connectivity of cages/channels, which are closely related to the performance of these materials in adsorption and catalysis. However, there are significant challenges in structural analysis due to small crystal size, electron-beam sensitivity, and local defects. Due to the strong interaction between electrons and matter, electron microscopy (EM) can provide rich structural information, which at the same time can also cause structural damage to samples. As early as 1960s, EM had been used to directly observe the lattice fringes of zeolites. Subsequently, the structures of many nanoporous crystals were solved and structural details such as defects, intergrowths, and surface structures were revealed by exploiting EM during the past decades. With the development of three-dimensional electron diffraction (3D ED) and low-dose high-resolution electron microscopy imaging, these approaches become more routine for solving the structure of nanocrystals and for revealing the local structural details. In this Account, we present our previous work on EM studies of several typical nanoporous materials, including SMCs, zeolites, MOFs, the TiO2@MIL-101 composite, and COFs. Various methods and strategies were developed and applied to different materials based on the characteristics of their structures. For example, 3D electrostatic potential maps of SMCs can be reconstructed by Fourier synthesis of crystal structure factors obtained from high-resolution TEM images, leading to the discovery of many 3D mesostructures. New zeolites/MOFs/COFs structures, which were not previously solved due to their structural complexity and small crystal size, have been determined using 3D ED data from nanosized crystals or using a combination of electron diffraction and high-resolution imaging. In addition, EM methods for determining the handedness of nanocrystals have also been developed and successfully applied to SMCs and STW zeolite based on high-resolution EM imaging or dynamical electron diffraction. Recently, a new strategy involving a combination of 3D ED and cryogenic protocol was proposed to study the structure, dynamics, and the host–guest interactions in a COF material. The direct-space strategy for structure solution, implemented using a genetic algorithm, was also demonstrated to be a successful approach for solving structures from low-resolution 3D ED data. By now, EM has become one of the most widely used methods in the study of nanoporous materials. We hope this Account will promote further developments of EM and stimulate the design and synthesis of new functional nanoporous materials.

Probing Molecular Motions in Metal-Organic Frameworks by Three-Dimensional Electron Diffraction.

Flexible metal–organic frameworks (MOFs) are known for their vast functional diversities and variable pore architectures. Dynamic motions or perturbations are among the highly desired flexibilities, which are key to guest diffusion processes. Therefore, probing such motions, especially at an atomic level, is crucial for revealing the unique properties and identifying the applications of MOFs. Nuclear magnetic resonance (NMR) and single-crystal X-ray diffraction (SCXRD) are the most important techniques to characterize molecular motions but require pure samples or large single crystals (>5 × 5 × 5 μm3), which are often inaccessible for MOF synthesis. Recent developments of three-dimensional electron diffraction (3D ED) have pushed the limits of single-crystal structural analysis. Accurate atomic information can be obtained by 3D ED from nanometer- and submicrometer-sized crystals and samples containing multiple phases. Here, we report the study of molecular motions by using the 3D ED method in MIL-140C and UiO-67, which are obtained as nanosized crystals coexisting in a mixture. In addition to an ab initio determination of their framework structures, we discovered that motions of the linker molecules could be revealed by observing the thermal ellipsoid models and analyzing the atomic anisotropic displacement parameters (ADPs) at room temperature (298 K) and cryogenic temperature (98 K). Interestingly, despite the same type of linker molecule occupying two symmetry-independent positions in MIL-140C, we observed significantly larger motions for the isolated linkers in comparison to those reinforced by π–π stacking. With an accuracy comparable to that of SCXRD, we show for the first time that 3D ED can be a powerful tool to investigate dynamics at an atomic level, which is particularly beneficial for nanocrystalline materials and/or phase mixtures.

Determination of Spinel Content in Cycled Li1.2Ni0.13Mn0.54Co0.13O2 Using Three-Dimensional Electron Diffraction and Precession Electron Diffraction

Among lithium battery cathode materials, Li1.2Ni0.13Mn0.54Co0.13O2 (LR-NMC) has a high theoretical capacity, but suffers from voltage and capacity fade during cycling. This is partially ascribed to transition metal cation migration, which involves the local transformation of the honeycomb layered structure to spinel-like nano-domains. Determination of the honeycomb layered/spinel phase ratio from powder X-ray diffraction data is hindered by the nanoscale of the functional material and the domains, diverse types of twinning, stacking faults, and the possible presence of the rock salt phase. Determining the phase ratio from transmission electron microscopy imaging can only be done for thin regions near the surfaces of the crystals, and the intense beam that is needed for imaging induces the same transformation to spinel as cycling does. In this article, it is demonstrated that the low electron dose sufficient for electron diffraction allows the collection of data without inducing a phase transformation. Using calculated electron diffraction patterns, we demonstrate that it is possible to determine the volume ratio of the different phases in the particles using a pair-wise comparison of the intensities of the reflections. Using this method, the volume ratio of spinel structure to honeycomb layered structure is determined for a submicron sized crystal from experimental three-dimensional electron diffraction (3D ED) and precession electron diffraction (PED) data. Both twinning and the possible presence of the rock salt phase are taken into account. After 150 charge–discharge cycles, 4% of the volume in LR-NMC particles was transformed irreversibly from the honeycomb layered structure to the spinel structure. The proposed method would be applicable to other multi-phase materials as well.

The Complex Crystal Structure and Abundant Local Defects of Zeolite EMM-17 Unraveled by Combined Electron Crystallography and Microscopy.

In this study, we successfully solve polymorphs A and B of zeolite EMM-17, which can only crystallize in sub-micrometer-sized crystals while containing complex stacking disorders, from the three-dimensional (3D) electron diffraction (ED) data. This is the first time that the atomic structure of this polymorph has been ab initio solved, and the result reveals a unique 10(12)×10(12)×11-ring channel system. Moreover, we acquire the first atomic-resolution images of EMM-17 using integrated differential phase-contrast scanning transmission electron microscopy. The images allow us to directly observe polymorphs B and C and discover a large number of local structural defects. Based on structural features unraveled from the reciprocal-space 3D ED data and real-space images, we propose a series of energetically feasible local structures in EMM-17. We also demonstrate that the unique porous structure of EMM-17 enables efficient kinetic separation of C6 alkane isomers.

Molybdenum Disorder in Hydrated Sedovite, Ideally U(MoO4)2·nH2O, a Microporous Nanocrystalline Mineral Characterized by Three-Dimensional Electron Diffraction, Density Functional Theory Computations, and Complexity Analysis.

Sedovite, U4+(Mo6+O4)2·nH2O, is reported as being one of the earliest supergene minerals formed of the secondary zone. The difficulty of isolating enough pure material limits studies to techniques that can access the nanoscale combined with theoretical analyses. The crystal structure of sedovite has been solved and refined using the dynamical approach from three-dimensional electron diffraction data collected on natural nanocrystals found among iriginite. At 100 K, sedovite is monoclinic a ≈ 6.96 Å, b ≈ 9.07 Å, c ≈ 12.27 Å, and V ≈ 775 Å3 with space group C2/c. The microporous structure presents a characteristic framework built from uranium polyhedra and disordered Mo pyramids creating pore hosting water molecules. To confirm the formula U4+(Mo6+O4)2·nH2O, the possible presence of a hydroxyl group that would promote Mo5+ was tested with density functional theory (DFT) computations at the ambient temperature. DFT predicts that sedovite is a ferromagnetic insulator with a fundamental bandgap of Eg ∼ 1.7 eV with its chemical and physical properties dominated by U4+ rather than Mo6+. The structural complexity, IG,tot, of sedovite was evaluated in order to get indirect information about the missing formation conditions.

Uranotungstite, the only natural uranyl tungstate: Crystal structure revealed from 3D electron diffraction

Abstract Uranotungstite is an uranyl-tungstate mineral that was until recently only partially characterized with a formula originally given as (Fe2+,Ba,Pb)(UO2)2(WO4)(OH)4·12H2O and an unknown crystal structure. This mineral has been reinvestigated by electron microprobe analysis coupled with three-dimensional electron diffraction. According to the electron microprobe data, the holotype material from the Menzenschwand uranium deposit (Black Forest, Germany) has the empirical formula (Ba0.35Pb0.27)Σ0.62[(U6+O2)2(W0.986+☐0.75)O4.7(OH)2.5(H2O)1.75](H2O)1.67 (average of 8 points calculated on the basis of 2U apfu; H2O content derived from the structure). According to the precession-assisted 3D ED data, holotype uranotungstite from Menzenschwand is monoclinic, P21/m, with a = 6.318(5) Å, b = 7.388(9) Å, c = 13.71(4) Å, β = 99.04(13)°, and V = 632(2) Å3 (Z = 2). The structure refinement of the 3D ED data using the dynamical approach (Robs = 0.0846 for 3287 independent observed reflections) provided a structure model composed of heteropolyhedral sheets. A β-U3O8-type sheet of idealized composition [(UO2)2W6+Fe0.253+☐0.75O4.75(OH)1.5(H2O)1.75]0.25– is composed of UO7 polyhedra linked by (W,Fe)O5 polyhedra in which the W:Fe ratio is variable as well as the bulk occupancy of this site; the W site may also host a minor proportion of Cu, Mg, or V. In uranotungstite, the interlayer spaces between adjacent U-W-O sheets host water on one side and, on the other side, a partially occupied cation site mostly occupied by Ba and, to a lesser extent, Pb, as well as a partially occupied H2O site. This work is the first structural description of a natural uranyl-tungstate mineral and confirms the great structural and chemical flexibility of β-U3O8 type of sheets.

Structure determination, thermal stability and dissolution rate of δ-indomethacin

The structure solution of the δ-polymorph of indomethacin was obtained using three-dimensional electron diffraction. This form shows a significantly enhanced dissolution rate compared with the more common and better studied α- and γ-polymorphs, indicating better biopharmaceutical properties for medicinal applications. The structure was solved in non-centrosymmetric space group P21 and comprises two molecules in the asymmetric unit. Packing and molecule conformation closely resemble indomethacin methyl ester and indomethacin methanol solvate. Knowledge of the structure allowed the rational interpretation of spectroscopic IR and Raman data for δ-polymorph and a tentative interpretation for still unsolved indomethacin polymorphs. Finally, we observed a solid–solid transition from δ-polymorph to α-polymorph that can be driven by similarities in molecular conformation.

Elucidation of linker motion in metal–organic frameworks by three-dimensional electron diffraction

Elucidation of linker motion in metal–organic frameworks by three-dimensional electron diffraction

On the quality of three-dimensional electron diffraction data for direct location of guest molecules in open-framework materials

On the quality of three-dimensional electron diffraction data for direct location of guest molecules in open-framework materials

Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments.

Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.

Low Dose Structural Analysis of Fragile Materials by Three-Dimensional Electron Diffraction

Low Dose Structural Analysis of Fragile Materials by Three-Dimensional Electron Diffraction

On the completeness of three-dimensional electron diffraction data for structural analysis of metal–organic frameworks

On the completeness of three-dimensional electron diffraction data for structural analysis of metal–organic frameworks

Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction

Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys. 43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

Isoreticular Chemistry of Group 13 Metal-Organic Framework Compounds Based on V-Shaped Linker Molecules: Exceptions to the Rule?

Following the concept of isoreticular chemistry, we carried out a systematic study on Ga-containing metal-organic frameworks (MOFs) using six V-shaped linker molecules of differing sizes, geometries, and additional functional groups. The linkers included three isophthalic acid derivatives (m-H2BDC-R, R = CH3, OCH3, NHCOCH3), thiophene-2,5-dicarboxylic acid (H2TDC), and two 4,4'-sulfonyldibenzoic acid derivatives (H2SDBA, DPSTA). The crystal structures of seven compounds were elucidated by a combination of model building, single-crystal X-ray diffraction (SCXRD), three-dimensional electron diffraction (3D ED), and Rietveld refinements against powder X-ray diffraction (PXRD) data. Four new Ga-MOFs that are isoreticular with their aluminum counterparts, i.e. Ga-CAU-10-R (Ga(OH)(m-BDC-R); R = OCH3, NHCOCH3), Ga-CAU-11 (Ga(OH)(SDBA)), and Ga-CAU-11-COOH (Ga(OH)(H2DPSTC)), were obtained. For the first time large single crystals of a MOF crystallizing in the CAU-10 structure type could be isolated, i.e. Ga-CAU-10-OCH3, which permitted a detailed structural characterization. In addition, the use of 5-methylisophthalic acid and thiophene-2,5-dicarboxylic acid resulted in two new Ga-MOFs denoted Ga-CAU-49 and Ga-CAU-51, respectively, which are not isostructural with any known Al-MOF. The crystal structure of Ga-CAU-49 ([Ga4(m-HBDC-CH3)2(m-BDC-CH3)3(OH)4(H2O)]) contains an unprecedented rod-shaped inorganic building unit (IBU) of the formula ∞1{Ga16(OH)18O60}, composed of corner-sharing GaO5 and GaO6 polyhedra. In Ga-CAU-51 ([Ga(OH)(C5H2O2S)]) chains of alternating cis and trans corner-sharing GaO6 polyhedra form the IBU. A detailed characterization of the title compounds was carried out, including nitrogen gas and water vapor sorption measurements. Ga-CAU-11 was the only compound exhibiting porosity toward nitrogen with a type I isotherm, a specific surface area of aS,BET = 210 m2/g, and a micropore volume of Vmic = 0.09 cm3/g. The new MOF Ga-CAU-51 exhibits exceptional water sorption properties with a reversible S-shaped isotherm and a high uptake around p/p0 = 0.38 of mads = 370 mg/g.

Serial Electron Diffraction Data Processing With diffractem and CrystFEL.

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.