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.

Absolute structure determination of Berkecoumarin by X-ray and electron diffraction.

X-ray and electron diffraction methods independently identify the S-enantiomer of Berkecoumarin [systematic name: (S)-8-hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one]. Isolated from Berkeley Pit Lake Penicillium sp., Berkecoumarin is a natural product with a light-atom composition (C13H14O5) that challenges in-house absolute structure determination by anomalous scattering. This study further demonstrates the utility of dynamical refinement of electron-diffraction data for absolute structure determination.

Dynamical refinement with multipolar electron scattering factors.

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petrícek & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction.

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Šand ß = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.

Refining short-range order parameters from the three-dimensional diffuse scattering in single-crystal electron diffraction data.

Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Šfor the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Šfor the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.

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.

Optimal estimated standard uncertainties of reflection intensities for kinematical refinement from 3D electron diffraction data.

Estimating the error in the merged reflection intensities requires a full understanding of all the possible sources of error arising from the measurements. Most diffraction-spot integration methods focus mainly on errors arising from counting statistics for the estimation of uncertainties associated with the reflection intensities. This treatment may be incomplete and partly inadequate. In an attempt to fully understand and identify all the contributions to these errors, three methods are examined for the correction of estimated errors of reflection intensities in electron diffraction data. For a direct comparison, the three methods are applied to a set of organic and inorganic test cases. It is demonstrated that applying the corrections of a specific model that include terms dependent on the original uncertainty and the largest intensity of the symmetry-related reflections improves the overall structure quality of the given data set and improves the final Rall factor. This error model is implemented in the data reduction software PETS2.

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.

Catching a New Zeolite as a Transition Material during Deconstruction.

Zeolites are key materials in both basic research and industrial applications. However, their synthesis is neither diverse nor applicable to labile frameworks because classical procedures require harsh hydrothermal conditions, whereas post-synthesis methods are limited to a few suitable parent materials. Remaining frameworks can fail due to amorphization, dissolution, and other decomposition processes. Nevertheless, stopping degradation at intermediate structures could yield new zeolites. Here, by optimizing the design and synthesis parameters of the parent zeolite IWV, we "caught" a new, highly crystalline, and siliceous zeolite during its degradation. IWV seed-assisted crystallization followed by gentle transformation into the water-alcohol system yielded the highly crystalline daughter zeolite IPC-20, whose structure was solved by precession-assisted three-dimensional electron diffraction. Without additional requirements, as in conventional (direct or post-synthesis) strategies, our approach may be applied to any chemically labile material with a staged structure.

Preparation and Characterization of Metalloporphyrin Tröger's and Spiro-Tröger's Base Derivatives.

A series of metalloporphyrin dimers as Tröger's bases 1 or spiro-Tröger's bases 2 was prepared starting from five different C4-symmetry porphyrin derivatives substituted in meso-positions by Ph, 3-MeO-Ph, 4-MeO-Ph, 3,4-(MeO)2-Ph, or 3,5-(MeO)2-Ph. Free-base porphyrins were converted to metalloporphyrins, which were subsequently nitrated with nickel(II), copper(II), or zinc(II) nitrate to give ß-nitrometalloporphyrins. These were further reduced to ß-aminometalloporphyrins and treated with a methanal equivalent under acidic conditions to selectively obtain Tröger's base 1, spiro-Tröger's base 2, or a mixture of both, in yields up to 41% of 1 and 45% of 2 depending on the reaction conditions used. The ratio of 1 to 2 was influenced by the methanal equivalent used, the strength of the acid, and, above all, the solvent. The presence of a metal ion within the porphyrin core and the use of a chlorinated solvent were found to be essential for the formation of spiro-Tröger's base 2. The molecular structure of spiroTB 2a-Ni2 was proven by electron diffraction.

Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions.

Determination of lattice parameters from 3D electron diffraction (3D ED) data measured in a transmission electron microscope is hampered by a number of effects that seriously limit the achievable accuracy. The distortion of the diffraction patterns by the optical elements of the microscope is often the most severe problem. A thorough analysis of a number of experimental datasets shows that, in addition to the well known distortions, namely barrel-pincushion, spiral and elliptical, an additional distortion, dubbed parabolic, may be observed in the data. In precession electron diffraction data, the parabolic distortion leads to excitation-error-dependent shift and splitting of reflections. All distortions except for the elliptical distortion can be determined together with lattice parameters from a single 3D ED data set. However, the parameters of the elliptical distortion cannot be determined uniquely due to correlations with the lattice parameters. They can be determined and corrected either by making use of the known Laue class of the crystal or by combining data from two or more crystals. The 3D ED data can yield lattice parameter ratios with an accuracy of about 0.1% and angles with an accuracy better than 0.03°.

Design of metastable oxychalcogenide phases by topochemical (de)intercalation of sulfur in La2O2S2.

Designing and synthesising new metastable compounds is a major challenge of today's material science. While exploration of metastable oxides has seen decades-long advancement thanks to the topochemical deintercalation of oxygen as recently spotlighted with the discovery of nickelate superconductor, such unique synthetic pathway has not yet been found for chalcogenide compounds. Here we combine an original soft chemistry approach, structure prediction calculations and advanced electron microscopy techniques to demonstrate the topochemical deintercalation/reintercalation of sulfur in a layered oxychalcogenide leading to the design of novel metastable phases. We demonstrate that La2O2S2 may react with monovalent metals to produce sulfur-deintercalated metastable phases La2O2S1.5 and oA-La2O2S whose lamellar structures were predicted thanks to an evolutionary structure-prediction algorithm. This study paves the way to unexplored topochemistry of mobile chalcogen anions.

Synthesis of Discrete CHA Zeolite Nanocrystals without Organic Templates for Selective CO2 Capture.

Small-pore zeolites such as chabazite (CHA) are excellent candidates for the selective separation of CO2 ; however, the current synthesis involves several steps and the use of organic structure-directing agent (OSDA), increasing their cost and energy requirements. We report the synthesis of small-pore zeolite crystals (aluminosilicate) with CHA-type framework structure by direct synthesis in a colloidal suspension containing a mixture of inorganic cations only (Na+ , K+ , and Cs+ ). The location of CO2 molecules in the host structure was revealed by 3D electron diffraction (3D ED). The high sorption capacity for CO2 (3.8 mmol g-1 at 121 kPa), structural stability and regenerability of the discreate CHA zeolite nanocrystals is maintained for 10 consecutive cycles without any visible degradation. The CHA zeolite (Si:Al=2) reaches an almost perfect CO2 storage capacity (8 CO2 per unit cell) and high selectivity (no CH4 was adsorbed).

Modulated structure determination and ion transport mechanism of oxide-ion conductor CeNbO4+δ.

CeNbO4+δ, a family of oxygen hyperstoichiometry materials with varying oxygen content (CeNbO4, CeNbO4.08, CeNbO4.25, CeNbO4.33) that shows mixed electronic and oxide ionic conduction, has been known for four decades. However, the oxide ionic transport mechanism has remained unclear due to the unknown atomic structures of CeNbO4.08 and CeNbO4.33. Here, we report the complex (3 + 1)D incommensurately modulated structure of CeNbO4.08, and the supercell structure of CeNbO4.33 from single nanocrystals by using a three-dimensional electron diffraction technique. Two oxide ion migration events are identified in CeNbO4.08 and CeNbO4.25 by molecular dynamics simulations, which was a synergic-cooperation knock-on mechanism involving continuous breaking and reformation of Nb2O9 units. However, the excess oxygen in CeNbO4.33 hardly migrates because of the high concentration and the ordered distribution of the excess oxide ions. The relationship between the structure and oxide ion migration for the whole series of CeNbO4+δ compounds elucidated here provides a direction for the performance optimization of these compounds.

Cleaving silicene-terminated calcium disilicide in the transmission electron microscope.

Silicene, a monolayer of silicon atoms arranged in a honeycomb lattice, is excellently compatible with the materials used in today's semiconductor manufacturing. In this paper, silicene-terminated CaSi2 is cleaved inside a transmission electron microscope using an in situ manipulator. HRTEM studies on a standard lift-out lamella performed from several crystallographic orientations confirm the cell parameters of a = 3.7 Å and c = 30.60 Å, and allow to determine its exact orientation in the SEM/FIB system. A FIB procedure with corrected tilting and rotating angles has been developed to ensure that the tensile force applied by the manipulator is perpendicular to the (0 0 1) plane, and that the [1 0 0] pole axis could be used for HRTEM imaging. A sharp and flat cleavage interface with a length of more than 1 µm was observed in one in situ experiment. HRTEM images from multiple regions confirm that the flat cleavage follows the (0 0 3) plane of the CaSi2 crystal. The current in situ study demonstrates that a surface sheet with silicene-like atomic arrangement can be mechanically exfoliated from silicide compounds.

3D Electron Diffraction: The Nanocrystallography Revolution.

Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.

SSZ-27: A Small-Pore Zeolite with Large Heart-Shaped Cavities Determined by Using Multi-crystal Electron Diffraction.

The high-silica zeolite SSZ-27 was synthesized using one of the isomers of the organic structure-directing agent that is known to produce the large-pore zeolite SSZ-26 (CON). The structure of the as-synthesized form was solved using multi-crystal electron diffraction data. Data were collected on eighteen crystals, and to obtain a high-quality and complete data set for structure refinement, hierarchical cluster analysis was employed to select the data sets most suitable for merging. The framework structure of SSZ-27 can be described as a combination of two types of cavities, one of which is shaped like a heart. The cavities are connected through shared 8-ring windows to create straight channels that are linked together in pairs to form a one-dimensional channel system. Once the framework structure was known, molecular modelling was used to find the best fitting isomer, and this, in turn, was isolated to improve the synthesis conditions for SSZ-27.

Stacking sequence variations in vaterite resolved by precession electron diffraction tomography using a unified superspace model.

As a metastable phase, vaterite is involved in the first step of crystallization of several carbonate-forming systems including the two stable polymorphs calcite and aragonite. Its complete structural determination would consequently shed important light to understand scaling formation and biomineralization processes. While vaterite's hexagonal substructure (a0 ~ 4.1 Å and c0 ~ 8.5 Å) and the organization of the carbonate groups within a single layer is known, conflicting interpretations regarding the stacking sequence remain and preclude the complete understanding of the structure. To resolve the ambiguities, we performed precession electron diffraction tomography (PEDT) to collect single crystal data from 100 K to the ambient temperature. The structure was solved ab initio and described over all the temperature range using a unified modulated structure model in the superspace group C12/c1(α0γ)00 with a = a0 = 4.086(3) Å, b = [Formula: see text]a0 = 7.089(9) Å, c = c0 = 8.439(9) Å, α = ß = γ = 90° and q = [Formula: see text]a* + γc*. At 100 K the model presents a pure 4-layer stacking sequence with γ = [Formula: see text] whereas at the ambient temperature, ordered stacking faults are introduced leading to γ < [Formula: see text]. The model was refined against PEDT data using the dynamical refinement procedure including modulation and twinning as well as against x-ray powder data by the Rietveld refinement.

Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal.

Determination of the absolute configuration of organic molecules is essential in drug development and the subsequent approval process. We show that this determination is possible through electron diffraction using nanocrystalline material. Ab initio structure determination by electron diffraction has so far been limited to compounds that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure analysis of a pharmaceutical cocrystal of sofosbuvir and l-proline, which is about one order of magnitude less stable. Data collection on multiple positions of a crystal and an advanced-intensity extraction procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous determination of the absolute structure of material composed of light scatterers.

Homoleptic Imidophosphorane Stabilization of Tetravalent Cerium.

The homoleptic complexes of cerium with the tris(piperidinyl)imidophosphorane ligand, [NP(pip)3]-, present the most negative Ce3+/4+ redox couple known (<-2.64 V vs Fc/Fc+). This dramatic stabilization of the cerium tetravalent oxidation state [>4.0 V shift from the Ce3+/4+ couple in 1 M HClO4(aq)] is established through reactivity studies. Spectroscopic studies (UV-vis, electron paramagnetic resonance, and Ce L3-edge X-ray absorption spectroscopy), in conjunction with density functional theory studies, reveal the dominant covalent metal-ligand interactions underlying the observed redox chemistry and the dependence of the redox potential on the binding of potassium in the inner coordination sphere.