Double conical beam-rocking system for measurement of integrated electron diffraction intensities

Optimization of three-dimensional electron diffuse scattering data acquisition

The diffraction patterns of crystalline materials with local order contain sharp Bragg reflections as well as highly structured diffuse scattering. In this study, we quantitatively show how the diffuse scattering in three-dimensional electron diffraction (3D ED) data is influenced by various parameters, including the data acquisition mode, the detector type and the use of an energy filter. We found that diffuse scattering data used for quantitative analysis are preferably acquired in selected area electron diffraction (SAED) mode using a CCD and an energy filter. In this study, we also show that the diffuse scattering in 3D ED data can be obtained with a quality comparable to that from single-crystal X-ray diffraction. As electron diffraction requires much smaller crystal sizes than X-ray diffraction, this opens up the possibility to investigate the local structure of many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.

Autoencoder latent space sensitivity to material structure in convergent-beam low energy electron diffraction

The convergent-beam low energy electron diffraction technique has been proposed as a novel method to gather local structural and electronic information from crystalline surfaces during low-energy electron microscopy. However, the approach suffers from high complexity of the resulting diffraction patterns. We show that Convolutional Autoencoders trained on CBLEED patterns achieve a highly structured latent space. The latent space is then used to estimate structural parameters with sub-angstrom accuracy. The low complexity of the neural networks enables real time application of the approach during experiments with low latency.

Electron Diffraction Tomography on Two-Phase Nanolamellae of Topochemically Synthesized Cu(Sb2S3)Cl

The dark red semiconductor Cu(Sb2S3)Cl was obtained by leaching the layered precursor Cu(Sb2S3)[AlCl4] in a 0.1 M aqueous HCl solution. The selective extraction of AlCl3 yielded a mica-like lamellar product of poor crystallinity. Misalignment of lamellae down to the nanoscale prevented structure determination by conventional single-crystal X-ray diffraction, but a combination of transmission electron microscopy, selected area electron diffraction, and selected area electron precession diffraction tomography on a nanoscale spot with largely ordered crystalline lamellae revealed the crystal structures of two intergrown modifications. Orthorhombic o-Cu(Sb2S3)Cl and monoclinic m-Cu(Sb2S3)Cl have similar layers to the precursor and differ only in the stacking of the layers. These consist of uncharged Sb2S3 strands, whose sulfide ions, together with chloride ions, coordinate the copper(I) cations. Only one chloride ion remained from the [AlCl4]- group. DFT calculations confirm the structure solution for the orthorhombic form and suggest that the monoclinic structure is metastable against transformation to o-Cu(Sb2S3)Cl.

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.

Improved ACOM pattern matching in 4D-STEM through adaptive sub-pixel peak detection and image reconstruction

The technique known as 4D-STEM has recently emerged as a powerful tool for the local characterization of crystalline structures in materials, such as cathode materials for Li-ion batteries or perovskite materials for photovoltaics. However, the use of new detectors optimized for electron diffraction patterns and other advanced techniques requires constant adaptation of methodologies to address the challenges associated with crystalline materials. In this study, we present a novel image-processing method to improve pattern matching in the determination of crystalline orientations and phases. Our approach uses sub-pixel adaptive image processing to register and reconstruct electron diffraction signals in large 4D-STEM datasets. By using adaptive prominence and linear filters, we can improve the quality of the diffraction pattern registration. The resulting data compression rate of 103 is well-suited for the era of big data and provides a significant enhancement in the performance of the entire ACOM data processing method. Our approach is evaluated using dedicated metrics, which demonstrate a high improvement in phase recognition. Several features are extracted from the registered data to map properties such as the spot count, and various virtual dark fields, which are used to enhance the handling of the results maps. Our results demonstrate that this data preparation method not only enhances the quality of the resulting image but also boosts the confidence level in the analysis of the outcomes related to determining crystal orientation and phase. Additionally, it mitigates the impact of user bias that may occur during the application of the method through the manipulation of parameters.

High precision orientation mapping from 4D-STEM precession electron diffraction data through quantitative analysis of diffracted intensities

The association of scanning transmission electron microscopy (STEM) and detection of a diffraction pattern at each probe position (so-called 4D-STEM) represents one of the most promising approaches to analyze structural properties of materials with nanometric resolution and low irradiation levels. This is widely used for texture analysis of materials using automated crystal orientation mapping (ACOM). Herein, we perform orientation mapping in InP nanowires exploiting precession electron diffraction (PED) patterns acquired by an axial CMOS camera. Crystal orientation is determined at each probe position by the quantitative analysis of diffracted intensities minimizing a residue comparing experiments and simulations in analogy to x-ray structural refinement. Our simulations are based on the two-beam dynamical diffraction approximation and yield a high angular precision (∼0.03°), much lower than the traditional ACOM based on pattern matching algorithms (∼1°). We anticipate that simultaneous exploration of both spot positions and high precision crystal misorientation will allow the exploration of the whole potentiality provided by PED-based 4D-STEM for the characterization of deformation fields in nanomaterials.

Diffraction-Based Multiscale Residual Strain Measurements

Modern analytical tools, from microfocus X-ray diffraction (XRD) to electron microscopy-based microtexture measurements, offer exciting possibilities of diffraction-based multiscale residual strain measurements. The different techniques differ in scale and resolution, but may also yield significantly different strain values. This study, for example, clearly established that high-resolution electron backscattered diffraction (HR-EBSD) and high-resolution transmission Kikuchi diffraction (HR-TKD) [sensitive to changes in interplanar angle (Δθθ)], provide quantitatively higher residual strains than micro-Laue XRD and transmission electron microscope (TEM) based precession electron diffraction (PED) [sensitive to changes in interplanar spacing (Δdd)]. Even after correcting key known factors affecting the accuracy of HR-EBSD strain measurements, a scaling factor of ∼1.57 (between HR-EBSD and micro-Laue) emerged. We have then conducted "virtual" experiments by systematically deforming an ideal lattice by either changing an interplanar angle (α) or a lattice parameter (a). The patterns were kinematically and dynamically simulated, and corresponding strains were measured by HR-EBSD. These strains showed consistently higher values for lattice(s) distorted by α, than those altered by a. The differences in strain measurements were further emphasized by mapping identical location with HR-TKD and TEM-PED. These measurements exhibited different spatial resolution, but when scaled (with ∼1.57) provided similar lattice distortions numerically.

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.

Multi-exposure diffraction pattern fusion applied to enable wider-angle transmission Kikuchi diffraction with direct electron detectors

Diffraction pattern analysis can be used to reveal the crystalline structure of materials, and this information is used to nano- and micro-structure of advanced engineering materials that enable modern life. For nano-structured materials typically diffraction pattern analysis is performed in the transmission electron microscope (TEM) and TEM diffraction patterns typically have a limited angular range (less than a few degrees) due to the long camera length, and this requires analysis of multiple patterns to probe a unit cell. As a different approach, wide angle Kikuchi patterns can be captured using an on-axis detector in the scanning electron microscope (SEM) with a shorter camera length. These 'transmission Kikuchi diffraction' (TKD) patterns present a direct projection of the unit cell and can be routinely analysed using EBSD-based methods and dynamical diffraction theory. In the present work, we enhance this analysis significantly and present a multi-exposure diffraction pattern fusion method that increases the dynamic range of the detected patterns captured with a Timepix3-based direct electron detector (DED). This method uses an easy-to-apply exposure fusion routine to collect data and extend the dynamic range, as well as normalise the intensity distribution within these very wide (>95°) angle patterns. The potential of this method is demonstrated with full diffraction sphere reprojection and highlight potential of the approach to rapidly probe the structure of nano-structured materials in the scanning electron microscope.

Modelling dynamical 3D electron diffraction intensities. II. The role of inelastic scattering

The strong interaction of high-energy electrons with a crystal results in both dynamical elastic scattering and inelastic events, particularly phonon and plasmon excitation, which have relatively large cross sections. For accurate crystal structure refinement it is therefore important to uncover the impact of inelastic scattering on the Bragg beam intensities. Here a combined Bloch wave-Monte Carlo method is used to simulate phonon and plasmon scattering in crystals. The simulated thermal and plasmon diffuse scattering are consistent with experimental results. The simulations also confirm the empirical observation of a weaker unscattered beam intensity with increasing energy loss in the low-loss regime, while the Bragg-diffracted beam intensities do not change significantly. The beam intensities include the diffuse scattered background and have been normalized to adjust for the inelastic scattering cross section. It is speculated that the random azimuthal scattering angle during inelastic events transfers part of the unscattered beam intensity to the inner Bragg reflections. Inelastic scattering should not significantly influence crystal structure refinement, provided there are no artefacts from any background subtraction, since the relative intensity of the diffracted beams (which includes the diffuse scattering) remains approximately constant in the low energy loss regime.

Structural analysis of nanocrystals by pair distribution function combining electron diffraction with crystal tilting

As an important characterization method, pair distribution function (PDF) has been extensively used in structural analysis of nanomaterials, providing key insights into the degree of crystallinity, atomic structure, local disorder etc. The collection of scattering signals with good statistics is necessary for a reliable structural analysis. However, current conventional electron diffraction experiments using PDF (ePDF) are limited in their ability to acquire continuous diffraction rings for large nanoparticles. Herein, a new method - tilt-ePDF - is proposed to improve the data quality and compatibility of ePDF by a combination of electron diffraction and specimen tilting. In the present work, a tilt-series of electron diffraction patterns was collected from gold nanoparticles with three different sizes and a standard sample polycrystalline aluminium film for ePDF analysis. The results show that tilt-ePDF can not only enhance the continuity of diffraction rings, but can also improve the signal-to-noise ratio in the high scattering angle range. As a result, compared with conventional ePDF data, tilt-ePDF data provide structure parameters with a better accuracy and lower residual factors in the refinement against the crystal structure. This method provides a new way of utilizing ePDF to obtain accurate local structure information from nanoparticles.

Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

Beam sensitive nanomaterials such as zeolites or metal-organic frameworks (MOF) represent a great challenge for crystallographic structure determination and refinement. The strong electron-matter interaction and the high spatial resolution achievable make electron diffraction the technique of choice for particles of sizes below a micrometer and many different 3-dimensional electron diffraction (3D ED) techniques have been developed in recent years. Nevertheless, beam sensitivity of the samples can lead to the crystal structure being damaged during the data acquisition impeding the determination of its structure. A simple way to reduce beam damage is to lower the dose during the experiment. However, this implies weaker diffraction intensities which can become problematic for the exploitation of the data. In order to obtain complete data sets with strong intensities without damaging the crystals, we developed the dose symmetric electron diffraction tomography (DS-EDT) method, combining the low-dose electron diffraction tomography (LD-EDT) technique with the dose-symmetric tomography scheme known from cryo-EM. In order to reduce the dose on an individual crystal and still obtain enough data for a structure solution and refinement, we partition the dose over several crystals. The individual datasets are then merged in order to achieve the necessary completeness. On two test structures we first show that merging of data from small domains of the reciprocal space is indeed sufficient to obtain reliable data for structure solution and refinement. Second, we show on the beam sensitive manganese formate that high-quality data can be obtained on a few frames while the frames that have suffered from beam damage can still be used to determine the orientation matrix and the unit cell of the crystals. The results from the dynamical refinement on the obtained data show a high accuracy of the atom positions. In this way, DS-EDT can reduce the total dose on an individual crystal by an order of magnitude with respect to the already very dose-efficient LD-EDT.

Scanning precession electron diffraction data analysis approaches for phase mapping of precipitates in aluminium alloys

Mapping the spatial distribution of crystal phases with nm-scale spatial resolution is an important characterisation task in studies of multi-phase materials. One popular approach is to use scanning precession electron diffraction which enables semi-automatic phase mapping at the nanoscale by collecting a single precession electron diffraction pattern at every probe position over regions spanning up to a few micrometers. For a successful phase mapping each diffraction pattern must be correctly identified. In this work four different approaches for phase mapping of embedded precipitates in an Al-Cu-Li alloy are compared on a sample containing three distinct crystal phases. These approaches are based on: non-negative matrix factorisation, vector matching, template matching and artificial neural networks. To evaluate the success of each approach a ground truth phase map was manually created from virtual images based on characteristic phase morphologies and compared with the deduced phase maps. The percentage accuracy of all methods when compared to the ground truth was satisfactory, with all approaches obtaining scores above 98%. The optimal method depends on the specific task at hand. Non-negative matrix factorisation is suitable with limited prior data knowledge but performs best with few unique diffraction patterns and requires substantial post-processing. It has the advantage of reducing the dimensionality of the dataset and handles weak diffracted intensities well given that they occur repeatedly. The current vector matching implementation is fast, simple, based only on the Bragg spot geometry and requires few parameters. It does however demand that each Bragg spot is accurately detected in each pattern and the current implementation is limited to zone axis patterns. Template matching handles a large range of orientations, including off-axis patterns. However, achieving successful and reliable results often require thorough data pre-processing and do require adequate diffraction simulations. For artificial neural networks a substantial setup effort is demanded but once trained it excels for routine tasks, offering fast predictions. The implemented codes and the data used are available open-source. These resources and the detailed assessment of the methods will allow others to make informed decisions when selecting a data analysis approach for 4D-STEM phase mapping tasks on other material systems.

Applications and limitations of electron 3D crystallography

Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.

The crystal structure of the killer fibre erionite from Tuzköy (Cappadocia, Turkey)

Erionite is a non-asbestos fibrous zeolite classified by the International Agency for Research on Cancer (IARC) as a Group 1 carcinogen and is considered today similar to or even more carcinogenic than the six regulated asbestos minerals. Exposure to fibrous erionite has been unequivocally linked to cases of malignant mesothelioma (MM) and this killer fibre is assumed to be directly responsible for more than 50% of all deaths in the population of the villages of Karain and Tuzköy in central Anatolia (Turkey). Erionite usually occurs in bundles of thin fibres and very rarely as single acicular or needle-like fibres. For this reason, a crystal structure of this fibre has not been attempted to date although an accurate characterization of its crystal structure is of paramount importance for our understanding of the toxicity and carcinogenicity. In this work, we report on a combined approach of microscopic (SEM, TEM, electron diffraction), spectroscopic (micro-Raman) and chemical techniques with synchrotron nano-single-crystal diffraction that allowed us to obtain the first reliable ab initio crystal structure of this killer zeolite. The refined structure showed regular T-O distances (in the range 1.61-1.65 Å) and extra-framework content in line with the chemical formula (K2.63Ca1.57Mg0.76Na0.13Ba0.01)[Si28.62Al7.35]O72·28.3H2O. The synchrotron nano-diffraction data combined with three-dimensional electron diffraction (3DED) allowed us to unequivocally rule out the presence of offretite. These results are of paramount importance for understanding the mechanisms by which erionite induces toxic damage and for confirming the physical similarities with asbestos fibres.

Unraveling the Complex Solid-State Phase Transition Behavior of 1-Iodoadamantane, a Material for Which Ostensibly Identical Crystals Undergo Different Transformation Pathways

Phase transitions in crystalline molecular solids have important implications in the fundamental understanding of materials properties and in the development of materials applications. Herein, we report the solid-state phase transition behavior of 1-iodoadamantane (1-IA) investigated using a multi-technique strategy [synchrotron powder X-ray diffraction (XRD), single-crystal XRD, solid-state NMR, and differential scanning calorimetry (DSC)], which reveals complex phase transition behavior on cooling from ambient temperature to ca. 123 K and on subsequent heating to the melting temperature (348 K). Starting from the known phase of 1-IA at ambient temperature (phase A), three low-temperature phases are identified (phases B, C, and D); the crystal structures of phases B and C are reported, together with a re-determination of the structure of phase A. Remarkably, single-crystal XRD shows that some individual crystals of phase A transform to phase B, while other crystals of phase A transform instead to phase C. Results (from powder XRD and DSC) on cooling a powder sample of phase A are fully consistent with this behavior while also revealing an additional transformation pathway from phase A to phase D. Thus, on cooling, a powder sample of phase A transforms partially to phase C (at 229 K), partially to phase D (at 226 K) and partially to phase B (at 211 K). During the cooling process, each of the phases B, C, and D is formed directly from phase A, and no transformations are observed between phases B, C, and D. On heating the resulting triphasic powder sample of phases B, C, and D from 123 K, phase B transforms to phase D (at 211 K), followed by the transformation of phase D to phase C (at 255 K), and finally, phase C transforms to phase A (at 284 K). From these observations, it is apparent that different crystals of phase A, which are ostensibly identical at the level of information revealed by XRD, must actually differ in other aspects that significantly influence their low-temperature phase transition pathways. This unusual behavior will stimulate future studies to gain deeper insights into the specific properties that control the phase transition pathways in individual crystals of this material.

A reference-area-free strain mapping method using precession electron diffraction data

In this work, we developed a method using precession electron diffraction data to map the residual elastic strain at the nano-scale. The diffraction pattern of each pixel was first collected and denoised. Template matching was then applied using the center spot as the mask to identify the positions of the diffraction disks. Statistics of distances between the selected diffracted disks enable the user to make an informed decision on the reference and to generate strain maps. Strain mapping on an unstrained single crystal sapphire shows the standard deviation of strain measurement is 0.5%. With this method, we were able to successfully measure and map the residual elastic strain in VO₂ on sapphire and martensite in a Ni_50.3Ti_29.7Hf₂₀ shape memory alloy. This approach does not require the user to select a "strain-free area" as a reference and can work on datasets even with the crystals oriented away from zone axes. This method is expected to provide a robust and more accessible alternative means of studying the residual strain of various material systems that complements the existing algorithms for strain mapping.

Solving the crystallographic phase problem using dynamical scattering in electron diffraction

Solving crystal structures from kinematical X-ray or electron diffraction patterns of single crystals requires many more diffracted beams to be recorded than there are atoms in the structure, since the phases of the structure factors can only be retrieved from such data if the atoms can be resolved as sharply peaked objects. Here a method is presented by which the fact that multiple scattering encodes structure factor phases in the diffracted intensities is being used for solving the crystallographic phase problem. The retrieval of both amplitudes and phases of electron structure factors from diffraction patterns recorded with varying angle of incidence will be demonstrated. No assumption about the scattering potential itself is being made. In particular, the resolution in the diffraction data does not need to be sufficient to resolve atoms, making this method potentially interesting for electron crystallography of 2-dimensional protein crystals and other beam-sensitive complex structures.

Effect of Pore Formation on Redox-Driven Phase Transformation

When solid-state redox-driven phase transformations are associated with mass loss, vacancies are produced that develop into pores. These pores can influence the kinetics of certain redox and phase transformation steps. We investigated the structural and chemical mechanisms in and at pores in a combined experimental-theoretical study, using the reduction of iron oxide by hydrogen as a model system. The redox product (water) accumulates inside the pores and shifts the local equilibrium at the already reduced material back toward reoxidation into cubic Fe_{1-x}O (where x refers to Fe deficiency, space group Fm3[over ¯]m). This effect helps us to understand the sluggish reduction of cubic Fe_{1-x}O by hydrogen, a key process for future sustainable steelmaking.

Electron crystallography and dedicated electron-diffraction instrumentation

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

Correcting for probe wandering by precession path segmentation

Precession electron diffraction has in the past few decades become a powerful technique for structure solving, strain analysis, and orientation mapping, to name a few. One of the benefits of precessing the electron beam, is increased reciprocal space resolution, albeit at a loss of spatial resolution due to an effect referred to as 'probe wandering'. Here, a new methodology of precession path segmentation is presented to counteract this effect and increase the resolution in reconstructed virtual images from scanning precession electron diffraction data. By utilizing fast pixelated electron detector technology, multiple frames are recorded for each azimuthal rotation of the beam, allowing for the probe wandering to be corrected in post-acquisition processing. Not only is there an apparent increase in the resolution of the reconstructed images, but probe wandering due to instrument misalignment is reduced, potentially easing an already difficult alignment procedure.

Synthesis and Structure Evolution in Metal Carbazole Diphosphonates Followed by Electron Diffraction

To access porous metal phosphonates, a new V-shaped, rigid, and sterically demanding diphosphonic acid, namely 3,6-diphosphono-9H-carbazole (H₄L), was designed and employed in a high-throughput investigation. Screening of different metal salts and subsequent optimization studies resulted in the isolation of two porous metal phosphonates [Cu₂(H₂O)₂(L)]·2H₂O (CAU-37) and [Zn_6.75(H₂O)_1.5(HL)_2.5(L)_1.5]·8H₂O (CAU-57). Structure determination was accomplished by electron diffraction and the dehydration behavior of CAU-37 was followed in situ. A rare case of intralayer water de-/adsorption in CAU-37 was found which leads to a cell volume change of 11.9%. Rod-shaped inorganic building units (IBUs) are connected to layers and structural flexibility is due to "accordion-like" structural changes within the layers. In contrast, in CAU-57 a layered IBU is found, which usually results in the formation of dense structures. Due to the shape and rigidity of the linker, the interconnection of the IBUs results in the formation of pores. Water sorption measurements in combination with powder X-ray diffraction data confirmed the reversibility under structural retention.

Modelling fine-sliced three dimensional electron diffraction data with dynamical Bloch-wave simulations

Recent interest in structure solution and refinement using electron diffraction (ED) has been fuelled by its inherent advantages when applied to crystals of sub-micrometre size, as well as its better sensitivity to light elements. Currently, data are often processed with software written for X-ray diffraction, using the kinematic theory of diffraction to generate model intensities - despite the inherent differences in diffraction processes in ED. Here, dynamical Bloch-wave simulations are used to model continuous-rotation electron diffraction data, collected with a fine angular resolution (crystal orientations of ∼0.1°). This fine-sliced data allows a re-examination of the corrections applied to ED data. A new method is proposed for optimizing crystal orientation, and the angular range of the incident beam and the varying slew rate are taken into account. Observed integrated intensities are extracted and accurate comparisons are performed with simulations using rocking curves for a (110) lamella of silicon 185 nm thick. R₁ is reduced from 26% with the kinematic model to 6.8% using dynamical simulations.

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°.

Electron Diffraction of 3D Molecular Crystals

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

3D electron diffraction for structure determination of small-molecule nanocrystals: A possible breakthrough for the pharmaceutical industry

Nanomedicine is among the most fascinating areas of research. Most of the newly discovered pharmaceutical polymorphs, as well as many new synthesized or isolated natural products, appear only in form of nanocrystals. The development of techniques that allow investigating the atomic structure of nanocrystalline materials is therefore one of the most important frontiers of crystallography. Some unique features of electrons, like their non-neutral charge and their strong interaction with matter, make this radiation suitable for imaging and detecting individual atoms, molecules, or nanoscale objects down to sub-angstrom resolution. In the recent years the development of three-dimensional (3D) electron diffraction (3D ED) has shown that electron diffraction can be successfully used to solve the crystal structure of nanocrystals and most of its limiting factors like dynamical scattering or limited completeness can be easily overcome. This article is a review of the state of the art of this method with a specific focus on how it can be applied to beam sensitive samples like small-molecule organic nanocrystals. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Quantitative analysis of diffuse electron scattering in the lithium-ion battery cathode material Li1.2Ni0.13Mn0.54Co0.13O2

In contrast to perfectly periodic crystals, materials with short-range order produce diffraction patterns that contain both Bragg reflections and diffuse scattering. To understand the influence of short-range order on material properties, current research focuses increasingly on the analysis of diffuse scattering. This article verifies the possibility to refine the short-range order parameters in submicrometre-sized crystals from diffuse scattering in single-crystal electron diffraction data. The approach was demonstrated on Li1.2Ni0.13Mn0.54Co0.13O2, which is a state-of-the-art cathode material for lithium-ion batteries. The intensity distribution of the 1D diffuse scattering in the electron diffraction patterns of Li1.2Ni0.13Mn0.54Co0.13O2 depends on the number of stacking faults and twins in the crystal. A model of the disorder in Li1.2Ni0.13Mn0.54Co0.13O2 was developed and both the stacking fault probability and the percentage of the different twins in the crystal were refined using an evolutionary algorithm in DISCUS. The approach was applied on reciprocal space sections reconstructed from 3D electron diffraction data since they exhibit less dynamical effects compared with in-zone electron diffraction patterns. A good agreement was achieved between the calculated and the experimental intensity distribution of the diffuse scattering. The short-range order parameters in submicrometre-sized crystals can thus successfully be refined from the diffuse scattering in single-crystal electron diffraction data using an evolutionary algorithm in DISCUS.

A structure determination protocol based on combined analysis of 3D-ED data, powder XRD data, solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine

We report the crystal structure of a new polymorph of l-tyrosine (denoted the β polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic 13C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state 13C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the β polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and β polymorphs.

ReciPro: free and open-source multipurpose crystallographic software integrating a crystal model database and viewer, diffraction and microscopy simulators, and diffraction data analysis tools

ReciPro is a comprehensive multipurpose crystallographic program equipped with an intuitive graphical user interface (GUI), and it is completely free and open source. This software has a built-in crystal database consisting of over 20 000 crystal models, and the visualization system can seamlessly display a specified crystal model as an attractive three-dimensional graphic. The comprehensive features are not confined to these crystal model databases and viewers. It can smoothly and quantitatively simulate not only single-crystal and/or polycrystalline (powder) diffraction patterns of X-ray, electron and neutron diffraction of a selected crystal model, based on the kinematic scattering theory, but also various electron diffraction patterns and high-resolution transmission electron microscopy (TEM) images, based on the dynamical scattering theory. The features of stereographic projection of crystal planes/axes to explore crystal orientation relationships and the semi-automatic diffraction spot indexing function for experimental diffraction patterns assist diffraction experiments and analyses. These features are linked through a user-friendly GUI, and the results can be synchronously displayed almost in real time. ReciPro will assist a wide range of crystallographers (including beginners) using X-ray, electron and neutron diffraction crystallography and TEM.

Two New Organic Co-Crystals Based on Acetamidophenol Molecules

Herein we present two new organic co-crystals obtained through a simple solution growth process based on an acetamidophenol molecule, either paracetamol or metacetamol, and on 7,7,8,8-tetracyanoquinodimethane (TCNQ). These co-crystals are part of a family of potential organic charge transfer complexes, where the acetamidophenol molecule behaves as an electron donor and TCNQ behaves as an electron acceptor. Due to the sub-micron size of the crystalline domains, 3D electron diffraction was employed for the structure characterization of both systems. Paracetamol-TCNQ structure was solved by standard direct methods, while the analysis of metacetamol-TCNQ was complicated by the low resolution of the available diffraction data and by the low symmetry of the system. The structure determination of metacetamol-TCNQ was eventually achieved after merging two data sets and combining direct methods with simulated annealing. Our study reveals that both paracetamol-TCNQ and metacetamol-TCNQ systems crystallize in a 1:1 stoichiometry, assembling in a mixed-stack configuration and adopting a non-centrosymmetric P1 symmetry. It appears that paracetamol and metacetamol do not form a strong structural scaffold based on hydrogen bonding, as previously observed for orthocetamol-TCNQ and orthocetamol-TCNB (1,2,4,5-tetracyanobenzene) co-crystals.

Precise strain mapping of nano-twinned axial ZnTe/CdTe hetero-nanowires by scanning nanobeam electron diffraction

The occurrence of strain is inevitable for the growth of lattice mismatched heterostructures. It affects greatly the mechanical, electrical and optical properties of nano-objects. It is also the case for nanowires which are characterized by a high surface to volume ratio. Thus, the knowledge of the strain distribution in nano-objects is critically important for their implementation into devices. This paper presents an experimental data for II-VI semiconductor system. Scanning nanobeam electron diffraction strain mapping technique for hetero-nanowires characterized by a large lattice mismatch (>6% in the case of CdTe/ZnTe) and containing segments with nano-twins has been described. The spatial resolution of about 2 nm is 10 times better than obtained in synchrotron nanobeam systems. The proposed approach allows us to overcome the difficulties related to nanowire thickness variations during the acquisition of the nano-beam electron diffraction data. In addition, the choice of optimal parameters used for the acquisition of nano-beam diffraction data for strain mapping has been discussed. The knowledge of the strain distribution enables, in our particular case, the improvement of the growth model of extremely strained axial nanowires synthetized by vapor-liquid solid growth mechanism. However, our method can be applied for the strain mapping in nanowire heterostructures grown by any other method.

Low-Dose Electron Crystallography: Structure Solution and Refinement

There is a wealth of materials that are beam sensitive and only exist in nanometric crystals, because the growth of bigger crystals is either impossible or so complicated that it is not reasonable to spend enough time and resources to grow big crystals before knowing their potential for research or applications. This difficulty is encountered in minerals, zeolites, metal-organic frameworks or molecular crystals, including pharmaceuticals and biological crystals. In order to study these crystals a structure determination method for beam sensitive crystals of nanometric size is needed. The nanometric size makes them destined for electron diffraction, since electrons interact much more strongly with matter than X-rays or neutrons. In addition, for the same amount of beam damage, electron diffraction yields more information than X-rays. The recently developed low-dose electron diffraction tomography (LD-EDT) not only combines the advantages inherent in electron diffraction, but is also optimized for minimizing the electron dose used for the data collection. The data quality is high, allowing not only the solution of complex unknown structures, but also their refinement taking into account the dynamical diffraction effects. Here we present several examples of crystals solved and refined by this method. The range of the crystals presented includes two synthetic oxides, Sr5CuGe9O24 and (Na2/3Mn1/3)3Ge5O12, a natural mineral (bulachite), and a metal organic framework (Mn-formiate). The dynamical refinement can be successfully performed on data sets that needed less than 0.1 e−/Å2 for the entire data set.

Three-Dimensional Electron Diffraction: A Powerful Structural Characterization Technique for Crystal Engineering

Understanding crystal structures and behaviors is crucial for constructing and engineering crystalline materials with various properties and functions. Recent advancement in three-dimensional electron diffraction (3D ED) and its application on...

Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination

Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.

Self-Assembly of Pulverized Nanoparticles: An Approach to Realize Large-Capacity, Long-Lasting, and Ultra-Fast-Chargeable Na-Ion Batteries

The fabrication of battery anodes simultaneously exhibiting large capacity, fast charging capability, and high cyclic stability is challenging because these properties are mutually contrasting in nature. Here, we report a rational strategy to design anodes outperforming the current anodes by simultaneous provision of the above characteristics without utilizing nanomaterials and surface modifications. This is achieved by promoting spontaneous structural evolution of coarse Sn particles to 3D-networked nanostructures during battery cycling in an appropriate electrolyte. The anode steadily exhibits large capacity (∼480 mAhg^-1) and energy retention capability (99.9%) during >1500 cycles even at an ultrafast charging rate of 12 690 mAg^-1 (15C). The structural and chemical origins of the measured properties are explained using multiscale simulations combining molecular dynamics and density functional theory calculations. The developed method is simple, scalable, and expandable to other systems and provides an alternative robust route to obtain nanostructured anode materials in large quantities.

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 ų 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 E_g ∼ 1.7 eV with its chemical and physical properties dominated by U⁴⁺ rather than Mo⁶⁺. The structural complexity, I_G,tot, of sedovite was evaluated in order to get indirect information about the missing formation conditions.

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

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

Hexagonal Si-Ge Class of Semiconducting Alloys Prepared by Using Pressure and Temperature

Multi-anvil and laser-heated diamond anvil methods have been used to subject Ge and Si mixtures to pressures and temperatures of between 12 and 17 GPa and 1500-1800 K, respectively. Synchrotron angle dispersive X-ray diffraction, precession electron diffraction and chemical analysis using electron microscopy, reveal recovery at ambient pressure of hexagonal Ge-Si solid solutions (P6₃ /mmc). Taken together, the multi-anvil and diamond anvil results reveal that hexagonal solid solutions can be prepared for all Ge-Si compositions. This hexagonal class of solid solutions constitutes a significant expansion of the bulk Ge-Si solid solution family, and is of interest for optoelectronic applications.

Exploring the origins of the indentation size effect at submicron scales

The origin of the indentation size effect has been extensively researched over the last three decades, following the establishment of nanoindentation as a broadly used small-scale mechanical testing technique that enables hardness measurements at submicrometer scales. However, a mechanistic understanding of the indentation size effect based on direct experimental observations at the dislocation level remains limited due to difficulties in observing and quantifying the dislocation structures that form underneath indents using conventional microscopy techniques. Here, we employ precession electron beam diffraction microscopy to "look beneath the surface," revealing the dislocation characteristics (e.g., distribution and total length) as a function of indentation depth for a single crystal of nickel. At smaller depths, individual dislocation lines can be resolved, and the dislocation distribution is quite diffuse. The indentation size effect deviates from the Nix-Gao model and is controlled by dislocation source starvation, as the dislocations are very mobile and glide away from the indented zone, leaving behind a relatively low dislocation density in the plastically deformed volume. At larger depths, dislocations become highly entangled and self-arrange to form subgrain boundaries. In this depth range, the Nix-Gao model provides a rational description because the entanglements and subgrain boundaries effectively confine dislocation movement to a small hemispherical volume beneath the contact impression, leading to dislocation interaction hardening. The work highlights the critical role of dislocation structural development in the small-scale mechanistic transition in indentation size effect and its importance in understanding the plastic deformation of materials at the submicron scale.

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 La₂O₂S_1.5 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.

Great progress has been made in topochemistry of mobile oxygen anions, but metastable compounds have not yet been achieved by deintercalation of sulfur anions. Here, the authors prepare metastable oxychalcogenide phases by taking advantage of redox-reactive sulfur dimers embedded in a layered oxysulfide.

Synthesis and electrochemical properties of metal(ii)-carboxyethylphenylphosphinates

We report herein the synthesis, structural characterization and electrocatalytic properties of three new coordination polymers, resulting from the combination of divalent metal (Ca²⁺, Cd²⁺ or Co²⁺) salts with (2-carboxyethyl)(phenyl)phosphinic acid. In addition to the usual hydrothermal procedure, the Co²⁺ derivative could also be prepared by microwave-assisted synthesis, in much shorter times. The crystal structures were solved by ab initio calculations, from powder diffraction data. Compounds M^II[O₂P(CH₂CH₂COOH)(C₆H₅)]₂ {M = Cd (1) or Ca (2)} crystallize in the monoclinic system and display a layered topology, with the phenyl groups pointing toward the interlayer space in a interdigitated fashion. Compound Co₂[(O₂P(CH₂CH₂COO)(C₆H₅)(H₂O)]₂·2H₂O (3) presents a 1D structure composed of zig-zag chains, formed by edge-sharing cobalt octahedra, with the phenyl groups pointing outside. Packing of these chains is favored by hydrogen bond interactions via lattice water molecules. In addition, H-bonds along the chains are established with the participation of the water molecules and the hydrophilic groups from the ligand. However, the solid exhibits a low proton conductivity, attributed to the isolation of the hydrophilic regions caused by the arrangement of hydrophobic phenyl groups. Preliminary studies on the electrocatalytic performance for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) have been conducted for compound 3 and its pyrolytic derivatives, which were previously thoroughly characterized. By comparison, another Co²⁺ phosphinate, 4, obtained by microwave-assisted synthesis, but with distinct stoichiometry and a known structure was also tested. For the OER, the best performance was achieved with a derivative of 3, prepared by heating this compound in N₂ at 200 °C. This derivative showed overpotential (339 mV, at a current density of 10 mA cm^-2) and Tafel slope (51.7 mV dec^-1) values comparable to those of other Co²⁺ related materials.

A new electron diffraction approach for structure refinement applied to Ca3Mn2O7

The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.

Crystallographic Orientation Analysis of Nanocrystalline Tungsten Thin Film Using TEM Precession Electron Diffraction and SEM Transmission Kikuchi Diffraction

Two advanced, automated crystal orientation mapping techniques suited for nanocrystalline materials—precession electron diffraction (PED) in transmission electron microscopy (TEM) and on-axis transmission Kikuchi diffraction (TKD) in scanning electron microscopy (SEM)—are evaluated by comparing the orientation maps obtained from the identical location on a 30 nm-thick nanocrystalline tungsten (W) thin film. A side-by-side comparison of the orientation maps directly showed that the large-scale orientation features are almost identical. However, there are differences in the fine details, which arise from the fundamentally different nature of the spot pattern and Kikuchi line pattern in terms of the excitation volume and the angular resolution. While TEM-PED is more reliable to characterize grains oriented along low-index zone axes, the high angular resolution of SEM-TKD allows the detection of small misorientation between grains and thus yields better quantification and statistical analysis of grain orientation. Given that both TEM-PED and SEM-TKD orientation mapping techniques are complementary tools for nanocrystalline materials, one can be favorably selected depending on the requirements of the analysis, as they have competitive performance in terms of angular resolution and texture quantification.