Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

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

All crystalline materials in nature, whether inorganic, organic, or biological, macroscopic or microscopic, have their own chemical and physical properties, which strongly depend on their atomic structures. Therefore, structure determination is extremely important in chemistry, physics, materials science, etc. In the past centuries, many techniques have been developed for structure determination. The most widely used one is X-ray crystallography (single-crystal X-ray diffraction (SCXRD) and powder X-ray diffraction (PXRD)), and it remains the most important technique for structure determination of crystalline materials. Although SCXRD and PXRD are successful in many cases, a number of reasons limit their applications, such as SCXRD for nanosized crystals, intergrowth, and defects and PXRD for complex structures, multiphasic samples, impurities, peak overlaps, etc. Another most valuable technique for structure determination is electron crystallography (EC). With the electron as a probe, EC alone can also be used for structure determination, especially for crystals that are too small to be studied by SCXRD or too complex for PXRD. As electrons interact much more strongly with matter than X-rays do, both electron diffraction (ED) patterns and high-resolution transmission electron microscopy (HRTEM) images can be obtained from nanosized crystals. However, collecting a complete set of ED patterns or recording a good HRTEM image requires considerable expertise on the operation of electron microscopes and crystallography. The strong interactions between electrons and materials can also lead to dynamical effects and beam damage. These difficulties make structure determination from ED patterns and HRTEM images not straightforward. Recently, two three-dimensional (3D) electron diffraction techniques, automated electron diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed, which perform the data collection in an automated manner. Although the dynamical effects in the newly developed 3D electron diffraction techniques (ADT, RED) are reduced significantly, for some structures there are still problems with obtaining an initial model because of beam damage. The X-ray diffraction and EC methods discussed above are both powerful techniques but have their own limitations. In many complicated cases, one technique alone is not enough to solve the crystal structure, and different techniques that supply complementary structural information have to support each other for the complete structure determination. In this Account, we provide a summary of the advantages and disadvantages of X-ray diffraction (PXRD and SCXRD) and EC (HRTEM and ED) for structure determination and include a review of applications of X-ray diffraction and EC for solving complex structure problems such as peak overlap, impurities, pseudosymmetry and twinning, disordered frameworks, locating guests, aperiodic structures, etc. Some of the latest advances in structure determination are also presented briefly, namely, revealing hydrogen positions by ED, protein crystal structure solution by 3D electron diffraction, and structure determination using an X-ray free electron laser (XFEL).

Magnetically frustrated materials have been the subject of many studies over the last decades. In search for a 3-dimensional quantum spin liquid, where quantum-mechanical fluctuations prevent magnetic order, different phases of stoichiometry Ba3NiSb2O9 have recently [1] been synthesized some of them at high pressure. Two of these phases are hexagonal. The hexagonal phases (space groups P63/mmc and P63mc, respectively) have different structures but cell parameters that differ by less than 1%. Similar phases have been obtained with Cu [2] or Co [3]. These phases are well distinguished by powder X-ray diffraction when they appear in sufficient quantity in a newly synthesized powder. When these phases are present only in minor quantities, which is a common situation when synthesizing new materials, only transmission electron microscopy can give structural information on a very local scale. However, the accuracy of unit cell parameter determination by electron diffraction (usually 1% or worse) and the identical extinction conditions for the 2 space groups don't permit to distinguish between the two phases. Convergent beam electron diffraction could show the difference between the centrosymmetric and non-centrosymmetric space groups provided a suitably oriented particle can be found. In this work we propose a different method of distinguishing structures in such complicated cases by actually solving the structure. Sufficient in-zone axis precession electron diffraction and/or electron diffraction tomography data can be obtained from any crystal regardless of its orientation. In the subsequent structure solution we have tested both space groups. The quality (or absence thereof) of the structure solutions obtained clearly makes it possible to distinguish between the two hexagonal structures.

Pair Distribution Function Obtained from Electron Diffraction: An Advanced Real-Space Structural Characterization Tool

Electron diffraction tomography (EDT) data are in many ways similar to X-ray diffraction data. However, they also present certain specifics. One of the most noteworthy is the specific rocking curve observed for EDT data collected using the precession electron diffraction method. This double-peaked curve (dubbed `the camel') may be described with an approximation based on a circular integral of a pseudo-Voigt function and used for intensity extraction by profile fitting. Another specific aspect of electron diffraction data is the high likelihood of errors in the estimation of the crystal orientation, which may arise from the inaccuracies of the goniometer reading, crystal deformations or crystal movement during the data collection. A method for the refinement of crystal orientation for each frame individually is proposed based on the least-squares optimization of simulated diffraction patterns. This method provides typical angular accuracy of the frame orientations of less than 0.05°. These features were implemented in the computer program PETS 2.0. The implementation of the complete data processing workflow in the program PETS and the incorporation of the features specific for electron diffraction data is also described.

Structure determination of intermetallic phases in bulk Al alloys by 3D electron diffraction tomography

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, Petříček & 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.

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.

Strain engineering is an efficient way to modify the ground state of epitaxial thin films in order to induce new features or improve existing properties.One of the challenges in this approach is to quantify structural changes occurring in these films.While X-ray diffraction is the most widely used technique to obtain accurate structural information on bulk materials, severe limitations appear in the case of epitaxial thin films due to the presence of a thick substrate (mm range) for a film thickness usually well below 100 nm.This last decade, 3D electron diffraction (3D ED) [1], and notably precession electron diffraction tomography (PEDT), has shown its usefulness in the determination of new, metastable, phases stabilized in the form of thin films.While challenging, the determination of unknown structures does actually not represent the major need for thin films.In most cases, the deposited materials have a known structure.The question is not to solve the structure but to know how it differs from the bulk [2].In this context, our aim is to develop a standard dataset acquisition technique in order to accurately quantify the structure of nano-sized domains in thin films.This can be done by combining the standard PEDT procedure with, for each tilt angle, a line or an area scan across the film section (Fig. 1).Known as scanning precession electron diffraction tomography (SPEDT) and already used for nanocrystalline microstructures analysis [3], this approach has the potential to become the standard procedure to characterize films as thin as 10 nm thanks to constant improvements in the illumination and detection systems of transmission electron microscopes.For thicker films, where strain relaxation might occur, line scan shall be sufficient to obtain structural information about the evolution of the structure versus thickness (Fig. 1a).Executed on an area of the film containing several domains (Fig. 1b), diffracted intensities related to each domain could be recorded and used for structure solution and refinement, increasing in this way the amount of information that can be obtained from a single acquisition.These results are obtained within the framework of the European project NanED (Electron Nanocrystallography -H2020-MSCA-ITN GA956099).

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

In recent years, electron diffraction (ED) and structural imaging have undergone a major resurgence in the scientific community, driven by continuous advancements in transmission electron microscopy (TEM) instrumentation, such as Cs correctors, direct detection cameras and automation, and the development or expansion of analytical methods, such as cryo-EM, beam precession, 4D Scanning Electron Diffraction, 3D electron diffraction, 4D-STEM, and ptychography [...]

Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.

3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.

In recent years, we have seen remarkable progress in the field of 3D Electron Diffraction (3D ED).These improvements encompass various aspects, including instrumentation, data collection strategies, mitigation of radiation damage, data processing, handling of dynamical scattering, and refinement.During the refinement stage, it seems to be essential to use appropriate atomic scattering factors.These are usually calculated based on the Independent Atom Model (IAM), which presumes atoms are spherical and do not interact with each other.However, in reality, the electron densities and electrostatic potentials of atoms within molecules or crystals are not perfectly spherical, and the point charges associated with them deviate from the formal charge.Advanced electron density models have been utilized in X-ray crystallography for many years [1,2].When high-quality and highresolution X-ray data is available, these models allow for the extraction of detailed information about electron density directly from the experimental data [3].Even with more routine X-ray data of standard resolution, it is still possible to benefit from using more sophisticated models.This can be achieved by using scattering factors based on advanced models, which are either obtained from theoretical calculations [4] or transferred from appropriate databanks [5].More complex models of electrostatic potential have also been incorporated into electron crystallography.During the lecture, I will provide a summary of what we have recently learned from applying the Transferable Aspherical Atom Model (TAAM) [6,7,8], based on the MATTS databank, and other multipole models to the currently available 3D ED data for organic crystals.I will attempt to answer the question of what benefits we gain by using these models in the case of data of varying quality, different resolution, and the use of kinematical or dynamical refinement.

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) Å and β = 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.