3D electron crystallography has emerged as a method with great potential for the structure determination of small molecules and macromolecules complementing traditional single-crystal X-ray crystallography and powder X-ray diffraction (PXRD). It offers the unique capability of determining the structures of small molecules and macromolecules from micro- and nanocrystals. In this study, using 3D electron diffraction (3D ED), we determined the single-crystal structure of commercially sourced arginine directly from its bottle. The 3D ED analysis of micro-sized single crystals identified two distinct forms: the L-arginine enantiomer and the racemic mixture DL-arginine. At the time of writing, neither the Cambridge Structural Database nor the Crystallographic Open Database contain a single-crystal structure of isolated L-arginine (sum formula C6H14N4O2), which has been solved in this work by 3D ED. We also present a comparison of the structures of these molecules solved by 3D ED and PXRD.

• Klíčová slova
• 3D ED, 3D electron crystallography, crystal structure, l-arginine, trace impurity,
• Publikační typ
• časopisecké články MeSH

Over the past decade, advances in electron diffraction (ED) have significantly improved the determination and refinement of crystal structures, making it a viable alternative to traditional X-ray diffraction (XRD), especially for very small volumes, such as nanoparticles (NPs). This work evaluates the application of advanced 3D ED techniques to the analysis of isolated NPs, focusing on their efficacy and limitations in terms of crystal size and accuracy of results. Our investigation begins by addressing the challenges of obtaining 3D ED data for NPs, including sample preparation, instrument capabilities, and the choice of 3D ED methods. We find that 3D ED can provide highly accurate structure refinements for crystals in the 50-100 nm range and is also effective for the analysis of NPs as small as 10 nm. While kinematical approximations often provide accurate refinements similar to those obtained from powder XRD, the accuracy depends on the specific data set and may not always align with traditional reliability indicators. Our study shows that dynamical scattering effects, even in tiny crystals, challenge the assumption that they are negligible in thin crystal scenarios. Addressing these effects through full dynamical refinement significantly improves the accuracy and reliability of the structure determination. This report suggests a paradigm shift in viewing dynamic scattering effects not as mere obstacles but as opportunities to explore crystal structures in greater detail on smaller scales. By embracing these complexities, 3D ED can provide precise and reliable structural insights that are critical to the advancement of nanotechnology and materials science.

• Klíčová slova
• crystallography, dynamical refinement, electron diffraction, electron microscopy, oxide nanoparticles,
• Publikační typ
• časopisecké články MeSH

The accurate characterization of highly sensitive materials using 3D electron diffraction (3D ED) is often challenged by sample degradation caused by exposure to moisture, air, temperature variations and high vacuum during the transfer and introduction into the transmission electron microscope (TEM). A cryogenic sample-transfer protocol is presented here, designed to enable the safe and effective transfer of reactive samples into the TEM, ensuring an inert and moisture-free environment throughout the process. The protocol was validated by redetermining the crystal structures of the moisture-sensitive, strongly oxidizing and highly reactive compounds XeF2, XeF4 and XeF2·XeF4 cocrystal. Crystal structures of all three compounds were successfully solved ab initio and dynamically refined, yielding results that showed good agreement with the previously reported X-ray and neutron diffraction structures. This approach holds significant promise for advancing the study of other reactive and moisture-sensitive samples, enabling precise structural characterization in cases where traditional TEM sample preparation is unsuitable.

• Klíčová slova
• 3D electron diffraction, cryotransfer, noble-gas compounds, xenon fluorides,
• Publikační typ
• časopisecké články MeSH

A new platinate was recently discovered when Nd2O3 was explored as a platinum capture material in the Ostwald process, formed by a direct reaction between gaseous PtO2 and Nd2O3. The crystal structure of this new platinate and its composition, Nd10.67Pt4O24, are here reported for the first time. The compound is synthesized either by a direct reaction between PtO2(g) and Nd2O3 or by the citric acid chemical route. Based on 3-dimensional electron diffraction data and Rietveld refinement of high-resolution synchrotron and neutron powder diffraction data, we describe its crystal structure in space group I41/a. The compound is structurally related to the Ln11-x Sr x Ir4O24 (Ln = La, Pr, Nd, and Sm) phases with a double perovskite (A2BB'O6)-like crystal structure with A-site cation deficiency. Owing to the fixed oxidation state of Pt(IV), two of the four Nd sites are partly occupied to provide charge neutrality, with Nd4 taking a split position. On heating, Nd10.67Pt4O24 decomposes into Nd2O3 and Pt. A plateau in the thermogravimetric curves measured in 33 vol % O2 in N2 indicates the presence of an intermediate Pt(II) phase at around 960 °C, probably isostructural with La4PtO7.

• Publikační typ
• časopisecké články MeSH

Conventional refinement strategies used for three-dimensional electron diffraction (3D ED) data disregard the bonding effects between the atoms in a molecule by assuming a pure spherical model called the Independent Atom model (IAM) and may lead to an inaccurate or biased structure. Here we show that it is possible to perform a refinement going beyond the IAM with electron diffraction data. We perform kappa refinement which models charge transfers between atoms while assuming a spherical model. We demonstrate the procedure by analysing five inorganic samples; quartz, natrolite, borane, lutecium aluminium garnet, and caesium lead bromide. Implementation of kappa refinement improved the structure model obtained over conventional IAM refinements and provided information on the ionisation of atoms. The results were validated against periodic DFT calculations. The work presents an extension of the conventional refinement of 3D ED data for a more accurate structure model which enables charge density information to be extracted.

• Publikační typ
• časopisecké články MeSH

Recent advances in 3D electron diffraction (3D ED) have succeeded in matching the capabilities of single-crystal X-ray diffraction (SCXRD), while requiring only submicron crystals for successful structural investigations. One of the many diverse areas to benefit from the 3D ED structural analysis is main-group chemistry, where compounds are often poorly crystalline or single-crystal growth is challenging. A facile method for loading and transferring highly air-sensitive and strongly oxidizing samples at low temperatures to a transmission electron microscope (TEM) for 3D ED analysis was successfully developed and tested on xenon(II) compounds from the XeF2-MnF4 system. The crystal structures determined on nanometer-sized crystallites by dynamical refinement of the 3D ED data are in complete agreement with the results obtained by SCXRD on micrometer-sized crystals and by periodic density-functional theory (DFT) calculations, demonstrating the applicability of this approach for structural studies of noble-gas compounds and highly reactive species in general. The compounds 3XeF2·2MnF4, XeF2·MnF4, and XeF2·2MnF4 are rare examples of structurally fully characterized xenon difluoride-metal tetrafluoride adducts and thus advance our knowledge of the diverse structural chemistry of these systems, which also includes the hitherto poorly characterized first noble-gas compound, "XePtF6".

• Publikační typ
• časopisecké články MeSH

Detoxification of heme in Plasmodium depends on its crystallization into hemozoin. This pathway is a major target of antimalarial drugs. The crystalline structure of hemozoin was established by X-ray powder diffraction using a synthetic analog, β-hematin. Here, we apply emerging methods of in situ cryo-electron tomography and 3D electron diffraction to obtain a definitive structure of hemozoin directly from ruptured parasite cells. Biogenic hemozoin crystals take a striking polar morphology. Like β-hematin, the unit cell contains a heme dimer, which may form four distinct stereoisomers: two centrosymmetric and two chiral enantiomers. Diffraction analysis, supported by density functional theory analysis, reveals a selective mixture in the hemozoin lattice of one centrosymmetric and one chiral dimer. Absolute configuration has been determined by morphological analysis and confirmed by a novel method of exit-wave reconstruction from a focal series. Atomic disorder appears on specific facets asymmetrically, and the polar morphology can be understood in light of water binding. Structural modeling of the heme detoxification protein suggests a function as a chiral agent to bias the dimer formation in favor of rapid growth of a single crystalline phase. The refined structure of hemozoin should serve as a guide to new drug development.

• Publikační typ
• časopisecké články MeSH

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.

• Klíčová slova
• 3D ED, MicroED, electron diffraction, microcrystal electron diffraction,
• MeSH
• elektronová kryomikroskopie * MeSH
• průběh práce MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH

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.

• Klíčová slova
• 3D electron diffraction, dynamical refinement, electron crystallography, microcrystal electron diffraction, multipolar scattering factors, quantum crystallography, transferable aspherical atom model,
• Publikační typ
• časopisecké články MeSH

Many long-lasting insecticidal bed nets for protection against disease vectors consist of poly(ethylene) fibers in which insecticide is incorporated during manufacture. Insecticide molecules diffuse from within the supersaturated polymers to surfaces where they become bioavailable to insects and often crystallize, a process known as blooming. Recent studies revealed that contact insecticides can be highly polymorphic. Moreover, insecticidal activity is polymorph-dependent, with forms having a higher crystal free energy yielding faster insect knockdown and mortality. Consequently, the crystallographic characterization of insecticide crystals that form on fibers is critical to understanding net function and improving net performance. Structural characterization of insecticide crystals on bed net fiber surfaces, let alone their polymorphs, has been elusive owing to the minute size of the crystals, however. Using the highly polymorphous compound ROY (5-methyl-2-[(2-nitrophenyl)-amino]thiophene-3-carbonitrile) as a proxy for insecticide crystallization, we investigated blooming and crystal formation on the surface of extruded poly(ethylene) fibers containing ROY. The blooming rates, tracked from the time of extrusion, were determined by UV-vis spectroscopy after successive washes. Six crystalline polymorphs (of the 13 known) were observed on poly(ethylene) fiber surfaces, and they were identified and characterized by Raman microscopy, scanning electron microscopy, and 3D electron diffraction. These observations reveal that the crystallization and phase behavior of polymorphs forming on poly(ethylene) fibers is complex and dynamic. The characterization of blooming and microcrystals underscores the importance of bed net crystallography for the optimization of bed net performance.

• Publikační typ
• časopisecké články MeSH