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

The crystal structures of organic semiconductors are critical when they are integrated into optoelectronic devices, such as organic field-effect transistors (OFETs). In this study, we introduce a crystal engineering approach that leverages weak, nondirectional dispersion forces and steric effects, working together to govern the molecular packing. We investigated how the substitution at the peri-position affects the crystal structure in a series of oligorylene molecules. Upon elucidation of the crystal structures, we found a distinct difference between symmetrical and unsymmetrical derivatives. The unsymmetrical derivatives are prone to forming a sandwich herringbone (SHB) motif, while symmetrical derivatives exhibit a typical herringbone (HB) motif. In most of the rylene derivatives, substitutions at the peri-position triggered an "end-to-face" orientation within the HB structure, rather than an "edge-to-face" orientation, which occurs more often. Results from the Hirschfeld surface analysis provide evidence that the "end-to-face" orientation promotes C-H-π interactions between terminal methyl groups and the π-core of the molecules. While these C-Hmethyl---π interactions contribute to the overall stability of the packing structure, they remain ineffective in enhancing the charge transport properties. In contrast, a particular derivative, tetramethyl perylene (TMP), exhibits a HB structure with an edge-to-face orientation, promoting both C-H---π and π---π interactions. These interactions are crucial for improving the charge carrier mobility, as evidenced by mobility values. For TMP, we could obtain the mobility value of 0.05 cm2 V-1 s-1 in OFETs, whereas a slightly higher mobility of 0.2 cm2 V-1 s-1 was observed with Field-Induced Time-Resolved Microwave conductivity (FI-TRMC) technique.

• 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

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II), [Ru(C33H16F10N4)(CO)2] or Ru(CO)2[DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetrapyrrole complex. The neutral complex sports two carbonyls and an oligotetrapyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO)2[DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetrapyrrole ligand, but also the first metal biladiene complex in which the tetrapyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO)2[DMBil1] is weakly luminescent, displaying λem = 552 nm upon excitation at λex = 500 nm, supports two reversible 1 e- reductions at -1.45 and -1.73 V (versus Fc+/Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photocatalytic and photosensitization applications. While the structure of Ru(CO)2[DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. An independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.

• Klíčová slova
• biladiene, crystal structure, electron diffraction, reduction photocatalyst, ruthenium, tetrapyrrole,
• 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

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

• Klíčová slova
• Berkecoumarin, absolute structure determination, chromenone, coumarin, crystal structure, dynamical refinement, electron diffraction, microED, natural product,
• Publikační typ
• časopisecké články MeSH