Although the demonstration of noble-gas reactivity represents one of the most significant breakthroughs of 20th-century inorganic chemistry, the first noble-gas compound, XePtF6 (XeF2·PtF4), lacks comprehensive structural characterization, and its structure remains to be elucidated. In this study, the XeF2-PtF4 and XeF2-PdF4 systems were reexplored, resulting in the crystal structure determination of XeF2·2PtF4 and XeF2·2PdF4 by 3D electron diffraction, marking the first successful structural characterization of compounds from these systems. Both compounds are isostructural with the previously characterized XeF2·2MnF4, featuring corrugated zigzag double-chain motifs formed by interconnected octahedral fluoridometallate(IV) units. Periodic density functional theory calculations were employed to evaluate the structural models of XeF2·PtF4, which were derived from experimentally determined crystal structures of XeF2-MF4 (M = Cr, Mn) analogues. The results reveal a preference for cis-bridging between adjacent platinum(IV) centers and show that a tetrameric ring structure and cis-chain polymorph, modeled after the crystal structure of XeF2·MnF4 and XeF2-deficient 3XeF2·2MnF4, respectively, emerge as energetically favored. The results of this study thus provide a direct structural link between platinum, palladium, and manganese analogues in the XeF2-MF4 systems and highlight the tetrameric ring structure and cis-chain as likely structural models of XeF2·PtF4.

• 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

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

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

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

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.

• Klíčová slova
• 3D electron diffraction, Alzheimer's disease, absolute structure, crystal structure, natural product,
• MeSH
• biologické přípravky * MeSH
• Cordyceps * MeSH
• elektrony MeSH
• krystalografie rentgenová MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• biologické přípravky * MeSH