Dynamical refinement with multipolar electron scattering factors.

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, Petrícek & 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.

ROY Crystallization on Poly(ethylene) Fibers, a Model for Bed Net Crystallography.

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.

Chlorfenapyr Crystal Polymorphism and Insecticidal Activity.

Four crystalline polymorphs of the proinsecticide chlorfenapyr [4-bromo-2-(4-chlorophenyl)-1-ethoxymethyl-5-trifluoromethyl-1H-pyrrole-3-carbonitrile] have been identified and characterized by polarized light optical microscopy, differential scanning calorimetry, Raman spectroscopy, X-ray diffraction, and electron diffraction. Three of the four structures were considered polytypic. Chlorfenapyr polymorphs show similar lethality against fruit flies (Drosophila melanogaster) and mosquitoes (Anopheles quadrimaculatus) with the least stable polymorph showing slightly higher lethality. Similar activities may be expected to be consistent with structural similarities. Knockdown kinetics, however, depend on an internal metabolic activating step, which further complicates polymorph-dependent bioavailability.

Unveiling the topology of partially disordered micro-crystalline nitro-perylenediimide with X-aggregate stacking: an integrated approach.

Profound knowledge of the molecular structure and supramolecular organization of organic molecules is essential to understand their structure-property relationships. Herein we demonstrate the packing arrangement of partially disordered nitro-perylenediimide (NO2-PDI), revealing that the perylenediimide units exhibit an X-shaped packing pattern. The packing of NO2-PDI is derived using a complementary approach that utilises solid-state NMR (ssNMR) and 3D electron diffraction (3D ED) techniques. Perylenediimide (PDI) molecules are captivating due to their high luminescence efficiency and optoelectronic properties, which are related to supramolecular self-assembly. Increasing the alkyl chain length on the imide substituent poses a more significant challenge in crystallizing the resulting molecule. In addition to the alkyl tails, other functional groups, like the nitro group attached as a bay substituent, can also cause disorder. Such heterogeneity could lead to diffuse scattering, which then complicates the interpretation of diffraction experiment data, where perfect periodicity is expected. As a result, there is an unmet need to develop a methodology for solving the structures of difficult-to-crystallize materials. A synergistic approach is utilised in this manuscript to understand the packing arrangement of the disordered material NO2-PDI by making use of 3D ED, ssNMR and density functional theory calculations (DFT). The combination of these experimental and theoretical approaches provides great promise in enabling the structural investigation of novel materials with customized properties across various applications, which are, due to the internal disorder, very difficult to study by diffraction techniques. By effectively addressing these challenges, our methodology opens up new avenues for material characterization, thereby driving exciting advancements in the field.

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°.

Phosphinate MOFs Formed from Tetratopic Ligands as Proton-Conductive Materials.

Metal-organic frameworks (MOFs) are attracting attention as potential proton conductors. There are two main advantages of MOFs in this application: the possibility of rational design and tuning of the properties and clear conduction pathways given by their crystalline structure. We hereby present two new MOF structures, ICR-10 and ICR-11, based on tetratopic phosphinate ligands. The structures of both MOFs were determined by 3D electron diffraction. They both crystallize in the P3̅ space group and contain arrays of parallel linear pores lined with hydrophilic noncoordinated phosphinate groups. This, together with the adsorbed water molecules, facilitates proton transfer via the Grotthuss mechanism, leading to a proton conductivity of up to 4.26 × 10-4 S cm-1 for ICR-11. The presented study demonstrates the high potential of phosphinate MOFs for the fabrication of proton conductors.

Preparation of High-Entropy (Ti, Zr, Hf, Ta, Nb) Carbide Powder via Solution Chemistry.

High-entropy ceramics is a new class of materials having a great potential and wide application. The carbide of Ti, Zr, Hf, Ta, Nb is a typical member of this group. It has been synthesized mostly through blending, milling, and high-temperature solid-state reaction of metal carbide precursors for each metal. This route needs extremely high temperature (2300 °C), which makes it energy and technology demanding. We have developed a chemical route for high-entropy carbide powder that needs a synthetic temperature that is several hundred degrees Celsius lower. A solution of desired metal citrates with an excess of citric acid was converted into a metal oxide/active carbon nanocomposite. Starting from a solution enabled ideal mixing of precursors on a molecular level, allowing us to skip any milling and blending steps. The nanocomposite was treated in vacuum at 1600 °C, giving a phase-pure high-entropy carbide. The intermediate compounds and products were characterized by means of solid-state analysis.

Synthesis of Discrete CHA Zeolite Nanocrystals without Organic Templates for Selective CO2 Capture.

Small-pore zeolites such as chabazite (CHA) are excellent candidates for the selective separation of CO2 ; however, the current synthesis involves several steps and the use of organic structure-directing agent (OSDA), increasing their cost and energy requirements. We report the synthesis of small-pore zeolite crystals (aluminosilicate) with CHA-type framework structure by direct synthesis in a colloidal suspension containing a mixture of inorganic cations only (Na+ , K+ , and Cs+ ). The location of CO2 molecules in the host structure was revealed by 3D electron diffraction (3D ED). The high sorption capacity for CO2 (3.8 mmol g-1 at 121 kPa), structural stability and regenerability of the discreate CHA zeolite nanocrystals is maintained for 10 consecutive cycles without any visible degradation. The CHA zeolite (Si:Al=2) reaches an almost perfect CO2 storage capacity (8 CO2 per unit cell) and high selectivity (no CH4 was adsorbed).

Magnetic nanoparticles of Ga-substituted ε-Fe2 O3 for biomedical applications: Magnetic properties, transverse relaxivity, and effects of silica-coated particles on cytoskeletal networks.

Magnetic nanoparticles of ε-Fe1.76 Ga0.24 O3 with the volume-weighted mean size of 17 nm were prepared by thermal treatment of a mesoporous silica template impregnated with metal nitrates and were coated with silica shell of four different thicknesses in the range 6-24 nm. The bare particles exhibited higher magnetization than the undoped compound, 22.4 Am2 kg-1 at 300 K, and were characterized by blocked state with the coercivity of 1.2 T at 300 K, being thus the very opposite of superparamagnetic iron oxides. The relaxometric study of the silica-coated samples at 0.47 T revealed promising properties for MRI, specifically, transverse relaxivity of 89-168 s-1 mmol(f.u.)-1 L depending on the shell thickness was observed. We investigated the effects of the silica-coated nanoparticles on human A549 and MCF-7 cells. Cell viability, proliferation, cell cycle distribution, and the arrangement of actin cytoskeleton were assessed, as well as formation and maturation of focal adhesions. Our study revealed that high concentrations of silica-coated particles with larger shell thicknesses of 16-24 nm interfere with the actin cytoskeletal networks, inducing thus morphological changes. Consequently, the focal adhesion areas were significantly decreased, resulting in impaired cell adhesion.

Cleaving silicene-terminated calcium disilicide in the transmission electron microscope.

Silicene, a monolayer of silicon atoms arranged in a honeycomb lattice, is excellently compatible with the materials used in today's semiconductor manufacturing. In this paper, silicene-terminated CaSi2 is cleaved inside a transmission electron microscope using an in situ manipulator. HRTEM studies on a standard lift-out lamella performed from several crystallographic orientations confirm the cell parameters of a = 3.7 Å and c = 30.60 Å, and allow to determine its exact orientation in the SEM/FIB system. A FIB procedure with corrected tilting and rotating angles has been developed to ensure that the tensile force applied by the manipulator is perpendicular to the (0 0 1) plane, and that the [1 0 0] pole axis could be used for HRTEM imaging. A sharp and flat cleavage interface with a length of more than 1 µm was observed in one in situ experiment. HRTEM images from multiple regions confirm that the flat cleavage follows the (0 0 3) plane of the CaSi2 crystal. The current in situ study demonstrates that a surface sheet with silicene-like atomic arrangement can be mechanically exfoliated from silicide compounds.

Cerium Oxalate Morphotypes: Synthesis and Conversion into Nanocrystalline Oxide.

Cerium dioxide is a scientifically and technologically important material with a wide range of potential applications, particularly in solid oxide fuel cells and catalysis. Herein, we report a study focusing on the synthesis of nanocrystalline cerium dioxide via thermal decomposition of the oxalate salt. Simply by changing reaction conditions (temperature, concentration, acidity, strike) during the precipitation of the cerium solution with oxalic acid, we were able to obtain different morphologies. The main reaction parameters were mapped and linked to the morphology of the final products. Additionally, it was proved that oxalate precipitation is a robust reaction proceeding at relatively extreme contitions. Moreover, the conversion of cerium oxalate to nanocrystalline oxide was followed to monitor the progress of the reaction, the texture evolution, and the grain growth. The results showed that, for unvaried heating cycle, the grain size of converted material is linked to morphology. The thinner was the original microcrystal the smaller were the CeO2 nanocrystals after calcination. In addition, the grains were found smaller near the edges of the ex-oxalate microcrystals. In both cases, this behavior results from asymmetrical limitations of diffusion during grain growth.

Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal.

Determination of the absolute configuration of organic molecules is essential in drug development and the subsequent approval process. We show that this determination is possible through electron diffraction using nanocrystalline material. Ab initio structure determination by electron diffraction has so far been limited to compounds that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure analysis of a pharmaceutical cocrystal of sofosbuvir and l-proline, which is about one order of magnitude less stable. Data collection on multiple positions of a crystal and an advanced-intensity extraction procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous determination of the absolute structure of material composed of light scatterers.

Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0.

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.

Phosphinic Acid Based Linkers: Building Blocks in Metal-Organic Framework Chemistry.

Metal-organic frameworks (MOFs) are a chemically and topologically diverse family of materials composed of inorganic nodes and organic linkers bound together by coordination bonds. Presented here are two significant innovations in this field. The first is the use of a new coordination group, phenylene-1,4-bis(methylphosphinic acid) (PBPA), a phosphinic acid analogue of the commonly used terephtalic acid. Use of this new linker group leads to the formation of a hydrothermally stable and permanently porous MOF structure. The second innovation is the application of electron-diffraction tomography, coupled with dynamic refinement of the EDT data, to the elucidation of the structure of the new material, including the localization of hydrogen atoms.

TaS3 Nanofibers: Layered Trichalcogenide for High-Performance Electronic and Sensing Devices.

Layered materials, like transition metal dichalcogenides, exhibit broad spectra with outstanding properties with huge application potential, whereas another group of related materials, layered transition metal trichalcogenides, remains unexplored. Here, we show the broad application potential of this interesting structural type of layered tantalum trisulfide prepared in a form of nanofibers. This material shows tailorable attractive electronic properties dependent on the tensile strain applied to it. Structure of this so-called orthorhombic phase of TaS3 grown in a form of long nanofibers has been solved and refined. Taking advantage of these capabilities, we demonstrate a highly specific impedimetric NO gas sensor based on TaS3 nanofibers as well as construction of photodetectors with excellent responsivity and field-effect transistors. Various flexible substrates were used for the construction of a NO gas sensor. Such a device exhibits a low limit of detection of 0.48 ppb, well under the allowed value set by environmental agencies for NOx (50 ppb). Moreover, this NO gas sensor also showed excellent selectivity in the presence of common interferences formed during fuel combustion. TaS3 nanofibers produced in large scale exhibited excellent broad application potential for various types of devices covering nanoelectronic, optoelectronic, and gas-sensing applications.

Crystal structures of η''-Cu3+xSi and η'''-Cu3+xSi.

The binary phase diagram of Cu-Si is unexpectedly complex in the vicinity of Cu3+xSi. The low-temperature region contains three closely related incommensurately modulated phases denoted, in order of increasing temperature of stability, η''', η'' and η'. The structure analysis of η' has been reported previously [Palatinus et al. (2011). Inorg. Chem. 50, 3743]. Here the structure model for the phases η'' and η''' is reported. The structures could be solved in superspace, but no superspace structure model could be constructed due to the complexity of the modulation functions. Therefore, the structures were described in a supercell approximation, which involved a 4 × 4 × 3 supercell for the η'' phase and a 14 × 14 × 3 supercell for the η''' phase. Both structures are very similar and differ only by a subtle symmetry lowering from η'' to η'''. A comparison of the structure models of η'' and η''' with the reported structure of η' suggests that the reported structure model of η' contains an incorrect assignment of atomic types.