Can NbO Keep nbo Topology under Electrons? -Unveiling Novel Aspects of Niobium Monoxide at the Atomic Scale.

A precise investigation of NbO has been carried out by advanced electron microscopy combined with powder and single crystal X-ray diffraction (XRD). The structure of pristine NbO has been determined as Pm-3 m space group (SG) with a = 4.211 Šand the positions of Nb and O at the 3c and 3d Wyckoff positions, respectively, which is consistent with previous report based on powder XRD data. Electron beams induced a structural transition, which was investigated and explained by combining electron diffraction and atomic-resolution imaging. The results revealed that the electron beam stimulated both Nb and O atom-migrations within each fcc sublattice, and that the final structure was SG Fm-3 m with a = 4.29 Å, Nb and O at the 4a and 4b with 75 % occupancy and same chemical composition. Antiphase planar defects were discovered in the pristine NbO and related to the structural transformation. Theoretical calculations performed by density functional theory (DFT) supported the experimental conclusions.

Fine Pore-Structure Engineering by Ligand Conformational Control of Naphthalene Diimide-Based Semiconducting Porous Coordination Polymers for Efficient Chemiresistive Gas Sensing.

Exploring new porous coordination polymers (PCPs) that have tunable structure and conductivity is attractive but remains challenging. Herein, fine pore structure engineering by ligand conformation control of naphthalene diimide (NDI)-based semiconducting PCPs with π stacking-dependent conductivity tunability is achieved. The π stacking distances and ligand conformation in these isoreticular PCPs were modulated by employing metal centers with different coordination geometries. As a result, three conjugated PCPs (Co-pyNDI, Ni-pyNDI, and Zn-pyNDI) with varying pore structure and conductivity were obtained. Their crystal structures were determined by three-dimensional electron diffraction. The through-space charge transfer and tunable pore structure in these PCPs result in modulated selectivity and sensitivity in gas sensing. Zn-pyNDI can serve as a room-temperature operable chemiresistive sensor selective to acetone.

Selective and Reversible Solvent Uptake in Tetra-4-(4-pyridyl)phenylmethane-based Supramolecular Organic Frameworks.

The dynamic behavior of supramolecular organic frameworks (SOFs) based on the rigid tetra-4-(4-pyridyl)phenylmethane (TPPM) organic tecton has been elucidated through 3D electron diffraction, X-ray powder diffraction and differential scanning calorimetry (DSC) analysis. The SOF undergoes a reversible single-crystal-to-single-crystal transformation when exposed to vapours of selected organic solvents, moving from a closed structure with isolated small voids to an expanded structure with solvated channels along the b axis. The observed selectivity is dictated by the fitting of the guest in the expanded SOF, following the degree of packing coefficient. The effect of solvent uptake on TPPM solid-state fluorescence was investigated, evidencing a significant variation in the emission profile only in the presence of chloroform.

Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM.

A semi-automated protocol has been developed for rotational data collection of electron diffraction patterns by combined use of SerialEM and ParallEM, where SerialEM is used for positioning of sample crystals and ParallEM for rotational data collection. ParallEM calls standard camera control software through an AutoIt script, which adapts to software operational changes and to new GUI programs guiding other cameras. Development included periodic flashing and pausing of data collection during overnight or day-long recording with a cold field-emission beam. The protocol proved to be efficient and accurate in data collection of large-scale rotational series from two JEOL electron microscopes, a general-purpose JEM-2100 and a high-end CRYO ARM 300. Efficiency resulted from simpler steps and task specialization. It is possible to collect 12-20 rotational series from ~-68° to ~68° at a rotation speed of 1°/s in one hour without human supervision.

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).

Applying 3D ED/MicroED workflows toward the next frontiers.

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.

TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

Data collection is your last experiment.

Exciting developments are unfolding in the realm of chemical crystallography, especially with the profound impact of electron diffraction and the remarkable progress it has witnessed in recent years.

Three-dimensional electron diffraction on clinkers: the belite α'H incommensurate modulated structure.

Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure.

3D ED/MicroED entering a new era.

Aragon et al. [Acta Cryst. (2024), C80, 179-189], by reporting the discussion and the final conclusions of a round table held during a symposium at the National Center for CryoEM Access and Training, well describe all the advances that have been made for the application of 3D ED/MicroED to pharmaceutical and macromolecular nanocrystals and propose possible future scenarios.

The crystal structure of olanzapine form III.

The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.

Structure solution and refinement of beam-sensitive nano-crystals.

Radiation sensitive materials are among the most difficult materials to study, even more so if they exist only as nanometer-sized particles, where their size is either intentional because of enhanced properties at the nano-scale or it is unintentional because it is impossible to obtain bigger particles of the same structure. In both cases characterization methods need to be optimized to get the most information out of these particles before the radiation damages them to a point where their structure is altered. When the particles are crystallized, both characteristics, the small size and the beam sensitivity, call for electron diffraction as a privileged investigation tool. The strong interaction of electrons (as compared to X-rays) with matter allows single crystal diffraction experiments on nanometer-sized crystals and for the same amount of beam damage, electron diffraction yields more information than X-rays. These inherent advantages of electron diffraction are optimized in the recently developed low-dose electron diffraction tomography (LD-EDT) by minimizing the necessary dose for a complete data collection. In this contribution we show that in some cases even doses as low as 2 e-/Ų can induce damage in crystal structures that inhibit a correct structure refinement. However, by LD-EDT we can obtain data using extremely low doses that don't alter the structure which make it then possible not only to solve crystal structures but also to refine them using dynamical diffraction theory. Here a synthetic oxide containing volatile Na and a metal-organic framework are given as examples. A dynamical refinement of the structures is possible with data sets requiring a dose of less than 0.15 e-/Ų.

Parameterized absorptive electron scattering factors.

In electron diffraction, thermal atomic motion produces incoherent scattering over a relatively wide angular range, which appears as a diffuse background that is usually subtracted from measurements of Bragg spot intensities in structure solution methods. The transfer of electron flux from Bragg spots to diffuse scatter is modelled using complex scattering factors f + if' in the Bloch wave methodology. In a two-beam Einstein model the imaginary `absorptive' scattering factor f' can be obtained by the evaluation of an integral containing f over all possible scattering angles. While more sophisticated models of diffuse scatter are widely used in the electron microscopy community, it is argued in this paper that this simple model is appropriate for current structure solution and refinement methods. The two-beam model is a straightforward numerical calculation, but even this simplistic approach can become time consuming for simulations of materials with large numbers of atoms in the unit cell and/or many incident beam orientations. Here, a parameterized form of f' is provided for 103 elements as neutral, spherical atoms that reduces calculation time considerably.

On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors.

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.

Applications and limitations of electron 3D crystallography.

Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.

Modelling fine-sliced three dimensional electron diffraction data with dynamical Bloch-wave simulations.

Recent interest in structure solution and refinement using electron diffraction (ED) has been fuelled by its inherent advantages when applied to crystals of sub-micrometre size, as well as its better sensitivity to light elements. Currently, data are often processed with software written for X-ray diffraction, using the kinematic theory of diffraction to generate model intensities - despite the inherent differences in diffraction processes in ED. Here, dynamical Bloch-wave simulations are used to model continuous-rotation electron diffraction data, collected with a fine angular resolution (crystal orientations of ∼0.1°). This fine-sliced data allows a re-examination of the corrections applied to ED data. A new method is proposed for optimizing crystal orientation, and the angular range of the incident beam and the varying slew rate are taken into account. Observed integrated intensities are extracted and accurate comparisons are performed with simulations using rocking curves for a (110) lamella of silicon 185 nm thick. R1 is reduced from 26% with the kinematic model to 6.8% using dynamical simulations.

Polytypism in mcalpineite: a study of natural and synthetic Cu3TeO6.

Synthetic and naturally occurring forms of tricopper orthotellurate, CuII3TeVIO6 (the mineral mcalpineite) have been investigated by 3D electron diffraction (3D ED), X-ray powder diffraction (XRPD), Raman and infrared (IR) spectroscopic measurements. As a result of the diffraction analyses, CuII3TeVIO6 is shown to occur in two polytypes. The higher-symmetric CuII3TeVIO6-1C polytype is cubic, space group Ia3, with a = 9.537 (1) Šand V = 867.4 (3) Å3 as reported in previous studies. The 1C polytype is a well characterized structure consisting of alternating layers of CuIIO6 octahedra and both CuIIO6 and TeVIO6 octahedra in a patchwork arrangement. The structure of the lower-symmetric orthorhombic CuII3TeVIO6-2O polytype was determined for the first time in this study by 3D ED and verified by Rietveld refinement. The 2O polytype crystallizes in space group Pcca, with a = 9.745 (3) Å, b = 9.749 (2) Å, c = 9.771 (2) Šand V = 928.3 (4) Å3. High-precision XRPD data were also collected on CuII3TeVIO6-2O to verify the lower-symmetric structure by performing a Rietveld refinement. The resultant structure is identical to that determined by 3D ED, with unit-cell parameters a = 9.56157 (19) Å, b = 9.55853 (11) Å, c = 9.62891 (15) Šand V = 880.03 (2) Å3. The lower symmetry of the 2O polytype is a consequence of a different cation ordering arrangement, which involves the movement of every second CuIIO6 and TeVIO6 octahedral layer by (1/4, 1/4, 0), leading to an offset of TeVIO6 and CuIIO6 octahedra in every second layer giving an ABAB* stacking arrangement. Syntheses of CuII3TeVIO6 showed that low-temperature (473 K) hydrothermal conditions generally produce the 2O polytype. XRPD measurements in combination with Raman spectroscopic analysis showed that most natural mcalpineite is the orthorhombic 2O polytype. Both XRPD and Raman spectroscopy measurements may be used to differentiate between the two polytypes of CuII3TeVIO6. In Raman spectroscopy, CuII3TeVIO6-1C has a single strong band around 730 cm-1, whereas CuII3TeVIO6-2O shows a broad double maximum with bands centred around 692 and 742 cm-1.

Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data.

Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.

How to get maximum structure information from anisotropic displacement parameters obtained by three-dimensional electron diffraction: an experimental study on metal-organic frameworks.

Three-dimensional electron diffraction (3D ED) has been used for ab initio structure determination of various types of nanocrystals, such as metal-organic frameworks (MOFs), zeolites, metal oxides and organic crystals. These crystals are often obtained as polycrystalline powders, which are too small for single-crystal X-ray diffraction (SCXRD). While it is now possible to obtain accurate atomic positions of nanocrystals by adopting kinematical refinement against 3D ED data, most new structures are refined with isotropic displacement parameters (U eq), which limits the detection of possible structure disorders and atomic motions. Anisotropic displacement parameters (ADPs, Uij ) obtained by anisotropic structure refinement, on the other hand, provide information about the average displacements of atoms from their mean positions in a crystal, which can provide insights with respect to displacive disorder and flexibility. Although ADPs have been obtained from some 3D ED studies of MOFs, they are seldom mentioned or discussed in detail. We report here a detailed study and interpretation of structure models refined anisotropically against 3D ED data. Three MOF samples with different structural complexity and symmetry, namely ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc) (1,4-ndcH2 is naphthalene-1,4-dicarboxylic acid), were chosen for the studies. We compare the ADPs refined against individual data sets and how they are affected by different data-merging strategies. Based on our results and analysis, we propose strategies for obtaining accurate structure models with interpretable ADPs based on kinematical refinement against 3D ED data. The ADPs of the obtained structure models provide clear and unambiguous information about linker motions in the MOFs.

Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method.

Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R 1 values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.