Structure of the new mineral sarrabusite, Pb5CuCl4(SeO3)4, solved by manual electron-diffraction tomography

Molybdenum Disorder in Hydrated Sedovite, Ideally U(MoO4)2·nH2O, a Microporous Nanocrystalline Mineral Characterized by Three-Dimensional Electron Diffraction, Density Functional Theory Computations, and Complexity Analysis

Sedovite, U⁴⁺(Mo⁶⁺O₄)₂·nH₂O, is reported as being one of the earliest supergene minerals formed of the secondary zone. The difficulty of isolating enough pure material limits studies to techniques that can access the nanoscale combined with theoretical analyses. The crystal structure of sedovite has been solved and refined using the dynamical approach from three-dimensional electron diffraction data collected on natural nanocrystals found among iriginite. At 100 K, sedovite is monoclinic a ≈ 6.96 Å, b ≈ 9.07 Å, c ≈ 12.27 Å, and V ≈ 775 ų with space group C2/c. The microporous structure presents a characteristic framework built from uranium polyhedra and disordered Mo pyramids creating pore hosting water molecules. To confirm the formula U⁴⁺(Mo⁶⁺O₄)₂·nH₂O, the possible presence of a hydroxyl group that would promote Mo⁵⁺ was tested with density functional theory (DFT) computations at the ambient temperature. DFT predicts that sedovite is a ferromagnetic insulator with a fundamental bandgap of E_g ∼ 1.7 eV with its chemical and physical properties dominated by U⁴⁺ rather than Mo⁶⁺. The structural complexity, I_G,tot, of sedovite was evaluated in order to get indirect information about the missing formation conditions.

Hydrogen-Bond-Assisted Alignment of [MCu(SeO3)4Cl(H2O)]4- (M = Fe, Ga) Anionic Layers to Form Two Polar Oxychlorides: Pb2MCu(SeO3)4Cl(H2O)

Two novel selenite oxychlorides Pb₂MCu(SeO₃)₄Cl(H₂O) (M = Fe, Ga) were hydrothermally synthesized and structurally characterized. They are isostructural and crystallize in the two-dimensional [MCu(SeO₃)₄Cl(H₂O)]^4- anionic layer structure mediated with hydrogen bonds and aligned between neighboring layers which assist in building the three-dimensional framework with a polar space group. Optical properties measurements revealed that the optical band gaps are 2.61 and 3.22 eV for Pb₂FeCu(SeO₃)₄Cl(H₂O) (1) and Pb₂GaCu(SeO₃)₄Cl(H₂O) (2) and the SHG responses are about 0.12 and 0.18 times that of KDP, respectively. Furthermore, 1 exhibits an interesting metamagnetic phenomenon under varied applied fields from around 1 to 4 T at 2 K, and 2 behaves with potential ferromagnetic ordering at low temperature.

Structural analysis of metastable pharmaceutical loratadine form II, by 3D electron diffraction and DFT+D energy minimisation

Coupling 3D electron diffraction and density functional theory provided the metastable pharmaceutical crystal structure within nanometre range, under ambient conditions.

3D Electron Diffraction: The Nanocrystallography Revolution

Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.

Automated electron diffraction tomography - development and applications

Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.

3D electron diffraction techniques

3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.

Daliranite, PbHgAs2S5: determination of the incommensurately modulated structure and revision of the chemical formula

The incommensurately modulated crystal structure of the mineral daliranite has been determined using 3D electron diffraction data obtained on nanocrystalline domains. Daliranite is orthorhombic with a = 21, b = 4.3, c = 9.5 Å and shows modulation satellites along c. The solution of the average structure in the Pnma space group together with energy-dispersive X-ray spectroscopy data obtained on the same domains indicate a chemical formula of PbHgAs2S5, which has one S fewer than previously reported. The crystal structure of daliranite is built from columns of face-sharing PbS8 bicapped trigonal prisms laterally connected by [2+4]Hg polyhedra and (As3+ 2S5)4− groups. The excellent quality of the electron diffraction data allows a structural model to be built for the modulated structure in superspace, which shows that the modulation is due to an alternated occupancy of a split As site.

Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction

The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile. The compound crystallizes in a noncentrosymmetric space group, P2₁2₁2₁. The molecular conformation in the crystal structure was used to calculate the molecular dipole moment of 3.22 Debye, which enables the material to show nonlinear optical effects.

Transition Metal Selenite Halides: A Fascinating Family of Magnetic Compounds

The problem of searching for low-dimensional magnetic systems has been a topical subject and has attracted attention of the chemistry and physics community for the last decade. In low-dimensional magnetic systems, magnetic ions are distributed anisotopically and form different groups such as dimers, chains, ladders, or planes. In 3D frameworks, the distances between magnetic ions are equal in all directions while in low-dimensional systems the distances within groups are different from those between groups. The main approach of searching for desired systems is a priori crystal chemical design expecting the needed distribution of transition metal ions in the resulting structure. One of the main concepts of this structural design is the incorporation of the p-element ions with stereochemically active electron pairs and ions acting as spacers in the composition. Transition metal selenite halides, substances that combine SeO32− groups and halide ions in the structure, seem to be a promising object of investigation. Up to now, there are 33 compounds that are structurally described, magnetically characterized, and empirically tested on different levels. The presented review will summarize structural peculiarities and observed magnetic properties of the known transition metal selenite halides. In addition, the known compounds will be analyzed as possible low-dimensional magnetic systems.

Single-crystal analysis of nanodomains by electron diffraction tomography: mineralogy at the order-disorder borderline

Electron diffraction tomography is a powerful emerging method for the structure characterization of materials available only as sub-micrometric grains. This technique can in fact deliver complete 3D information from a single crystal of few hundreds or few tens of nanometers, allowing the analysis of polyphasic or polytypic mixtures that generally cannot be fully addressed by X-ray methods. In this paper, we report and discuss three mineralogy-related study cases where electron diffraction tomography was the only way for achieving a proper description of the sample, by the identification and the structure determination of all the phases or all the polytypes within. We also show how electron diffraction tomography and dynamical refinement can be combined for finding accurate atomic positions and localizing hydrogen atoms at room conditions. Finally, we stress the future potential of this method in the fields of mineralogy and experimental petrology, where till now many samples cannot be properly described because nanocrystalline, polyphasic or disordered. Electron diffraction tomography can be used for detecting unexpected or unknown phases in high-pressure synthetic yields or for the characterization of fine rocks formed under extreme conditions, like impactites or meteorites. Eventually, this method allows the structure characterization of single domains that are ordered only at the scale of few cell repetitions, and therefore it makes possible investigating those materials at the borderline between crystalline and amorphous matter and delivers crucial and unique elements for the understanding of the first stages of solid matter organization.

Pb3(SeO3)Br4: a new nonlinear optical material with enhanced SHG response designedviaan ion-substitution strategy

A new NLO material has been designedviaion-substitution from a similar structure. It shows an enhanced SHG response equalling to that of KH₂PO₄(KDP) and a high laser damage threshold of 67 MW cm⁻¹.

Divalent metal phosphonates – new aspects for syntheses, in situ characterization and structure solution

Divalent metal phosphonates are promising hybrid materials with a broad field of application. The rich coordination chemistry of the phosphonate linkers enables the formation of structures with different dimensionalities ranging from isolated complexes and layered structures to porous frameworks incorporating various functionalities through the choice of the building blocks. In brief, metal phosphonates offer an interesting opportunity for the design of multifunctional materials. Here, we provide a short review on the class of divalent metal phosphonates discussing their syntheses, structures, and applications. We present the advantages of the recently introduced mechanochemical pathway for the synthesis of divalent phosphonates as a possibility to generate new, in certain cases metastable compounds. The benefits of

Crystal structure of disordered nanocrystalline αII-quinacridone determined by electron diffraction

The nanocrystalline α^II-phase of the industrially produced organic pigment quinacridone was studied by 3D electron diffraction. The average crystal structure was obtained directly from the data and validated by energy minimization. A model describing the experimentally observed diffuse scattering was proposed.

[NaCl][Cu(HSeO3)2], NaCl-intercalated Cu(HSeO3)2: synthesis, crystal structure and comparison with related compounds

Single crystals of [NaCl][Cu(HSeO3)2] have been prepared by the chemical vapor transport reactions. Its crystal structure (monoclinic, C2/c, a = 13.9874(7), b = 7.2594(4), c = 9.0421(5) Å, β = 127.046(2)°, V = 732.81(7) Å3) is based upon electroneutral [Cu(HSeO3)2] sheets formed by corner sharing between the [CuO4] squares and (HSeO3) groups that are parallel to the (100) plane. Each (SeO2OH)– group forms the Oh1...O2 hydrogen bond to an adjacent hydroselenite group to constitute a [(SeO2OH)2]2– dimer that provides additional stabilization of the copper diselenite sheet. The [Cu(HSeO3)2] sheets alternate with the sheets consisting of zigzag–Na–Cl–Na–Cl–chains formed by Cl atoms and disordered Na sites. The chains are parallel to the c axis. The linkage between the alternating electroneutral [Cu(HSeO3)2] and [NaCl] sheets is provided by the Cu–Cl and Na–O bonds. The coordination of Na is fivefold and consists of three O and two Cl atoms. [NaCl][Cu(HSeO3)2] is a new member of the group of compounds based upon the M(HSeO3)2 layers (M2+ = Cu, Co, Cd). The prototype structure for this group is [Cu(HSeO3)2] that does not have any chemical species separating the copper hydroselenite layers. In other compounds, the interlayer space between the [Cu(HSeO3)2]0 layers is occupied by structural units of different complexity. [NaCl][Cu(HSeO3)2] can be considered as [Cu(HSeO3)2] intercalated with the NaCl layers consisting of one-dimensional–Na–Cl–Na–Cl–chains.

Fast electron diffraction tomography

A fast and fully automatic procedure for collecting electron diffraction tomography data is presented. In the case of a very stable goniometer it is demonstrated how, by variation of the tilting speed and the CCD detector parameters, it is possible to obtain fully automatic precession-assisted electron diffraction tomography data collections, rotation electron diffraction tomography data collections or new integrated electron diffraction tomography data collections, in which the missing wedge of the reciprocal space between the patterns is recorded by longer exposures during the crystal tilt. It is shown how automatic data collection of limited tilt range can be used to determine the unit-cell parameters, while data of larger tilt range are suitable to solve the crystal structureabinitiowith direct methods. The crystal structure of monoclinic MgMoO4has been solved in this way as a test structure. In the case where the goniometer is not stable enough to guarantee a steady position of the crystal over large tilt ranges, an automatic method for tracking the crystal during continuous rotation of the sample is proposed.

Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders

Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Structure refinement from precession electron diffraction data

Electron diffraction is a unique tool for analysing the crystal structures of very small crystals. In particular, precession electron diffraction has been shown to be a useful method for ab initio structure solution. In this work it is demonstrated that precession electron diffraction data can also be successfully used for structure refinement, if the dynamical theory of diffraction is used for the calculation of diffracted intensities. The method is demonstrated on data from three materials - silicon, orthopyroxene (Mg,Fe)(2)Si(2)O(6) and gallium-indium tin oxide (Ga,In)(4)Sn(2)O(10). In particular, it is shown that atomic occupancies of mixed crystallographic sites can be refined to an accuracy approaching X-ray or neutron diffraction methods. In comparison with conventional electron diffraction data, the refinement against precession diffraction data yields significantly lower figures of merit, higher accuracy of refined parameters, much broader radii of convergence, especially for the thickness and orientation of the sample, and significantly reduced correlations between the structure parameters. The full dynamical refinement is compared with refinement using kinematical and two-beam approximations, and is shown to be superior to the latter two.