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3D Electron Diffraction: The Nanocrystallography Revolution

  • Mauro Gemmi*
    Mauro Gemmi
    Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
    *E-mail: [email protected]
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    Orcidhttp://orcid.org/0000-0001-9542-3783
  • , 
  • Enrico Mugnaioli
    Enrico Mugnaioli
    Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
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  • , 
  • Tatiana E. Gorelik
    Tatiana E. Gorelik
    University of Ulm, Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
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  • , 
  • Ute Kolb
    Ute Kolb
    Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
    Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
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  • , 
  • Lukas Palatinus
    Lukas Palatinus
    Department of Structure Analysis, Institute of Physics of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
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  • , 
  • Philippe Boullay
    Philippe Boullay
    CRISMAT, Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France
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    Orcidhttp://orcid.org/0000-0002-2867-8986
  • , 
  • Sven Hovmöller
    Sven Hovmöller
    Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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  • , and 
  • Jan Pieter Abrahams
    Jan Pieter Abrahams
    Center for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland
    Department of Biology and Chemistry, Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
    Leiden Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Cite this: ACS Cent. Sci. 2019, 5, 8, 1315–1329
Publication Date (Web):July 19, 2019
https://doi.org/10.1021/acscentsci.9b00394

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Abstract

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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.

Synopsis

3D electron diffraction allows the atomic structure determination of inorganic, organic, and macromolecular materials that remained hitherto unknown because of their limited crystal size.

1. Introduction

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Accelerated electrons have been long considered the less promising among the radiation types used in crystallography for attaining diffraction data suitable for atomic structure determination. In fact, the large majority of structural models deposited in crystallographic databases (1−5) have been obtained by means of X-ray diffraction, and most of what is left has been derived from neutron diffraction or spectroscopic methods. Although still limited, the use of electron diffraction has grown rapidly over the past decade, mostly due to the introduction of 3D methods for the systematic acquisition and analysis of diffracted intensities. Here, we would like to examine how the use of parallel beam electron diffraction for structure determination has evolved from a mostly qualitative technique, used only by few specialists, to a quantitative approach accessible to a much larger community.
To understand the full picture of this (r)evolution, it is important to focus on the strengths of accelerated electrons for crystallography. First, the possibility to have parallel electron probes with a size of a few nanometers allows collecting diffraction data from sample volumes 2 or 3 orders of magnitude smaller than the ones suitable for synchrotron microfocused X-ray beams. Second, the ability to deliver both diffraction and imaging from the same nanovolume allows the combination of reciprocal and direct space information and the experimental determination of crystallographic phases. Third, the strong Coulomb interaction between electrons and matter allows a good signal-to-noise ratio even from very thin samples and an easier identification of light atoms, like lithium and hydrogen, when compared with X-rays.
However, the strong scattering of electrons is also the reason why electron diffraction (ED) was disregarded for many years for structure analysis. The occurrence of multiple scattering events (dynamical effects) while electrons pass through the sample has a significant impact on the intensities of Bragg reflections. (6,7) In diffraction data, the structure information dwells in the relative differences between reflection intensities, and it is evidently lost or jeopardized when such intensities are leveled out, or their ranking is scrabbled due to multiple scattering.
ED experienced a true rebirth in the past 20 years of the past century, thanks to the research of Dorset and co-workers (8,9) and Hovmöller and co-workers, (10,11) that demonstrated how ED data acquired in a transmission electron microscope (TEM) can be used for the structure characterization of both organic and inorganic nanocrystalline samples, despite the presence of dynamical effects. Shortly after, Gonen et al. (12) also showed that ED can be used for the structure determination of 2D protein crystals at almost-atomic resolution. Still, the occurrence of multiple scattering (13) and the difficulty in merging intensities between different ED patterns (14) hindered the application of classical crystallographic routines for structure determination and restricted ED to a very time-consuming and niche technique, whose fallouts often needed a further validation.
Only in 2007 researchers started to realize that limitations of ED were mostly related with the data collection strategy. Thus far, ED data were always acquired after orienting a target crystal along low-index and well recognizable crystallographic axes. This procedure evidently cuts down the number of recorded reflections. Additionally, in low-index in-zone patterns dynamical effects are just maximized by the simultaneous excitation of many, geometrically related reflections.
As an alternative, Kolb and co-workers (15−18) proposed acquiring ED patterns off-zone, after tilting the sample in fixed angular steps around an arbitrary, noncrystallographic axis. In fact, this procedure just mimics data acquisition by a simple monoaxial diffractometer equipped with an area detector. Each single diffraction pattern cannot be easily interpreted alone, but once the angular relationship between the patterns is known, the whole data set can be reconstructed into a 3D volume from which cell parameters, extinction rules, and reflection intensities are conveniently extracted by dedicated software.
Since 2007, the three-dimensional ED method has spread with an exponential trend. Very soon, still in the hand of few specialists, it allowed the structure determination of landmark samples, mostly inorganic, that were considered impracticable for X-ray methods. (19−28) Later, the introduction of ultrafast data acquisition procedures and of more sensitive detectors allowed establishing robust experimental protocols also for organic and metalorganic materials. (29−35) Finally, three-dimensional ED found successful applications for macromolecules (36−45) and other structures of biologic interest. (46−50) The growing attention on three-dimensional ED is confirmed by the number and impact of related publications in the very last year, (51−77) and by the fact that this method has been considered one of the most important recent scientific breakthroughs. (78)
The fast spread-out of the technique without the availability of dedicated instrumentations has brought researchers to develop different experimental set-ups for data acquisition (as will be described in detail in the next section). Consequently, several acronyms are found in the literature, like automated diffraction tomography (ADT), (16) electron diffraction tomography (EDT), (79) single-crystal electron diffraction (SCED), (53) precession-assisted electron diffraction tomography (PEDT), (80) rotation electron diffraction (RED), (81,82) continuous rotation electron diffraction (cRED), (68) and microcrystal electron diffraction (MicroED). (32,38) Nonetheless, we argue that all these variants share the same core concept, i.e., the idea of sampling the whole available three-dimensional reciprocal space by a tilt of the sample around an arbitrary axis. In this Outlook we will therefore use the generic term 3D ED when broadly referring to all of them.
Compared to conventional in-zone ED patterns, the most obvious advantage of 3D ED is that all reflections reachable in the tilt range of the TEM goniometer are sampled, thus maximizing data completeness. All at once, dynamical effects are drastically reduced, because less geometrically related reflections are excited at the same time. In fact, ab initio structure determination by 3D ED data is normally achieved with the same routines developed for X-ray crystallography (83−85) and without any special treatment for multiple scattering. Finally, data acquisition is significantly faster, easier, and more reproducible, allowing sampling many crystals in a short time and working on very beam sensitive materials.
3D ED is conceptually comparable to single-crystal X-ray but allows data collection from much smaller volumes. Typical crystals for 3D ED range from 100 to 10–4 μm3. Even if XFEL radiation allows diffraction data from comparable crystals, the accessibility of dedicated facilities is still rather limited for general users. (86) Moreover, ED can easily access single crystals even in polyphasic mixtures or embedded in a solid matrix (Figure 1).

Figure 1

Figure 1. Examples of crystals suitable for 3D ED data collection. (A) Cu2–xTe nanoplatelets, with lateral size of 100–200 nm and thickness of few tens of nanometers. (B) Submicrometric Eu2Si2O7 grains embedded in a ground mass of nanocrystalline quartz. (C) Submicrometric cronstedtite pyramidal crystals in a focused ion beam (FIB) lamella, sampled from the carbonaceous meteorite Paris. (D) Micrometric pharmaceutical crystal.

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X-ray powder diffraction (XRPD) is an option for dealing with crystals with a size of few hundreds or few tens of nanometers. This method has also developed into a reliable structure analysis technique in the past decades and is remarkably accurate for what concerns cell and structure refinement. However, XRPD is intrinsically limited by the projection of the information onto one dimension. Systematic and accidental peak overlap is a well-known issue when dealing with structures with long cell parameters or pseudosymmetries. A small crystal size and occurrence of defects result in peak broadening and asymmetry, which in turn emphasize overlapping. Moreover, when the sample of interest is a polyphasic mixture, the XRPD signal is the superposition of reflections from all crystalline components, further hampering any structural interpretation.
In the past years, the potential of electrons for crystallography has become evident due to the outburst of cryo-EM imaging for macromolecule single-particle determination. (87,88) Similarly, 3D ED requires relatively small crystals and can be applied to crystallization products that are considered failures in the eyes of X-ray crystallographers. (31,32) Additionally, ED allows for a better structural resolution and requires an electron dose much lower than any imaging technique, as testified by the successful structure determinations of very beam sensitive materials, (21,26,30,35,46−50,56,68,73) possibly even without the need of cooling down the sample. (24,29,34,55,62)

3D ED requires relatively small crystals and can be applied to crystallization products that are considered failures in the eyes of X-ray crystallographers

2. Data Collection Protocols

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A 3D ED data set is essentially a sequence of diffraction patterns recorded sequentially at different tilt angles of the TEM goniometer. The tilt axis is the goniometer axis of the TEM stage, and its angular range is limited by the presence of the objective lens pole pieces, so that in a standard setup the tilt range cannot exceed 120° (±60°). Thus, differently from singly-crystal X-ray diffraction, there is an intrinsic limitation to the reciprocal space coverage due to the fact the TEM is primarily built to perform as a microscope and not as a diffractometer.
The simplest data collection strategy consists in a stepwise tilt of the crystal in fixed angular steps, with the acquisition of an ED pattern at each tilt stage (Figure 2A). (15) The reciprocal space reconstructed from the collected patterns allows for a reliable unit cell determination. (16) However, the recorded diffraction intensities suffer from an imprecise integration due to the gap between two sequential positions. (89) This missing wedge can be physically filled by collecting the patterns in precession mode (Figure 2B). In precession electron diffraction, the beam is tilted away from the optical axis and precessed at high speed on a conical surface with the vertex fixed on the sample plane. (90) The beam movement makes the Ewald sphere sweep the reciprocal space around the plane normal to the optical axis. This data collection procedure is often referred to as precession-assisted electron diffraction tomography (PEDT), and it has been the first 3D ED method with a high degree of success for structure determination. (17,18)

Figure 2

Figure 2. Sketches of the four main 3D ED data collection protocols. (A) Simple stepwise acquisition performed with fixed mechanical tilt steps (brown arrows) and steady beam (in green). The tilt step is normally 0.5–2°. (B) Stepwise acquisition performed with fixed mechanical tilt steps (brown arrows) while the beam is precessing around a conical surface pointed on the sample (green arrow). The Ewald sphere is also precessing (blue cones), and this movement allows a better integration of the Bragg reflection intensities. (C) Stepwise RED acquisition. Large mechanical tilt steps (brown arrows) are followed by small beam tilt steps (green arrows) obtained by the deflection coils of the TEM. The beam tilt step may be smaller than 0.1°. (D) Continuous rotation acquisition. The sample is mechanically tilted within the whole goniometer range (brown arrow) while the detector is acquiring a sequence of patterns. The acquisition tilt step is determined by the sum of exposure time (blue) and readout time (yellow). The latter is also responsible for the nonsampled wedges between two consecutive patterns. The beam is stationary during the whole data acquisition, and the main limit is given by the goniometer stability, because the sample tends to shift laterally during the tilt and therefore may go out from the illuminated area. The not sampled missing wedge is exaggerated in the figures and is colored in red. It is the same for all acquisition protocols, as it depends only on the mechanical limit of the TEM goniometer.

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An alternative stepwise approach is the so-called rotation electron diffraction (RED), where the missing wedge is filled by fine beam tilt steps achieved using the TEM deflection coils (Figure 2C). (81,82) The angular step is this way reduced to less than 0.1°. A complete RED data collection is implemented by consecutive large mechanical tilts (2–3°), followed every time by a sequence of patterns collected in fine electrical beam tilts. The total number of patterns is on the order of 1000, about 10 times more than in PEDT.
The crystals analyzed in 3D ED are usually smaller than 1 μm; therefore, any mechanical instability of the goniometer can easily bring the crystal out of the illuminated area. In both RED and PEDT, after each mechanical tilt step the crystal position is checked by recording a TEM or STEM image, and if necessary, unwanted sample shifts are corrected by recentering the crystal under the beam. The first 3D ED data collection protocol that appeared in the literature, generally referred as automated diffraction tomography (ADT), is entirely working in STEM mode with a nanosized and adjustable quasiparallel beam. An automatic crystal tracking by STEM imaging allows compensating the mechanical drift through an equivalent shift of the electron beam. (15,91)
The third and most recent approach to 3D ED is based on a continuous data collection while the goniometer is rotating (Figure 2D). (36) In this case the missing wedge is directly sampled by the detector, which is recording the diffracted intensities during the rotation, as it is done in oscillation singly-crystal X-ray diffraction. Differently from X-rays, the rotation never stops during data collection to minimize any mechanical instability. Thus, the relation between the detector exposure and the goniometer rotation speed determines the effective angular step. The continuous data collection relies on the high stability of the goniometer, since crystal recentering is impossible, and on the speed of the detector, which should be fast enough to avoid loss of reciprocal space sampling during readout time. Data collection in continuous rotation is known under different names, as MicroED, (38) IEDT, (89) or cRED. (30) This data collection strategy is the one that guarantees the minimum electron dose on the sample and currently is the one most commonly used for structure determination of beam sensitive materials like small organic molecules, (29−32) proteins, (38−44) and protein fragments. (46−50)
Regardless of the chosen data collection protocol (PEDT, RED, or continuous rotation) the crystal can be illuminated either in selected area mode (SAED) or in parallel nanodiffraction mode (NED). In SAED mode the target area is selected by an SAED diaphragm located in the postsample image plane, and therefore, the illuminated portion of the sample is larger than the area used for collecting diffraction data. If the sample is beam sensitive, the beam damages the whole crystal and not only the area visible inside the SAED aperture. On the contrary, in NED mode the diffracting area is selected by inserting a small presample condenser aperture. The sample is illuminated with a parallel beam having a size in the 50–200 nm range, thus avoiding damaging the part of the crystal which is not diffracting. NED gives full control on the beam diameter used and in principle also allows collecting data on a smaller area with respect to SAED. Consequently it is the method of choice in the case of low crystallinity, high mosaicity, or order–disorder polytypism at the nanoscale. (20,45,58,61,92−95)
PEDT and RED, allowing crystal tracking and recentering in image mode, guarantee that the crystal is always perfectly illuminated up to the tilt limit of the TEM goniometer and therefore always allow the maximum reciprocal space coverage. However, in both cases the crystal is illuminated longer than is strictly required for the diffraction data collection, with an obvious increase of the total electron dose. The continuous rotation method, instead, assures at the same time the maximum speed and the minimum electron dose on the sample. Its implementation has been boosted by the development of radiation hard hybrid detectors that are sensible to single-electron arrivals and are very fast, with negligible readout times. (33,36,96) Exploiting the speed and the sensitivity of such detectors, it is possible to collect a full ED data set in few tens of seconds, with electron doses on the order of 0.01 el s–1 Å–2 and without any reasonable loss of reciprocal space information. However, continuous rotation does not allow crystal tracking and recentering, and therefore the crystal of interest may move out from the illuminated area, especially at high tilt. This may be a serious issue if other crystals or phases are present in the surroundings.
In the case of slow detectors with a long readout time that would be incompatible with a fast continuous data collection, data can be collected in PEDT mode by blanking the beam during the rotation and avoiding any recentering, provided the goniometer is stable. In this way the total dose coincides with the dose of a continuous rotation, and the missing gaps are sampled by precession. (97)
Usually, very sensitive samples are studied in low-temperature conditions. (21,30) However, the high sensitivity of the new hybrid detectors combined with fast rotation or STEM imaging for crystal searching may allow data collection at room temperature before critical sample deterioration. (24,29,55,62)
The speed in data collection introduced by continuous rotation protocols makes 3D ED usable also as an overall sample checking routine for nanocrystalline polyphasic mixtures or assembles. Surveys of continuous data collection have been used for the identification of known and unknown phases (32,92,98) and may foresee possible applications of 3D ED as a quality control technique for chemical synthesis.
All the described 3D ED protocols have in common a proper integration of the reflections over the reciprocal space and a minimization of the dynamical scattering, because reflections are generally collected far from low-index zone axis orientations. Nowadays, several software suites exist for 3D ED data reduction, which allow the accurate refinement of experimental parameters, the reconstruction of the 3D diffraction volume, the 3D visualization of the data set, the determination of cell parameters, and the integration of reflection intensities (Figure 3): ADT3D, (18) EDT-PROCESS, (79) PETS, (73) and RED. (82) Moreover, software developed for X-ray crystallography can be also adapted for the analysis of ED data, like DIALS, (99) MOSFLM, (100) and XDS. (41) 3D ED intensity data can be subsequently used as kinematical “X-ray-like” input for ab initio structure solution via direct methods, charge flipping, simulated annealing, or molecular replacement in almost all possible kinds of crystalline compounds, both organic and inorganic (Figure 4).

3D ED intensity data can be subsequently used as kinematical “X-ray-like” input for ab initio structure solution via direct methods, charge flipping, simulated annealing, or molecular replacement in almost all possible kinds of crystalline compounds, both organic and inorganic

Figure 3

Figure 3. Exemplary diffraction volume of the trigonal mineral franzinite reconstructed from 3D ED data (a = 12.9 Å, c = 26.6 Å). (A) View along a*. (B) View along b*. (C) View along c*. (D) View along the tilt axis of the acquisition. Note that these are projections of a 3D volume and not conventional 2D oriented ED patterns. Cell edges are sketched in yellow. a* vector is in red, b* vector in green, and c* vector in blue. Data resolution is about 0.8 Å. The figure is made by ADT3D software. (18)

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Figure 4

Figure 4. Sketch showing some representative structures solved by 3D ED method for different classes of materials. Starting from the upper left and going anticlockwise: the mineral karibibite, (133) a tunnel (Na,Mn)-oxide for electrolytic applications, (124) the aperiodic structure of SrBi7NbO24, (122) the extra-large-pore silicoaluminophosphate ITQ-51, (25) the cobat tetraphosphonate MOF Co-CAU-36, (66) the pharma compound carbamazepine-III, (29) the amyloid core of the Sup35 prion protein, (47) and a new monoclinic polymorph of lysozyme. (45)

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3. Dynamical Refinement

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Even if dynamical scattering is significantly reduced in 3D ED data, still a pure kinematical approximation during refinement normally results in high figures of merit, when compared to typical values for X-ray diffraction. Also, the refined structure models are generally less accurate, and there is a limited sensitivity to subtle structural features, like displacement parameters, partial atomic occupancies, and coordinates of light atoms like hydrogen.
An alternative refinement procedure was developed by Palatinus et al. (101,102) In this procedure the model intensities for the least-squares refinement are calculated using the dynamical diffraction theory. (103,104) The calculation of the intensities uses the Bloch-wave formalism, which is well-suited for the intensity calculation in general, off-zone crystal orientations. The input to the refinement procedure is diffracted intensities from a 3D ED data set obtained with beam precession. (17,90) The intensities are extracted frame by frame and are treated separately for each frame. Only reflections sufficiently integrated by the precession are used in the refinement. In addition to structural parameters, the thickness of the crystal is also refined. Attempts to use data collected without beam precession have so far failed.
The dynamical refinement improves the accuracy of the structure parameters typically by a factor of 2–3 when compared to the kinematical refinement. The average error of atomic positions is reduced to about 0.02 Å. (102) Dynamical refinement also allows a more accurate determination of atomic partial occupancies (102,105) and the location of hydrogen atoms in organic, organometallic, and even inorganic materials (Figure 5A). (56,95,105) Thanks to this enhanced sensitivity, the dynamical refinement also allows for the discrimination of atomic species with close scattering powers, like in the alloy Ni8Ti5, (106) and for the investigation of positional and occupational disorder in layered materials. (107)

Figure 5

Figure 5. Hydrogen atoms localization by 3D ED. (A) Perspective view of the Co1.13Al2P4O20H11.74 structure (105) with a superimposed difference potential map showing maxima at the positions of the hydrogen atoms. Isosurface levels are at 2σ[ΔV(r)] (light gray) and 3σ[ΔV(r)] (yellow). CoO6, AlO6, and PO4 polyhedra are represented in blue, green, and orange, respectively, while oxygen atoms are in red. This difference potential map enlightening the hydrogen positions is obtained thanks to the use of dynamical refinement. The hydrogen positions (in black) are stable once incorporated to the dynamical refinement. (B) Two adjacent orthocetamol chains (34) with the superimposed difference Fourier map. The maximum residual potential (in blue and yellow) corresponds to the hydrogen atom responsible for the intermolecular bonding. Carbon atoms are drawn in brown, oxygen atoms in red, and nitrogen atoms in gray.

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An important feature of dynamical refinement is its strong sensitivity to the absolute configuration of noncentrosymmetric crystal structures. The correct absolute structure can be determined unambiguously not only in inorganic materials with heavy scatterers (102,108) but also in organic materials and pharmaceuticals. (73)
The calculations involving dynamical diffraction theory are much more computationally demanding than the ones necessary with a kinematical approximation. Therefore, the computing time needed for the dynamical refinement is longer than the time for the kinematical refinement and may reach several hours per refinement cycle for large structures. The computing time becomes prohibitively large for macromolecular structures, and therefore no dynamical refinement of a macromolecular crystal structure has been performed so far.

4. Applications in Materials Sciences

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The main strength of ED is evidently the ability of performing single-crystal diffraction on areas of few hundreds or few tens of nanometers. The probe size is eventually limited by the convergence and the coherence of the beam, which may introduce distortions in the recorded patterns. Thus far, the smallest beam size reported for 3D ED is about 30–50 nm when working in NED mode with a small condenser aperture. (15,18)
3D ED is therefore the technique of choice for the analysis of nanocrystalline mixtures, where XRPD interpretation is hampered by the overlapping signals from multiple different phases. 3D ED allows a first screening of the sample through the analysis of several single crystal grains, with a time frame of a few minutes per sampled spot. (92,98) Even faster automated systems, able to perform multiple data acquisitions from different areas of the sample, have been recently proposed. (53,109) Cell parameters can be coupled with chemical information obtained by electron-dispersive X-ray spectroscopy (EDX or EDS), allowing unequivocal recognition of all the phases already reported in crystallographic databases. Additionally, if unknown or unrecognized phases are identified, a more accurate analysis of 3D ED data should provide ab initio their structure determination. Remarkably, such an analytical protocol can be performed on extremely small sample batches, which cannot be conveniently prepared for XFEL, or even for conventional XRPD. Moreover, 3D ED screening does not destroy the sample, thus allowing future further investigations on the same batch or even on exactly the already analyzed crystal grains.
It is worth mentioning that structural complexity does not appear to be a real limit, at least for inorganic materials. For example, the intermetallic quasicrystal approximant Al77Rh15Ru8 (110) and the mineral charoite (20) were solved despite their asymmetric units containing 78 and 90 atoms, respectively. Also, electrons are more sensitive to light atoms, and therefore, they are able to locate more easily species like lithium (18,111) and possibly hydrogen. (56,95,105)

electrons are more sensitive to light atoms, and therefore, they are able to locate more easily species like lithium and possibly hydrogen

3D ED is rather efficient also for the characterization of materials with pervasive disorder. The small probe size allows spotting locally ordered sample areas (92−94) and single crystal individua in twinned samples. (60,112) This ability is particularly crucial for materials where different order–disorder sequences may arise due to modifications in structural packing. (20,61,95) Additionally, recent studies quantitatively correlated 3D diffuse scattering features with structural disorder. (58,113−115)

4.1. Functional Materials

Thanks to the high sampling resolution, 3D ED allows collecting structural data from single nanoparticles, nanowires, or nanodevices. Birkel et al. (19) in one of the first pioneering papers determined the structure of a new Zn1+xSb phase obtained as 50 nm particles in a yield containing also ZnSb impurities. More recently, Willhammar et al. (116) and Mugnaioli et al. (60) analyzed the structure modulations in plasmonic Cu2–xTe particles combining 3D ED and high-resolution TEM and STEM imaging. Baraldi et al. (117) performed the structure determination of a new Eu2Si2O7 phase recovered as nanoprecipitates inside a quartz matrix. Mayence et al. (118) also proposed the application of 3D ED for the study of twinned metallic particle seeds.
3D ED is an extremely promising technique for the structure determination of functional layered oxides, even if characterized by disorder (119,120) or incommensurate modulations. (64,80,121,122) 3D ED was also used for the analysis of structure modifications caused by the thermal annealing of Ni/Au electrodes, (123) and for the study of materials engineered for electrochemical applications. (59,111,124) In this regard, Karakulina et al. (57) performed the first in situ charge/discharge experiment on a (Li)FePO4 electrode.
Another application for 3D ED resides in the structure analysis of epitaxial thin films. In addition to their intrinsically small diffracting volume, these films are clamped onto a thick crystalline substrate that significantly complicates their analysis by X-ray diffraction and limits the number of measurable reflections. 3D ED was recently used for the characterization of the multiferroic compound Bi3(Mn,Fe)4O11 (28) and the antiferromagnetic compound CuMnAs. (65) Additionally, 3D ED allows a straight comparison between the structure of the known bulk material and the one observed in thin films. (125) A very promising application of dynamical refinements is foreseen for such cases where the main goal is to point out subtle structural changes. Steciuk et al. (76) showed that the structure of a thin film of CaTiO3 grown on SrTiO3 can be refined even in the presence of twinning and that the evolution of the thin film structure as a function of the distance from the substrate may also be observed.
The 3D ED ability of analyzing single components in a nanocrystalline mixture was also applied for the study of HP syntheses (126,127) and metallic alloys. (51) 3D ED is also a powerful instrument for the characterization of intermediate synthetic snapshots, to follow a specific reaction pathway. (128,129)

4.2. Minerals

Several mineral species can be found only in the form of nanocrystals inside complex polyphasic parageneses. Moreover, many of them show polytypism, disorder, and twinning at a very fine scale, possibly associated with pseudosymmetry and severe peak overlap in XRPD. For such samples, 3D ED looks like the only technique able to deliver comprehensive structural information. This technique has already allowed the structure determination of several minerals that have been recognized for decades but whose structures were still lacking because no crystal suitable for single-crystal X-ray diffraction actually exists. (74,75,130−133) Charoite (20) and denisovite (94) embody two emblematic cases which highlight the strengths of the 3D ED method. These extremely complex minerals appear only as submicrometric fibers, typically made of different polytypic sequences stacked one next to the other in areas of few unit cell repetitions.
3D ED is also a valid option for the study of alteration products, (134) biomineralizations, (135) metamict minerals, (136) and first nucleating crystalline seeds. In this regard, it allowed the structure characterization of several hydrated and dehydrated CaCO3 cryptocrystalline polymorphs. (61,77,137) Dynamical refinement also allowed a reliable refinement of Mg/Fe partial occupancies in orthopyroxene. (102) Additionally, meteorites (138) and rocks formed at nonequilibrated and extreme conditions, like seismogenic mirror faults and shock-metamorphic impactites, typically host polyphasic grains and cryptocrystalline matrices and therefore constitute ideal candidates for the 3D ED method. (139)
3D ED is also an excellent option for the study of recovered samples from experimental mineralogy and petrology, typically consisting of small yields and nanocrystalline polyphasic assemblies. (72,92,140−142) Finally, a recent study showed interesting applications of 3D ED for the characterization of archeological finds. (69)

4.3. Porous Materials

Zeolites and other inorganic molecular sieves are optimal targets for the 3D ED method. They usually consist of rather complex 3D frameworks, associated with long cell parameters that produce XRPD peak overlap already at medium resolution. Additionally, they are typically electron beam sensitive and difficult to study by means of high-resolution TEM imaging. New frameworks are continuously engineered to tune chemical and physical properties, which are mostly structure-dependent. Still, it is not always possible to grow single crystals for X-ray diffraction, and therefore, 3D ED has quickly become one of the reference techniques for the structure determination of molecular sieves, (22,25,27,63,70,143−146) also in the presence of polyphasic mixtures. (98) In addition to the structure determination of the framework, there is a large interest in locating templates or extra molecules hosted inside cavities (66,147) and in properly modeling the polytypic disorder in the framework. (54,58)
Metal–organic frameworks (MOFs), (21,56,62,66,68,112) covalent organic frameworks (COFs), (148) and hybrid layered compounds (149) are porous materials whose structures rely on organic linkers. They are generally developed to extend the typical pore size of conventional inorganic zeolites. In cases where single crystals could not be grown, 3D ED proved a robust protocol also for the structure investigation for such hybrid and organic compounds. All kinds of porous materials may suffer fast deterioration under the electron beam, but cooling the sample at liquid N2 temperature (21,22,148) and collecting data in fast continuous mode (68,70,145) generally allow a complete and reliable data acquisition.

4.4. Aperiodic Materials

Aperiodic materials are a specific class of materials that exhibit long-range order but cannot be described within a 3D periodic system. Periodicity can be recovered by using a crystallographic description in a higher dimensional space. (150,151) Although not common, aperiodic structures appear in all classes of materials. In the most simple cases, incommensurately modulated phases have only one modulation vector, and only one extra dimension (3 + 1)D is sufficient to describe their system. Their diffraction patterns combine strong “main” reflections related to the average cell with much weaker “satellite” reflections related to the periodic perturbation (the modulation), which can be found in irrational positions with respect to the average cell. This makes them very difficult to identify and to analyze when only powder diffraction data is available. For this reason, incommensurately modulated structures have been the subject of study by 3D ED methods from the early days. (23) Following this work, Boullay et al. (80) and Steciuk et al. (64,122) deduced the incommensurately modulated structures of several Aurivillius related compounds in the system Bi5Nb3O15–ABi2Nb2O9 (A = Ba, Sr, and Pb). Buixaderas et al. (52) analyzed the temperature-dependent structural changes of the tetragonal-tungsten–bronze type compound Sr0.35Ba0.69Nb2O6.04. Lanza et al. (74) determined and refined the natural modulated structure of the mineral daliranite (PbHgAs2S5). Recently the dynamical refinement was generalized to the case of modulated structures and applied to deduce the structure of Hf3Ta2O11. (67)
Another level of complexity can be found in structures that need the application of a (3 + 2)D superspace. The first incommensurately modulated structure solved by 3D ED methods was actually the two-dimensionally modulated structure of tricopper silicide-germanide. (23) The same need applies to composite structures that can be seen as the imbrication of two distinct 3D average cells, whose coexistence induces a periodical perturbation of both systems. When stabilized in the form of thin films, such a system represents a challenge that only 3D ED can elucidate thanks to the possibility to map reciprocal space from nanosized areas. (152)
Lastly, quasicrystals are aperiodic materials characterized by the presence of forbidden rotational symmetries (5-, 8-, 10-, or 12-fold) that require the use of either (3 + 2)D or (3 + 3)D superspace groups and for which the structure determination from diffraction data is extremely rare. To date, no quasicrystalline material has been solved using 3D ED, but this method has been successfully applied for the study of 3D periodic “approximants” of quasicrystals. (110,153)

5. Applications in Life Sciences

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In most current TEM applications to life sciences, the diffracted electrons are refocused into an image by the electromagnetic lenses. Recently, the method achieved spectacular breakthroughs culminating in the award of the 2017 Nobel Prize in Chemistry to Henderson, Frank, and Dubochet for the development of the cryo-EM method. (87,88) A remarkable advantage of cryo-EM is that frozen samples, vitrified at liquid nitrogen temperature, can be studied without the need of growing crystals and in their native, hydrated environment, while the low temperature reduces the effects of radiation damage.
The study of 2D protein crystals by directly measuring the diffracted intensities, i.e., by ED, was surely a scientific focus at the end of the past century. (154−156) Gonen et al. (12) were able to solve and refine AQP0 junctions at 1.9 Å resolution, and preliminary, low-resolution determinations of 3D structures were also attempted. (157) However, the structural study of proteins by electron diffraction lost most of its luster until recently, when 3D crystals definitely became the object of study. (36−45) Such renewed interest was fueled by technical developments and insights.
First, experimental evidence indicated that dynamical scattering affects ED data from 3D protein crystals to a far lesser extent (41,42) than anticipated by theoretical considerations. (158,159) Also, a significantly higher signal-to-noise ratio is expected in ED, as predicted by first principles calculations. (160) Thus, even when technology would allow the development of the ideal electron microscope, measuring in diffraction mode will still result in significantly better data. The improved signal comes at a price, though: the crystallographic phase information, which is lost in diffraction, has to be reconstructed a posteriori.
A biological or pharmaceutical sample can tolerate only a limited electron dose, before radiation damage destroys its functional structure. (161−163) This implies that data are limited by counting statistics. The advent of direct electron detectors (164) was essential for cryo-EM imaging. Such detectors have been successfully used also for ED, (49) but they are not always suited for measuring electron diffraction, because of their inadequate dynamic range and radiation hardness. On the other hand, conventional detectors for ED, like CCD and CMOS, quantify electrons indirectly from the release of photons emitted when high-energy electrons hit a phosphor.
New-generation hybrid pixel detectors are more sensitive as their pixels count electrons directly and without readout noise. (29,33,36,96,165) These detectors are based on the charge separation within a semiconductor upon absorption of the full energy of the incident diffracted electrons. Hybrid pixel detectors can reach count rates higher than 108 electron hits per second per pixel, without readout noise. Their data accuracy is entirely determined by quantization—counting statistics—of the high-energy electrons, while their readout speed, of 1000 frames per second and higher, allows full data sets to be collected in just a handful of seconds. Hybrid detectors have recently become available commercially and are quickly becoming standard retrofits to existing TEMs in many electron crystallography laboratories.
Current applications of ED in life sciences are mainly found in the crystallographic structure determination of “small-molecule” organic compounds and proteins. Although peptides and proteins are both polyamino acids, from a crystallographic, methodological, and experimental perspective, peptides—and protein fragments in general—are closer to crystals of anhydrous organic compounds. In particular, peptides allow collecting diffraction data up to atomic resolution, and therefore, their structure determination can be often achieved ab initio by direct methods.

5.1. Small-Molecule Organic Compounds: Pharmaceuticals and Peptides

Nowadays, different kinds of spectroscopic methods, and in particular NMR, allow an easy determination of the molecule connectivity for crystalline and noncrystalline organic materials. Still, many molecular compounds can pack into different polymorphic arrangements, which in turn have different physical, chemical, and therapeutic properties. A comprehensive structure determination, including polymorphism, requires therefore diffraction data, which are normally obtained by X-ray methods. In this perspective, 3D ED allows structure analysis of single, far smaller crystalline domains. This ability allows structure determination without the need for growing large coherent crystals, as required for X-ray diffraction, a procedure that may be time-consuming, complicated, or even fully unfeasible for certain pharmaceutical compounds or biological derivates. (31,32)
The main difficulty, when working with ED on organics, is that such compounds quickly get damaged by the electron beam. Cryo-plunging or just cooling the sample at liquid N2 temperature is a common experimental procedure for slowing down the crystal deterioration induced by the electron beam. (31,32,46−50) On the other hand, when nano- or microcrystals of peptides and other organic compounds do not contain much disordered bulk solvent, their preservation in the vacuum of the microscope is relatively straightforward, and they can even be measured at ambient temperature if a sufficiently sensitive detector is available. (29,55) At any rate, continuous rotation 3D ED would be the method of choice for data acquisition to minimize the total electron dose on the sample. (36,38,40,89)
In addition to cryo-cooling, the limitations on data quality imposed by radiation sensitivity can be mitigated by the implementation of serial crystallography data collection strategies, in which many individual, static nanocrystals are illuminated to destruction. (53,109,166,167) A second way for lessening the drawback of beam damage is to diffract from somewhat larger crystals. This will partially compromise data quality by increasing the dynamical scattering contribution, but for organics, such an effect only becomes important beyond a crystal thickness of about 100 nm. (24,160)
When data resolution is around 1 Å or better, phase determination can normally be obtained ab initio by direct methods. (29,31,32,34,35,47) In certain cases, even hydrogen atoms can be spotted directly in the potential map after ab initio phasing (Figure 5B) (34,46) or can be determined after treatment for dynamical effects. (35,105) If data to such a resolution are not available, global optimization methods like simulated annealing can be still successful, given the limitation that they rely on the a priori knowledge of the molecular compound. (55) 3D ED was already successfully employed for unveiling the structure of unknown pharmaceuticals (34) and protein fragments (46−49) that could not be addressed by X-ray methods because they could not be grown in large crystals, and in certain cases even for determining their absolute configuration. (73)
Dynamical diffraction will hamper proper structure refinement and validation. For very high-quality X-ray data of small organic molecular compounds, the refinement residual R1 can be as low as 2.5%, while samples with R1 values close to 5% and goodness-of-fit (GooF) values close to 1 are generally considered good. For ED data taken from crystals thicker than 100 nm, typical refinement statistics range from 18% to 40% in R1, and GooF ranges from 1.4 to 2.8. (31,32) These relatively poor statistics reveal significant inadequacies of the kinematical diffraction approximation, which prevents a confident validation of fine details in the atomic structures of unknown compounds.
Systematic deviations in the measured data due to dynamical diffraction can be reduced by including the effects of dynamical scattering in the crystal refinement. For instance, full unrestrained dynamical refinement of the paracetamol structure, based on 3D ED data taken from a 90 nm thick crystal, allowed a R1 of 9% and a GooF of 2.5. (105) A statistical correction for dynamical scattering allowed instead the refinement of C16O5H18 and C18O6N2S2H16 structures up to a R1 of 12% and a GooF of 0.9, starting from data collected on crystals with thicknesses of about 100–200 nm. (35) Both approaches were shown to be sensitive to hydrogen atom positions.
Hence, current approaches in 3D ED allow confident ab initio structure determination using single submicrometer crystals. Also, methods for dealing with the adverse effects of dynamical diffraction are now quickly progressing toward full and unrestrained refinement of hydrogen atoms and toward the reliable identification of atomic species, alternate and partial occupied positions, and anisotropic displacement parameters.

methods for dealing with the adverse effects of dynamical diffraction are now quickly progressing toward full and unrestrained refinement of hydrogen atoms and toward the reliable identification of atomic species, alternate and partial occupied positions, and anisotropic displacement parameters

5.2. Proteins

Protein crystals contain 50% of disordered matter on average. Mostly, this is water located between the globular protein molecules, but crystals of membrane proteins also contain substantial amounts of disordered detergent. Moreover, water is volatile under the TEM vacuum, and its loss definitely compromises the crystallinity of the sample. Therefore, protein crystals must be vitrified and kept frozen to allow their study by cryo-EM or ED. Also, the relatively large unit cell, combined with a high amount of disordered volume, compromises the resolution and intensity of the Bragg reflections of protein crystals.
Collecting diffraction data by rotating the crystal around a random axis normal to the beam has been the standard approach in X-ray protein crystallography over the past four decades. (168) All recent attempts to collect 3D ED data were then performed with a similar experimental setup. The continuous rotation method, where a series of diffraction patterns are collected while the crystal is continuously rotated between subsequent exposures, is the most common approach for ED data collection. (36,38,40) Recently Lanza et al. (45) showed that it is also possible to acquire data stepwise by a precession-assisted nanobeam, while crystal tracking is done in STEM imaging mode. The main advantage of employing a nanobeam is that a small portion of the crystal is illuminated per time, allowing the sampling of smaller features and exploiting more efficiently the protein diffracting volume.
The first protein structure successfully determined was the most common tetragonal polymorph of lysozyme. (37,38) Later, Gonen and co-workers also succeeded in the structure determination of a number of protein species, with resolution below 2.0 Å. (42) They also showed that is possible to obtain information about the binding interactions between a small-molecule inhibitor and the surrounding HIV-1 Gag. (43)
Meanwhile, Yonekura et al. (39) demonstrated the advantage of energy-filtering ED data for a better definition of charged amino acid residues and metals. Xu et al. (44) stressed the improvement in the potential map definition derived by data redundancy. Eventually Lanza et al. (45) reported a polymorphic form of lysozyme that was also independently discovered with powder X-ray diffraction (169) but could be solved only by 3D ED. The same authors also showed how 3D ED and microfocused X-ray diffraction can be coupled for following protein crystallogenesis and growth.
Protein crystals hardly ever diffract to a resolution that is sufficiently high for phasing by direct methods, so other phasing methods are required. Crystallographic phasing by imaging has been successful for two-dimensional, (156) but so far not for three-dimensional, protein crystals. To date, most proteins determined by 3D ED data are proteins whose crystal structure was known from previous X-ray analyses. This is related with the fact that, at present, there is no satisfactory way of determining the phases of protein ED data other than molecular replacement, which is a very robust phasing method when the atomic structure of a similar molecule is available. Still, independent validation methods are evidently required. A potential validation is obtained removing parts of the model and checking if difference Fourier mapping reveals residual density corresponding to the missing parts. Nevertheless, for this procedure it is essential that an independent model is used and that no refinement was done before the difference Fourier mapping.
Undoubtedly, unmodeled dynamical scattering contributes to reduce accuracy and worsen agreement factors. Protein structures are currently too complex for a full dynamical refinement, (101,102,105) but recently a statistical correction for estimating dynamical scattering has been proposed. (35) This procedure allows a small, but significant, improvement of the models. For instance, in the case of lysozyme nanocrystals, this statistical correction resulted in a reduction of Rcomplete from 29% to 26%. (35,41)
We conclude that the electron diffraction of protein crystals may yield structural information that is almost as good as what can be achieved with X-ray diffraction, while requiring diffracted volumes that can be reduced by up to 6 orders of magnitude. However, several theoretical and experimental problems remain to be fully answered, and for general applications it will be indispensable to develop alternative phasing methods that do not rely on molecular replacement.

6. Outlook

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This paper outlines the strengths of electron crystallography for the analysis of nanocrystalline materials and the advances this technique experienced in the past decade. The impressive numbers of crystal structures determined by 3D ED in any domain of materials and life sciences testify to how advanced and powerful this method has become by now.
Robust and reliable protocols have been developed for ED data acquisition based on different approaches: sequential stage tilt with electron beam precession, combined stage-beam tilt, and continuous stage rotation. A common line for the data processing has been established using either dedicated programs for electron diffraction or modified X-ray packages. Most existing structure analysis and phase retrieval methods were successfully tested with 3D ED data. Meanwhile, the amount of structures characterized by 3D ED is continuously growing, including new complex material systems like proteins.
Taken together, 3D ED is rapidly gaining ground. The remaining steps concern the availability of dedicated instruments optimized for 3D ED. TEM is designed as imaging instruments, and their illumination systems and sample stages are not part of an electron diffractometer, which should provide 3D ED data on nanocrystals of any beam sensitivity. The mechanical stability of the sample stages should be improved to reduce the sample movement during tilt. The instruments should be equipped with single-electron detectors for diffraction, and the illumination system should provide parallel nanobeams smaller than 100 nm. The crystal search should be completely automatized with the possibility of performing ED in low dose conditions. Once such instruments will be available, 3D ED will be the gold standard every time the grain size goes beyond the micron size.
The overview that is provided in this Outlook aims to inform the research community beyond the current users of the method. Thereby, we encourage the outreach of 3D ED toward new materials and new scientific topics, and we foster cooperation among diverse research fields, such as materials and life sciences.

Author Information

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  • Corresponding Author
  • Authors
    • Enrico Mugnaioli - Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
    • Tatiana E. Gorelik - University of Ulm, Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
    • Ute Kolb - Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany;  Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
    • Lukas Palatinus - Department of Structure Analysis, Institute of Physics of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
    • Philippe Boullay - CRISMAT, Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France;  Orcidhttp://orcid.org/0000-0002-2867-8986
    • Sven Hovmöller - Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
    • Jan Pieter Abrahams - Center for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland;  Department of Biology and Chemistry, Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland;  Leiden Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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M.G. and E.M. are grateful to Regione Toscana for funding through the FELIX project (Por CREO FESR 2014-2020 action). T.E.G. is grateful to DFG (DFG) project CRC 1279 for the financial support. U.K. thanks the Stipendienstiftung Rheinland-Pfalz and the Johannes Gutenberg-University Mainz for research funding.

References

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    The ideal of solving unknown crystal structures from exptl. electron-diffraction intensities and high-resoln. electron micrographs has remained a controversial topic in the 60 yr history of electron crystallog. In this review refs. the application of modern direct phasing techniques, familiar to x-ray crystallographers, has decisively proven that such ab initio detns. are, in fact, possible. This statement does not, by any means, refute the existence of the several significant scattering perturbations identified by diffraction physicists. Rather, it does affirm that exptl. parameters can be controlled to ensure that a 'quasi-kinematical' data set can be collected from many types of specimens. Numerous applications were made to various types of specimens, ranging from small orgs. to proteins, and also some inorg. materials. While electron crystallog. may not be the optimal means for detg. accurate bonding parameters, it is often the method of choice when only microcryst. specimens are available.
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  10. 10
    Weirich, T. E.; Ramlau, R.; Simon, A.; Hovmöller, S.; Zou, X. A crystal structure determined with 0.02 Å accuracy by electron microscopy. Nature 1996, 382, 144– 146,  DOI: 10.1038/382144a0
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    10
    A crystal structure determined with 0.02 Å accuracy by electron microscopy
    Weirich, Thomas E.; Ramlau, Reiner; Simon, Arndt; Hovmoeller, Sven; Zou, Xiaodong
    Nature (London) (1996), 382 (6587), 144-146CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)
    The complete detn. of an unknown structure, Ti11Se4, was detd. by electron crystallog. Crystals that are too small for single-crystal x-ray diffraction and difficult to solve by powder diffraction may nevertheless be amenable to accurate structure detn. by electron crystallog. Ti11Se4 is monoclinic, space group C2/m, with a 25.516(11), b 3.4481(14), c 19.201(6) Å, and β 117.84(3)°; R = 14.7% for 408 reflections.
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  11. 11
    Weirich, T. E.; Zou, X.; Ramlau, R.; Simon, A.; Cascarano, G. L.; Giacovazzo, C.; Hovmöller, S. Structures of nanometre-size crystals determined from selected-area electron diffraction data. Acta Crystallogr., Sect. A: Found. Crystallogr. 2000, 56, 29– 35,  DOI: 10.1107/S0108767399009605
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    11
    Structures of nanometre-size crystals determined from selected-area electron diffraction data
    Weirich, Thomas E.; Zou, Xiaodong; Ramlau, Reiner; Simon, Arndt; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Hovmoller, Sven
    Acta Crystallographica, Section A: Foundations of Crystallography (2000), A56 (1), 29-35CODEN: ACACEQ; ISSN:0108-7673. (Munksgaard International Publishers Ltd.)
    The structure of a new modification of Ti2Se, the β-phase, and several related inorg. crystal structures contg. elements with at. nos. between 16 and 40 were solved by quasi-automatic direct methods from single-crystal electron diffraction patterns of nanometer-size crystals, using the kinematical approxn.. The crystals were several thousand times smaller than the min. size required for single-crystal x-ray diffraction. At. coordinates were found with an av. accuracy of 0.2 Å or better. Exptl. data were obtained by standardized techniques for recording and quantifying electron diffraction patterns. The SIR97 program for solving crystal structures from three-dimensional x-ray diffraction data by direct methods was modified to work also with two-dimensional electron diffraction data. At. coordinates are given for β-Ti2Se.
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  12. 12
    Gonen, T.; Cheng, Y.; Sliz, P.; Hiroaki, Y.; Fujiyoshi, Y.; Harrison, S. C.; Walz, T. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 2005, 438, 633– 638,  DOI: 10.1038/nature04321
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    12
    Lipid-protein interactions in double-layered two-dimensional AQP0 crystals
    Gonen, Tamir; Cheng, Yifan; Sliz, Piotr; Hiroaki, Yoko; Fujiyoshi, Yoshinori; Harrison, Stephen C.; Walz, Thomas
    Nature (London, United Kingdom) (2005), 438 (7068), 633-638CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fiber cells. Here we describe a 1.9 Å resoln. structure of junctional AQP0, detd. by electron crystallog. of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic amino and carboxy termini. In the center of the water pathway, the closed pore in junctional AQP0 retains only three water mols., which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the cryst. array are mediated by lipid mols., which assume preferred conformations. We were therefore able to build an at. model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.
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  13. 13
    Dorset, D. L.; Roth, W. J.; Gilmore, C. J. Electron crystallography of zeolites – the MWW family as a test of direct 3D structure determination. Acta Crystallogr., Sect. A: Found. Crystallogr. 2005, 61, 516– 527,  DOI: 10.1107/S0108767305024670
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    13
    Electron crystallography of zeolites - the MWW family as a test of direct 3D structure determination
    Dorset, Douglas L.; Roth, Wieslaw J.; Gilmore, Christopher J.
    Acta Crystallographica, Section A: Foundations of Crystallography (2005), A61 (5), 516-527CODEN: ACACEQ; ISSN:0108-7673. (Blackwell Publishing Ltd.)
    The efficacy of direct methods for solving the crystal structures of zeolites from electron diffraction data is evaluated for related materials, i.e. MCM-22, MCM-49 and ITQ-1. First, it is established by tilting expts. that all materials share the same MWW framework. The calcined product of a delaminated MCM-22 precursor, ITQ-2, also shares this framework structure within the limited no. of stacked unit cells. For all materials, the underlying space group is P6/mmm where a ≃ 14.21, c ≃ 24.94 Å. Traditional direct methods are useful for detg. the projected structure down the hexagonal axis but are not very effective for finding the three-dimensional structure. However, max.-entropy and likelihood approaches are effective for detg. either 2-dimensional projections or 3-dimensional frameworks. The major restriction to 3-dimensional detns. by direct methods is the limited goniometric tilt range of the electron microscope, hence the 'missing cone' of information. Potential maps from the most accurate phase sets are, therefore, obsd. as continuous d. envelopes to the true structure. Some improvement is found when the Sayer equation predicts missing amplitudes and phases but better specimen prepn. methods are required to include projections contg. the c* axis of the reciprocal lattice.
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  14. 14
    Gemmi, M.; Zou, X.; Hovmöller, S.; Migliori, A.; Vennström, M.; Andersson, Y. Structure of Ti2P solved by three-dimensional electron diffraction data collected with the precession technique and high-resolution electron microscopy. Acta Crystallogr., Sect. A: Found. Crystallogr. 2003, 59, 117– 126,  DOI: 10.1107/S0108767302022559
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    14
    Structure of Ti2P solved by three-dimensional electron diffraction data collected with the precession technique and high-resolution electron microscopy
    Gemmi, Mauro; Zou, Xiaodong; Hovmoeller, Sven; Migliori, Andrea; Vennstroem, Marie; Andersson, Yvonne
    Acta Crystallographica, Section A: Foundations of Crystallography (2003), A59 (2), 117-126CODEN: ACACEQ; ISSN:0108-7673. (Blackwell Munksgaard)
    The crystal structure of Ti2P was analyzed using electron diffraction and high-resoln. electron-microscopy techniques. A new unit cell was found, the compd. is hexagonal with a 19.969(1) and c 3.4589(1) Å. The structure was 1st solved in space group P‾62m in projection using direct methods on electron diffraction data from the [001] zone axis. Crystallog. data and at. coordinates are given. A three-dimensional soln. was obtained using again direct methods but on a three-dimensional set of electron diffraction data recorded with the precession technique. Ti2P is a distorted Fe2P structure and, based on high-resoln. images, it is possible to explain that the tripling of the unit cell is due to the ordering of P vacancies that reduces the symmetry to P‾6.
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  15. 15
    Kolb, U.; Gorelik, T.; Kübel, C.; Otten, M. T.; Hubert, D. Towards automated diffraction tomography: Part I—Data acquisition. Ultramicroscopy 2007, 107, 507– 513,  DOI: 10.1016/j.ultramic.2006.10.007
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    15
    Towards automated diffraction tomography: Part I-Data acquisition
    Kolb, U.; Gorelik, T.; Kuebel, C.; Otten, M. T.; Hubert, D.
    Ultramicroscopy (2007), 107 (6-7), 507-513CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    The ultimate aim of electron diffraction data collection for structure anal. is to sample the reciprocal space as accurately as possible to obtain a high-quality data set for crystal structure detn. Besides a more precise lattice parameter detn., fine sampling is expected to deliver superior data on reflection intensities, which is crucial for subsequent structure anal. Traditionally, three-dimensional (3D) diffraction data are collected by manually tilting a crystal around a selected crystallog. axis and recording a set of diffraction patterns (a tilt series) at various crystallog. zones. In a second step, diffraction data from these zones are combined into a 3D data set and analyzed to yield the desired structure information. Data collection can also be performed automatically, with the recent advances in tomog. acquisition providing a suitable basis. An exptl. software module has been developed for the Tecnai microscope for such an automated diffraction pattern collection while tilting around the goniometer axis. The module combines STEM imaging with diffraction pattern acquisition in nanodiffraction mode. It allows automated recording of diffraction tilt series from nanoparticles with a size down to 5 nm.
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  16. 16
    Kolb, U.; Gorelik, T.; Otten, M. T. Towards automated diffraction tomography. Part II—Cell parameter determination. Ultramicroscopy 2008, 108, 763– 772,  DOI: 10.1016/j.ultramic.2007.12.002
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    16
    Towards automated diffraction tomography. Part II-Cell parameter determination
    Kolb, U.; Gorelik, T.; Otten, M. T.
    Ultramicroscopy (2008), 108 (8), 763-772CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    Automated diffraction tomog. (ADT) allows the collection of three-dimensional (3d) diffraction data sets from crystals down to a size of only few nanometers. Imaging is done in STEM mode, and diffraction data are collected with quasi-parallel beam nanoelectron diffraction (NED). Here, we present a set of developed processing steps necessary for automatic unit-cell parameter detn. from the collected 3d diffraction data. Cell parameter detn. is done via extn. of peak positions from a recorded data set (called the data redn. path) followed by subsequent cluster anal. of difference vectors. The procedure of lattice parameter detn. is presented in detail for a beam-sensitive org. material. Independently, we demonstrate a potential (called the full integration path) based on 3d reconstruction of the reciprocal space visualising special structural features of materials such as partial disorder. Furthermore, we describe new features implemented into the acquisition part.
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  17. 17
    Mugnaioli, E.; Gorelik, T.; Kolb, U. Ab Initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. Ultramicroscopy 2009, 109, 758– 765,  DOI: 10.1016/j.ultramic.2009.01.011
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    17
    "Ab initio" structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique
    Mugnaioli, E.; Gorelik, T.; Kolb, U.
    Ultramicroscopy (2009), 109 (6), 758-765CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    Using a combination of our recently developed automated diffraction tomog. (ADT) module with precession electron technique (PED), quasi-kinematical 3D diffraction data sets of an inorg. salt (BaSO4) were collected. The lattice cell parameters and their orientation within the data sets were found automatically. The extd. intensities were used for "ab initio" structure anal. by direct methods. The data set covered almost the complete set of possible sym. equiv. reflections for an orthorhombic structure. The structure soln. in one step delivered all heavy (Ba, S) as well as light atoms (O). Results of the structure soln. using direct methods, charge flipping and max. entropy algorithms as well as structure refinement for 3 different 3D electron diffraction data sets were presented.
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  18. 18
    Kolb, U.; Mugnaioli, E.; Gorelik, T. E. Automated electron diffraction tomography – A new tool for nano crystal structure analysis. Cryst. Res. Technol. 2011, 46, 542– 554,  DOI: 10.1002/crat.201100036
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    18
    Automated electron diffraction tomography - a new tool for nanocrystal structure analysis
    Kolb, U.; Mugnaioli, E.; Gorelik, T. E.
    Crystal Research and Technology (2011), 46 (6), 542-554CODEN: CRTEDF; ISSN:0232-1300. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Automated electron Diffraction Tomog. (ADT) comprises an upcoming method for "ab intio" structure anal. of nanocrystals. ADT allows fine sampling of the reciprocal space by sequential collection of electron diffraction patterns while tilting a nano crystal in fixed tilt steps around an arbitrary axis. Electron diffraction is collected in nano diffraction mode (NED) with a semi-parallel beam with a diam. down to 50 nm. For crystal tracking micro-probe STEM imaging is used. Full automation of the acquisition procedure allowed optimization of the electron dose distribution and therefore anal. of highly beam sensitive samples. Cell parameters, space group and reflection intensities can be detd. directly within a reconstructed 3d diffraction vol. using a dedicated software package (ADT3D). Intensity data sets extd. from such a vol. usually show a high coverage and significantly reduced dynamical effects due to "off-zone" acquisition. The use of this data for "ab initio" structure soln. by direct methods implemented in std. programs for X-ray crystallog. is demonstrated. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).
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  19. 19
    Birkel, C. S.; Mugnaioli, E.; Gorelik, T.; Kolb, U.; Panthöfer, M.; Tremel, W. Solution synthesis of a new thermoelectric Zn1+xSb nanophase and its structure determination using automated electron diffraction tomography. J. Am. Chem. Soc. 2010, 132, 9881– 9889,  DOI: 10.1021/ja1035122
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    19
    Solution Synthesis of a New Thermoelectric Zn1+xSb Nanophase and Its Structure Determination Using Automated Electron Diffraction Tomography
    Birkel, Christina S.; Mugnaioli, Enrico; Gorelik, Tatiana; Kolb, Ute; Panthoefer, Martin; Tremel, Wolfgang
    Journal of the American Chemical Society (2010), 132 (28), 9881-9889CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Engineering materials with specific phys. properties have recently focused on the effect of nanoscopic inhomogeneities at the 10 nm scale. Such features are expected to scatter medium- and long-wavelength phonons thereby lowering the thermal cond. of the system. Low thermal cond. is a prerequisite for effective thermoelec. materials, and the challenge is to limit the transport of heat by phonons, without simultaneously decreasing charge transport. A soln.-phase technique was devised for synthesis of thermoelec. "Zn4Sb3" nanocrystals as a precursor for phase segregation into ZnSb and a new Zn-Sb intermetallic phase, Zn1+δSb, in a peritectoid reaction. Our approach uses activated metal nanoparticles as precursors for the synthesis of this intermetallic compd. The small particle size of the reactants ensures min. diffusion paths, low activation barriers, and low reaction temps., thereby eliminating solid-solid diffusion as the rate-limiting step in conventional bulk-scale solid-state synthesis. Both phases were identified and structurally characterized by automated electron diffraction tomog. combined with precession electron diffraction. An ab initio structure soln. based on electron diffraction data revealed two different phases. The new pseudo-hexagonal phase, Zn1+δSb, was identified and classified within the structural diversity of the Zn-Sb phase diagram.
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  20. 20
    Rozhdestvenskaya, I.; Mugnaioli, E.; Czank, M.; Depmeier, W.; Kolb, U.; Reinholdt, A.; Weirich, T. The structure of charoite, (K,Sr,Ba,Mn)15–16(Ca,Na)32[(Si70(O,OH)180)](OH,F)4.0·nH2O, solved by conventional and automated electron diffraction. Mineral. Mag. 2010, 74, 159– 177,  DOI: 10.1180/minmag.2010.074.1.159
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    20
    The structure of charoite, (K,Sr,Ba,Mn)15-16(Ca,Na)32[(Si70(O,OH)180)](OH,F)4.0·nH2O, solved by conventional and automated electron diffraction
    Rozhdestvenskaya, I.; Mugnaioli, E.; Czank, M.; Depmeier, W.; Kolb, U.; Reinholdt, A.; Weirich, T.
    Mineralogical Magazine (2010), 74 (1), 159-177CODEN: MNLMBB; ISSN:0026-461X. (Mineralogical Society)
    Charoite, ideally (K,Sr,Ba,Mn)15-16(Ca,Na)32[(Si70(O,OH)180)](OH,F)4.0·nH2O, a rare mineral from the Murun massif in Yakutia, Russia, was studied using high-resoln. transmission electron microscopy, selected-area electron diffraction, x-ray spectroscopy, precession electron diffraction, and the newly developed technique of automated electron-diffraction tomog. The structure of charoite (a = 31.96(6) Å, b = 19.64(4) Å, c = 7.09(1) Å, β = 90.0(1)°, V = 4450(24) Å3, space group P21/m) was solved ab initio by direct methods from 2878 unique obsd. reflections and refined to R1/wR2 = 0.17/0.21. The structure can be visualized as being composed of 3 different dreier silicate chains: a double dreier chain, [Si6O17]10-; a tubular loop-branched dreier triple chain, [Si12O30]12-; and a tubular hybrid dreier quadruple chain, [Si17O43]18-. The silicate chains occur between ribbons of edge-sharing Ca and Na-octahedra. The chains of tetrahedra and the ribbons of octahedra extend parallel to the z axis. K+, Ba2+, Sr2+, Mn2+, and H2O mols. lie inside tubes and channels of the structure. On the basis of microprobe analyses and occupancy refinement of the cation sites, the crystal chem. formula of this charoite can be written as (Z = 1): (K13.88Sr1.0Ba0.32Mn0.36)Σ15.56(Ca25.64Na6.36)Σ32[(Si6O11(O,OH)6)2(Si12O18(O,OH)12)2(Si17O25(O,OH)18)2](OH,F)4.0·3.18H2O.
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  21. 21
    Denysenko, D.; Grzywa, M.; Tonigold, M.; Streppel, B.; Krkljus, I.; Hirscher, M.; Mugnaioli, E.; Kolb, U.; Hanss, J.; Volkmer, D. Elucidating gating effects for hydrogen sorption in MFU-4-type triazolate-based metal–organic frameworks featuring different pore sizes. Chem. - Eur. J. 2011, 17, 1837– 1848,  DOI: 10.1002/chem.201001872
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    21
    Elucidating Gating Effects for Hydrogen Sorption in MFU-4-Type Triazolate-Based Metal-Organic Frameworks Featuring Different Pore Sizes
    Denysenko, Dmytro; Grzywa, Maciej; Tonigold, Markus; Streppel, Barbara; Krkljus, Ivana; Hirscher, Michael; Mugnaioli, Enrico; Kolb, Ute; Hanss, Jan; Volkmer, Dirk
    Chemistry - A European Journal (2011), 17 (6), 1837-1848, S1837/1-S1837/5CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A highly porous member of isoreticular MFU-4-type frameworks, [Zn5Cl4(BTDD)3] (MFU-4l(large)) (H2-BTDD=bis(1H-1,2,3-triazolo[4,5-b],[4',5'-i])dibenzo[1,4]dioxin), has been synthesized using ZnCl2 and H2-BTDD in N,N-dimethylformamide as a solvent. MFU-4l represents the first example of MFU-4-type frameworks featuring large pore apertures of 9.1 Å. Here, MFU-4l serves as a ref. compd. to evaluate the origin of unique and specific gas-sorption properties of MFU-4, reported previously. The latter framework features narrow-sized pores of 2.5 Å that allow passage of sufficiently small mols. only (such as hydrogen or water), whereas mols. with larger kinetic diams. (e.g., argon or nitrogen) are excluded from uptake. The crystal structure of MFU-4l has been solved ab initio by direct methods from 3D electron-diffraction data acquired from a single nanosized crystal through automated electron diffraction tomog. (ADT) in combination with electron-beam precession. Independently, it has been solved using powder X-ray diffraction. Thermogravimetric anal. (TGA) and variable-temp. X-ray powder diffraction (XRPD) expts. carried out on MFU-4l indicate that it is stable up to 500 °C (N2 atmosphere) and up to 350 °C in air. The framework adsorbs 4 wt % hydrogen at 20 bar and 77 K, which is twice the amt. compared to MFU-4. The isosteric heat of adsorption starts for low surface coverage at 5 kJ mol-1 and decreases to 3.5 kJ mol-1 at higher H2 uptake. In contrast, MFU-4 possesses a nearly const. isosteric heat of adsorption of ca. 7 kJ mol-1 over a wide range of surface coverage. Moreover, MFU-4 exhibits a H2 desorption max. at 71 K, which is the highest temp. ever measured for hydrogen physisorbed on metal-org. frameworks (MOFs).
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  22. 22
    Jiang, J.; Jorda, J. L.; Yu, J.; Baumes, L. A.; Mugnaioli, E.; Diaz-Cabanas, M. J.; Kolb, U.; Corma, A. Synthesis and structure determination of the hierarchical meso-microporous zeolite ITQ-43. Science 2011, 333, 1131– 1134,  DOI: 10.1126/science.1208652
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    22
    Synthesis and structure determination of the hierarchical meso-microporous zeolite ITQ-43
    Jiang, Jiuxing; Jorda, Jose L.; Yu, Jihong; Baumes, Laurent A.; Mugnaioli, Enrico; Diaz-Cabanas, Maria J.; Kolb, Ute; Corma, Avelino
    Science (Washington, DC, United States) (2011), 333 (6046), 1131-1134CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    The formation of mesopores in microporous zeolites is generally performed by postsynthesis acid, basic, and steam treatments. The hierarchical pore systems thus formed allow better adsorption, diffusion, and reactivity of these materials. By combining org. and inorg. structure-directing agents and high-throughput methodologies, we were able to synthesize a zeolite with a hierarchical system of micropores and mesopores, with channel openings delimited by 28 tetrahedral atoms. Its complex cryst. structure was solved with the use of automated diffraction tomog.
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  23. 23
    Palatinus, L.; Klementová, M.; Dřínek, V.; Jarošova, M.; Petříček, V. An incommensurately modulated structure of η’-phase of Cu3+xSi determined by quantitative electron diffraction tomography. Inorg. Chem. 2011, 50, 3743– 3751,  DOI: 10.1021/ic200102z
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    23
    An Incommensurately Modulated Structure of η'-Phase of Cu3+xSi Determined by Quantitative Electron Diffraction Tomography
    Palatinus, Lukas; Klementova, Mariana; Drinek, Vladislav; Jarosova, Marketa; Petricek, Vaclav
    Inorganic Chemistry (2011), 50 (8), 3743-3751CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The diffraction data of η'-Cu3+x(Si,Ge) were collected by 3-dimensional quant. electron diffraction tomog. on a submicrometer-sized sample, and the structure was solved by the charge-flipping algorithm in superspace. The structure is trigonal, and it is incommensurately modulated with two modulation vectors q1 = (α, α, 1/3) and q2 = (-2α, α, 1/3), superspace group P‾3m(α, α, 1/3)000(-2α, α, 1/3)000. The modulation functions of some atoms are very complicated and reach amplitudes comparable with the unit cell dimensions. The modulated structure can be described as sheets of Cu clusters sepd. by honeycomb layers of mixed Si/Ge positions. The shape of the Cu clusters in the sheets strongly varies with the modulation phase, and the predominant form is an icosahedron. The striving of the Cu layers to form icosahedral clusters is deemed to be the main driving force of the modulation. The combination of methods used in this work can be applied to other structures that are difficult to crystallize in large crystals and opens new perspectives, esp. for studies of aperiodic or otherwise complex metallic alloys.
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  24. 24
    Gorelik, T. E.; van de Streek, J.; Kilbinger, A. F. M.; Brunklaus, G.; Kolb, U. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data. Acta Crystallogr., Sect. B: Struct. Sci. 2012, 68, 171– 181,  DOI: 10.1107/S0108768112003138
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    24
    Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data
    Gorelik, Tatiana E.; van de Streek, Jacco; Kilbinger, Andreas F. M.; Brunklaus, Gunther; Kolb, Ute
    Acta Crystallographica, Section B: Structural Science (2012), 68 (2), 171-181CODEN: ASBSDK; ISSN:0108-7681. (International Union of Crystallography)
    The crystal structure of the oligo p-benzamide contg. four benzamide units (OPBA4) was solved ab initio from electron diffraction data. The structure soln. and refinement strategy was validated on the known structure of OPBA3 and then applied to OPBA4. Ab-initio crystal structure anal. of org. materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomog. (ADT) technique. The structure soln. and refinement route is 1st validated from the known crystal structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual H-bonding scheme is realized; the H-bonding scheme is, however, in perfect agreement with solid-state NMR data. Crystallog. data are given.
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  25. 25
    Martínez-Franco, R.; Moliner, M.; Yun, Y.; Sun, J.; Wan, W.; Zou, X.; Corma, A. Synthesis of an extra-large molecular sieve using proton sponges as organic structure-directing agents. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 3749– 3754,  DOI: 10.1073/pnas.1220733110
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    25
    Synthesis of an extra-large molecular sieve using proton sponges as organic structure-directing agents
    Martinez-Franco, Raquel; Moliner, Manuel; Yun, Yifeng; Sun, Junliang; Wan, Wei; Zou, Xiaodong; Corma, Avelino
    Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (10), 3749-3754, S3749/1-S3749/21CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    The synthesis of cryst. microporous materials contg. large pores is in high demand by industry, esp. for the use of these materials as catalysts in chem. processes involving bulky mols. An extra-large-pore silicoaluminophosphate with 16-ring openings, ITQ-51, has been synthesized by the use of bulky arom. proton sponge 1,8-bis (dimethylamino)naphthalene (DMAN) as org. structure-directing agent. Proton sponges show exceptional properties for directing extra-large zeolites because of their unusually high basicity combined with their large size and rigidity. This extra-large-pore material is stable after calcination, being one of the very few examples of hydrothermally stable mol. sieves contg. extra-large pores. The structure of ITQ-51 was solved from submicrometer-sized crystals using the rotation electron diffraction method. Finally, several hypothetical zeolites related to ITQ-51 have been proposed.
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  26. 26
    Förster, C.; Gorelik, T. E.; Kolb, U.; Ksenofontov, V.; Heinze, K. Crystalline non-equilibrium phase of a cobalt(II) complex with tridentate ligands. Eur. J. Inorg. Chem. 2015, 2015, 920– 924,  DOI: 10.1002/ejic.201403200
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    Guo, P.; Shin, J.; Greenaway, A. G.; Min, J. G.; Su, J.; Choi, H. J.; Liu, L.; Cox, P. A.; Hong, S. B.; Wright, P. A.; Zou, X. A Zeolite Family with expanding structural complexity and embedded isoreticular structures. Nature 2015, 524, 74– 78,  DOI: 10.1038/nature14575
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    A zeolite family with expanding structural complexity and embedded isoreticular structures
    Guo, Peng; Shin, Jiho; Greenaway, Alex G.; Min, Jung Gi; Su, Jie; Choi, Hyun June; Liu, Leifeng; Cox, Paul A.; Hong, Suk Bong; Wright, Paul A.; Zou, Xiaodong
    Nature (London, United Kingdom) (2015), 524 (7563), 74-78CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    The prediction and synthesis of new crystal structures enable the targeted prepn. of materials with desired properties. Among porous solids, this has been achieved for metal-org. frameworks, but not for the more widely applicable zeolites, where new materials are usually discovered using exploratory synthesis. Although millions of hypothetical zeolite structures have been proposed, not enough is known about their synthesis mechanism to allow any given structure to be prepd. Here the authors present an approach that combines structure soln. with structure prediction, and inspires the targeted synthesis of new super-complex zeolites. The authors used electron diffraction to identify a family of related structures and to discover the structural 'coding' within them. This allowed the authors to det. the complex, and previously unknown, structure of zeolite ZSM-25 (ref. 8), which has the largest unit-cell vol. of all known zeolites (91,554 cubic angstroms) and demonstrates selective CO2 adsorption. By extending the authors' method, the authors were able to predict other members of a family of increasingly complex, but structurally related, zeolites and to synthesize two more-complex zeolites in the family, PST-20 and PST-25, with much larger cell vols. (166,988 and 275,178 cubic angstroms, resp.) and similar selective adsorption properties. Members of this family have the same symmetry, but an expanding unit cell, and are related by hitherto unrecognized structural principles; the authors call these family members embedded isoreticular zeolite structures.
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  28. 28
    Zhang, W.; Li, M.; Chen, A.; Li, L.; Zhu, Y.; Xia, Z.; Lu, P.; Boullay, P.; Wu, L.; Zhu, Y.; MacManus-Driscoll, J. L.; Jia, Q.; Zhou, H.; Narayan, J.; Zhang, X.; Wang, H. Two-dimensional layered oxide structures tailored by self-assembled layer stacking via interfacial strain. ACS Appl. Mater. Interfaces 2016, 8, 16845– 16851,  DOI: 10.1021/acsami.6b03773
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    28
    Two-Dimensional Layered Oxide Structures Tailored by Self-Assembled Layer Stacking via Interfacial Strain
    Zhang, Wenrui; Li, Mingtao; Chen, Aiping; Li, Leigang; Zhu, Yuanyuan; Xia, Zhenhai; Lu, Ping; Boullay, Philippe; Wu, Lijun; Zhu, Yimei; MacManus-Driscoll, Judith L.; Jia, Quanxi; Zhou, Honghui; Narayan, Jagdish; Zhang, Xinghang; Wang, Haiyan
    ACS Applied Materials & Interfaces (2016), 8 (26), 16845-16851CODEN: AAMICK; ISSN:1944-8244. (American Chemical Society)
    Study of layered complex oxides emerge as one of leading topics in fundamental materials science because of the strong interplay among intrinsic charge, spin, orbital, and lattice. As a fundamental basis of heteroepitaxial thin film growth, interfacial strain can be used to design materials that exhibit new phenomena beyond their conventional forms. Here, the authors report a strain-driven self-assembly of bismuth-based supercell (SC) with a two-dimensional (2D) layered structure. With combined exptl. anal. and 1st-principles calcns., the authors studied the full SC structure and elucidated the fundamental growth mechanism achieved by the strain-enabled self-assembled at. layer stacking. The unique SC structure exhibits room-temp. ferroelectricity, enhanced magnetic responses, and a distinct optical bandgap from the conventional double perovskite structure. This study reveals the important role of interfacial strain modulation and at. rearrangement in self-assembling a layered singe-phase multiferroic thin film, which opens up a promising avenue in the search for and design of novel 2-dimensional layered complex oxides with enormous promise.
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  29. 29
    van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Acta Crystallogr., Sect. A: Found. Adv. 2016, 72, 236– 242,  DOI: 10.1107/S2053273315022500
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    29
    Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector
    van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.
    Acta Crystallographica, Section A: Foundations and Advances (2016), 72 (2), 236-242CODEN: ACSAD7; ISSN:2053-2733. (International Union of Crystallography)
    Until recently, structure detn. by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomog. data collection at liq.-nitrogen temp., in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive org. compds. Low-dose electron diffraction data (∼0.013 e- Å-2 s-1) were collected at room temp. with the rotation method. It was ascertained that the data were of sufficient quality for structure soln. using direct methods using software developed for X-ray crystallog. (XDS, SHELX) and for electron crystallog. (ADT3D/PETS, SIR2014).
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  30. 30
    Wang, Y.; Takki, S.; Cheung, O.; Xu, H.; Wan, W.; Öhrström, L.; Inge, A. K. Elucidation of the elusive structure and formula of the active pharmaceutical ingredient bismuth subgallate by continuous rotation electron diffraction. Chem. Commun. 2017, 53, 7018– 7021,  DOI: 10.1039/C7CC03180G
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    30
    Elucidation of the elusive structure and formula of the active pharmaceutical ingredient bismuth subgallate by continuous rotation electron diffraction
    Wang, Yunchen; Takki, Sofia; Cheung, Ocean; Xu, Hongyi; Wan, Wei; Oehrstroem, Lars; Inge, A. Ken
    Chemical Communications (Cambridge, United Kingdom) (2017), 53 (52), 7018-7021CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    Bismuth subgallate has been used in wound and gastrointestinal therapy for over a century. The combination of continuous rotation electron diffraction and sample cooling finally revealed its structure as a coordination polymer. The structure provides insight regarding its formula, poor soly., acid resistance and previously unreported gas sorption properties.
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  31. 31
    Gruene, T.; Wennmacher, J. T. C.; Zaubitzer, C.; Holstein, J. J.; Heidler, J.; Fecteau-Lefebvre, A.; De Carlo, S.; Müller, E.; Goldie, K. N.; Regeni, I.; Li, T.; Santiso-Quinones, G.; Steinfeld, G.; Handschin, S.; van Genderen, E.; van Bokhoven, J. A.; Clever, G. H.; Pantelic, R. Rapid structure determination of microcrystalline molecular compounds using electron diffraction. Angew. Chem., Int. Ed. 2018, 57, 16313– 16317,  DOI: 10.1002/anie.201811318
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    Rapid Structure Determination of Microcrystalline Molecular Compounds Using Electron Diffraction
    Gruene, Tim; Wennmacher, Julian T. C.; Zaubitzer, Christan; Holstein, Julian J.; Heidler, Jonas; Fecteau-Lefebvre, Ariane; De Carlo, Sacha; Mueller, Elisabeth; Goldie, Kenneth N.; Regeni, Irene; Li, Teng; Santiso-Quinones, Gustavo; Steinfeld, Gunther; Handschin, Stephan; van Genderen, Eric; van Bokhoven, Jeroen A.; Clever, Guido H.; Pantelic, Radosav
    Angewandte Chemie, International Edition (2018), 57 (50), 16313-16317CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Chemists of all fields currently publish about 50 000 crystal structures per yr, the vast majority of which are X-ray structures. We detd. two mol. structures by employing electron rather than X-ray diffraction. For this purpose, an EIGER hybrid pixel detector was fitted to a transmission electron microscope, yielding an electron diffractometer. The structure of a new methylene blue deriv. was detd. at 0.9 Å resoln. from a crystal smaller than 1 × 2 μm2. Several thousand active pharmaceutical ingredients (APIs) are only available as submicrocryst. powders. To illustrate the potential of electron crystallog. for the pharmaceutical industry, we also detd. the structure of an API from its pill. We demonstrate that electron crystallog. complements X-ray crystallog. and is the technique of choice for all unsolved cases in which submicrometer-sized crystals were the limiting factor.
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  32. 32
    Jones, C. G.; Martynowycz, M. W.; Hattne, J.; Fulton, T. J.; Stoltz, B. M.; Rodriguez, J. A.; Nelson, H. M.; Gonen, T. The cryoEM method MicroED as a powerful tool for small molecule structure determination. ACS Cent. Sci. 2018, 4, 1587– 1592,  DOI: 10.1021/acscentsci.8b00760
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    The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination
    Jones, Christopher G.; Martynowycz, Michael W.; Hattne, Johan; Fulton, Tyler J.; Stoltz, Brian M.; Rodriguez, Jose A.; Nelson, Hosea M.; Gonen, Tamir
    ACS Central Science (2018), 4 (11), 1587-1592CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
    In the many scientific endeavors that are driven by org. chem., unambiguous identification of small mols. is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous detn. of a small mol.'s structure requires X-ray and/or neutron diffraction studies. In practice, however, X-ray crystallog. is rarely applied in routine org. chem. due to intrinsic limitations of both the analytes and the technique. Here, we report the use of the electron cryo-microscopy (cryoEM) method microcrystal electron diffraction (MicroED) to provide routine and unambiguous structural detn. of small org. mols. From simple powders, with minimal sample prepn., we could collect high-quality MicroED data from nanocrystals (∼100 nm, ∼10-15 g) resulting in at. resoln. (<1 Å) crystal structures in minutes.
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  33. 33
    Tinti, G.; Fröjdh, E.; van Genderen, E.; Gruene, T.; Schmitt, B.; de Winter, D. A. M.; Weckhuysen, B. M.; Abrahams, J. P. Electron crystallography with the EIGER detector. IUCrJ 2018, 5, 190– 199,  DOI: 10.1107/S2052252518000945
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    Electron crystallography with the EIGER detector
    Tinti, Gemma; Frojdh, Erik; van Genderen, Eric; Gruene, Tim; Schmitt, Bernd; Matthijs de Winter, D. A.; Weckhuysen, Bert M.; Abrahams, Jan Pieter
    IUCrJ (2018), 5 (2), 190-199CODEN: IUCRAJ; ISSN:2052-2525. (International Union of Crystallography)
    Electron crystallog. is a discipline that currently attracts much attention as method for inorg., org. and macromol. structure soln. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 μm2, frame rates up to 23 kHz and a dead time between frames as low as 3 μs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure detn. of a SAPO-34 zeotype from electron diffraction data.
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  34. 34
    Andrusenko, I.; Hamilton, V.; Mugnaioli, E.; Lanza, A.; Hall, C.; Potticary, J.; Hall, S. R.; Gemmi, M. The crystal structure of orthocetamol solved by 3D electron diffraction. Angew. Chem., Int. Ed. 2019, in press. DOI: 10.1002/anie.201904564 .
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    Clabbers, M. T. B.; Gruene, T.; van Genderen, E.; Abrahams, J. P. Reducing dynamical electron scattering reveals hydrogen atoms. Acta Crystallogr., Sect. A: Found. Adv. 2019, 75, 82– 93,  DOI: 10.1107/S2053273318013918
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    35
    Reducing dynamical electron scattering reveals hydrogen atoms
    Clabbers, Max T. B.; Gruene, Tim; van Genderen, Eric; Abrahams, Jan Pieter
    Acta Crystallographica, Section A: Foundations and Advances (2019), 75 (1), 82-93CODEN: ACSAD7; ISSN:2053-2733. (International Union of Crystallography)
    Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure soln. and its effects can only be modelled in specific cases. Dynamical scattering can be reduced exptl. by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometer-sized crystals from org. pharmaceuticals allow positional refinement of the hydrogen atoms, even while ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resoln.
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  36. 36
    Nederlof, I.; van Genderen, E.; Li, Y.-W.; Abrahams, J. P. A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2013, 69, 1223– 1230,  DOI: 10.1107/S0907444913009700
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    36
    A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals
    Nederlof, Igor; van Genderen, Eric; Li, Yao-Wang; Abrahams, Jan Pieter
    Acta Crystallographica, Section D: Biological Crystallography (2013), 69 (7), 1223-1230CODEN: ABCRE6; ISSN:0907-4449. (International Union of Crystallography)
    When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irresp. of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e- Å-2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resoln., indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that vols. of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-anal. software (MOSFLM and SCALA) from X-ray protein crystallog. can be used in principle for analyzing electron-diffraction data from three-dimensional nanocrystals of proteins.
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    Shi, D.; Nannenga, B. L.; Iadanza, M. G.; Gonen, T. Three-dimensional electron crystallography of protein microcrystals. eLife 2013, 2, e01345  DOI: 10.7554/eLife.01345
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    Three-dimensional electron crystallography of protein microcrystals
    Shi, Dan; Nannenga, Brent L.; Iadanza, Matthew G.; Gonen, Tamir
    eLife (2013), 2 (), e01345/1-e01345/17, 17 pp.CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)
    We demonstrate that it is feasible to det. high-resoln. protein structures by electron crystallog. of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resoln. The authors developed a data collection protocol to collect a full-tilt series in electron diffraction to at. resoln. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. The authors indexed the data from three crystals and used them for structure detn. of lysozyme by mol. replacement followed by crystallog. refinement to 2.9 Å resoln. This proof of principle paves the way for the implementation of a new technique, which the authors name 'MicroED', that may have wide applicability in structural biol.
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    Nannenga, B. L.; Shi, D.; Leslie, A. G. W.; Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods 2014, 11, 927– 930,  DOI: 10.1038/nmeth.3043
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    High-resolution structure determination by continuous-rotation data collection in MicroED
    Nannenga, Brent L.; Shi, Dan; Leslie, Andrew G. W.; Gonen, Tamir
    Nature Methods (2014), 11 (9), 927-930CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)
    MicroED uses very small three-dimensional protein crystals and electron diffraction for structure detn. We present an improved data collection protocol for MicroED called 'continuous rotation'. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallog. software tool MOSFLM, which resulted in improved resoln. for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biol.
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    Yonekura, K.; Kato, K.; Ogasawara, M.; Tomita, M.; Toyoshima, C. Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 3368– 3373,  DOI: 10.1073/pnas.1500724112
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    Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges
    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi
    Proceedings of the National Academy of Sciences of the United States of America (2015), 112 (11), 3368-3373CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    Membrane proteins and macromol. complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallog. could provide a powerful means for structure detn. with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallog. yields Coulomb potential maps rather than electron d. maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodol. for electron crystallog. of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resoln., resp., obtained from Ca2+-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build at. models from such crystals and even to det. the charged states of amino acid residues in the Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase.
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  40. 40
    Shi, D.; Nannenga, B. L.; De La Cruz, M. J.; Liu, J.; Sawtelle, S.; Calero, G.; Reyes, E. F.; Hattne, J.; Gonen, T. The collection of MicroED data for macromolecular crystallography. Nat. Protoc. 2016, 11, 895– 904,  DOI: 10.1038/nprot.2016.046
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    The collection of MicroED data for macromolecular crystallography
    Shi, Dan; Nannenga, Brent L.; de la Cruz, M. Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E.; Hattne, Johan; Gonen, Tamir
    Nature Protocols (2016), 11 (5), 895-904CODEN: NPARDW; ISSN:1750-2799. (Nature Publishing Group)
    The formation of large, well-ordered crystals for crystallog. expts. remains a crucial bottleneck to the structural understanding of many important biol. systems. To help alleviate this problem in crystallog., we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biol. material. In this approach, liq. solns. contg. protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liq. ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by neg.-stain electron microscopy in samples obtained from std. protein crystn. expts. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording exptl. parameters in diffraction image metadata. Identifying microcrystals, prepg. samples and setting up the microscope for diffraction data collection take approx. half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resoln. structures can be obtained from a single crystal or by merging data from multiple crystals.
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  41. 41
    Clabbers, M. T. B.; van Genderen, E.; Wan, W.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P. Protein structure determination by electron diffraction using a single three-dimensional nanocrystal. Acta Crystallogr. D 2017, 73, 738– 748,  DOI: 10.1107/S2059798317010348
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    41
    Protein structure determination by electron diffraction using a single three-dimensional nanocrystal
    Clabbers, M. T. B.; van Genderen, E.; Wan, W.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.
    Acta Crystallographica, Section D: Structural Biology (2017), 73 (9), 738-748CODEN: ACSDAD; ISSN:2059-7983. (International Union of Crystallography)
    Three-dimensional nanometer-sized crystals of macromols. currently resist structure elucidation by single-crystal X-ray crystallog. Here, a single nanocrystal with a diffracting vol. of only 0.14μm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to det. the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallog. This is at least an order of magnitude smaller than was previously possible. The mol.-replacement soln., based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain d., and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel inhouse-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favorable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallog. can provide an attractive alternative in detg. biol. structures.
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  42. 42
    de la Cruz, M. J.; Hattne, J.; Shi, D.; Seidler, P.; Rodriguez, J.; Reyes, F. E.; Sawaya, M. R.; Cascio, D.; Weiss, S. C.; Kim, S. K.; Hinck, C. S.; Hinck, A. P.; Calero, G.; Eisenberg, D.; Gonen, T. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Nat. Methods 2017, 14, 399– 402,  DOI: 10.1038/nmeth.4178
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    Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED
    de la Cruz, M. J.; Hattne, Johan; Shi, Dan; Seidler, Paul; Rodriguez, Jose; Reyes, Francis E.; Sawaya, Michael R.; Cascio, Duilio; Weiss, Simon C.; Kim, Sun Kyung; Hinck, Cynthia S.; Hinck, Andrew P.; Calero, Guillermo; Eisenberg, David; Gonen, Tamir
    Nature Methods (2017), 14 (4), 399-402CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)
    Traditionally, crystallog. anal. of macromols. has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resoln. structure detn. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resoln. structure detn. by the cryoEM method MicroED and potentially by serial femtosecond crystallog.
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  43. 43
    Purdy, M. D.; Shi, D.; Chrustowicz, J.; Hattne, J.; Gonen, T.; Yeager, M. MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 13258– 13263,  DOI: 10.1073/pnas.1806806115
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    43
    MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat
    Purdy, Michael D.; Shi, Dan; Chrustowicz, Jakub; Hattne, Johan; Gonen, Tamir; Yeager, Mark
    Proceedings of the National Academy of Sciences of the United States of America (2018), 115 (52), 13258-13263CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-A MicroED structure revealed that a single BVM mol. stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.
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  44. 44
    Xu, H.; Lebrette, H.; Yang, T.; Srinivas, V.; Hovmöller, S.; Högbom, M.; Zou, X. A rare lysozyme crystal form solved using highly redundant multiple electron diffraction datasets from micron-sized crystals. Structure 2018, 26, 667– 675,  DOI: 10.1016/j.str.2018.02.015
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    A Rare Lysozyme Crystal Form Solved Using Highly Redundant Multiple Electron Diffraction Datasets from Micron-Sized Crystals
    Xu, Hongyi; Lebrette, Hugo; Yang, Taimin; Srinivas, Vivek; Hovmoeller, Sven; Hoegbom, Martin; Zou, Xiaodong
    Structure (Oxford, United Kingdom) (2018), 26 (4), 667-675.e3CODEN: STRUE6; ISSN:0969-2126. (Elsevier Ltd.)
    Recent developments of novel electron diffraction techniques have shown to be powerful for detn. of at. resoln. structures from micron- and nano-sized crystals, too small to be studied by single-crystal X-ray diffraction. In this work, the structure of a rare lysozyme polymorph is solved and refined using continuous rotation MicroED data and std. X-ray crystallog. software. Data collection was performed on a std. 200 kV transmission electron microscope (TEM) using a highly sensitive detector with a short readout time. The data collection is fast (∼3 min per crystal), allowing multiple datasets to be rapidly collected from a large no. of crystals. We show that merging data from 33 crystals significantly improves not only the data completeness, overall I/σ and the data redundancy, but also the quality of the final at. model. This is extremely useful for electron beam-sensitive crystals of low symmetry or with a preferred orientation on the TEM grid.
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  45. 45
    Lanza, A.; Margheritis, E.; Mugnaioli, E.; Cappello, V.; Garau, G.; Gemmi, M. Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme. IUCrJ 2019, 6, 178– 188,  DOI: 10.1107/S2052252518017657
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    45
    Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme
    Lanza, Arianna; Margheritis, Eleonora; Mugnaioli, Enrico; Cappello, Valentina; Garau, Gianpiero; Gemmi, Mauro
    IUCrJ (2019), 6 (2), 178-188CODEN: IUCRAJ; ISSN:2052-2525. (International Union of Crystallography)
    Recent advances in 3D electron diffraction have allowed the structure detn. of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallog. Here, the first new protein structure detd. by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystn. conditions. Remarkably, the data were collected using a low-dose stepwise exptl. setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was addnl. validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromol. crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction expts. Addnl., the anal., which was performed on both nanocrystals and microcrystals from the same crystn. drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the mol. dynamics during protein crystal growth.
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  46. 46
    Rodriguez, J. A.; Ivanova, M. I.; Sawaya, M. R.; Cascio, D.; Reyes, F. E.; Shi, D.; Sangwan, S.; Guenther, E. L.; Johnson, L. M.; Zhang, M.; Jiang, L.; Arbing, M. A.; Nannenga, B. L.; Hattne, J.; Whitelegge, J.; Brewster, A. S.; Messerschmidt, M.; Boutet, S.; Sauter, N. K.; Gonen, T.; Eisenberg, D. S. Structure of the toxic core of α-synuclein from invisible crystals. Nature 2015, 525, 486– 490,  DOI: 10.1038/nature15368
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    Structure of the toxic core of α-synuclein from invisible crystals
    Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.; Cascio, Duilio; Reyes, Francis E.; Shi, Dan; Sangwan, Smriti; Guenther, Elizabeth L.; Johnson, Lisa M.; Zhang, Meng; Jiang, Lin; Arbing, Mark A.; Nannenga, Brent L.; Hattne, Johan; Whitelegge, Julian; Brewster, Aaron S.; Messerschmidt, Marc; Boutet, Sebastien; Sauter, Nicholas K.; Gonen, Tamir; Eisenberg, David S.
    Nature (London, United Kingdom) (2015), 525 (7570), 486-490CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    α-Synuclein is the main component of Lewy bodies, the neuron-assocd. aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which the authors term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here, the authors describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure detn. by synchrotron x-ray diffraction, the authors used micro-electron diffraction to det. the structure at at. resoln. The 1.4-Å-resoln. structure demonstrated that this method can det. previously unknown protein structures and here yielded, to the authors' knowledge, the highest resoln. achieved by any cryo-electron microscopy method to date. The structure exhibited protofibrils built of pairs of face-to-face β-sheets. X-ray fiber diffraction patterns showed the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a 2nd segment, inspired a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.
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    Sawaya, M. R.; Rodriguez, J.; Cascio, D.; Collazo, M. J.; Shi, D.; Reyes, F. E.; Hattne, J.; Gonen, T.; Eisenberg, D. S. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 11232– 11236,  DOI: 10.1073/pnas.1606287113
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    Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED
    Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Hattne, Johan; Gonen, Tamir; Eisenberg, David S.
    Proceedings of the National Academy of Sciences of the United States of America (2016), 113 (40), 11232-11236CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    Electrons, because of their strong interaction with matter, produce high-resoln. diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure detn. of complex biol. macromols., which cannot be coaxed to form crystals large enough for conventional crystallog. or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystd. mol. The second obstacle is the lack of a proven means of de novo phase detn., as is required if the mol. crystd. is insufficiently similar to one that has been previously detd. The authors show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resoln. is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in x-ray diffraction. The success of these four expts. dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromols. can also be detd. by direct methods.
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  48. 48
    Gallagher-Jones, M.; Glynn, C.; Boyer, D. R.; Martynowycz, M. W.; Hernandez, E.; Miao, J.; Zee, C.-T.; Novikova, I. V.; Goldschmidt, L.; McFarlane, H. T.; Helguera, G. F.; Evans, J. E.; Sawaya, M. R.; Cascio, D.; Eisenberg, D. S.; Gonen, T.; Rodriguez, J. A. Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp. Nat. Struct. Mol. Biol. 2018, 25, 131– 134,  DOI: 10.1038/s41594-017-0018-0
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    Sub-angstrom cryo-EM structure of a prion protofibril reveals a polar clasp
    Gallagher-Jones, Marcus; Glynn, Calina; Boyer, David R.; Martynowycz, Michael W.; Hernandez, Evelyn; Miao, Jennifer; Zee, Chih-Te; Novikova, Irina V.; Goldschmidt, Lukasz; McFarlane, Heather T.; Helguera, Gustavo F.; Evans, James E.; Sawaya, Michael R.; Cascio, Duilio; Eisenberg, David S.; Gonen, Tamir; Rodriguez, Jose A.
    Nature Structural & Molecular Biology (2018), 25 (2), 131-134CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)
    The at. structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-angstrom-resoln. structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
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    Guenther, E. L.; Ge, P.; Trinh, H.; Sawaya, M. R.; Cascio, D.; Boyer, D. R.; Gonen, T.; Zhou, Z. H.; Eisenberg, D. S. Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2. Nat. Struct. Mol. Biol. 2018, 25, 311– 319,  DOI: 10.1038/s41594-018-0045-5
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    Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2
    Guenther, Elizabeth L.; Ge, Peng; Trinh, Hamilton; Sawaya, Michael R.; Cascio, Duilio; Boyer, David R.; Gonen, Tamir; Zhou, Z. Hong; Eisenberg, David S.
    Nature Structural & Molecular Biology (2018), 25 (4), 311-319CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)
    Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the mol. level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathol. amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the 247DLIIKGISVHI257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These assocns. include seven distinct interfaces displaying five different symmetry classes of steric zippers. Addnl., we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the mol. level how amyloid proteins can form diverse fibril structures.
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  50. 50
    Zee, C.-T.; Glynn, C.; Gallagher-Jones, M.; Miao, J.; Santiago, C. G.; Cascio, D.; Gonen, T.; Sawaya, M. R.; Rodriguez, J. A. Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ. IUCrJ 2019, 6, 197– 205,  DOI: 10.1107/S2052252518017621
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    50
    Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ
    Zee, Chih-Te; Glynn, Calina; Gallagher-Jones, Marcus; Miao, Jennifer; Santiago, Carlos G.; Cascio, Duilio; Gonen, Tamir; Sawaya, Michael R.; Rodriguez, Jose A.
    IUCrJ (2019), 6 (2), 197-205CODEN: IUCRAJ; ISSN:2052-2525. (International Union of Crystallography)
    The ice-nucleation protein InaZ from Pseudomonas syringae contains a large no. of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. Ab initio structures of this repeat segment, resolved to 1.1 A by microfocus X-ray crystallog. and to 0.9 A by the cryo-EM method MicroED, were detd. from both racemic and homochiral crystals. The benefits of racemic protein crystals for structure detn. by MicroED were evaluated and it was confirmed that the phase restriction introduced by crystal centrosymmetry increases the no. of successful trials during the ab initio phasing of the electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel β-sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all-left-handed sheets mate with their all-right-handed counterparts. This detn. of racemic amyloid assemblies by MicroED reveals complex amyloid architectures and illustrates the racemic advantage in macromol. crystallog., now with submicrometer-sized crystals.
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    Bowden, D.; Krysiak, Y.; Palatinus, L.; Tsivoulas, D.; Plana-Ruiz, S.; Sarakinou, E.; Kolb, U.; Stewart, D.; Preuss, M. A high-strength silicide phase in a stainless steel alloy designed for wear-resistant applications. Nat. Commun. 2018, 9, 1374,  DOI: 10.1038/s41467-018-03875-9
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    A high-strength silicide phase in a stainless steel alloy designed for wear-resistant applications
    Bowden D; Tsivoulas D; Sarakinou E; Preuss M; Krysiak Y; Plana-Ruiz S; Kolb U; Palatinus L; Tsivoulas D; Plana-Ruiz S; Sarakinou E; Stewart D
    Nature communications (2018), 9 (1), 1374 ISSN:.
    Hardfacing alloys provide strong, wear-resistant and corrosion-resistant coatings for extreme environments such as those within nuclear reactors. Here, we report an ultra-high-strength Fe-Cr-Ni silicide phase, named π-ferrosilicide, within a hardfacing Fe-based alloy. Electron diffraction tomography has allowed the determination of the atomic structure of this phase. Nanohardness testing indicates that the π-ferrosilicide phase is up to 2.5 times harder than the surrounding austenite and ferrite phases. The compressive strength of the π-ferrosilicide phase is exceptionally high and does not yield despite loading in excess of 1.6 GPa. Such a high-strength silicide phase could not only provide a new type of strong, wear-resistant and corrosion-resistant Fe-based coating, replacing more costly and hazardous Co-based alloys for nuclear applications, but also lead to the development of a new class of high-performance silicide-strengthened stainless steels, no longer reliant on carbon for strengthening.
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    Buixaderas, E.; Kempa, M.; Bovtun, V.; Kadlec, C.; Savinov, M.; Borodavka, F.; Vaněk, P.; Steciuk, G.; Palatinus, L.; Dec, J. Multiple polarization mechanisms across the ferroelectric phase transition of the tetragonal tungsten-bronze Sr0.35Ba0.69Nb2O6.04. Physical Review Materials 2018, 2, 124402,  DOI: 10.1103/PhysRevMaterials.2.124402
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    Multiple polarization mechanisms across the ferroelectric phase transition of the tetragonal tungsten-bronze Sr0.35Ba0.69Nb2O6.04
    Buixaderas, E.; Kempa, M.; Bovtun, V.; Kadlec, C.; Savinov, M.; Borodavka, F.; Vanek, P.; Steciuk, G.; Palatinus, L.; Dec, J.
    Physical Review Materials (2018), 2 (12), 124402CODEN: PRMHBS; ISSN:2475-9953. (American Physical Society)
    A review. The broadband dielec. response of the uniaxial ferroelec. strontium barium niobate with 35% Sr has been studied from 1 kHz to 30 THz along the polar c axis using high-frequency and low-frequency dielec. spectroscopies, time-domain terahertz spectroscopy, and far-IR reflectivity, in the wide temp. interval 20-600 K. The mechanisms that contribute to the ferroelec. phase transition and to the dielec. anomaly in this material are the softening of an anharmonic excitation in the THz range related to cation hopping and the slowing down of a relaxation in the GHz range, which sats. below TC near 1 MHz. In the ferroelec. phase, a relaxation, related to domain-wall dynamics, appears in the sub-GHz range and hardens on cooling up to 10 GHz. The ferroelec.-paraelec. transition, investigated by electron diffraction, has been assessed to the appearance of a supplementary mirror plane perpendicular to the polar axis.
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    Cichocka, M. O.; Ångström, J.; Wang, B.; Zou, X.; Smeets, S. High-throughput continuous rotation electron diffraction data acquisition via software automation. J. Appl. Crystallogr. 2018, 51, 1652– 1661,  DOI: 10.1107/S1600576718015145
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    High-throughput continuous rotation electron diffraction data acquisition via software automation
    Cichocka, Magdalena Ola; Aangstroem, Jonas; Wang, Bin; Zou, Xiaodong; Smeets, Stef
    Journal of Applied Crystallography (2018), 51 (6), 1652-1661CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    Single-crystal electron diffraction (SCED) is emerging as an effective technique to det. and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the no. of successful expts. with larger rotation ranges and turned cRED data collection into a high-throughput method. The exptl. parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addn., it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.
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    Cichocka, M. O.; Lorgouilloux, Y.; Smeets, S.; Su, J.; Wan, W.; Caullet, P.; Bats, N.; McCusker, L. B.; Paillaud, J.-L.; Zou, X. Multidimensional disorder in zeolite IM-18 revealed by combining transmission electron microscopy and X-ray powder diffraction analyses. Cryst. Growth Des. 2018, 18, 2441– 2451,  DOI: 10.1021/acs.cgd.8b00078
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    54
    Multidimensional Disorder in Zeolite IM-18 Revealed by Combining Transmission Electron Microscopy and X-ray Powder Diffraction Analyses
    Cichocka, Magdalena O.; Lorgouilloux, Yannick; Smeets, Stef; Su, Jie; Wan, Wei; Caullet, Philippe; Bats, Nicolas; McCusker, Lynne B.; Paillaud, Jean-Louis; Zou, Xiaodong
    Crystal Growth & Design (2018), 18 (4), 2441-2451CODEN: CGDEFU; ISSN:1528-7483. (American Chemical Society)
    A new medium-pore germanosilicate, denoted IM-18, with a 3-dimensional 8 × 8 × 10-ring channel system, was prepd. hydrothermally using 4-dimethylaminopyridine as an org. structure-directing agent (OSDA). Due to the presence of stacking disorder, the structure elucidation of IM-18 was challenging, and a combination of different techniques, including electron diffraction, high-resoln. TEM (HRTEM), and Rietveld refinement using synchrotron powder diffraction data, was necessary to elucidate the details of the structure and to understand the nature of the disorder. Rotation electron diffraction data were used to det. the av. structure of IM-18, HRTEM images to characterize the stacking disorder, and Rietveld refinement to locate the Ge in the framework and the OSDA occluded in the channels.
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  55. 55
    Das, P. P.; Mugnaioli, E.; Nicolopoulos, S.; Tossi, C.; Gemmi, M.; Galanis, A.; Borodi, G.; Pop, M. M. Crystal structures of two important pharmaceuticals solved by 3D precession electron diffraction tomography. Org. Process Res. Dev. 2018, 22, 1365– 1372,  DOI: 10.1021/acs.oprd.8b00149
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    55
    Crystal Structures of Two Important Pharmaceuticals Solved by 3D Precession Electron Diffraction Tomography
    Das, Partha P.; Mugnaioli, Enrico; Nicolopoulos, Stavros; Tossi, Camilla; Gemmi, Mauro; Galanis, Athanasios; Borodi, Gheorghe; Pop, Mihaela M.
    Organic Process Research & Development (2018), 22 (10), 1365-1372CODEN: OPRDFK; ISSN:1083-6160. (American Chemical Society)
    The crystal structures of two important marketed pharmaceuticals, namely, ramelteon (RAM) and tolvaptan (TOL), were detd. for the first time using 3D precession electron diffraction tomog. (PEDT) on 500 nm-sized crystals. The results were compared with the same structures detd. by single-crystal X-ray diffraction on subsequently grown 50-200 μm single crystals, indicating a good match of mol. conformation, crystal packing, and unit cell parameters. The X-ray crystal structures were used to validate the developed work-flow of data acquisition and structure soln. with electron diffraction. This study highlights that 3D PEDT alone is able to provide accurate crystal structures from pharmaceutical nanocrystals that will suffice for most practical applications when no larger crystals can be grown.
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  56. 56
    Hynek, J.; Brázda, P.; Rohlíček, J.; Londesborough, M. G. S.; Demel, J. Phosphinic acid based linkers: Building blocks in metal–organic framework chemistry. Angew. Chem., Int. Ed. 2018, 57, 5016– 5019,  DOI: 10.1002/anie.201800884
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    Phosphinic Acid Based Linkers: Building Blocks in Metal-Organic Framework Chemistry
    Hynek, Jan; Brazda, Petr; Rohlicek, Jan; Londesborough, Michael G. S.; Demel, Jan
    Angewandte Chemie, International Edition (2018), 57 (18), 5016-5019CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Metal-org. frameworks (MOFs) are a chem. and topol. diverse family of materials composed of inorg. nodes and org. 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 analog of the commonly used terephthalic acid. Use of this new linker group gives a hydrothermally stable and permanently porous MOF structure. The second innovation is the application of electron-diffraction tomog., coupled with dynamic refinement of the EDT data, to the elucidation of the structure of the new material, including the localization of hydrogen atoms.
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  57. 57
    Karakulina, O. M.; Demortière, A.; Dachraoui, W.; Abakumov, A. M.; Hadermann, J. In situ electron diffraction tomography using a liquid-electrochemical transmission electron microscopy cell for crystal structure determination of cathode materials for Li-ion batteries. Nano Lett. 2018, 18, 6286– 6291,  DOI: 10.1021/acs.nanolett.8b02436
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    57
    In Situ Electron Diffraction Tomography Using a Liquid-Electrochemical Transmission Electron Microscopy Cell for Crystal Structure Determination of Cathode Materials for Li-Ion batteries
    Karakulina, Olesia M.; Demortiere, Arnaud; Dachraoui, Walid; Abakumov, Artem M.; Hadermann, Joke
    Nano Letters (2018), 18 (10), 6286-6291CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    It is demonstrated that changes in the unit cell structure of lithium battery cathode materials during electrochem. cycling in liq. electrolyte can be detd. for particles of just a few hundred nanometers in size using in situ transmission electron microscopy (TEM). The at. coordinates, site occupancies (including lithium occupancy), and cell parameters of the materials can all be reliably quantified. This was achieved using electron diffraction tomog. (EDT) in a sealed electrochem. cell with conventional liq. electrolyte (LP30) and LiFePO4 crystals, which have a well-documented charged structure to use as ref. In situ EDT in a liq. environment cell provides a viable alternative to in situ X-ray and neutron diffraction expts. due to the more local character of TEM, allowing for single crystal diffraction data to be obtained from multiphased powder samples and from submicrometer- to nanometer-sized particles. EDT is the first in situ TEM technique to provide information at the unit cell level in the liq. environment of a com. TEM electrochem. cell. Its application to a wide range of electrochem. expts. in liq. environment cells and diverse types of cryst. materials can be envisaged.
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  58. 58
    Krysiak, Y.; Barton, B.; Marler, B.; Neder, R. B.; Kolb, U. Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography. Acta Crystallogr., Sect. A: Found. Adv. 2018, 74, 93– 101,  DOI: 10.1107/S2053273317018277
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    58
    Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography
    Krysiak, Yasar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B.; Kolb, Ute
    Acta Crystallographica, Section A: Foundations and Advances (2018), 74 (2), 93-101CODEN: ACSAD7; ISSN:2053-2733. (International Union of Crystallography)
    Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and sepn. processes. In order to understand the properties of such materials, current research focuses increasingly on the detn. of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at at. level by std. crystallog. methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomog. (ADT), crystal disorder modeling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extd. from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was detd. by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.
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  59. 59
    Mayorga-Martinez, C. C.; Sofer, Z.; Luxa, J.; Huber, Š.; Sedmidubský, D.; Brázda, P.; Palatinus, L.; Mikulics, M.; Lazar, P.; Medlín, R.; Pumera, M. TaS3 nanofibers: Layered trichalcogenide for high-performance electronic and sensing devices. ACS Nano 2018, 12, 464– 473,  DOI: 10.1021/acsnano.7b06853
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    TaS3 nanofibers: Layered trichalcogenide for high-performance electronic and sensing devices
    Mayorga-Martinez, Carmen C.; Sofer, Zdenek; Luxa, Jan; Huber, Stepan; Sedmidubsky, David; Brazda, Petr; Palatinus, Lukas; Mikulics, Martin; Lazar, Petr; Medlin, Rostislav; Pumera, Martin
    ACS Nano (2018), 12 (1), 464-473CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    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 prepd. 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.
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  60. 60
    Mugnaioli, E.; Gemmi, M.; Tu, R.; David, J.; Bertoni, G.; Gaspari, R.; De Trizio, L.; Manna, L. Ab initio structure determination of Cu2–xTe plasmonic nanocrystals by precession-assisted electron diffraction tomography and HAADF-STEM imaging. Inorg. Chem. 2018, 57, 10241– 10248,  DOI: 10.1021/acs.inorgchem.8b01445
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    60
    Ab Initio Structure Determination of Cu2-xTe Plasmonic Nanocrystals by Precession-Assisted Electron Diffraction Tomography and HAADF-STEM Imaging
    Mugnaioli, Enrico; Gemmi, Mauro; Tu, Renyong; David, Jeremy; Bertoni, Giovanni; Gaspari, Roberto; De Trizio, Luca; Manna, Liberato
    Inorganic Chemistry (2018), 57 (16), 10241-10248CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The authors studied pseudo-cubic Cu2-xTe nanosheets using electron diffraction tomog. and high-resoln. HAADF-STEM imaging. The structure of this metastable nanomaterial, which has a strong localized surface plasmon resonance in the near-IR region, was detd. ab initio by 3-dimensional electron diffraction data recorded in low-dose nanobeam precession mode, using a new generation background-free single-electron detector. The presence of 2 different, crystallog. defined modulations creates a 3-dimensional connected vacancy channel system, which may account for the strong plasmonic response of this material. Also, a pervasive rotational twinning is obsd. for nanosheets as thin as 40 nm, resulting in a tetragonal pseudo-symmetry.
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  61. 61
    Németh, P.; Mugnaioli, E.; Gemmi, M.; Czuppon, G.; Demény, A.; Spötl, C. A nanocrystalline monoclinic CaCO3 precursor of metastable aragonite. Sci. Adv. 2018, 4, eaau6178  DOI: 10.1126/sciadv.aau6178
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    Portolés-Gil, N.; Lanza, A.; Aliaga-Alcalde, N.; Ayllón, J. A.; Gemmi, M.; Mugnaioli, E.; López-Periago, A. M.; Domingo, C. Crystalline curcumin bioMOF obtained by precipitation in supercritical CO2 and structural determination by electron diffraction tomography. ACS Sustainable Chem. Eng. 2018, 6, 12309– 12319,  DOI: 10.1021/acssuschemeng.8b02738
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    62
    Crystalline Curcumin bioMOF Obtained by Precipitation in Supercritical CO2 and Structural Determination by Electron Diffraction Tomography
    Portoles-Gil, Nuria; Lanza, Arianna; Aliaga-Alcalde, Nuria; Ayllon, Jose A.; Gemmi, Mauro; Mugnaioli, Enrico; Lopez-Periago, Ana M.; Domingo, Concepcion
    ACS Sustainable Chemistry & Engineering (2018), 6 (9), 12309-12319CODEN: ASCECG; ISSN:2168-0485. (American Chemical Society)
    This article analyzes the use of supercrit. CO2 green technol. in the reactive crystn. processes involved in the formation of a bioMOF that contains curcumin and ZnII metal centers. A new phase with a [Zn(curcumin)]n compn., termed s.c.-CCMOF-1, is presented. The developed scCO2 protocol allows high yields of the small-sized cryst. material, which was characterized by the use of the recently developed electron diffraction tomog. method applied to the resoln. of submicrometric crystals. A remarkable 3D macrostructure with a complex morphol. was obtained. To analyze the crystn. mechanism, multiple identical runs were performed under similar exptl. conditions to study in each time period the crystal growth progress ex situ by X-ray diffraction and SEM. These expts. indicated that the process to achieve the s.c.-CCMOF-1 in a cryst. form involves the formation of amorphous or semicryst. metastable phases that derived into hierarchical stable and cryst. nanoflower aggregates. In addn., a potential therapeutic application of the bioMOF has been tested by studying the released of the curcumin mol. at neutral pH.
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    Seo, S.; Yang, T.; Shin, J.; Jo, D.; Zou, X.; Hong, S. B. Two aluminophosphate molecular sieves built from pairs of enantiomeric structural building units. Angew. Chem., Int. Ed. 2018, 57, 3727– 3732,  DOI: 10.1002/anie.201800791
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    Two Aluminophosphate Molecular Sieves Built from Pairs of Enantiomeric Structural Building Units
    Seo, Seungwan; Yang, Taimin; Shin, Jiho; Jo, Donghui; Zou, Xiaodong; Hong, Suk Bong
    Angewandte Chemie, International Edition (2018), 57 (14), 3727-3732CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Herein we report the synthesis and structures of two new small-pore aluminophosphate mol. sieves PST-13 and PST-14 with mutually connected 8-ring channels. The structure of PST-13, synthesized using diethylamine as an org. structure-directing agent, contains penta-coordinated framework Al atoms bridged by hydroxy groups and thus edge-sharing 3- and 5-rings. Upon calcination, PST-13 undergoes a transformation to PST-14 with loss of bridging hydroxy groups and occluded org. species. The structures of both materials consist "nonjointly" of pairs of previously undiscovered 1,5- and 1,6-open double 4-rings (d4rs) which are mirror images of each other. We also present a series of novel chem. feasible hypothetical structures built from 1-open d4r (sti) or 1,3-open d4r (nsc) units, as well as from these two enantiomeric structural building units.
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    Steciuk, G.; Barrier, N.; Pautrat, A.; Boullay, P. Stairlike Aurivillius Phases in the pseudobinary Bi5Nb3O15–ABi2Nb2O9 (A = Ba and Sr) system: A comprehensive analysis using superspace group formalism. Inorg. Chem. 2018, 57, 3107– 3115,  DOI: 10.1021/acs.inorgchem.7b03026
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    Stairlike Aurivillius Phases in the Pseudobinary Bi5Nb3O15-ABi2Nb2O9 (A = Ba and Sr) System: A Comprehensive Analysis Using Superspace Group Formalism
    Steciuk, Gwladys; Barrier, Nicolas; Pautrat, Alain; Boullay, Philippe
    Inorganic Chemistry (2018), 57 (6), 3107-3115CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The possibility of extending the so-called stairlike Aurivilius phases in the pseudobinary Bi5Nb3O15-ABi2Nb2O9 (A = Ba and Sr) over a wide range of compns. is reported. These phases are characterized by a discontinuous stacking of [Bi2O2] slabs and perovskite blocks, leading to long-period intergrowths stabilized as a single phase. When analyses from precession electron diffraction tomog. and x-ray and neutron powder diffraction are combined, the monoclinic incommensurately modulated structure with q = αa* + γc* previously proposed for the ABi7Nb5O24 compn. could be generalized to the Bi5Nb3O15-ABi2Nb2O9 (A = Ba and Sr) compds. Considering the compns. expressed as (A,Bi)1-xNbxO3-3x, the stacking sequence assocd. with compns. ranging from x = 2/5 to 3/8 is governed by the component γ of the modulation vector and can be predicted following a Farey tree hierarchy independently to the A cation. The length of the steps, characteristic of the stairlike nature, is controlled by the α component and depends on the substitution ratio A/Bi and the nature of A (A = Ba and Sr). This study highlights the compositional flexibility of stairlike Aurivillius phases.
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  65. 65
    Veis, M.; Minár, J.; Steciuk, G.; Palatinus, L.; Rinaldi, C.; Cantoni, M.; Kriegner, D.; Tikuišis, K. K.; Hamrle, J.; Zahradník, M.; Antoš, R.; Železný, J.; Šmejkal, L.; Marti, X.; Wadley, P.; Campion, R. P.; Frontera, C.; Uhlířová, K.; Duchoň, T.; Kužel, P.; Novák, V.; Jungwirth, T.; Výborný, K. Band structure of CuMnAs probed by optical and photoemission spectroscopy. Phys. Rev. B: Condens. Matter Mater. Phys. 2018, 97, 125109,  DOI: 10.1103/PhysRevB.97.125109
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    Wang, B.; Rhauderwiek, T.; Inge, A. K.; Xu, H.; Yang, T.; Huang, Z.; Stock, N.; Zou, X. A porous cobalt tetraphosphonate metal–organic framework: Accurate structure and guest molecule location determined by continuous-rotation electron diffraction. Chem. - Eur. J. 2018, 24, 17429– 17433,  DOI: 10.1002/chem.201804133
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    66
    A Porous Cobalt Tetraphosphonate Metal-Organic Framework: Accurate Structure and Guest Molecule Location Determined by Continuous-Rotation Electron Diffraction
    Wang, Bin; Rhauderwiek, Timo; Inge, A. Ken; Xu, Hongyi; Yang, Taimin; Huang, Zhehao; Stock, Norbert; Zou, Xiaodong
    Chemistry - A European Journal (2018), 24 (66), 17429-17433CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Synthesis is presented of a novel porous Co metal-org. framework (MOF) with 1D channels, [Co2(Ni-H4TPPP)].2DABCO.6H2O, (denoted Co-CAU-36; DABCO = 1,4-diazabicyclo[2.2.2]octane), and its structure detn. using continuous-rotation electron diffraction (cRED) data. By combining a fast hybrid electron detector with low sample temp. (96 K), high resoln. (0.83-1.00 Å) cRED data could be obtained from 8 Co-CAU-36 crystals. Independent structure detns. were conducted using each of the 8 cRED datasets. All atoms in the MOF framework could be located. Org. mols. in the pores, which were previously difficult to find, could be located using the cRED data. A comparison of 8 independent structure detns. using different datasets shows that structural models differ only on av. by 0.03(2) Å for the framework atoms and 0.10(6) and 0.16(12) Å for DABCO and H2O mols., resp.
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  67. 67
    Wiedemann, D.; Lüdtke, T.; Palatinus, L.; Willinger, E.; Willinger, M. G.; Mühlbauer, M. J.; Lerch, M. At the Gates: The tantalum-rich phase Hf3Ta2O11 and its commensurately modulated structure. Inorg. Chem. 2018, 57, 14435– 14442,  DOI: 10.1021/acs.inorgchem.8b02642
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    67
    At the Gates: The Tantalum-Rich Phase Hf3Ta2O11 and its Commensurately Modulated Structure
    Wiedemann, Dennis; Luedtke, Tobias; Palatinus, Lukas; Willinger, Elena; Willinger, Marc G.; Muehlbauer, Martin J.; Lerch, Martin
    Inorganic Chemistry (2018), 57 (22), 14435-14442CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    Generic mixts. in the system (Zr,Hf)O2(Nb,Ta)2O5 are employed as tunable gate materials for field-effect transistors. Whereas prodn. processes and target compns. are well-defined, resulting crystal structures are vastly unexplored. The authors summarize the sparse reported findings and present the new phase Hf3Ta2O11 as synthesized via a sol-gel route. Its commensurately modulated structure represents the hitherto unknown, metal(V)-richest member of the family (Zr,Hf)x(Nb,Ta)2O2x+5. Based on electron, neutron, and x-ray diffraction, the crystal structure is described within modern superspace [Hf1.2Ta0.8O4.4, Z = 2, a 4.7834(13), b 5.1782(17), c 5.064(3) Å, q = 1/5c*, orthorhombic, superspace group Xmcm(00γ)s00] and supercell formalisms [Hf3Ta2O11, Z = 4, a 4.7834(13), b 5.1782(17), c 25.320(13) Å, orthorhombic, space group Pbnm]. TEM shows the microscopic structure from film-like aggregates down to at. resoln. Cation ordering within the different available coordination environments is possible, but no significant hint at it is found within the limits of std. diffraction techniques. Hf3Ta2O11 is an unpredicted compd. in the above-mentioned oxide systems, in which stability ranges were disputably fuzzy and established only by syntheses via solid-state routes so far.
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  68. 68
    Yuan, S.; Qin, J.-S.; Xu, H.-Q.; Su, J.; Rossi, D.; Chen, Y.; Zhang, L.; Lollar, C.; Wang, Q.; Jiang, H.-L.; Son, D. H.; Xu, H.; Huang, Z.; Zou, X.; Zhou, H.-C. [Ti8Zr2O12(COO)16] cluster: An ideal inorganic building unit for photoactive metal–organic frameworks. ACS Cent. Sci. 2018, 4, 105– 111,  DOI: 10.1021/acscentsci.7b00497
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    68
    [Ti8Zr2O12(COO)16] Cluster: An Ideal Inorganic Building Unit for Photoactive Metal-Organic Frameworks
    Yuan, Shuai; Qin, Jun-Sheng; Xu, Hai-Qun; Su, Jie; Rossi, Daniel; Chen, Yuanping; Zhang, Liangliang; Lollar, Christina; Wang, Qi; Jiang, Hai-Long; Son, Dong Hee; Xu, Hongyi; Huang, Zhehao; Zou, Xiaodong; Zhou, Hong-Cai
    ACS Central Science (2018), 4 (1), 105-111CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
    Metal-org. frameworks (MOFs) based on Ti-oxo clusters (Ti-MOFs) represent a naturally self-assembled superlattice of TiO2 nanoparticles sepd. by designable org. linkers as antenna chromophores, epitomizing a promising platform for solar energy conversion. However, despite the vast, diverse, and well-developed Ti-cluster chem., only a scarce no. of Ti-MOFs have been documented. The synthetic conditions of most Ti-based clusters are incompatible with those required for MOF crystn., which has severely limited the development of Ti-MOFs. This challenge was met herein by the discovery of the [Ti8Zr2O12(COO)16] cluster as a nearly ideal building unit for photoactive MOFs. A family of isoreticular photoactive MOFs were assembled, and their orbital alignments were fine-tuned by rational functionalization of org. linkers under computational guidance. These MOFs demonstrate high porosity, excellent chem. stability, tunable photoresponse, and good activity toward photocatalytic H evolution reactions. The discovery of the [Ti8Zr2O12(COO)16] cluster and the facile construction of photoactive MOFs from this cluster shall pave the way for the development of future Ti-MOF-based photocatalysts.
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  69. 69
    Zacharias, N.; Karavassili, F.; Das, P.; Nicolopoulos, S.; Oikonomou, A.; Galanis, A.; Rauch, E.; Arenal, R.; Portillo, J.; Roque, J.; Casablanca, J.; Margiolaki, I. A novelty for cultural heritage material analysis: transmission electron microscope (TEM) 3D electron diffraction tomography applied to Roman glass tesserae. Microchem. J. 2018, 138, 19– 25,  DOI: 10.1016/j.microc.2017.12.023
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    A novelty for cultural heritage material analysis: Transmission Electron Microscope (TEM) 3D electron diffraction tomography applied to Roman glass tesserae
    Zacharias, N.; Karavassili, F.; Das, P.; Nicolopoulos, S.; Oikonomou, A.; Galanis, A.; Rauch, E.; Arenal, R.; Portillo, J.; Roque, J.; Casablanca, J.; Margiolaki, I.
    Microchemical Journal (2018), 138 (), 19-25CODEN: MICJAN; ISSN:0026-265X. (Elsevier B.V.)
    We present a novel electron diffraction technique (Automated precession 3D diffraction tomog. - ADT) based on a Transmission Electron Microscope (TEM) to precisely det. unit cell parameters, Space Group symmetry and at. structure of various pigment/opacifier crystallites of submicron dimensions and commonly present in colored Roman glass tesserae. Such technique can operate at nanometer scale and it is possible to distinguish even between mineralogical phases of similar/same chem. compn., but different crystal structures.
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    Zhang, C.; Kapaca, E.; Li, J.; Liu, Y.; Yi, X.; Zheng, A.; Zou, X.; Jiang, J.; Yu, J. An extra-large-pore zeolite with 24 × 8 × 8-ring channels using a structure-directing agent derived from traditional Chinese medicine. Angew. Chem., Int. Ed. 2018, 57, 6486– 6490,  DOI: 10.1002/anie.201801386
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    An Extra-Large-Pore Zeolite with 24×8×8-Ring Channels Using a Structure-Directing Agent Derived from Traditional Chinese Medicine
    Zhang, Chuanqi; Kapaca, Elina; Li, Jiyang; Liu, Yunling; Yi, Xianfeng; Zheng, Anmin; Zou, Xiaodong; Jiang, Jiuxing; Yu, Jihong
    Angewandte Chemie, International Edition (2018), 57 (22), 6486-6490CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Extra-large-pore zeolites have attracted much interest because of their important applications because for processing larger mols. Although great progress was made in academic science and industry, it is challenging to synthesize these materials. A new extra-large-pore zeolite SYSU-3 (Sun Yat-sen University no. 3) was synthesized by using a novel sophoridine deriv. as an org. structure-directing agent (OSDA). The framework structure was solved and refined using continuous rotation electron diffraction (cRED) data from nanosized crystals. SYSU-3 exhibits a new zeolite framework topol., which has the 1st 24×8×8-ring extra-large-pore system and a framework d. (FD) ≥11.4 T/1000 Å3. The unique skeleton of the OSDA plays an essential role in the formation of the distinctive zeolite structure. This work provides a new perspective for developing new zeolitic materials by using alkaloids as cost-effective OSDAs.
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    Zhou, Z.; Qiu, Y.; Liang, F.; Palatinus, L.; Poupon, M.; Yang, T.; Cong, R.; Lin, Z.; Sun, J. CsSiB3O7: A beryllium-free deep-ultraviolet nonlinear optical material discovered by the combination of electron diffraction and first-principles calculations. Chem. Mater. 2018, 30, 2203– 2207,  DOI: 10.1021/acs.chemmater.8b00545
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    CsSiB3O7: A Beryllium-Free Deep-Ultraviolet Nonlinear Optical Material Discovered by the Combination of Electron Diffraction and First-Principles Calculations
    Zhou, Zhengyang; Qiu, Yi; Liang, Fei; Palatinus, Lukas; Poupon, Morgane; Yang, Tao; Cong, Rihong; Lin, Zheshuai; Sun, Junliang
    Chemistry of Materials (2018), 30 (7), 2203-2207CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
    The accelerated exploration on new nonlinear optical (NLO) materials urgently demands new methods. The recently developed approach of dynamical refinements of precession electron diffraction tomog. (PEDT) data were adopted to discover a new Be-free borosilicate CsSiB3O7, which was originally found as a minor impurity in a multi-phase sample. The 0.8 × KH2PO4 second-harmonic generation (SHG) response and the <200 nm cut-off edge of CsSiB3O7 are confirmed by the optical measurements on pure polycryst. samples. The 1st-principles calcns. reveal that CsSiB3O7 exhibits a short absorption edge (∼166 nm), indicating a promising candidate for deep UV NLO materials. This study provides a powerful combinational method for searching new NLO materials effectively and efficiently.
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    Ångström, J.; Jenei, I. Z.; Spektor, K.; Häussermann, U. Formation of hydrous, pyroxene-related phases from LiAlSiO4 glass in high-pressure hydrothermal environments. ACS Earth Space Chem. 2019, 3, 8– 16,  DOI: 10.1021/acsearthspacechem.8b00091
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    Brázda, P.; Palatinus, L.; Babor, M. Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science 2019, 364, 667– 669,  DOI: 10.1126/science.aaw2560
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    Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal
    Brazda, Petr; Palatinus, Lukas; Babor, Martin
    Science (Washington, DC, United States) (2019), 364 (6441), 667-669CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    Detn. of the abs. configuration of org. mols. is essential in drug development and the subsequent approval process. We show that this detn. is possible through electron diffraction using nanocryst. material. Ab initio structure detn. by electron diffraction has so far been limited to compds. that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure anal. 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 extn. procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous detn. of the abs. structure of material composed of light scatterers.
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    Lanza, A. E.; Gemmi, M.; Bindi, L.; Mugnaioli, E.; Paar, W. H. Daliranite, PbHgAs2S5: determination of the incommensurately modulated structure and revision of the chemical formula. Acta Crystallogr. B 2019, in press. DOI: 10.1107/S2052520619007340 .
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    Rondeau, B.; Devouard, B.; Jacob, D.; Roussel, J.; Stephant, N.; Boulet, C.; Mollé, V.; Corre, M.; Fritsch, E.; Ferraris, C.; Parodi, G. C. Lasnierite, (Ca,Sr)(Mg,Fe)2Al(PO4)3, a new phosphate accompanying lazulite from Mt. Ibity, Madagascar: an example of structural characterization from dynamical refinement of precession electron diffraction data on submicrometre sample. Eur. J. Mineral. 2019, 31, 379– 388,  DOI: 10.1127/ejm/2019/0031-2817
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    Steciuk, G.; David, A.; Petricek, V.; Palatinus, L.; Mercey, B.; Prellier, W.; Pautrat, A.; Boullay, P. Precession electron diffraction tomography on twinned crystals: Application to CaTiO3 thin films. J. Appl. Crystallogr. 2019, 52, 626– 636,  DOI: 10.1107/S1600576719005569
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    Precession electron diffraction tomography on twinned crystals: application to CaTiO3 thin films
    Steciuk, Gwladys; David, Adrian; Petricek, Vaclav; Palatinus, Lukas; Mercey, Bernard; Prellier, Wilfrid; Pautrat, Alain; Boullay, Philippe
    Journal of Applied Crystallography (2019), 52 (3), 626-636CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    Strain engineering via epitaxial thin-film synthesis is an efficient way to modify the crystal structure of a material in order to induce new features or improve existing properties. One of the challenges in this approach is to quantify structural changes occurring in these films. While X-ray diffraction is the most widely used technique for obtaining accurate structural information from bulk materials, severe limitations appear in the case of epitaxial thin films. This past decade, precession electron diffraction tomog. has emerged as a relevant technique for the structural characterization of nano-sized materials. While its usefulness has already been demonstrated for solving the unknown structure of materials deposited in the form of thin films, the frequent existence of orientation variants within the film introduces a severe bias in the structure refinement, even when using the dynamical diffraction theory to calc. diffracted intensities. By taking into account twinning in the structural anal., it is shown that the structure of the CaTiO3 films can be refined with an accuracy comparable to that obtained by dynamical refinement from non-twinned data. The introduction of the possibility to handle twin data sets is undoubtedly a valuable add-on and, notably, paves the way for a successful use of precession electron diffraction tomog. for accurate structural analyses of thin films.
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    Zou, Z.; Habraken, W. J. E. M.; Matveeva, G.; Jensen, A. C. S.; Bertinetti, L.; Hood, M. A.; Sun, C.; Gilbert, P. U. P. A.; Polishchuk, I.; Pokroy, B.; Mahamid, J.; Politi, Y.; Weiner, S.; Werner, P.; Bette, S.; Dinnebier, R.; Kolb, U.; Zolotoyabko, E.; Fratzl, P. A hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate. Science 2019, 363, 396– 400,  DOI: 10.1126/science.aav0210
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    A hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate
    Zou, Zhaoyong; Habraken, Wouter J. E. M.; Matveeva, Galina; Jensen, Anders C. S.; Bertinetti, Luca; Hood, Matthew A.; Sun, Chang-yu; Gilbert, Pupa U. P. A.; Polishchuk, Iryna; Pokroy, Boaz; Mahamid, Julia; Politi, Yael; Weiner, Steve; Werner, Peter; Bette, Sebastian; Dinnebier, Robert; Kolb, Ute; Zolotoyabko, Emil; Fratzl, Peter
    Science (Washington, DC, United States) (2019), 363 (6425), 396-400CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    As one of the most abundant materials in the world, calcium carbonate, CaCO3, is the main constituent of the skeletons and shells of various marine organisms. It is used in the cement industry and plays a crucial role in the global carbon cycle and formation of sedimentary rocks. For more than a century, only three polymorphs of pure CaCO3-calcite, aragonite, and vaterite-were known to exist at ambient conditions, as well as two hydrated crystal phases, monohydrocalcite (CaCO3·1H2O) and ikaite (CaCO3·6H2O). While investigating the role of magnesium ions in crystn. pathways of amorphous calcium carbonate, we unexpectedly discovered an unknown cryst. phase, hemihydrate CaCO3·1/2H2O, with monoclinic structure. This discovery may have important implications in biomineralization, geol., and industrial processes based on hydration of CaCO3.
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    Hand, E.; Vogel, G.; Garber, K.; Kaiser, J.; Servick, K.; Clery, D.; Service, R. F.; Wadman, M. Runners-up. Science 2018, 362, 1346– 1351,  DOI: 10.1126/science.362.6421.1346
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    Ice age impact
    Hand, Eric
    Science (Washington, DC, United States) (2018), 362 (6421), 1346-1351CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    There is no expanded citation for this reference.
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    Gemmi, M.; Oleynikov, P. Scanning reciprocal space for solving unknown structures: energy filtered diffraction tomography and rotation diffraction tomography methods. Z. Kristallogr. - Cryst. Mater. 2013, 228, 51– 58,  DOI: 10.1524/zkri.2013.1559
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    Scanning reciprocal space for solving unknown structures: energy filtered diffraction tomography and rotation diffraction tomography methods
    Gemmi, Mauro; Oleynikov, Peter
    Zeitschrift fuer Kristallographie - Crystalline Materials (2013), 228 (1), 51-58CODEN: ZKCMAJ; ISSN:2194-4946. (Oldenbourg Wissenschaftsverlag GmbH)
    Structure solns. of CaFe2O4 from energy filtered and unfiltered precession electron diffraction tomog. and rotation electron diffraction tomog. data, collected on two different microscopes, are reported. The collected data are analyzed with three available software packages (ADT3D, PETS and EDT-PROCESS) and the obtained results are compared. In all cases the structure soln. is successfully achieved. Energy filtered precession electron diffraction tomog., performed here for the 1st time, gives sharper diffraction peaks and less background compared to the unfiltered data and the final recovered model is closer to the x-ray refinement. Simultaneously the 1st crystal structure soln. obtained from the rotation electron diffraction tomog. data is reported.
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    Boullay, P.; Palatinus, L.; Barrier, N. Precession electron diffraction tomography for solving complex modulated structures: The case of Bi5Nb3O15. Inorg. Chem. 2013, 52, 6127– 6135,  DOI: 10.1021/ic400529s
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    Precession Electron Diffraction Tomography for Solving Complex Modulated Structures: the Case of Bi5Nb3O15
    Boullay, Philippe; Palatinus, Lukas; Barrier, Nicolas
    Inorganic Chemistry (2013), 52 (10), 6127-6135CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The crystal structure of the 1D incommensurately modulated phase Bi5Nb3O15 [superspace group X2mb(0b0)000, a = 5.46781(7) Å, b = 5.47381(8) Å, c = 41.9005(5) Å, and q = 0.17588(8)b*] is solved by electron diffraction using a tomog. technique combined with precession of the electron beam. The (3 + 1)D structure is further validated by a refinement against powder X-ray diffraction (PXRD). A coherent picture of the true nature of this compd. is obtained, conciliating exptl. observations made by different groups using transmission electron microscopy and PXRD. Bi5Nb3O15 does not have a mixed-layer Aurivillius-type structure but does contain structural elements, [Bi2O2]2+ slabs, and perovskite-like blocks, characteristic of Aurivillius phases. The presence of aperiodic crystallog. shear planes (CSPs) along the modulated direction b leads to the formation of an original layered structure contg. both continuous and discontinuous [Bi2O2]2+ and perovskite-like octahedral layers. Between CSPs, the stacking of these two structural elements exhibits an unprecedented nonuniform sequence referring to Aurivillius phases.
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    Zhang, D.; Oleynikov, P.; Hovmöller, S.; Zou, X. Collecting 3D electron diffraction data by the rotation method. Z. Kristallogr. 2010, 225, 94– 102,  DOI: 10.1524/zkri.2010.1202
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    Collecting 3D electron diffraction data by the rotation method
    Zhang, Daliang; Oleynikov, Peter; Hovmoeller, Sven; Zou, Xiaodong
    Zeitschrift fuer Kristallographie - Crystalline Materials (2010), 225 (2-3), 94-102CODEN: ZKCMAJ; ISSN:2194-4946. (Oldenbourg Wissenschaftsverlag GmbH)
    A new method for collecting complete 3-dimensional electron diffraction data is described. Diffraction data is collected by combining electron beam tilt at many very small steps, with rotation of the crystal in a few but large steps. A no. of practical considerations are discussed, as well as advantages and disadvantages compared to other methods of collecting electron diffraction data.
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    Wan, W.; Sun, J.; Su, J.; Hovmöller, S.; Zou, X. Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing. J. Appl. Crystallogr. 2013, 46, 1863– 1873,  DOI: 10.1107/S0021889813027714
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    Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing
    Wan, Wei; Sun, Junliang; Su, Jie; Hovmoeller, Sven; Zou, Xiaodong
    Journal of Applied Crystallography (2013), 46 (6), 1863-1873CODEN: JACGAR; ISSN:0021-8898. (International Union of Crystallography)
    Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20°) are combined with goniometer tilts at a coarse step (2.0-3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are detd. from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indexes and intensities is output. The data processing program also includes a visualizer to view and analyze three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
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    Palatinus, L.; Chapuis, G. SUPERFLIP – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. J. Appl. Crystallogr. 2007, 40, 786– 790,  DOI: 10.1107/S0021889807029238
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    SUPERFLIP. A computer program for the solution of crystal structures by charge flipping in arbitrary dimensions
    Palatinus, Lukas; Chapuis, Gervais
    Journal of Applied Crystallography (2007), 40 (4), 786-790CODEN: JACGAR; ISSN:0021-8898. (International Union of Crystallography)
    SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from x-ray and neutron diffraction data. Structure soln. from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure. SUPERFLIP is written in Fortran90 and is distributed as a source code and as precompiled binaries. It was successfully compiled and tested on a variety of operating systems.
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    Sheldrick, G. M. A short history of SHELX. Acta Crystallogr., Sect. A: Found. Crystallogr. 2008, 64, 112– 122,  DOI: 10.1107/S0108767307043930
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    A short history of SHELX
    Sheldrick, George M.
    Acta Crystallographica, Section A: Foundations of Crystallography (2008), 64 (1), 112-122CODEN: ACACEQ; ISSN:0108-7673. (International Union of Crystallography)
    An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addn. to identifying useful innovations that have come into general use through their implementation in SHELX, a crit. anal. is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photog. intensity data, punched cards and computers over 10000 times slower than an av. modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-mol. refinement and SHELXS and SHELXD are often employed for structure soln. despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromols. against high-resoln. or twinned data; SHELXPRO acts as an interface for macromol. applications. SHELXC, SHELXD and SHELXE are proving useful for the exptl. phasing of macromols., esp. because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure detn.
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    Burla, M. C.; Caliandro, R.; Carrozzini, B.; Cascarano, G. L.; Cuocci, C.; Giacovazzo, C.; Mallamo, M.; Mazzone, A.; Polidori, G. Crystal structure determination and refinement via SIR2014. J. Appl. Crystallogr. 2015, 48, 306– 309,  DOI: 10.1107/S1600576715001132
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    Crystal structure determination and refinement via SIR2014
    Burla, Maria Cristina; Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Cuocci, Corrado; Giacovazzo, Carmelo; Mallamo, Mariarosaria; Mazzone, Annamaria; Polidori, Giampiero
    Journal of Applied Crystallography (2015), 48 (1), 306-309CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    SIR2014 is the latest program of the SIR suite for crystal structure soln. of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (std. or modern direct methods, Patterson techniques, Vive la Difference) and non-ab initio (simulated annealing, mol. replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-d. maps via suitable viewers.
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    Grimes, J. M.; Hall, D. R.; Ashton, A. W.; Evans, G.; Owen, R. L.; Wagner, A.; McAuley, K. E.; von Delft, F.; Orville, A. M.; Sorensen, T.; Walsh, M. A.; Ginn, H. M.; Stuart, D. I. Where is crystallography going?. Acta Crystallogr. D 2018, 74, 152– 166,  DOI: 10.1107/S2059798317016709
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    Where is crystallography going?
    Grimes, Jonathan M.; Hall, David R.; Ashton, Alun W.; Evans, Gwyndaf; Owen, Robin L.; Wagner, Armin; McAuley, Katherine E.; von Delft, Frank; Orville, Allen M.; Sorensen, Thomas; Walsh, Martin A.; Ginn, Helen M.; Stuart, David I.
    Acta Crystallographica, Section D: Structural Biology (2018), 74 (2), 152-166CODEN: ACSDAD; ISSN:2059-7983. (International Union of Crystallography)
    Macromol. crystallog. (MX) has been a motor for biol. for over half a century and this continues apace. A series of revolutions, including the prodn. of recombinant proteins and cryo-crystallog., have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron expts. In addn., X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallog. in rude health, or will imaging methods, esp. single-particle electron microscopy, render it obsolete for the most interesting biol., while electron diffraction enables structure detn. from even the smallest crystals. We will lay out some information to help you decide.
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    Amunts, A.; Brown, A.; Bai, X.-C.; Llácer, J. L.; Hussain, T.; Emsley, P.; Long, F.; Murshudov, G.; Scheres, S. H. W.; Ramakrishnan, V. Structure of the yeast mitochondrial large ribosomal subunit. Science 2014, 343, 1485– 1489,  DOI: 10.1126/science.1249410
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    Structure of the yeast mitochondrial large ribosomal subunit
    Amunts, Alexey; Brown, Alan; Bai, Xiao-chen; Llacer, Jose L.; Hussain, Tanweer; Emsley, Paul; Long, Fei; Murshudov, Garib; Scheres, Sjors H. W.; Ramakrishnan, V.
    Science (Washington, DC, United States) (2014), 343 (6178), 1485-1489CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. Here, the authors report the soln. of the structure of the yeast (Saccharomyces cerevisiae) mitoribosomal large subunit using single-particle cryo-electron microscopy. The resoln. of 3.2 Å enabled a nearly complete at. model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure revealed a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.
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    Single-Particle Cryo-EM at Crystallographic Resolution
    Cheng, Yifan
    Cell (Cambridge, MA, United States) (2015), 161 (3), 450-457CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
    A review. Until only a few years ago, single-particle electron cryo-microscopy (cryo-EM) was usually not the first choice for many structural biologists due to its limited resoln. in the range of nanometer to subnanometer. Now, this method rivals x-ray crystallog. in terms of resoln. and can be used to det. at. structures of macromols. that are either refractory to crystn. or difficult to crystallize in specific functional states. In this review, the recent breakthroughs in both hardware and software that transformed cryo-microscopy, enabling understanding of complex biomols. and their functions at at. level are discussed.
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    Gemmi, M.; La Placa, M. G. I.; Galanis, A. S.; Rauch, E. F.; Nicolopoulos, S. Fast electron diffraction tomography. J. Appl. Crystallogr. 2015, 48, 718– 727,  DOI: 10.1107/S1600576715004604
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    Fast electron diffraction tomography
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    Journal of Applied Crystallography (2015), 48 (3), 718-727CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    A fast and fully automatic procedure for collecting electron diffraction tomog. 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 tomog. data collections, rotation electron diffraction tomog. data collections or new integrated electron diffraction tomog. 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 det. the unit-cell parameters, while data of larger tilt range are suitable to solve the crystal structure ab initio with direct methods. The crystal structure of monoclinic MgMoO4 has 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.
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    Vincent, R.; Midgley, P. A. Double conical beam-rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy 1994, 53, 271– 282,  DOI: 10.1016/0304-3991(94)90039-6
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    Double conical beam-rocking system for measurement of integrated electron diffraction intensities
    Vincent, R.; Midgley, P. A.
    Ultramicroscopy (1994), 53 (3), 271-82CODEN: ULTRD6; ISSN:0304-3991.
    The performance of a scanning system for a transmission electron microscope is described, where the focused beam is scanned at a const. angle around the optic axis. Below the specimen, the beam is de-scanned, the net effect being equiv. to precessing the specimen around a stationary beam focused to a probe size of 0.1 μm for typical precession and convergence angles. Unlike std. convergent beam electron diffraction (CBED) patterns aligned on a zone axis, precessed patterns include many reflections intercepted by the Ewald sphere, where the diffracted intensities are detd. by integration through the Bragg condition. The double conical scanning system was designed to collect a large data set of integrated intensities that are more suitable for structure detn. by electron diffraction, both by removing excitation errors due to curvature of the Ewald sphere and also by reducing nonsystematic dynamic effects. Exptl. patterns obtained from the Si<110> axis are discussed, followed by anal. of the intensities diffracted into the higher order Laue zones of a rare earth pyrogermanate (Er2Ge2O7) with a large unit cell. The scanning system is equally suitable for collection of precessed spot patterns from radiation-sensitive specimens such as org. crystals.
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    Plana-Ruiz, S.; Portillo, J.; Estradé, S.; Peiró, F.; Kolb, U.; Nicolopoulos, S. Quasi-parallel precession diffraction: Alignment method for scanning transmission electron microscopes. Ultramicroscopy 2018, 193, 39– 51,  DOI: 10.1016/j.ultramic.2018.06.005
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    Quasi-parallel precession diffraction: Alignment method for scanning transmission electron microscopes
    Plana-Ruiz, S.; Portillo, J.; Estrade, S.; Peiro, F.; Kolb, Ute; Nicolopoulos, S.
    Ultramicroscopy (2018), 193 (), 39-51CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    A general method to set illuminating conditions for selectable beam convergence and probe size is presented in this work for Transmission Electron Microscopes (TEM) fitted with μs/pixel fast beam scanning control, (S)TEM, and an annular dark field detector. The case of interest of beam convergence and probe size, which enables diffraction pattern indexation, is then used as a starting point in this work to add 100 Hz precession to the beam while imaging the specimen at a fast rate and keeping the projector system in diffraction mode. The described systematic alignment method for the adjustment of beam precession on the specimen plane while scanning at fast rates is mainly based on the sharpness of the precessed STEM image. The complete alignment method for parallel condition and precession, Quasi-Parallel PED-STEM, is presented in block diagram scheme, as it has been tested on a variety of instruments. The immediate application of this methodol. is that it renders the TEM column ready for the acquisition of Precessed Electron Diffraction Tomogs. (EDT) as well as for the acquisition of slow Precessed Scanning Nanometer Electron Diffraction (SNED). Examples of the quality of the Precessed Electron Diffraction (PED) patterns and PED-STEM alignment images are presented with corresponding probe sizes and convergence angles.
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    Gemmi, M.; Merlini, M.; Palatinus, L.; Fumagalli, P.; Hanfland, M. Electron diffraction determination of 11.5 Å and HySo structures: Candidate water carriers to the Upper Mantle. Am. Am. Mineral. 2016, 101, 2645– 2654,  DOI: 10.2138/am-2016-5722
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    Wilke, M.; Kabelitz, A.; Gorelik, T. E.; Guilherme Buzanich, A.; Reinholz, U.; Kolb, U.; Rademann, K.; Emmerling, F. The crystallisation of copper(II) phenylphosphonates. Dalton T. 2016, 45, 17453– 17463,  DOI: 10.1039/C6DT02904C
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    Rozhdestvenskaya, I. V.; Mugnaioli, E.; Schowalter, M.; Schmidt, M. U.; Czank, M.; Depmeier, W.; Rosenauer, A. The structure of denisovite, a fibrous nanocrystalline polytypic disordered ‘very complex’ silicate, studied by a synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction. IUCrJ 2017, 4, 223– 242,  DOI: 10.1107/S2052252517002585
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    Structure of denisovite, fibrous nanocrystalline polytypic disordered very complex silicate, studied by synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction
    Rozhdestvenskaya, Ira V.; Mugnaioli, Enrico; Schowalter, Marco; Schmidt, Martin U.; Czank, Michael; Depmeier, Wulf; Rosenauer, Andreas
    IUCrJ (2017), 4 (3), 223-242CODEN: IUCRAJ; ISSN:2052-2525. (International Union of Crystallography)
    A denisovite is a rare mineral occurring as aggregates of ffibers typically 200500 nm diam. It was confirmed as a new mineral in 1984, but important facts about its chem. formula, lattice parameters, symmetry and structure have remained incompletely. Recently obtained results from studies using microprobe anal., X-ray powder diffraction (XRPD), electron crystallog., modeling and Rietveld refinement will be reported. The electron crystallog. methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resoln. transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomog. (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure soln. using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5)Å = 95.99 (3), V = 4310.1 (5) Å 3 and space group P12/a1. The structure consists of three topol. distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si6O17]10, and a tubular loop-branched dreier triple chain, [Si12O30]12-. The silicate chains occur between three walls of edge-sharing (Ca, Na). The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water mols. and K+ cations are located at the center of the tubular silicate chain. The latter also occupy positions close to the centers of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighboring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighboring layers being either z = c/4 or c/4. Such behavior is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections, but continuous diffuse streaks parallel to a* instead; only reflections with sharp. The diffuse scattering is caused by (100) nanolamellae sepd. by stacking faults and twin boundaries. The structure can be described according to the order-disorder (OD) theory as a stacking of layers parallel to (100).
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    Mugnaioli, E.; Gemmi, M. Single-crystal analysis of nanodomains by electron diffraction tomography: mineralogy at the order-disorder borderline. Z. Kristallogr. - Cryst. Mater. 2018, 233, 163– 178,  DOI: 10.1515/zkri-2017-2130
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    Single-crystal analysis of nanodomains by electron diffraction tomography: mineralogy at the order-disorder borderline
    Mugnaioli, Enrico; Gemmi, Mauro
    Zeitschrift fuer Kristallographie - Crystalline Materials (2018), 233 (3-4), 163-178CODEN: ZKCMAJ; ISSN:2194-4946. (Oldenbourg Wissenschaftsverlag GmbH)
    Electron diffraction tomog. 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 anal. of polyphasic or polytypic mixts. 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 tomog. was the only way for achieving a proper description of the sample, by the identification and the structure detn. of all the phases or all the polytypes within. We also show how electron diffraction tomog. and dynamical refinement can be combined for finding accurate at. positions and localizing hydrogen atoms at room conditions. Finally, we stress the future potential of this method in the fields of mineralogy and exptl. petrol., where till now many samples cannot be properly described because nanocryst., polyphasic or disordered. Electron diffraction tomog. 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 cryst. and amorphous matter and delivers crucial and unique elements for the understanding of the first stages of solid matter organization.
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  96. 96
    Georgieva, D.; Jansen, J.; Sikharulidze, I.; Jiang, L.; Zandbergen, H. W.; Abrahams, J. P. Evaluation of Medipix2 detector for recording electron diffraction data in low dose conditions. J. Instrum. 2011, 6, C01033,  DOI: 10.1088/1748-0221/6/01/C01033
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    Kodjikian, S.; Klein, H. Low-dose electron diffraction tomography (LD-EDT). Ultramicroscopy 2019, 200, 12– 19,  DOI: 10.1016/j.ultramic.2019.02.010
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    Low-dose electron diffraction tomography (LD-EDT)
    Kodjikian, Stephanie; Klein, Holger
    Ultramicroscopy (2019), 200 (), 12-19CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    A new electron diffraction tomog. method is presented that is aimed to enable high performance electron crystallog. expts. on beam sensitive materials using a std. TEM without any special equipment. Low-dose electron diffraction tomog. minimizes the electron dose necessary for obtaining data sets suitable for structure soln. by irradiating the crystal exclusively during the acquisition of the diffraction patterns. The performance of the method is successfully tested on two model structures, a complex oxide Sr5CuGe9O24 and the beam sensitive metal-org. framework (MOF) of manganese formiate. Even when the limited lifetime of a beam sensitive material only allows obtaining a data set of rather low completeness, the data quality is high enough for the structures to be solved to a high precision. Low-dose electron diffraction tomog. is easy to implement and doesn't require any special equipment or lengthy calibration processes, making it accessible to a large no. of scientists.
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  98. 98
    Yun, Y.; Wan, W.; Rabbani, F.; Su, J.; Xu, H.; Hovmöller, S.; Johnsson, M.; Zou, X. Phase identification and structure determination from multiphase crystalline powder samples by rotation electron diffraction. J. Appl. Crystallogr. 2014, 47, 2048– 2054,  DOI: 10.1107/S1600576714023875
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    Phase identification and structure determination from multiphase crystalline powder samples by rotation electron diffraction
    Yun, Yifeng; Wan, Wei; Rabbani, Faiz; Su, Jie; Xu, Hongyi; Hovmoeller, Sven; Johnsson, Mats; Zou, Xiaodong
    Journal of Applied Crystallography (2014), 47 (6), 2048-2054CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    Phase identification and structure characterization are important in synthetic and materials science. It is difficult to characterize the individual phases from multiphase cryst. powder samples, esp. if some of the phases are unknown. This problem can be solved by combining rotation electron diffraction (RED) and powder X-ray diffraction (PXRD). Four phases were identified on the same transmission electron microscopy grid from a multiphase sample in the Ni-Se-O-Cl system, and their structures were solved from the RED data. Phase 1 (NiSeO3) was found in the Inorg. Crystal Structure Database using the information from RED. Phase 2 (Ni3Se4O10Cl2) is an unknown compd., but it is isostructural to Co3Se4O10Cl2, which was recently solved by single-crystal X-ray diffraction. Phase 3 (Ni5Se6O16Cl4H2) and Phase 4 (Ni5Se4O12Cl2) are new compds. The fact that there are at least four different compds. in the as-synthesized material explains why the phase identification and structure detn. could not be done by PXRD alone. The RED method makes phase identification from such multiphase powder samples much easier than would be the case using powder X-ray diffraction. The RED method also makes structure detn. of submicrometer-sized crystals from multiphase samples possible.
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    Clabbers, M. T. B.; Gruene, T.; Parkhurst, J. M.; Abrahams, J. P.; Waterman, D. G. Electron diffraction data processing with DIALS. Acta Cryst. D 2018, 74, 506– 518,  DOI: 10.1107/S2059798318007726
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    Electron diffraction data processing with DIALS
    Clabbers, Max T. B.; Gruene, Tim; Parkhurst, James M.; Abrahams, Jan Pieter; Waterman, David G.
    Acta Crystallographica, Section D: Structural Biology (2018), 74 (6), 506-518CODEN: ACSDAD; ISSN:2059-7983. (International Union of Crystallography)
    Electron diffraction is a relatively novel alternative to X-ray crystallog. for the structure detn. of macromols. from three-dimensional nanometer-sized crystals. Nevertheless, the DIALS software package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings addnl. challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in exptl. geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are addnl. factors that complicate data processing. Here, recent features of DIALS as adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools in DIALS, make data integration and refinement feasible for electron crystallog., even in difficult cases.
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    Nannenga, B. L.; Shi, D.; Hattne, J.; Reyes, F. E.; Gonen, T. Structure of catalase determined by MicroED. eLife 2014, 3, e03600  DOI: 10.7554/eLife.03600
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    Structure of catalase determined by MicroED
    Nannenga, Brent L.; Shi, Dan; Hattne, Johan; Reyes, Francis E.; Gonen, Tamir
    eLife (2014), 3 (), e03600/1-e03600/11CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)
    MicroED is a recently developed method that uses electron diffraction for structure detn. from very small three-dimensional crystals of biol. material. Previously we used a series of still diffraction patterns to det. the structure of lysozyme at 2.9 Å resoln. with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase detd. from a single crystal at 3.2 Å resoln. by MicroED. The data were collected by continuous rotation of the sample under const. exposure and were processed and refined using std. programs for X-ray crystallog. The ability of MicroED to det. the structure of bovine liver catalase, a protein that has long resisted at. anal. by traditional electron crystallog., demonstrates the potential of this method for structure detn.
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    Palatinus, L.; Petříček, V.; Antunes Corrêa, C. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Crystallogr., Sect. A: Found. Adv. 2015, 71, 235– 244,  DOI: 10.1107/S2053273315001266
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    Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation
    Palatinus, Lukas; Petricek, Vaclav; Correa, Cinthia Antunes
    Acta Crystallographica, Section A: Foundations and Advances (2015), 71 (2), 235-244CODEN: ACSAD7; ISSN:2053-2733. (International Union of Crystallography)
    Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomog., possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallog.: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallog. computing system Jana2006.
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    Palatinus, L.; Corrêa, C. A.; Steciuk, G.; Jacob, D.; Roussel, P.; Boullay, P.; Klemantová, M.; Gemmi, M.; Kopeček, J.; Domeneghetti, M. C.; Cámara, F.; Petříček, V. Structure refinement using precession electron diffraction tomography and dynamical diffraction: Tests on experimental data. Acta Crystallogr., Sect. B: Struct. Sci., Cryst. Eng. Mater. 2015, 71, 740– 751,  DOI: 10.1107/S2052520615017023
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    Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data
    Palatinus, Lukas; Correa, Cinthia Antunes; Steciuk, Gwladys; Jacob, Damien; Roussel, Pascal; Boullay, Philippe; Klementova, Mariana; Gemmi, Mauro; Kopecek, Jaromir; Domeneghetti, M. Chiara; Camara, Fernando; Petricek, Vaclav
    Acta Crystallographica, Section B: Structural Science, Crystal Engineering and Materials (2015), 71 (6), 740-751CODEN: ACSBDA; ISSN:2052-5206. (International Union of Crystallography)
    The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of exptl. data sets from five different samples - Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable ref. structure was available. A large series of tests revealed that the method provides structure models with an av. error in at. positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approxn. for the calcn. of model intensities. The method also allows a reliable detn. of site occupancies and detn. of abs. structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.
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    Hirsch, P.; Howie, A.; Nicholson, R.; Pashley, D.; Whelan, M. Electron microscopy of thin crystals; Robert E. Krieger: Malabar, FL, 1977.
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    Zuo, J. M.; Spence, J. C. H. Automated structure factor refinement from convergent-beam patterns. Ultramicroscopy 1991, 35, 185– 186,  DOI: 10.1016/0304-3991(91)90071-D
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    Automated structure factor refinement from convergent-beam patterns
    Zuo, J. M.; Spence, J. C. H.
    Ultramicroscopy (1991), 35 (3-4), 185-96CODEN: ULTRD6; ISSN:0304-3991.
    An algorithm is described which automatically adjusts values of the low-order structure factors, crystal thickness and absorption coeffs. for the best fit to exptl. convergent-beam electron diffraction (CBED) patterns recorded in the systematics orientation. A fitting index is defined, by analogy with R factors used in neutron diffraction. A comparison of several least-squares optimization routines is made, and the Simplex method is most useful. An anal. of errors, background and noise is presented. The use of perturbation methods for the final 33-beam refinement reduces the computation time from 6 h to 30 min. An example of the use of the program is given. This algorithm may be used to measure and study any of the parameters on which crystal structure factors depend.
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    Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S. Hydrogen positions in single nanocrystals revealed by electron diffraction. Science 2017, 355, 166– 169,  DOI: 10.1126/science.aak9652
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    Hydrogen positions in single nanocrystals revealed by electron diffraction
    Palatinus, L.; Brazda, P.; Boullay, P.; Perez, O.; Klementova, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.
    Science (Washington, DC, United States) (2017), 355 (6321), 166-169CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    The localization of H atoms is an essential part of crystal structure anal., but it is difficult because of their small scattering power. The authors report the direct localization of H atoms in nanocryst. materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomog. data. This method was used to locate H atoms in both an org. (paracetamol) and an inorg. (framework Co aluminophosphate) material. The technique can reliably reveal fine structural details, including the positions of H atoms in single crystals with micro- to nanosized dimensions.
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    Klementová, M.; Karlík, M.; Novák, P.; Palatinus, P. Structure determination of a new phase Ni8Ti5 by electron diffraction tomography. Intermetallics 2017, 85, 110– 116,  DOI: 10.1016/j.intermet.2017.02.003
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    Structure determination of a new phase Ni8Ti5 by electron diffraction tomography
    Klementova, Mariana; Karlik, Miroslav; Novak, Pavel; Palatinus, Lukas
    Intermetallics (2017), 85 (), 110-116CODEN: IERME5; ISSN:0966-9795. (Elsevier Ltd.)
    The structure of Ni8Ti5 was solved and refined from precession electron diffraction tomog. data using dynamical refinement approach. It has trigonal symmetry R-3m (a = 12.24(5) Å, c = 15.33(5) Å) with a structure related to the structure of Ni4Ti3. The greatest challenge of the structure detn. was the assignment of at. types due to the proximity of scattering powers of Ti and Ni. Several approaches to detn. of atom type distribution over at. positions were used; (1) anal. of the Wyckoff position multiplicities, (2) refinement of displacement parameters, and (3) geometrical anal. of the structure and comparison with known structures. These approaches consistently pointed to one distribution, which was confirmed by a significant improvement of the refinement figures of merit.
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  107. 107
    Gonano, B.; Breard, Y.; Pelloquin, D.; Caignaert, V.; Perez, O.; Pautrat, A.; Boullay, P.; Bazin, P.; Le Breton, J. M. Combining multiscale approaches for the structure determination of an iron layered oxysulfate: Sr4Fe2.5O7.25(SO4)0.5. Inorg. Chem. 2017, 56, 15241– 15250,  DOI: 10.1021/acs.inorgchem.7b02572
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    Combining Multiscale Approaches for the Structure Determination of an Iron Layered Oxysulfate: Sr4Fe2.5O7.25(SO4)0.5
    Gonano, Bruno; Breard, Yohann; Pelloquin, Denis; Caignaert, Vincent; Perez, Olivier; Pautrat, Alain; Boullay, Philippe; Bazin, Philippe; Le Breton, Jean-Marie
    Inorganic Chemistry (2017), 56 (24), 15241-15250CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The new Fe layered oxysulfate Sr4Fe2.5O7.25(SO4)0.5 was prepd. by a solid-state reaction in closed ampuls into the form of ceramics and single crystals. Its at. structure was solved by spectroscopy, diffraction techniques, and high-resoln. electron microscopy. Sr4Fe2.5O7.25(SO4)0.5 is a layered structure that derives from the Ruddelsden-Popper (RP) phases with the layer stacking sequence SrO/SrFeO2.5/SrFe0.5(SO4)0.5O1.25/SrFeO2.5. Within the mixed Fe3+/SO42- layer, the S atoms are slightly shifted from the B site of the perovskite and each sulfate group shares 2 corners with Fe pyramids in the basal plan without any order phenomenon. The electronic cond. is thermally activated, while no ionic cond. is detected.
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  108. 108
    Klementová, M.; Motlochová, M.; Boháček, J.; Kupčík, J.; Palatinus, L.; Pližingrová, E.; Szatmáry, L.; Šubrt, J. Metatitanic acid pseudomorphs after titanyl sulfates: nanostructured sorbents and precursors for crystalline titania with desired particle size and shape. Cryst. Growth Des. 2017, 17, 6762– 6769,  DOI: 10.1021/acs.cgd.7b01349
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    Metatitanic Acid Pseudomorphs after Titanyl Sulfates: Nanostructured Sorbents and Precursors for Crystalline Titania with Desired Particle Size and Shape
    Klementova, Mariana; Motlochova, Monika; Bohacek, Jaroslav; Kupcik, Jaroslav; Palatinus, Lukas; Plizingrova, Eva; Szatmary, Lorant; Subrt, Jan
    Crystal Growth & Design (2017), 17 (12), 6762-6769CODEN: CGDEFU; ISSN:1528-7483. (American Chemical Society)
    A new prepn. method for the synthesis of TiO2 microrods in aq. media starting with solid hydrated titanyl sulfate crystals with defined morphol. is presented. The method is based on the extn. of sulfate ions from the crystals and their replacement with hydroxyl groups in aq. ammonia soln. leaving the Ti-O framework intact. The particle size and morphol. of the starting hydrated titanyl sulfate is closely preserved in the pseudomorphs of amorphous metatitanic acid including such details like the layered structure of the original hydrated titanyl sulfate crystals. When annealed ≤1200°, the rod-like morphol. of particles is retained, while the phase compn. changes to anatase/rutile. The rod-like particles of metatitanic acid possess excellent sorption properties towards radionuclides. The mechanism of pseudomorph formation is discussed based on the structures of the precursors, including the hitherto unknown structure of titanyl sulfate dihydrate detd. by electron diffraction tomog.
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  109. 109
    de la Cruz, M. J.; Martynowycz, M. W.; Hattne, J.; Gonen, T. MicroED data collection with SerialEM. Ultramicroscopy 2019, 201, 77– 80,  DOI: 10.1016/j.ultramic.2019.03.009
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    MicroED data collection with SerialEM
    de la Cruz, M. Jason; Martynowycz, Michael W.; Hattne, Johan; Gonen, Tamir
    Ultramicroscopy (2019), 201 (), 77-80CODEN: ULTRD6; ISSN:0304-3991. (Elsevier B.V.)
    The cryoEM method Microcrystal Electron Diffraction (MicroED) involves transmission electron microscope (TEM) and electron detector working in synchrony to collect electron diffraction data by continuous rotation. We previously reported several protein, peptide, and small mol. structures by MicroED using manual control of the microscope and detector to collect data. Here we present a procedure to automate this process using a script developed for the popular open-source software package SerialEM. With this approach, SerialEM coordinates stage rotation, microscope operation, and camera functions for automated continuous-rotation MicroED data collection. Depending on crystal and substrate geometry, more than 300 datasets can be collected overnight in this way, facilitating high-throughput MicroED data collection for large-scale data analyses.
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    Samuha, S.; Mugnaioli, E.; Grushko, B.; Kolb, U.; Meshi, L. Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data. Acta Crystallogr., Sect. B: Struct. Sci., Cryst. Eng. Mater. 2014, 70, 999– 1005,  DOI: 10.1107/S2052520614022033
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    Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data
    Samuha, Shmuel; Mugnaioli, Enrico; Grushko, Benjamin; Kolb, Ute; Meshi, Louisa
    Acta Crystallographica, Section B: Structural Science, Crystal Engineering and Materials (2014), 70 (6), 999-1005CODEN: ACSBDA; ISSN:2052-5206. (International Union of Crystallography)
    The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was detd. using modern direct methods (MDM) applied to automated electron diffraction tomog. (ADT) data. The Al77Rh15Ru8 E-phase is orthorhombic [Pbma, a = 23.40 (5), b = 16.20 (4) and c = 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique at. positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resoln. electron microscopy (HRTEM) images were used for the validation of the proposed at. model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al-Rh-Ru at close compns.
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    Drozhzhin, O. A.; Sumanov, V. D.; Karakulina, O. M.; Abakumov, A. M.; Hadermann, J.; Baranov, A. N.; Stevenson, K. J.; Antipov, E. V. Switching between solid solution and two-phase regimes in the Li1-xFe1-yMnyPO4 cathode materials during lithium (de)insertion: combined PITT, in situ XRPD and electron diffraction tomography study Electrochim. Electrochim. Acta 2016, 191, 149– 157,  DOI: 10.1016/j.electacta.2016.01.018
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    111
    Switching between solid solution and two-phase regimes in the Li1-xFe1-yMnyPO4 cathode materials during lithium (de)insertion: combined PITT, in situ XRPD and electron diffraction tomography study
    Drozhzhin, Oleg A.; Sumanov, Vasiliy D.; Karakulina, Olesia M.; Abakumov, Artem M.; Hadermann, Joke; Baranov, Andrey N.; Stevenson, Keith J.; Antipov, Evgeny V.
    Electrochimica Acta (2016), 191 (), 149-157CODEN: ELCAAV; ISSN:0013-4686. (Elsevier Ltd.)
    The electrochem. properties and phase transformations during (de)insertion of Li+ in LiFePO4, LiFe0.9Mn0.1PO4 and LiFe0.5Mn0.5PO4 were studied by galvanostatic cycling, potential intermittent titrn. technique (PITT) and in situ x-ray powder diffraction. Different modes of switching between the solid soln. and two-phase regimes are revealed which are influenced by the Mn content in Li1-xFe1-yMnyPO4. Addnl., an increase in electrochem. capacity with the Mn content is obsd. at high rates of galvanostatic cycling (10 C, 20 C), which is in good agreement with the numerically estd. contribution of the solid soln. mechanism detd. from PITT data. The obsd. asym. behavior of the phase transformations in Li1-xFe0.5Mn0.5PO4 during charge and discharge is discussed. For the 1st time, the crystal structures of electrochem. deintercalated Li1-xFe0.5Mn0.5PO4 with different Li content - LiFe0.5Mn0.5PO4, Li0.5Fe0.5Mn0.5PO4 and Li0.1Fe0.5Mn0.5PO4 - are refined, including the occupancy factors of the Li position. This refinement is done using electron diffraction tomog. data. The crystallog. analyses of Li1-xFe0.5Mn0.5PO4 reveal that at x = 0.5 and 0.9 the structure retains the Pnma symmetry and the main motif of the pristine x = 0 structure without noticeable short range order effects.
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    Feyand, M.; Mugnaioli, E.; Vermoortele, F.; Bueken, B.; Dieterich, J. M.; Reimer, T.; Kolb, U.; de Vos, D.; Stock, N. Automated diffraction tomography for the structure elucidation of twinned, sub-micrometer crystals of a highly porous, catalytically active bismuth metal–organic framework. Angew. Chem., Int. Ed. 2012, 51, 10373– 10376,  DOI: 10.1002/anie.201204963
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    Automated Diffraction Tomography for the Structure Elucidation of Twinned, Sub-micrometer Crystals of a Highly Porous, Catalytically Active Bismuth-Metal-Organic Framework
    Feyand, Mark; Mugnaioli, Enrico; Vermoortele, Frederik; Bueken, Bart; Dieterich, Johannes M.; Reimer, Tim; Kolb, Ute; de Vos, Dirk; Stock, Norbert
    Angewandte Chemie, International Edition (2012), 51 (41), 10373-10376, S10373/1-S10373/28CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Automated diffraction tomog. for structure elucidation of twinned, sub-micrometer crystals of highly porous, catalytically active bismuth-metal-org. framework is discussed, along with hydroxymethylation of hemicellulose-derived 2-methylfuran to 5-methylfurfuryl alc.
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    Brázda, P.; Palatinus, L.; Drahokoupil, J.; Knížek, K.; Buršík, J. Calcium-induced cation ordering and large resistivity decrease in Pr0.3CoO2. J. Phys. Chem. Solids 2016, 96–97, 10– 16,  DOI: 10.1016/j.jpcs.2016.04.012
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    Calcium-induced cation ordering and large resistivity decrease in Pr0.3CoO2
    Brazda, Petr; Palatinus, Lukas; Drahokoupil, Jan; Knizek, Karel; Bursik, Josef
    Journal of Physics and Chemistry of Solids (2016), 96-97 (), 10-16CODEN: JPCSAW; ISSN:0022-3697. (Elsevier Ltd.)
    Structure of layered cobaltates Pr0.3CoO2 and (PrCa)0.3CoO2 were investigated by electron diffraction tomog. and powder X-ray diffraction. The effect of the calcium substitution on thermoelec. properties was evaluated. The structure consists of hexagonal sheets of edge-sharing CoO6 octahedra interleaved by cationic monolayers. The cations form a 2-dimensional a√3×a√3 superstructure in the a-b plane. While Pr0.3CoO2 showed no layer order in the [001] direction, introduction of calcium resulted in the formation of a superstructure spanning over six cationic layers along the [001]. This superstructure model appears to be valid also for the description of the superstructures of CaxCoO2 and SrxCoO2 with x about 1/3. Thanks to the increased no. of charge carriers, the substitution of Ca2+ for Pr3+ significantly lowers the elec. resistivity, while keeping quite high thermopower around 100 μV K-1, though the character of resistivity remained semiconducting.
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    Neagu, A.; Tai, C.-W. Local disorder in Na0.5Bi0.5TiO3-piezoceramic determined by 3D electron diffuse scattering. Sci. Rep. 2017, 7, 12519,  DOI: 10.1038/s41598-017-12801-w
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    114
    Local disorder in Na0.5Bi0.5TiO3-piezoceramic determined by 3D electron diffuse scattering
    Neagu Alexandra; Tai Cheuk-Wai
    Scientific reports (2017), 7 (1), 12519 ISSN:.
    Local structural distortions in Na0.5Bi0.5TiO3-based solid solutions have been proved to play a crucial role in understanding and tuning their enhanced piezoelectric properties near the morphotropic phase boundary. In this work all local structural disorders in a lead-free ternary system, namely 85%Na0.5Bi0.5TiO3-10%Bi0.5K0.5TiO3-5%BaTiO3, were mapped in reciprocal space by 3D electron diffraction. Furthermore, a comprehensive model of the local disorder was developed by analysing the intensity and morphology of the observed weak diffuse scattering. We found that the studied ceramics consists of plate-like in-phase oxygen octahedral nanoscale domains randomly distributed in an antiphase tilted matrix. In addition, A-site chemical short-range order of Na/Bi and polar displacements contribute to different kinds of diffuse scattering. The proposed model explains all the observed diffraction features and offers insight into the ongoing controversy over the nature of local structural distortions in Na0.5Bi0.5TiO3-based solid solutions.
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    Zhao, H.; Krysiak, Y.; Hoffmann, K.; Barton, B.; Molina-Luna, L.; Neder, R. B.; Kleebe, H.-J.; Gesing, T. M.; Schneider, H.; Fischer, R. X.; Kolb, U. Elucidating structural order and disorder phenomena in mullite-type Al4B2O9 by automated electron diffraction tomography. J. Solid State Chem. 2017, 249, 114– 123,  DOI: 10.1016/j.jssc.2017.02.023
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    115
    Elucidating structural order and disorder phenomena in mullite-type Al4B2O9 by automated electron diffraction tomography
    Zhao, Haishuang; Krysiak, Yasar; Hoffmann, Kristin; Barton, Bastian; Molina-Luna, Leopoldo; Neder, Reinhard B.; Kleebe, Hans-Joachim; Gesing, Thorsten M.; Schneider, Hartmut; Fischer, Reinhard X.; Kolb, Ute
    Journal of Solid State Chemistry (2017), 249 (), 114-123CODEN: JSSCBI; ISSN:0022-4596. (Elsevier B.V.)
    The crystal structure and disorder phenomena of Al4B2O9, an Al borate from the mullite-type family, were studied using automated diffraction tomog. (ADT), a recently established method for collection and anal. of electron diffraction data. Al4B2O9, prepd. by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure detn. based on 3-dimensional electron diffraction data from single ordered crystals reveals that edge-connected AlO6 octahedra expanding along the b axis constitute the backbone. The ordered structure (A) was confirmed by TEM and HAADF-STEM images. Disordered crystals with diffuse scattering along the b axis are obsd. Anal. of the modulation pattern implies a mean superstructure (AAB) with a 3-fold b axis, where B corresponds to an A layer shifted by 0.5a and 0.5c. Diffraction patterns simulated for the AAB sequence including addnl. stacking disorder are in good agreement with exptl. electron diffraction patterns.
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    Willhammar, T.; Sentosun, K.; Mourdikoudis, S.; Goris, B.; Kurttepeli, M.; Bercx, M.; Lamoen, D.; Partoens, B.; Pastoriza-Santos, I.; Pérez-Juste, J.; Liz-Marzán, L. M.; Bals, S.; Van Tendeloo, G. Structure and vacancy distribution in copper telluride nanoparticles influence plasmonic activity in the near-infrared. Nat. Commun. 2017, 8, 14925,  DOI: 10.1038/ncomms14925
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    Structure and vacancy distribution in copper telluride nanoparticles influence plasmonic activity in the near-infrared
    Willhammar, Tom; Sentosun, Kadir; Mourdikoudis, Stefanos; Goris, Bart; Kurttepeli, Mert; Bercx, Marnik; Lamoen, Dirk; Partoens, Bart; Pastoriza-Santos, Isabel; Perez-Juste, Jorge; Liz-Marzan, Luis M.; Bals, Sara; Van Tendeloo, Gustaaf
    Nature Communications (2017), 8 (), 14925CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
    Copper chalcogenides find applications in different domains including photonics, photothermal therapy and photovoltaics. CuTe nanocrystals have been proposed as an alternative to noble metal particles for plasmonics. Although it is known that deviations from stoichiometry are a prerequisite for plasmonic activity in the near-IR, an accurate description of the material and its (optical) properties is hindered by an insufficient understanding of the at. structure and the influence of defects, esp. for materials in their nanocryst. form. We demonstrate that the structure of Cu1.5±xTe nanocrystals can be detd. using electron diffraction tomog. Real-space high-resoln. electron tomog. directly reveals the three-dimensional distribution of vacancies in the structure. Through first-principles d. functional theory, we furthermore demonstrate that the influence of these vacancies on the optical properties of the nanocrystals is detd. Since our methodol. is applicable to a variety of cryst. nanostructured materials, it is expected to provide unique insights concerning structure-property correlations.
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    Baraldi, A.; Buffagni, E.; Capelletti, R.; Mazzera, M.; Fasoli, M.; Lauria, A.; Moretti, F.; Vedda, A.; Gemmi, M. Eu incorporation into sol–gel silica for photonic applications: Spectroscopic and TEM evidences of α-quartz and Eu pyrosilicate nanocrystal growth. J. Phys. Chem. C 2013, 117, 26831– 26848,  DOI: 10.1021/jp4101174
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    117
    Eu Incorporation into Sol-Gel Silica for Photonic Applications: Spectroscopic and TEM Evidences of α-Quartz and Eu Pyrosilicate Nanocrystal Growth
    Baraldi, Andrea; Buffagni, Elisa; Capelletti, Rosanna; Mazzera, Margherita; Fasoli, Mauro; Lauria, Alessandro; Moretti, Federico; Vedda, Anna; Gemmi, Mauro
    Journal of Physical Chemistry C (2013), 117 (50), 26831-26848CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    The problem of Eu incorporation into SiO2 as dispersed dopants, clusters, sep.-phase nanoparticles, or nanocrystals, which is of key importance for applications in the fields of lasers and scintillators, is faced by applying to sol-gel SiO2 doped with 9 different Eu3+ concns. (0.001-10 mol % range) various spectroscopic techniques, including crystal field and vibrational mode anal. by Fourier transform absorption and microreflectivity (in the 200-6000 cm-1 and 9-300 K ranges), radioluminescence, and Raman scattering studies at 300 K. The variety of methods revealed the following concordant results: (1) amorphous Eu clusters grow when the Eu concn. is increased up to 3 mol % and (2) Si-OH groups are completely removed and ordered phase sepn. occurs at 10 mol % doping, as suggested by the remarkable narrowing of the spectral lines. Comparison with polycryst. Eu oxide, Eu silicates, and α-quartz spectra allowed the unequivocal identification of Eu2Si2O7 pyrosilicate and α-quartz as the main components of nanocrystals in 10 mol % Eu-doped SiO2. Such conclusions were brilliantly confirmed by TEM and electron diffraction anal. Phonon coupling and anharmonicity were analyzed and are discussed for a few vibrational modes of nanocrystals.
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    Mayence, A.; Wang, D.; Salaz-Alvarez, G.; Oleynikov, P.; Bergström, L. Probing planar defects in nanoparticle superlattices by 3D small-angle electron diffraction tomography and real space imaging. Nanoscale 2014, 6, 13803– 13808,  DOI: 10.1039/C4NR04156A
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    Probing planar defects in nanoparticle superlattices by 3D small-angle electron diffraction tomography and real space imaging
    Mayence, Arnaud; Wang, Dong; Salazar-Alvarez, German; Oleynikov, Peter; Bergstroem, Lennart
    Nanoscale (2014), 6 (22), 13803-13808CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
    We demonstrate how the acquisition and processing of 3D electron diffraction data can be extended to characterize structural features on the mesoscale, and show how lattice distortions in superlattices of self-assembled spherical Pd nanoparticles can be quantified by three-dimensional small-angle electron diffraction tomog. (3D SA-EDT). Transmission electron microscopy real space imaging and 3D SA-EDT reveal a high d. of stacking faults that was related to a competition between fcc and hcp arrangements during assembly. Information on the orientation of the stacking faults was used to make analogies between planar defects in the superlattices and Shockley partial dislocations in metallic systems.
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    Colmont, M.; Palatinus, L.; Huvé, M.; Kabbour, H.; Saitzek, S.; Djelal, N.; Roussel, P. On the use of dynamical diffraction theory to refine crystal structure from electron diffraction data: Application to KLa5O5(VO4)2, a material with promising luminescent properties. Inorg. Chem. 2016, 55, 2252– 2260,  DOI: 10.1021/acs.inorgchem.5b02663
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    On the Use of Dynamical Diffraction Theory To Refine Crystal Structure from Electron Diffraction Data: Application to KLa5O5(VO4)2, a Material with Promising Luminescent Properties
    Colmont, Marie; Palatinus, Lukas; Huve, Marielle; Kabbour, Houria; Saitzek, Sebastien; Djelal, Nora; Roussel, Pascal
    Inorganic Chemistry (2016), 55 (5), 2252-2260CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    A new lanthanum oxide, KLa5O5(VO4)2, was synthesized using a flux growth technique that involved solid-state reaction under an air atm. at 900 °C. The crystal structure was solved and refined using an innovative approach recently established and based on three-dimensional (3D) electron diffraction data, using precession of the electron beam and then validated against Rietveld refinement and denisty functional theory (DFT) calcns. It crystallizes in a monoclinic unit cell with space group C2/m and has unit cell parameters of a = 20.2282(14) Å, b = 5.8639(4) Å, c = 12.6060(9) Å, and β = 117.64(1)°. Its structure is built on Cresnel-like two-dimensional (2D) units (La5O5) of 4*3 (OLa4) tetrahedra, which run parallel to (001) plane, being surrounded by isolated VO4 tetrahedra. Four isolated vanadate groups create channels that host K+ ions. Substitution of K+ cations by another alkali metal is possible, going from lithium to rubidium. Li substitution led to a similar phase with a primitive monoclinic unit cell. A complementary selected area electron diffraction (SAED) study highlighted diffuse streaks assocd. with stacking faults obsd. on high-resoln. electron microscopy (HREM) images of the lithium compd. Finally, preliminary catalytic tests for ethanol oxidn. are reported, as well as luminescence evidence. This paper also describes how solid-state chemists can take advantages of recent progresses in electron crystallog., assisted by DFT calcns. and powder X-ray diffraction (PXRD) refinements, to propose new structural types with potential applications to the physicist community.
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    Lepoittevin, C. Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr5Fe6O15.4. J. J. Solid State Chem. 2016, 242, 228– 235,  DOI: 10.1016/j.jssc.2016.08.004
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    Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr5Fe6O15.4
    Lepoittevin, Christophe
    Journal of Solid State Chemistry (2016), 242 (Part_1), 228-235CODEN: JSSCBI; ISSN:0022-4596. (Elsevier B.V.)
    The crystal structure of the strontium ferrite Sr5Fe6O15.4, was solved by direct methods on electron diffraction tomog. data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern.
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  121. 121
    Rickert, K.; Boullay, P.; Malo, S.; Caignaert, V.; Poeppelmeier, K. R. A rutile chevron modulation in delafossite-like Ga3-xIn3TixO9-x/2. Inorg. Chem. 2016, 55, 4403– 4409,  DOI: 10.1021/acs.inorgchem.6b00147
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    121
    A Rutile Chevron Modulation in Delafossite-Like Ga3-xIn3TixO9+x/2
    Rickert, Karl; Boullay, Philippe; Malo, Sylvie; Caignaert, Vincent; Poeppelmeier, Kenneth R.
    Inorganic Chemistry (2016), 55 (9), 4403-4409CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The structure soln. of the modulated, delafossite-related, orthorhombic Ga3-xIn3TixO9+x/2 for x = 1.5 is reported here in conjunction with a model describing the modulation as a function of x for the entire system. Previously reported structures in the related A3-xIn3TixO9+x/2 (A = Al, Cr, or Fe) systems use X-ray diffraction to det. that the anion lattice is the source of modulation. Neutron diffraction, with its enhanced sensitivity to light atoms, offers a route to solving the modulation and is used here, in combination with precession electron diffraction tomog. (PEDT), to solve the structure of Ga1.5In3Ti1.5O9.75. We construct a model that describes the anion modulation through the formation of rutile chevrons as a function of x. This model accommodates the orthorhombic phase (1.5 ≤ x ≤ 2.1) in the Ga3-xIn3TixO9+x/2 system, which transitions to a biphasic mixt. (2.2 ≤ x ≤ 2.3) with a monoclinic, delafossite-related phase (2.4 ≤ x ≤ 2.5). The optical band gaps of this system are detd., and are stable at ∼3.4 eV before a ∼0.4 eV decrease between x = 1.9 and 2.0. After this decrease, stability resumes at ∼3.0 eV. Resistance to oxidn. and redn. is also presented.
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  122. 122
    Steciuk, G.; Boullay, P.; Pautrat, A.; Barrier, N.; Caignaert, V.; Palatinus, L. Unusual relaxor ferroelectric behavior in stairlike aurivillius phases. Inorg. Chem. 2016, 55, 8881– 8891,  DOI: 10.1021/acs.inorgchem.6b01373
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    122
    Unusual Relaxor Ferroelectric Behavior in Stairlike Aurivillius Phases
    Steciuk, Gwladys; Boullay, Philippe; Pautrat, Alain; Barrier, Nicolas; Caignaert, Vincent; Palatinus, Lukas
    Inorganic Chemistry (2016), 55 (17), 8881-8891CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    New ferroelec. layered materials were found in the pseudobinary system Bi5Nb3O15-ABi2Nb2O9 (A= Ba, Sr and Pb). Preliminary observations made by transmission electron microscopy indicate that these compds. exhibit a complex incommensurately modulated structure. A (3 + 1)D structural model is obtained using ab initio phasing by charge flipping based on the anal. of precession electron diffraction tomog. data. The (3 + 1)D structure is further validated by a refinement against neutron powder diffraction. These materials possess a layered structure with discontinuous [Bi2O2] slabs and perovskite blocks. While these structural units are characteristics of Aurivillius phases, the existence of periodic crystallog. shear planes offers strong similarities with collapsed or stairlike structures known in high-Tc superconductors and related compds. Using dielec. spectroscopy, the phase transitions of these new layered materials is studied. For A = Ba and Sr, a V.ovrddot.ogel-Fulcher-like behavior characteristic of the so-called relaxor ferroelecs. is obsd. and compared to "canonical" relaxors. For A = Sr, the absence of a Burns temp. sepd. from the freezing temp. appears as a rather unusual behavior.
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  123. 123
    David, J.; Rossella, F.; Rocci, M.; Ercolani, D.; Sorba, L.; Beltram, F.; Gemmi, M.; Roddaro, S. Crystal phases in hybrid metal–semiconductor nanowire devices. Nano Lett. 2017, 17, 2336– 2341,  DOI: 10.1021/acs.nanolett.6b05223
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    123
    Crystal Phases in Hybrid Metal-Semiconductor Nanowire Devices
    David, J.; Rossella, F.; Rocci, M.; Ercolani, D.; Sorba, L.; Beltram, F.; Gemmi, M.; Roddaro, S.
    Nano Letters (2017), 17 (4), 2336-2341CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    The authors study the metallic phases obsd. in hybrid metal-GaAs nanowire devices obtained by controlled thermal annealing of Ni/Au electrodes. Devices are fabricated onto a SiN membrane compatible with TEM studies. Energy dispersive x-ray spectroscopy allows the authors to show that the nanowire body includes two Ni-rich phases that thanks to an innovative use of electron diffraction tomog. can be unambiguously identified as Ni3GaAs and Ni5As2 crystals. The mechanisms of Ni incorporation leading to the obsd. phenomenol. are discussed.
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  124. 124
    Mugnaioli, E.; Gemmi, M.; Merlini, M.; Gregorkiewitz, M. (Na,)5[MnO2]13 nanorods: a new tunnel structure for electrode materials determined ab initio and refined through a combination of electron and synchrotron diffraction data. Acta Crystallogr., Sect. B: Struct. Sci., Cryst. Eng. Mater. 2016, 72, 893– 903,  DOI: 10.1107/S2052520616015651
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    124
    (Na,.box.)5[MnO2]13 nanorods: a new tunnel structure for electrode materials determined ab initio and refined through a combination of electron and synchrotron diffraction data
    Mugnaioli, Enrico; Gemmi, Mauro; Merlini, Marco; Gregorkiewitz, Michele
    Acta Crystallographica, Section B: Structural Science, Crystal Engineering and Materials (2016), 72 (6), 893-903CODEN: ACSBDA; ISSN:2052-5206. (International Union of Crystallography)
    (Nax.box.1 - x)5[MnO2]13 has been synthesized with x = 0.80 (4), corresponding to Na0.31[MnO2]. This well known material is usually cited as Na0.4[MnO2] and is believed to have a romanechite-like framework. Here, its true structure is detd., ab initio, by single-crystal electron diffraction tomog. (EDT) and refined both by EDT data applying dynamical scattering theory and by the Rietveld method based on synchrotron powder diffraction data (χ2 = 0.690, Rwp = 0.051, Rp = 0.037, RF2 = 0.035). The unit cell is monoclinic C2/m, a = 22.5199 (6), b = 2.83987 (6), c = 14.8815 (4) Å, β = 105.0925 (16)°, V = 918.90 (4) Å3, Z = 2. A hitherto unknown [MnO2] framework is found, which is mainly based on edge- and corner-sharing octahedra and comprises three types of tunnels: per unit cell, two are defined by S-shaped 10-rings, four by egg-shaped 8-rings, and two by slightly oval 6-rings of Mn polyhedra. Na occupies all tunnels. The so-detd. structure excellently explains previous reports on the electrochem. of (Na,.box.)5[MnO2]13. The trivalent Mn3+ ions conc. at two of the seven Mn sites where larger Mn-O distances and Jahn-Teller distortion are obsd. One of the Mn3+ sites is five-coordinated in a square pyramid which, on oxidn. to Mn4+, may easily undergo topotactic transformation to an octahedron suggesting a possible pathway for the transition among different tunnel structures.
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  125. 125
    Rotella, H.; Copie, O.; Steciuk, G.; Ouerdane, H.; Boullay, P.; Roussel, P.; Morales, M.; David, A.; Pautrat, A.; Mercey, B.; Lutterotti, L.; Chateigner, D.; Prellier, W. Structural analysis of strained LaVO3 thin films. J. Phys.: Condens. Matter 2015, 27, 175001,  DOI: 10.1088/0953-8984/27/17/175001
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    125
    Structural analysis of strained LaVO3 thin films
    Rotella H; Copie O; Steciuk G; Ouerdane H; Boullay P; Roussel P; Morales M; David A; Pautrat A; Mercey B; Lutterotti L; Chateigner D; Prellier W
    Journal of physics. Condensed matter : an Institute of Physics journal (2015), 27 (17), 175001 ISSN:.
    While structure refinement is routinely achieved for simple bulk materials, the accurate structural determination still poses challenges for thin films due on the one hand to the small amount of material deposited on the thicker substrate and, on the other hand, to the intricate epitaxial relationships that substantially complicate standard x-ray diffraction analysis. Using both electron and x-ray diffraction, we analyze the crystal structure of epitaxial LaVO3 thin films grown on (1 0 0)-oriented SrTiO3. Transmission electron microscopy study reveals that the thin films are epitaxially grown on SrTiO3 and points to the presence of 90° oriented domains. The mapping of the reciprocal space obtained by high resolution x-ray diffraction permits refinement of the lattice parameters. We finally deduce that strain accommodation imposes a monoclinic structure onto the LaVO3 film. The reciprocal space maps are numerically processed and the extracted data computed to refine the atomic positions, which are compared to those obtained using precession electron diffraction tomography.
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  126. 126
    Bhat, S.; Wiehl, L.; Molina-Luna, L.; Mugnaioli, E.; Lauterbach, S.; Sicolo, S.; Kroll, P.; Duerrschnabel, M.; Nishiyama, N.; Kolb, U.; Albe, K.; Kleebe, H.-J.; Riedel, R. High-pressure synthesis of novel boron oxynitride B6N4O3 with sphalerite type structure. Chem. Mater. 2015, 27, 5907– 5914,  DOI: 10.1021/acs.chemmater.5b01706
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    126
    High-Pressure Synthesis of Novel Boron Oxynitride B6N4O3 with Sphalerite Type Structure
    Bhat, Shrikant; Wiehl, Leonore; Molina-Luna, Leopoldo; Mugnaioli, Enrico; Lauterbach, Stefan; Sicolo, Sabrina; Kroll, Peter; Duerrschnabel, Michael; Nishiyama, Norimasa; Kolb, Ute; Albe, Karsten; Kleebe, Hans-Joachim; Riedel, Ralf
    Chemistry of Materials (2015), 27 (17), 5907-5914CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
    A novel cryst. B oxynitride (BON) phase was synthesized under static pressures exceeding 15 GPa and temps. >1900°, from molar mixts. of B2O3 and h-BN. The structure and compn. of the synthesized product were studied using high-resoln. TEM, electron diffraction, automated diffraction tomog., energy dispersive x-ray spectroscopy and EELS. BON shows a hexagonal cell (space group R3m, Z = 3) with a 2.55(5) and c 6.37(13) Å, and a crystal structure closely related to the cubic sphalerite type. The EELS quantification yielded 42 at.% B, 35 at % N, and 23 at % O (B:N:O ≈ 6:4:3). Electronic structure calcns. in the framework of D. Functional Theory were performed to assess the stabilities and properties of selected models B6N4O3. These models contain ordered structural vacancies and are superstructures of the sphalerite structure. The calcd. bulk moduli of the structure models with the lowest formation enthalpies are ∼300 GPa, higher than for any other known oxynitride.
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  127. 127
    Lepoittevin, C.; Jeanneau, J.; Toulemonde, P.; Sulpice, A.; Núñez-Regueiro, M. Ba19Cr12O45: A high pressure chromate with an original structure solved by electron diffraction tomography and powder X-ray diffraction. Inorg. Chem. 2017, 56, 6404– 6409,  DOI: 10.1021/acs.inorgchem.7b00481
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    127
    Ba19Cr12O45: A High Pressure Chromate with an Original Structure Solved by Electron Diffraction Tomography and Powder X-ray Diffraction
    Lepoittevin, Christophe; Jeanneau, Justin; Toulemonde, Pierre; Sulpice, Andre; Nunez-Regueiro, Manuel
    Inorganic Chemistry (2017), 56 (11), 6404-6409CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The discovery of a Ba-based chromate obtained by high pressure-high temp. treatment of the low pressure orthorhombic Ba2CrO4 phase is reported. By combining TEM and powder x-ray diffraction measurements, its crystallog. structure was detd. This new Cr-oxide has a cubic lattice with a 13.3106(6) built from a 3-dimensional network of 2 Cr sites, Cr1 and Cr2, both in octahedral environments, with face sharing between Cr1 and Cr2 octahedra and corner-sharing between 2 Cr1 octahedra. The resulting chem. compn. Ba19Cr12O45 and bond valence sum anal. suggest a possible charge disproportion between Cr4+ in the Cr1 site and Cr5+ in the Cr2 site. Anal. of magnetization measurements indicates antiferromagnetic correlations between Cr cations and also points toward a probable charge disproportion between Cr sites.
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  128. 128
    Andrusenko, I.; Mugnaioli, E.; Gorelik, T. E.; Koll, D.; Panthöfer, M.; Tremel, W.; Kolb, U. Structure analysis of titanate nanorods by automated electron diffraction tomography. Acta Crystallogr., Sect. B: Struct. Sci. 2011, 67, 218– 225,  DOI: 10.1107/S0108768111014534
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    128
    Structure analysis of titanate nanorods by automated electron diffraction tomography
    Andrusenko, Iryna; Mugnaioli, Enrico; Gorelik, Tatiana E.; Koll, Dominik; Panthoefer, Martin; Tremel, Wolfgang; Kolb, Ute
    Acta Crystallographica, Section B: Structural Science (2011), 67 (3), 218-225CODEN: ASBSDK; ISSN:0108-7681. (International Union of Crystallography)
    A hitherto unknown phase of sodium titanate, NaTi3O6(OH)·2H2O, was identified as the intermediate species in the synthesis of TiO2 nanorods. This new phase, prepd. as nanorods, was investigated by electron diffraction, X-ray powder diffraction, thermogravimetric anal. and high-resoln. transmission electron microscopy. The structure was detd. ab initio using electron diffraction data collected by the recently developed automated diffraction tomog. technique. NaTi3O6(OH)·2H2O crystallizes in the monoclinic space group C2/m. Corrugated layers of corner- and edge-sharing distorted TiO6 octahedra are intercalated with Na+ and water of crystn. The nanorods are typically affected by pervasive defects, such as mutual layer shifts, that produce diffraction streaks along c*. In addn., edge dislocations were obsd. in HRTEM images.
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  129. 129
    Weber, D.; Huber, M.; Gorelik, T. E.; Abakumov, A. M.; Becker, N.; Niehaus, O.; Schwickert, C.; Culver, S. P.; Boysen, H.; Senyshyn, A.; Pöttgen, R.; Dronskowski, R.; Ressler, T.; Kolb, U.; Lerch, M. Molybdenum oxide nitrides of the Mo2(O,N,□)5 type: On the way to Mo2O5. Inorg. Chem. 2017, 56, 8782– 8792,  DOI: 10.1021/acs.inorgchem.7b00551
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    129
    Molybdenum Oxide Nitrides of the Mo2(O,N,.box.)5 Type: On the Way to Mo2O5
    Weber, Dominik; Huber, Manop; Gorelik, Tatiana E.; Abakumov, Artem M.; Becker, Nils; Niehaus, Oliver; Schwickert, Christian; Culver, Sean P.; Boysen, Hans; Senyshyn, Anatoliy; Poettgen, Rainer; Dronskowski, Richard; Ressler, Thorsten; Kolb, Ute; Lerch, Martin
    Inorganic Chemistry (2017), 56 (15), 8782-8792CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    Blue-colored Mo oxide nitrides of the Mo2(O,N,.box.)5 type were synthesized by direct nitridation of com. available MoO3 with a mixt. of gaseous NH3 and O. Chem. compn., crystal structure, and stability of the obtained and hitherto unknown compds. are studied extensively. The av. oxidn. state of +5 for Mo is proven by Mo K near-edge x-ray absorption spectroscopy, the magnetic behavior is in agreement with compds. exhibiting MoVO6 units. The new materials are stable up to ∼773 K in an inert gas atm. At higher temps., decompn. is obsd. X-ray and neutron powder diffraction, electron diffraction and high resoln. TEM reveal the structure to be related to VNb9O24.9-type phases, however, with severe disorder hampering full structure detn. Still, the results demonstrate the possibility of a future synthesis of the potential binary oxide Mo2O5. Based on these findings, a tentative suggestion on the crystal structure of the potential compd. Mo2O5, backed by electronic-structure and phonon calcns. from 1st-principles, is given.
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  130. 130
    Gemmi, M.; Campostrini, I.; Demartin, F.; Gorelik, T. E.; Gramaccioli, C. M. Structure of the new mineral sarrabusite, Pb5CuCl4(SeO3)4, solved by manual electron-diffraction tomography. Acta Crystallogr., Sect. B: Struct. Sci. 2012, 68, 15– 23,  DOI: 10.1107/S010876811104688X
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    130
    Structure of the new mineral sarrabusite, Pb5CuCl4(SeO3)4, solved by manual electron-diffraction tomography
    Gemmi, Mauro; Campostrini, Italo; Demartin, Francesco; Gorelik, Tatiana E.; Gramaccioli, Carlo Maria
    Acta Crystallographica, Section B: Structural Science (2012), 68 (1), 15-23CODEN: ASBSDK; ISSN:0108-7681. (International Union of Crystallography)
    The crystal structure of the new mineral sarrabusite Pb5CuCl4(SeO3)4 was solved using a manual and an automated version of the new electron-diffraction tomog. technique combined with the precession of the electron beam. The new mineral sarrabusite Pb5CuCl4(SeO3)4 was discovered in the Sardinian mine of Baccu Locci, near Villaputzu. It occurs as small lemon-yellow spherical aggregates of tabular crystals (< 10 μm) of <100 μm in diam. The crystal structure was solved from and refined against electron diffraction of a microcrystal. Data sets were measured by both a manual and an automated version of the new electron-diffraction tomog. technique combined with the precession of the electron beam. The sarrabusite structure is monoclinic and consists of (010) layers of straight chains formed by alternating edge-sharing CuO4Cl2 and PbO8 polyhedra parallel to the c axis, which share corners laterally with two zigzag corner-sharing chains of PbO6Cl2 and PbO4Cl4 bicapped trigonal prisms. These blocks are linked together by SeO flat-pyramidal groups.
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  131. 131
    Plášil, J.; Palatinus, L.; Rohlíček, J.; Houdková, L.; Klementová, M.; Goliáš, V.; Škácha, P. Crystal structure of lead uranyl carbonate mineral widenmannite: Precession electron-diffraction and synchrotron powder-diffraction study. Am. Mineral. 2014, 99, 276– 282,  DOI: 10.2138/am.2014.4671
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    131
    Crystal structure of lead uranyl carbonate mineral widenmannite: precession electron-diffraction and synchrotron powder-diffraction study
    Plasil, Jakub; Palatinus, Lukas; Rohlicek, Jan; Houdkova, Lenka; Klementova, Mariana; Golias, Viktor; Skacha, Pavel
    American Mineralogist (2014), 99 (2-3), 276-282CODEN: AMMIAY; ISSN:0003-004X. (Mineralogical Society of America)
    The crystal structure of the lead uranyl-carbonate mineral widenmannite has been solved from precession electron-diffraction data and refined using both electron-diffraction data and synchrotron powder-diffraction data. Widenmannite is orthorhombic, Pmmn, with a = 4.9744(9), b = 9.3816(16), c = 8.9539(15) Å, and V = 417.86(12) Å3. The structure was solved by charge-flipping and refined to an R1 = 0.1911 on the basis of 301 unique, obsd. reflections from electron diffraction data, and to Rp of 0.0253 and RF of 0.0164 from X-ray powder data. The idealized structure formula of widenmannite is Pb2(OH)2[(UO2)(CO3)2], Z = 2. However, both data sets suggest that the widenmmanite structure is not that simple. There are two sym. independent, partly occupied U sites. The substitution mechanism can be written as U(1)O2 + Pb(OH)2 ↔ U(2)O2. When the U(2) site is occupied, the U(1)O2 group is absent, the two OH groups are substituted by O2- and one Pb2+-vacancy. The chem. formula of the real structure should be written as Pb2-x(OH)2-2x[(UO2)(CO3)2], where x is the probability of the substitution U(2) → U(1). The probability of occurrence of U(2) refines to x = 0.074(15) from the powder-diffraction data and to x = 0.176(4) from the electron-diffraction data. There is one Pb site (nearly fully occupied), which is coordinated by 11 anions (up to the distance of 3.5 Å), including O and OH-. The shorter Pb-O bonds form a sheet structure, which is linked by the weaker bonds to the uranyl-carbonate chains to form a three-dimensional framework structure.
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  132. 132
    Majzlan, J.; Palatinus, L.; Plášil, J. Crystal structure of Fe2(AsO4)(HAsO4)(OH)(H2O)3, a dehydration product of kaňkite. Eur. J. Mineral. 2016, 28, 63– 70,  DOI: 10.1127/ejm/2015/0027-2495
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    132
    Crystal structure of Fe2(AsO4)(HAsO4)(OH)(H2O)3, a dehydration product of kankite
    Majzlan, Juraj; Palatinus, Lukas; Plasil, Jakub
    European Journal of Mineralogy (2016), 28 (1), 63-70CODEN: EJMIER; ISSN:0935-1221. (E. SchweizerbartÏsche Verlagsbuchhandlung)
    We report the crystal structure of a dehydration product of the mineral kankite (FeAsO4 · 3.5H2O). The structure was solved and refined by precession electron diffraction tomog. Initially, we believed that we solved the structure of kankite; this mineral, however, decomps. in vacuum to Fe2(AsO4)(HAsO4)(OH)(H2O)3 ( = FeAsO4 · 2H2O). The crystal structure was solved in the space group Cc and the model was refined by the full-matrix least-squares method by Jana2006. The model converged to R(obs) = 12.02%,wR(obs) = 12.49% (with GOF = 6.39) for 1139 obsd. reflections with [Iobs > 3σ (I)]. The structure of the dehydration product of kankite consists of corrugated heteropolyhedral sheets. Pairs of Feφ6 octahedra, flanked by five adjacent arsenate tetrahedra, could be seen as the building units of the corrugated sheets. Variable-temp. powder X-ray diffraction showed that kankite dehydrates to FeAsO4 · 2H2O at 55-56°C. Based on the similar topol. of FeAsO4 · 2H2O and the mineral lausenite [Fe2(SO4)3 · 5H2O], and the structural relationship between lausenite and kornelite [Fe2(SO4)3 · 7.5H2O], we conjecture that the structure of kankite could be also built by corrugated sheets. One polyhedral linkage between an Feφ6 octahedron and an Asφ4 tetrahedron in the sheet of the dehydrated kankite needs to be broken to allow for stretching of the sheets, the introduction of an addnl. H2O mol. into the sheet and perhaps also addnl. H2O mols. in between the sheets.
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    Colombo, F.; Mugnaioli, E.; Vallcorba, O.; Garcia, A.; Goñi, A. R.; Rius, J. Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography. Mineral. Mag. 2017, 81, 1191– 1202,  DOI: 10.1180/minmag.2016.080.159
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    Capitani, G. C.; Mugnaioli, E.; Rius, J.; Gentile, P.; Catelani, T.; Lucotti, A.; Kolb, U. The Bi sulfates from the Alfenza Mine, Crodo, Italy: An automatic electron diffraction tomography (ADT) study. Am. Mineral. 2014, 99, 500– 510,  DOI: 10.2138/am.2014.4446
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    Mugnaioli, E.; Reyes-Gasga, J.; Kolb, U.; Hemmerlé, J.; Brès, É. F. Evidence of noncentrosymmetry of human tooth hydroxyapatite crystals. Chem. - Eur. J. 2014, 20, 6849– 6852,  DOI: 10.1002/chem.201402275
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    Evidence of Noncentrosymmetry of Human Tooth Hydroxyapatite Crystals
    Mugnaioli, Enrico; Reyes-Gasga, Jose; Kolb, Ute; Hemmerle, Joseph; Bres, Etienne F.
    Chemistry - A European Journal (2014), 20 (23), 6849-6852CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Herein, we investigate human single hydroxyapatite crystals (enamel and dentin) by convergent-beam electron diffraction (CBED) and automated electron-diffraction tomog. (ADT). The CBED pattern shows the absence of the mirror plane perpendicular to the c axis leading to the P63 space group instead of the P63/m space group considered for larger-scale crystals, this is confirmed by ADT. This exptl. evidence is of prime importance for understanding the morphogenesis and the architectural organization of calcified tissues.
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  136. 136
    Capitani, G. C.; Mugnaioli, E.; Guastoni, A. What is the actual structure of samarskite-(Y)? A TEM investigation of metamict samarskite from the Garnet Codera dike pegmatite (Central Italian Alps). Am. Mineral. 2016, 101, 1679– 1690,  DOI: 10.2138/am-2016-5605
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  137. 137
    Mugnaioli, E.; Andrusenko, I.; Schüler, T.; Loges, N.; Dinnebier, R. E.; Panthöfer, M.; Tremel, W.; Kolb, U. Ab initio structure determination of vaterite by automated electron diffraction. Angew. Chem., Int. Ed. 2012, 51, 7041– 7045,  DOI: 10.1002/anie.201200845
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    137
    Ab Initio Structure Determination of Vaterite by Automated Electron Diffraction
    Mugnaioli, Enrico; Andrusenko, Iryna; Schueler, Timo; Loges, Niklas; Dinnebier, Robert E.; Panthoefer, Martin; Tremel, Wolfgang; Kolb, Ute
    Angewandte Chemie, International Edition (2012), 51 (28), 7041-7045, S7041/1-S7041/35CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The power of the ADT (automated diffraction tomog.) approach was revealed by unveiling the structure of vaterite, the least stable anhyd. polymorph of CaCO3, which has eluded structure detn. for almost 100 years. For the ADT/PED investigation two samples of synthetic vaterite, prepd. by different routes, were analyzed. The first sample, prepd. by mixing aq. solns. of Ca(NO3)2 and Na2CO3 mainly consisted of spherical aggregates of vaterite NCs with diams. of over 1 μm and several micrometer sized crystals of calcite. The structure of vaterite was solved from ED data obtained by ADT from single crystals with a size not larger than 50 nm. The ADT structure model can explain the Raman spectra and all other exptl. findings for vaterite. Aside from the av. structure, an anal. of the 3D scattering vol. revealed a structural modulation. Intensities extd. based on this modulation were used to det. the modulated superstructure ab initio. Taking into account the inherent and not fully resolved drawback of dynamic scattering, electron-diffraction tomog. showed its great potential for studying the structure of nanomaterials that elude conventional methods because of a small crystal size, low purity, structural complexity, or low availability.
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  138. 138
    Pignatelli, I.; Marrocchi, Y.; Mugnaioli, E.; Bourdelle, F.; Gounelle, M. Mineralogical, crystallographic and redox features of the earliest stages of fluid alteration in CM chondrites. Geochim. Cosmochim. Acta 2017, 209, 106– 122,  DOI: 10.1016/j.gca.2017.04.017
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    138
    Mineralogical, crystallographic and redox features of the earliest stages of fluid alteration in CM chondrites
    Pignatelli, Isabella; Marrocchi, Yves; Mugnaioli, Enrico; Bourdelle, Franck; Gounelle, Matthieu
    Geochimica et Cosmochimica Acta (2017), 209 (), 106-122CODEN: GCACAK; ISSN:0016-7037. (Elsevier Ltd.)
    The CM chondrites represent the largest group of hydrated meteorites and span a wide range of conditions, from less altered (i.e., CM2) down to heavily altered (i.e., CM1). The Paris chondrite is considered the least altered CM and thus enables the earliest stages of aq. alteration processes to be deciphered. Here, we report results from a nanoscale study of tochilinite/cronstedtite intergrowths (TCIs) in Paris-TCIs being the emblematic secondary mineral assemblages of CM chondrites, formed from the alteration of Fe-Ni metal beads (type-I TCIs) and anhyd. silicates (type-II TCIs). We combined high-resoln. transmission electron microscopy, scanning transmission X-ray microscopy and electron diffraction tomog. to characterize the crystal structure, crystal chem. and redox state of TCIs. The data obtained are useful to reconstruct the alteration conditions of Paris and to compare them with those of other meteorites. Our results show that tochilinite in Paris is characterized by a high hydroxide layer content (n = 2.1-2.2) regardless of the silicate precursors. When examd. alongside other CMs, it appears that the hydroxide layer and iron contents of tochilinites correlate with the degree of alteration experienced by the chondrites. The Fe3+/ΣFe ratios of TCIs are high: 8-15% in tochilinite, 33-60% in cronstedtite and 70-80% in hydroxides. These observations suggest that alteration of CM chondrites took place under oxidizing conditions that could have been induced by significant H2 release during serpentinization. Similar results were recently reported in CR chondrites (Le Guillou et al., 2015), suggesting that the process(es) controlling the redox state of the secondary mineral assemblages were quite similar in the CM and CR parent bodies despite the different alteration conditions. According to our mineralogical and crystallog. survey, the formation of TCIs in Paris occurred at temps. lower than 100 °C, under neutral, slightly alk. conditions that favored the formation of both tochilinite and cronstedtite. During the course of alteration, the redn. in sulfur activity and/or the decrease of temp. prevented tochilinite crystn. and favored the formation of cronstedtite and iron hydroxides. We suggest that iron hydroxides probably formed as ferrihydrite and then progressively converted to goethite between 50° and 80 °C, a temp. range that is also favorable for cronstedtite formation. The presence of cronstedtite plays a key role in the reconstruction of the alteration history, demonstrating that the alteration of Paris took place by way of serpentinization processes similar to those described on the Earth.
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  139. 139
    Viti, C.; Brogi, A.; Liotta, D.; Mugnaioli, E.; Spiess, R.; Dini, A.; Zucchi, M.; Vannuccini, G. Seismic slip recorded in tourmaline fault mirrors from Elba Island (Italy). J. Struct. Geol. 2016, 86, 1– 12,  DOI: 10.1016/j.jsg.2016.02.013
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  140. 140
    Gemmi, M.; Fischer, J.; Merlini, M.; Poli, S.; Fumagalli, P.; Mugnaioli, E.; Kolb, U. A new hydrous Al-bearing pyroxene as a water carrier in subduction zones. Earth Planet. Sci. Lett. 2011, 310, 422– 428,  DOI: 10.1016/j.epsl.2011.08.019
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    140
    A new hydrous Al-bearing pyroxene as a water carrier in subduction zones
    Gemmi, Mauro; Fischer, Johannes; Merlini, Marco; Poli, Stefano; Fumagalli, Patrizia; Mugnaioli, Enrico; Kolb, Ute
    Earth and Planetary Science Letters (2011), 310 (3-4), 422-428CODEN: EPSLA2; ISSN:0012-821X. (Elsevier B.V.)
    A new Hydrous Al-bearing PYroxene (HAPY) phase has been synthesized at 5.4 GPa, 720° in the MgO-Al2O3-SiO2-H2O model system. It has the compn. Mg2.1Al0.9(OH)2Al0.9Si1.1O6, a C-centered monoclinic cell with a = 9.8827(2), b = 11.6254(2) c = 5.0828(1) Å, and β = 111.07(1)°. The calcd. d. is 3.175 g/cm3 and the water content is 6.9% H2O by wt. Its structure has been solved in space group C2/c by the recently developed automated electron diffraction tomog. method and refined by synchrotron X-ray powder diffraction. HAPY is a single chain inosilicate very similar to pyroxenes but with three instead of two cations in the octahedral layer, bonded to four oxygens and two hydroxyl groups. The Si tetrahedra are half occupied by Al and cation ordering appears in the octahedral layer with two sites occupied by Mg and one by Al. The stability of such previously unknown hydrous silicate beyond the chlorite pressure breakdown may significantly promote the H2O transport in the subduction channel to depths exceeding 150 km.
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  141. 141
    Pignatelli, I.; Mugnaioli, E.; Hybler, J.; Mosser-Ruck, R.; Cathelineau, M.; Michau, N. A multi-technique characterization of cronstedtite synthesized by iron-clay interaction in a step-by-step cooling procedure. Clays Clay Miner. 2013, 61, 277– 289,  DOI: 10.1346/CCMN.2013.0610408
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    141
    A multi-technique characterization of cronstedtite synthesized by iron-clay interaction in a step-by-step cooling procedure
    Pignatelli, I.; Mugnaioli, E.; Hybler, J.; Mosser-Ruck, R.; Cathelineau, M.; Michau, N.
    Clays and Clay Minerals (2013), 61 (3-4), 277-289CODEN: CLCMAB; ISSN:0009-8604. (Clay Minerals Society)
    The cooling of steel containers in radioactive-waste storage was simulated in a step-by-step expt. from 90 to 40°C. Among newly formed clay minerals obsd. in run products, cronstedtite was identified by a no. of anal. techniques (powder X-ray diffraction, transmission electron microscopy, and SEM). Cronstedtite has not previously been recognized to be so abundant and so well crystd. in an iron-clay interaction expt. The supersatn. of exptl. solns. with respect to cronstedtite was due to the availability of Fe and Si in soln., as a result of the dissoln. of iron metal powder, quartz, and minor amts. of other silicates. Cronstedtite crystals are characterized by various morphologies: pyramidal (truncated or not) with a triangular base and conical with a rounded or hexagonal cross-section. The pyramidal crystals occur more frequently and their polytypes (2M1, 1M, 3T) were identified by selected area electron diffraction patterns and by automated diffraction tomog. Cronstedtite is stable within the 90-60°C temp. range. At temps. of ≤ 50°C, the cronstedite crystals showed evidence of alteration.
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  142. 142
    Koch-Müller, M.; Mugnaioli, E.; Rhede, D.; Speziale, S.; Kolb, U.; Wirth, R. Synthesis of a quenchable high-pressure form of magnetite (h-Fe3O4) with composition Fe1(Fe2+0.75Mg0.26)Fe2(Fe3+0.70Cr0.15Al0.11Si0.04)2O4. Am. Mineral. 2014, 99, 2405– 2415,  DOI: 10.2138/am-2014-4944
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    Willhammar, T.; Burton, A. W.; Yun, Y.; Sun, J.; Afeworki, M.; Strohmaier, K. G.; Vroman, H.; Zou, X. EMM-23: A stable high-silica multidimensional zeolite with extra-large trilobe-shaped channels. J. Am. Chem. Soc. 2014, 136, 13570– 13573,  DOI: 10.1021/ja507615b
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    143
    EMM-23: A Stable High-Silica Multidimensional Zeolite with Extra-Large Trilobe-Shaped Channels
    Willhammar, Tom; Burton, Allen W.; Yun, Yifeng; Sun, Junliang; Afeworki, Mobae; Strohmaier, Karl G.; Vroman, Hilda; Zou, Xiaodong
    Journal of the American Chemical Society (2014), 136 (39), 13570-13573CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    A stable 3D extra-large pore aluminosilicate zeolite EMM-23 is reported. The crystal structure of EMM-23 was detd. from submicron-sized crystals by combining electron crystallog., solid-state NMR, and powder X-ray diffraction. The framework contains highly unusual trilobe-shaped pores that are bound by 21-24 tetrahedral atoms. These extra-large pores are intersected perpendicularly by a two-dimensional 10-ring channel system. Unlike most ideal zeolite frameworks that have tetrahedral sites with four next-nearest tetrahedral neighbors (Q4 species), this unusual zeolite possesses a high d. of Q2 and Q3 silicon species. It is the first zeolite prepd. directly with Q2 species that are intrinsic to the framework. EMM-23 is stable after calcination at 540°C. The formation of this highly interrupted structure is facilitated by the high d. of extra framework pos. charge introduced by the dicationic structure directing agent.
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  144. 144
    Jiang, J.; Yun, Y.; Zou, X.; Jorda, J. L.; Corma, A. ITQ-54: a multi-dimensional extra-large pore zeolite with 20 × 14 × 12-ring channels. Chem. Sci. 2015, 6, 480– 485,  DOI: 10.1039/C4SC02577F
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    144
    ITQ-54: a multi-dimensional extra-large pore zeolite with 20 × 14 × 12-ring channels
    Jiang, Jiuxing; Yun, Yifeng; Zou, Xiaodong; Jorda, Jose Luis; Corma, Avelino
    Chemical Science (2015), 6 (1), 480-485CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
    A multi-dimensional extra-large pore silicogermanate zeolite, named ITQ-54, has been synthesized by in situ decompn. of the N,N-dicyclohexylisoindolinium cation into the N-cyclohexylisoindolinium cation. Its structure was solved by 3D rotation electron diffraction (RED) from crystals of ca. 1 μm in size. The structure of ITQ-54 contains straight intersecting 20 × 14 × 12-ring channels along the three crystallog. axes and it is one of the few zeolites with extra-large channels in more than one direction. ITQ-54 has a framework d. of 11.1 T atoms per 1000 Å3, which is one of the lowest among the known zeolites. ITQ-54 was obtained together with GeO2 as an impurity. A heavy liq. sepn. method was developed and successfully applied to remove this impurity from the zeolite. ITQ-54 is stable up to 600 °C and exhibits permanent porosity. The structure was further refined using powder X-ray diffraction (PXRD) data for both as-made and calcined samples.
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  145. 145
    Simancas, J.; Simancas, R.; Bereciartua, P. J.; Jorda, J. L.; Rey, F.; Corma, A.; Nicolopoulos, S.; Das, P. P.; Gemmi, M.; Mugnaioli, E. Ultrafast electron diffraction tomography for structure determination of the new zeolite ITQ-58. J. Am. Chem. Soc. 2016, 138, 10116– 10119,  DOI: 10.1021/jacs.6b06394
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    145
    Ultrafast Electron Diffraction Tomography for Structure Determination of the New Zeolite ITQ-58
    Simancas, Jorge; Simancas, Raquel; Bereciartua, Pablo J.; Jorda, Jose L.; Rey, Fernando; Corma, Avelino; Nicolopoulos, Stavros; Pratim Das, Partha; Gemmi, Mauro; Mugnaioli, Enrico
    Journal of the American Chemical Society (2016), 138 (32), 10116-10119CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    A new ultrafast data collection strategy for electron diffraction tomog. is presented that allows reducing data acquisition time by 1 order of magnitude. This methodol. minimizes the radiation damage of beam-sensitive materials, such as microporous materials. This method, combined with the precession of the electron beam, provides high quality data enabling the detn. of very complex structures. The implementation of this new electron diffraction methodol. is easily affordable in any modern electron microscope. As a proof of concept, the authors have solved a new highly complex zeolitic structure named ITQ-58, with a very low symmetry (triclinic) and a large unit cell vol. (1874.6 Å3), contg. 16 Si and 32 O atoms in its asym. unit, which would be very difficult to solve with the state of the art techniques.
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  146. 146
    Willhammar, T.; Su, J.; Yun, Y.; Zou, X.; Afeworki, M.; Weston, S. C.; Vroman, H. B.; Lonergan, W. W.; Strohmaier, K. G. High-throughput synthesis and structure of zeolite ZSM-43 with two-directional 8-ring channels. Inorg. Chem. 2017, 56, 8856– 8864,  DOI: 10.1021/acs.inorgchem.7b00752
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    146
    High-Throughput Synthesis and Structure of Zeolite ZSM-43 with Two-Directional 8-Ring Channels
    Willhammar, Tom; Su, Jie; Yun, Yifeng; Zou, Xiaodong; Afeworki, Mobae; Weston, Simon C.; Vroman, Hilda B.; Lonergan, William W.; Strohmaier, Karl G.
    Inorganic Chemistry (2017), 56 (15), 8856-8864CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
    The aluminosilicate zeolite ZSM-43 was first synthesized more than three decades ago, but its chem. structure remained unsolved due to poor crystallinity and small crystal size. Here the synthesis optimization is presented of ZSM-43 using a high throughput approach and subsequent structure detn. by combination of electron crystallog. methods and powder X-ray diffraction. The synthesis required the use of a combination of both inorg. (Cs+ and K+) and org. (Choline) structure directing agents. High throughput synthesis enabled the screening of the synthesis conditions which made it possible to optimize the synthesis, despite its complexity, in order to obtain a material with significantly improved crystallinity. By applying both rotation electron diffraction (RED) and high resoln. transmission electron microscopy (HRTEM) imaging techniques, the structure of ZSM-43 is detd. The structure of ZSM-43 is a new zeolite framework type and possesses a unique 2-dimensional channel system limited by 8-channels. The ZSM-43 is stable upon calcination and sorption measurements show that the material is suitable for adsorption of CO2 as well as methane.
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  147. 147
    Rius, J.; Mugnaioli, E.; Vallcorba, O.; Kolb, U. Application of δ recycling to electron automated diffraction tomography data from inorganic crystalline nanovolumes. Acta Crystallogr., Sect. A: Found. Crystallogr. 2013, 69, 396– 407,  DOI: 10.1107/S0108767313009549
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    147
    Application of δ recycling to electron automated diffraction tomography data from inorganic crystalline nanovolumes
    Rius, Jordi; Mugnaioli, Enrico; Vallcorba, Oriol; Kolb, Ute
    Acta Crystallographica, Section A: Foundations of Crystallography (2013), 69 (4), 396-407CODEN: ACACEQ; ISSN:0108-7673. (International Union of Crystallography)
    δ Recycling is a simple procedure for directly extg. phase information from Patterson-type functions [Rius (2012) Acta Cryst. A68, 399-400]. This new phasing method has a clear theor. basis and was developed with ideal single-crystal x-ray diffraction data. However, introduction of the automated diffraction tomog. (ADT) technique has represented a significant advance in electron diffraction data collection [Kolb et al. (2007) Ultramicroscopy, 107, 507-513]. When combined with precession electron diffraction, it delivers quasi-kinematical intensity data even for complex inorg. compds., so that single-crystal diffraction data of nanometric vols. are now available for structure detn. by direct methods. To check the tolerance of δ recycling to missing data-collection corrections and to deviations from kinematical behavior of ADT intensities, δ recycling was applied to differently shaped nanocrystals of various inorg. materials. It can phase ADT data very efficiently. In some cases even more complete structure models than those derived from conventional direct methods and least-squares refinement were found. During this study the Wilson-plot scaling procedure is largely insensitive to sample thickness variations and missing absorption corrections affecting electron ADT intensities.
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  148. 148
    Zhang, Y.-B.; Su, J.; Furukawa, H.; Yun, Y.; Gándara, F.; Duong, A.; Zou, X.; Yaghi, O. M. Single-crystal structure of a covalent organic framework. J. Am. Chem. Soc. 2013, 135, 16336– 16339,  DOI: 10.1021/ja409033p
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    148
    Single-Crystal Structure of a Covalent Organic Framework
    Zhang, Yue-Biao; Su, Jie; Furukawa, Hiroyasu; Yun, Yifeng; Gandara, Felipe; Duong, Adam; Zou, Xiaodong; Yaghi, Omar M.
    Journal of the American Chemical Society (2013), 135 (44), 16336-16339CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    The crystal structure of a new covalent org. framework, termed COF-320, is detd. by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepd. by an imine condensation of tetra-(4-anilyl)-methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 °C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m2/g and a methane total uptake of 15.0 wt. % (176 cm3/cm3) at 25 °C and 80 bar. The successful detn. of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chem.
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  149. 149
    Bellussi, G.; Montanari, E.; Di Paola, E.; Millini, R.; Carati, A.; Rizzo, C.; O’Neil Parker, W., Jr.; Gemmi, M.; Mugnaioli, E.; Kolb, U.; Zanardi, S. ECS-3: a crystalline hybrid organic–inorganic aluminosilicate with open porosity. Angew. Chem., Int. Ed. 2012, 51, 666– 669,  DOI: 10.1002/anie.201105496
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    149
    ECS-3: A Crystalline Hybrid Organic-Inorganic Aluminosilicate with Open Porosity
    Bellussi, Giuseppe; Montanari, Erica; Di Paola, Eleonora; Millini, Roberto; Carati, Angela; Rizzo, Caterina; O'Neil Parker, Wallace; Gemmi, Mauro; Mugnaioli, Enrico; Kolb, Ute; Zanardi, Stefano
    Angewandte Chemie, International Edition (2012), 51 (3), 666-669, S666/1-S666/8CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    In conclusion, ECS-3 confirms the synthesis of microporous cryst. org.-inorg. aluminosilicate hybrids. In particular, ECS-3 is the first such hybrid with open microporosity produced by a regular arrangement of inorg. and org. layers. The intriguing crystal structure of ECS-3, whose framework contains 62 atoms in the asym. unit, is one of the most complex structures ever solved by electron diffraction, with a structural complexity comparable to zeolites like ITQ-22. This is remarkable considering the high beam sensitivity of the sample, due to the phenylene rings. ADT was indeed indispensable and could become widely utilized for structural investigation of hybrid nanocryst. microporous materials.
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    Janssen, T.; Chapuis, G.; de Boissieu, M. Aperiodic Crystals: from modulated phases to quasicrystals; Oxford University Press: New York, 2007.
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    van Smaalen, S. Incommensurate crystallography; Oxford University Press: New York, 2007.
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    Li, L.; Boullay, P.; Lu, P.; Wang, X.; Jian, J.; Huang, J.; Gao, X.; Misra, S.; Zhang, W.; Perez, O.; Steciuk, G.; Chen, A.; Zhang, X.; Wang, H. Novel layered supercell structure from Bi2AlMnO6 for multifunctionalities. Nano Lett. 2017, 17, 6575– 6582,  DOI: 10.1021/acs.nanolett.7b02284
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    152
    Novel layered supercell structure from Bi2AlMnO6 for multifunctionalities
    Li, Leigang; Boullay, Philippe; Lu, Ping; Wang, Xuejing; Jian, Jie; Huang, Jijie; Gao, Xingyao; Misra, Shikhar; Zhang, Wenrui; Perez, Olivier; Steciuk, Gwladys; Chen, Aiping; Zhang, Xinghang; Wang, Haiyan
    Nano Letters (2017), 17 (11), 6575-6582CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    Layered materials, e.g., graphene and transition metal (di)chalcogenides, holding great promises in nanoscale device applications were extensively studied in fundamental chem., solid state physics and materials research areas. In parallel, layered oxides (e.g., Aurivillius and Ruddlesden-Popper phases) present an attractive class of materials both because of their rich physics behind and potential device applications. The authors report a novel layered oxide material with self-assembled layered supercell structure consisting of two mismatch-layered sublattices of [Bi3O3+δ] and [MO2]1.84 (M = Al/Mn, simply named BAMO), i.e., alternative layered stacking of two mutually incommensurate sublattices made of a three-layer-thick Bi-O slab and a 1-layer-thick Al/Mn-O octahedra slab in the out-of-plane direction. Strong room-temp. ferromagnetic and piezoelec. responses as well as anisotropic optical property were demonstrated with great potentials in various device applications. The realization of the novel BAMO layered supercell structure in this work has paved an avenue toward exploring and designing new materials with multifunctionalities.
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  153. 153
    Singh, D.; Yun, Y.; Wan, W.; Grushko, B.; Zou, X.; Hovmöller, S. A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction. J. Appl. Crystallogr. 2014, 47, 215– 221,  DOI: 10.1107/S1600576713029294
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    153
    A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction
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    Journal of Applied Crystallography (2014), 47 (1), 215-221CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    Electron diffraction is a complementary technique to single-crystal x-ray diffraction and powder X-ray diffraction for structure soln. of unknown crystals. Crystals too small to be studied by single-crystal x-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction were the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. The intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometer-sized single crystal in <2 h. Here the RED method is applied for ab initio structure detn. of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, with a 46.4, b 64.6, c 8.2 Å. However, as with other approximants in the PD series, the reflections with odd l indexes are much weaker than those with l even, so it was decided to 1st solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parameters a 23.2, b 32.3, c 4.1 Å and space group Pnmm was solved. The structure with c 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with 5-fold rotational symmetry, which agrees with results from high-resoln. electron microscopy images. Simulated electron diffraction patterns for the structure model agree with the exptl. electron diffraction patterns obtained by RED.
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    Serial electron crystallog. is being developed as an alternative way to collect diffraction data on beam-sensitive polycryst. materials. Merging serial diffraction data from a large no. of snapshots is difficult, and the dynamical nature of electron diffraction prevents the use of existing methods that rely on precise measurement of kinematical reflection intensities. To overcome this problem, an alternative method that uses rank aggregation to combine the rankings of relative reflection intensities from a large no. of snapshots has been developed. The method does not attempt to accurately model the diffraction intensity, but instead optimizes the most likely ranking of reflections. As a consequence, the problem of scaling individual snapshots is avoided entirely, and requirements for the data quality and precision are low. The method works best when reflections can be fully measured, but the benefit over measuring partial intensities is small. Since there were no exptl. data available for testing rank-based merging, the validity of the approach was assessed through a series of simulated serial electron diffraction datasets with different nos. of frames and varying degrees of errors. Several programs have been used to show that these rank-merged simulated data are good enough for ab initio structure detn. using several direct methods programs.
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    Journal of Applied Crystallography (2018), 51 (6), 1671-1683CODEN: JACGAR; ISSN:1600-5767. (International Union of Crystallography)
    The effect of relative humidity (rH) on protein crystal structures, an area that has attracted high scientific interest during the past decade, is investigated in this study on hen egg-white lysozyme (HEWL) polycryst. ppts. via in situ lab. X-ray powder diffraction (XRPD) measurements. For this purpose, HEWL was crystd. at room temp. and pH 4.5, leading to a novel monoclinic HEWL phase which, to our knowledge, has not been reported before. Anal. of XRPD data collected upon rH variation revealed several structural modifications. These observations, on a well-studied mol. like HEWL, underline not only the high impact of humidity levels on biol. crystal structures, but also the significance of inhouse XRPD as an anal. tool in industrial drug development and its potential to provide information for enhancing manufg. of pharmaceuticals.
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  • Abstract

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    Figure 1

    Figure 1. Examples of crystals suitable for 3D ED data collection. (A) Cu2–xTe nanoplatelets, with lateral size of 100–200 nm and thickness of few tens of nanometers. (B) Submicrometric Eu2Si2O7 grains embedded in a ground mass of nanocrystalline quartz. (C) Submicrometric cronstedtite pyramidal crystals in a focused ion beam (FIB) lamella, sampled from the carbonaceous meteorite Paris. (D) Micrometric pharmaceutical crystal.

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    Figure 2

    Figure 2. Sketches of the four main 3D ED data collection protocols. (A) Simple stepwise acquisition performed with fixed mechanical tilt steps (brown arrows) and steady beam (in green). The tilt step is normally 0.5–2°. (B) Stepwise acquisition performed with fixed mechanical tilt steps (brown arrows) while the beam is precessing around a conical surface pointed on the sample (green arrow). The Ewald sphere is also precessing (blue cones), and this movement allows a better integration of the Bragg reflection intensities. (C) Stepwise RED acquisition. Large mechanical tilt steps (brown arrows) are followed by small beam tilt steps (green arrows) obtained by the deflection coils of the TEM. The beam tilt step may be smaller than 0.1°. (D) Continuous rotation acquisition. The sample is mechanically tilted within the whole goniometer range (brown arrow) while the detector is acquiring a sequence of patterns. The acquisition tilt step is determined by the sum of exposure time (blue) and readout time (yellow). The latter is also responsible for the nonsampled wedges between two consecutive patterns. The beam is stationary during the whole data acquisition, and the main limit is given by the goniometer stability, because the sample tends to shift laterally during the tilt and therefore may go out from the illuminated area. The not sampled missing wedge is exaggerated in the figures and is colored in red. It is the same for all acquisition protocols, as it depends only on the mechanical limit of the TEM goniometer.

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    Figure 3

    Figure 3. Exemplary diffraction volume of the trigonal mineral franzinite reconstructed from 3D ED data (a = 12.9 Å, c = 26.6 Å). (A) View along a*. (B) View along b*. (C) View along c*. (D) View along the tilt axis of the acquisition. Note that these are projections of a 3D volume and not conventional 2D oriented ED patterns. Cell edges are sketched in yellow. a* vector is in red, b* vector in green, and c* vector in blue. Data resolution is about 0.8 Å. The figure is made by ADT3D software. (18)

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    Figure 4

    Figure 4. Sketch showing some representative structures solved by 3D ED method for different classes of materials. Starting from the upper left and going anticlockwise: the mineral karibibite, (133) a tunnel (Na,Mn)-oxide for electrolytic applications, (124) the aperiodic structure of SrBi7NbO24, (122) the extra-large-pore silicoaluminophosphate ITQ-51, (25) the cobat tetraphosphonate MOF Co-CAU-36, (66) the pharma compound carbamazepine-III, (29) the amyloid core of the Sup35 prion protein, (47) and a new monoclinic polymorph of lysozyme. (45)

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    Figure 5

    Figure 5. Hydrogen atoms localization by 3D ED. (A) Perspective view of the Co1.13Al2P4O20H11.74 structure (105) with a superimposed difference potential map showing maxima at the positions of the hydrogen atoms. Isosurface levels are at 2σ[ΔV(r)] (light gray) and 3σ[ΔV(r)] (yellow). CoO6, AlO6, and PO4 polyhedra are represented in blue, green, and orange, respectively, while oxygen atoms are in red. This difference potential map enlightening the hydrogen positions is obtained thanks to the use of dynamical refinement. The hydrogen positions (in black) are stable once incorporated to the dynamical refinement. (B) Two adjacent orthocetamol chains (34) with the superimposed difference Fourier map. The maximum residual potential (in blue and yellow) corresponds to the hydrogen atom responsible for the intermolecular bonding. Carbon atoms are drawn in brown, oxygen atoms in red, and nitrogen atoms in gray.

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      The structure of a new modification of Ti2Se, the β-phase, and several related inorg. crystal structures contg. elements with at. nos. between 16 and 40 were solved by quasi-automatic direct methods from single-crystal electron diffraction patterns of nanometer-size crystals, using the kinematical approxn.. The crystals were several thousand times smaller than the min. size required for single-crystal x-ray diffraction. At. coordinates were found with an av. accuracy of 0.2 Å or better. Exptl. data were obtained by standardized techniques for recording and quantifying electron diffraction patterns. The SIR97 program for solving crystal structures from three-dimensional x-ray diffraction data by direct methods was modified to work also with two-dimensional electron diffraction data. At. coordinates are given for β-Ti2Se.
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      Gonen, T.; Cheng, Y.; Sliz, P.; Hiroaki, Y.; Fujiyoshi, Y.; Harrison, S. C.; Walz, T. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 2005, 438, 633– 638,  DOI: 10.1038/nature04321
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      Lipid-protein interactions in double-layered two-dimensional AQP0 crystals
      Gonen, Tamir; Cheng, Yifan; Sliz, Piotr; Hiroaki, Yoko; Fujiyoshi, Yoshinori; Harrison, Stephen C.; Walz, Thomas
      Nature (London, United Kingdom) (2005), 438 (7068), 633-638CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fiber cells. Here we describe a 1.9 Å resoln. structure of junctional AQP0, detd. by electron crystallog. of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic amino and carboxy termini. In the center of the water pathway, the closed pore in junctional AQP0 retains only three water mols., which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the cryst. array are mediated by lipid mols., which assume preferred conformations. We were therefore able to build an at. model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.
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      Dorset, D. L.; Roth, W. J.; Gilmore, C. J. Electron crystallography of zeolites – the MWW family as a test of direct 3D structure determination. Acta Crystallogr., Sect. A: Found. Crystallogr. 2005, 61, 516– 527,  DOI: 10.1107/S0108767305024670
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      Electron crystallography of zeolites - the MWW family as a test of direct 3D structure determination
      Dorset, Douglas L.; Roth, Wieslaw J.; Gilmore, Christopher J.
      Acta Crystallographica, Section A: Foundations of Crystallography (2005), A61 (5), 516-527CODEN: ACACEQ; ISSN:0108-7673. (Blackwell Publishing Ltd.)
      The efficacy of direct methods for solving the crystal structures of zeolites from electron diffraction data is evaluated for related materials, i.e. MCM-22, MCM-49 and ITQ-1. First, it is established by tilting expts. that all materials share the same MWW framework. The calcined product of a delaminated MCM-22 precursor, ITQ-2, also shares this framework structure within the limited no. of stacked unit cells. For all materials, the underlying space group is P6/mmm where a ≃ 14.21, c ≃ 24.94 Å. Traditional direct methods are useful for detg. the projected structure down the hexagonal axis but are not very effective for finding the three-dimensional structure. However, max.-entropy and likelihood approaches are effective for detg. either 2-dimensional projections or 3-dimensional frameworks. The major restriction to 3-dimensional detns. by direct methods is the limited goniometric tilt range of the electron microscope, hence the 'missing cone' of information. Potential maps from the most accurate phase sets are, therefore, obsd. as continuous d. envelopes to the true structure. Some improvement is found when the Sayer equation predicts missing amplitudes and phases but better specimen prepn. methods are required to include projections contg. the c* axis of the reciprocal lattice.
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