Automated Electron Diffraction Tomography Research Articles

Topochemical Fluorination of LaBaInO4 to LaBaInO3F2, Their Optical Characterization, and Photocatalytic Activities for Hydrogen Evolution.

We report on a nonoxidative topochemical route for the synthesis of a novel indate-based oxyfluoride, LaBaInO3F2, using a low-temperature reaction of Ruddlesden-Popper-type LaBaInO4 with polyvinylidene difluoride as a fluorinating agent. The reaction involves the replacement of oxide ions with fluoride ions as well as the insertion of fluoride ions into the interstitial sites. From the characterization via powder X-ray diffraction (PXRD) and Rietveld analysis as well as automated electron diffraction tomography (ADT), it is deduced that the fluorination results in a symmetry lowering from I4/mmm (139) to monoclinic C2/c (15) with an expansion perpendicular to the perovskite layers and a strong tilting of the octahedra in the ab plane. Disorder of the anions on the apical and interstitial sites seems to be favored. The most stable configuration for the anion ordering is estimated based on an evaluation of bond distances from the ADT measurements via bond valence sums (BVSs). The observed disordering of the anions in the oxyfluoride results in changes in the optical properties and thus shows that the topochemical anion modification can present a viable route to alter the optical properties. Partial densities of states (PDOSs) obtained from ab initio density functional theory (DFT) calculations reveal a bandgap modification upon fluoride-ion introduction which originates from the presence of the oxide anions on the interstitial sites. The photocatalytic performance of the oxide and oxyfluoride shows that both materials are photocatalytically active for hydrogen (H2) evolution.

AUTOMATED ELECTRON DIFFRACTION TOMOGRAPHY ON NANOANATASE AND GOYAZITE FROM CLAY COVER OF BAUXITE DEPOSITS IN THE AMAZON

Since naturally occurring minerals typically have particle sizes from microns to several nanometers, their investigation, from sampling to individual particle analysis, is a challenging task. This work reports the detection of anatase, which occurs mainly in tropical soils and upon weathering in laterite. Little knowledge of this omnipresent accessory nanomineral, showing strong affinity to the soil formation processes and lateritic profiles is presently available. In bauxites the nano-anatase crystal morphology have not been reported yet. The samples were collected in a bauxite mine south of the Amazon (Juruti, Brazil). The chemical enrichment of anatase was carried out with H2TiF6 and the resulting powders could be characterized with SEM, XRPD and EDX. Subsequently, transmission electron microscopy (TEM) was used to analyze the chemical composition of individual anatase particles by EDX and the unique method of automated electron diffraction tomography (ADT), which probes the reciprocal space of individual nanoparticles. Associated with anatase, crandallite mineral group was also detected. Keywords: kaolinite; iron oxyhydroxides; gorceixite; goyazite; Juruti

Fast-ADT: A fast and automated electron diffraction tomography setup for structure determination and refinement

Electron crystallography has focused in the last few years on the analyses of microcrystals, mainly organic compounds, triggered by recent publications on acquisition methods based on direct detection cameras and continuous stage tilting. However, the main capability of a transmission electron microscope is the access to features at the nanometre scale. In this context, a new acquisition method, called fast and automated diffraction tomography (Fast-ADT), has been developed in form of a general application in order to get the most of the diffraction space from a TEM. It consists of two subsequent tilt scans of the goniometric stage; one to obtain a crystal tracking file and a second one to acquire an electron diffraction tomography. This setup has been implemented on both TEM and STEM modes of the microscope, thus it can be installed on any TEM regardless of the availability of a scanning unit. BaSO4 crystals have been measured to demonstrate the validity of the technique for structure determination and refinement. A recently solved layered silicate, RUB-5, has been used to prove the method advantages for fine identification of disorder details. Last, a new polymorph of a DRED1 organic molecule has been solved ab initio and refined by X-ray powder diffraction to show the full application of the presented method.

A new microporous 12-ring zincosilicate THK-2 with many terminal silanols characterized by automated electron diffraction tomography

A newly synthesized microporous zincosilicate THK-2 (estimated structural composition: |(H2O)6.7(C6H13N)0.9|[Li0.5Zn3.1Si32O62.7(OH)9.3]) was characterized by single-crystal electron diffraction using the automated electron diffraction tomography (ADT) approach in combination with powder X-ray diffraction. The lattice constants and space group of as-synthesized THK-2 were a = 2.50377(7) nm, b = 1.43866(4) nm, c = 0.505369(8) nm, and Pccn (no. 56) with orthorhombic symmetry. Because the crystal lattice was almost identical to a hexagonal lattice (), the first several peaks in its powder X-ray diffraction data severely overlapped, which suppressed the structural information to decide the framework topology. In order to overcome this intrinsic difficulty, the structure model of THK-2 was initially obtained by the direct method based on ADT data and refined by the Rietveld method. Its 3-dimensional framework structure was elucidated and it consisted of 4-, 5-, 6-rings of tetrahedral Si and Zn atoms and a one-dimensional straight channel with a 12-ring pore opening. Zn atoms were incorporated into the framework as four-coordinated [ZnO4], although their distribution was confirmed to be disorderly. In the as-synthesized THK-2, the site occupancy of Zn was as low as 0.39; that is, more than 60% of the Zn sites were vacant. Hexamethyleneimine and water molecules were accommodated in the straight channel in a disordered manner. The material was stable upon calcination, and the BET specific surface area and micropore volume of calcined THK-2 were 240.6 m2 g-1 and 0.12 ml g-1, respectively.

Automated electron diffraction tomography - development and applications.

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

Expanding the Variety of Zirconium-based Inorganic Building Units for Metal-Organic Frameworks.

Two new zirconium-based metal-organic frameworks with the composition [Zr6 O4 (OH)4 (OAc)6 (BDC)3 ] (CAU-26) and [Zr5 O4 (OH)4 (OAc)4 (BDC)2 ] (CAU-27) are reported, which were synthesized from acetic acid, a rarely utilized but green and sustainable solvent (BDC2- : 1,4-benzenedicarboxylate). Structure determination aided by automated electron diffraction tomography revealed that CAU-26 is composed of layers of well-known {Zr6 O8 } clusters interconnected by terephthalate ions. In contrast CAU-27 exhibits a three-dimensional structure with a so far unknown type of one-dimensional inorganic building unit (IBU), which can be rationalized as condensed polyhedron-sharing chains of {Zr6 O8 } clusters. CAU-26 occurs as an intermediate of the CAU-27 synthesis and can be isolated easily, when reaction temperature and time are decreased. We were also able to synthesize two isoreticular derivatives of CAU-27 with extended linker molecules by implementing 4,4'-biphenyldicarboxylic acid (H2 BPDC) and 5,5'-dicarboxy-2,2'-bipyridine (H2 BIPY). All materials show high thermal and chemical stability as well as permanent microporosity. The excellent stability of CAU-27-BIPY was exploited to synthesize a performant iridium-supported heterogeneous MOF-based catalyst for the direct C-H borylation of arenes.

Expanding the Variety of Zirconium‐based Inorganic Building Units for Metal–Organic Frameworks

AbstractTwo new zirconium‐based metal–organic frameworks with the composition [Zr6O4(OH)4(OAc)6(BDC)3] (CAU‐26) and [Zr5O4(OH)4(OAc)4(BDC)2] (CAU‐27) are reported, which were synthesized from acetic acid, a rarely utilized but green and sustainable solvent (BDC2−: 1,4‐benzenedicarboxylate). Structure determination aided by automated electron diffraction tomography revealed that CAU‐26 is composed of layers of well‐known {Zr6O8} clusters interconnected by terephthalate ions. In contrast CAU‐27 exhibits a three‐dimensional structure with a so far unknown type of one‐dimensional inorganic building unit (IBU), which can be rationalized as condensed polyhedron‐sharing chains of {Zr6O8} clusters. CAU‐26 occurs as an intermediate of the CAU‐27 synthesis and can be isolated easily, when reaction temperature and time are decreased. We were also able to synthesize two isoreticular derivatives of CAU‐27 with extended linker molecules by implementing 4,4′‐biphenyldicarboxylic acid (H2BPDC) and 5,5′‐dicarboxy‐2,2′‐bipyridine (H2BIPY). All materials show high thermal and chemical stability as well as permanent microporosity. The excellent stability of CAU‐27‐BIPY was exploited to synthesize a performant iridium‐supported heterogeneous MOF‐based catalyst for the direct C−H borylation of arenes.

Optimization of automated electron diffraction tomography for challenging applications

Optimization of automated electron diffraction tomography for challenging applications

Application of X-ray Diffraction and Electron Crystallography for Solving Complex Structure Problems.

All crystalline materials in nature, whether inorganic, organic, or biological, macroscopic or microscopic, have their own chemical and physical properties, which strongly depend on their atomic structures. Therefore, structure determination is extremely important in chemistry, physics, materials science, etc. In the past centuries, many techniques have been developed for structure determination. The most widely used one is X-ray crystallography (single-crystal X-ray diffraction (SCXRD) and powder X-ray diffraction (PXRD)), and it remains the most important technique for structure determination of crystalline materials. Although SCXRD and PXRD are successful in many cases, a number of reasons limit their applications, such as SCXRD for nanosized crystals, intergrowth, and defects and PXRD for complex structures, multiphasic samples, impurities, peak overlaps, etc. Another most valuable technique for structure determination is electron crystallography (EC). With the electron as a probe, EC alone can also be used for structure determination, especially for crystals that are too small to be studied by SCXRD or too complex for PXRD. As electrons interact much more strongly with matter than X-rays do, both electron diffraction (ED) patterns and high-resolution transmission electron microscopy (HRTEM) images can be obtained from nanosized crystals. However, collecting a complete set of ED patterns or recording a good HRTEM image requires considerable expertise on the operation of electron microscopes and crystallography. The strong interactions between electrons and materials can also lead to dynamical effects and beam damage. These difficulties make structure determination from ED patterns and HRTEM images not straightforward. Recently, two three-dimensional (3D) electron diffraction techniques, automated electron diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed, which perform the data collection in an automated manner. Although the dynamical effects in the newly developed 3D electron diffraction techniques (ADT, RED) are reduced significantly, for some structures there are still problems with obtaining an initial model because of beam damage. The X-ray diffraction and EC methods discussed above are both powerful techniques but have their own limitations. In many complicated cases, one technique alone is not enough to solve the crystal structure, and different techniques that supply complementary structural information have to support each other for the complete structure determination. In this Account, we provide a summary of the advantages and disadvantages of X-ray diffraction (PXRD and SCXRD) and EC (HRTEM and ED) for structure determination and include a review of applications of X-ray diffraction and EC for solving complex structure problems such as peak overlap, impurities, pseudosymmetry and twinning, disordered frameworks, locating guests, aperiodic structures, etc. Some of the latest advances in structure determination are also presented briefly, namely, revealing hydrogen positions by ED, protein crystal structure solution by 3D electron diffraction, and structure determination using an X-ray free electron laser (XFEL).

Elucidating structural order and disorder phenomena in mullite-type Al4B2O9 by automated electron diffraction tomography

The crystal structure and disorder phenomena of Al4B2O9, an aluminum borate from the mullite-type family, were studied using automated diffraction tomography (ADT), a recently established method for collection and analysis of electron diffraction data. Al4B2O9, prepared by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure determination based on three-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. Furthermore, disordered crystals with diffuse scattering along the b axis are observed. Analysis of the modulation pattern implies a mean superstructure (AAB) with a threefold b axis, where B corresponds to an A layer shifted by ½a and ½c. Diffraction patterns simulated for the AAB sequence including additional stacking disorder are in good agreement with experimental electron diffraction patterns.

Solving the Hydrogen and Lithium Substructure of Poly(triazine imide)/LiCl Using NMR Crystallography

Poly(triazine imide) with incorporated lithium chloride has recently attracted substantial attention due to its photocatalytic activity for water splitting. However, an apparent H/Li disorder prevents the delineation of structure-property relationships, for example, with respect to band-gap tuning. Herein, we show that through a combination of one- and two-dimensional, multinuclear solid-state NMR spectroscopy, chemical modelling, automated electron diffraction tomography, and an analysis based on X-ray pair distribution functions, it is finally possible to resolve the H/Li substructure. In each cavity, one hydrogen atom is bound to a bridging nitrogen atom, while a second one protonates a triazine ring. The two lithium ions within each cavity are positioned between two nitrogen atoms of neighbouring triazine rings. The thereby induced local dipole moments cause slight buckling of the framework and lateral displacements of the Cl- ions at a coherence length below 2 nm. Nevertheless, the average structure conforms to space group P21 21 21 . In this way, we demonstrate that, in particular, the above-mentioned techniques allow for smart interplay in delineating the real structure of PTI/LiCl.

Solving Challenging Crystallographic Problems with Automated Electron Diffraction Tomography (ADT)

Journal Article Solving Challenging Crystallographic Problems with Automated Electron Diffraction Tomography (ADT) Get access Ute Kolb, Ute Kolb Institute of Inorganic and Analytical Chemistry, Johannes Gutenberg-University, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Bastian Barton, Bastian Barton Institute of Inorganic and Analytical Chemistry, Johannes Gutenberg-University, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Yasar Krysiak, Yasar Krysiak Institute of Inorganic and Analytical Chemistry, Johannes Gutenberg-University, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Haishuang Zhao Haishuang Zhao Institute of Inorganic and Analytical Chemistry, Johannes Gutenberg-University, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 22, Issue S3, 1 July 2016, Pages 496–497, https://doi.org/10.1017/S1431927616003330 Published: 25 July 2016

Structural Characterisation of Complex Layered Double Hydroxides and TGA-GC-MS Study on Thermal Response and Carbonate Contamination in Nitrate- and Organic-Exchanged Hydrotalcites.

Layered double hydroxides (LDHs) are versatile materials used for intercalating bioactive molecules in the fields of pharmaceuticals, nutraceuticals and cosmetics, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability and improving their pharmacokinetic properties and formulation stability. Moreover, LDHs are used in various technological applications to improve stability and processability. The crystal chemistry of hydrotalcite-like compounds was investigated by X-ray powder diffraction (XRPD), automated electron diffraction tomography (ADT) and thermogravimetric analysis (TGA)-GC-MS to shed light on the mechanisms involved in ion exchange and absorption of contaminants, mainly carbonate anions. For the first time, ADT allowed a structural model of LDH_NO3 to be obtained from experiment, shedding light on the conformation of nitrate inside LDH and on the loss of crystallinity due to the layer morphology. The ADT analysis of a hybrid LDH sample (LDH_EUS) clearly revealed an increase in defectivity in this material. XRPD demonstrated that the presence of carbonate can influence the intercalation of organic molecules into LDH, since CO3 -contaminated samples tend to adopt d spacings that are approximate multiples of the d spacing of LDH_CO3 . TGA-GC-MS allowed intercalated and surface- adsorbed organic molecules to be distinguished and quantified, the presence and amount of carbonate to be confirmed, especially at low concentrations (<2 wt %), and the different types and strengths of adsorption to be classified with respect to the temperature of elimination.

A structural study of cyanotrichite from Dachang by conventional and automated electron diffraction

The crystal structure of cyanotrichite, having general formula Cu4Al2(SO4)(OH)12·2H2O, from the Dachang deposit (China) was studied by means of conventional transmission electron microscopy, automated electron diffraction tomography (ADT) and synchrotron X-ray powder diffraction (XRPD). ADT revealed the presence of two different cyanotrichite-like phases. The same phases were also recognized in the XRPD pattern, allowing the perfect indexing of all peaks leading, after refinement to the following cell parameters: (1) a = 12.417(2) Å, b = 2.907(1) Å, c = 10.157(1) Å and β = 98.12(1); (2) a = 12.660(2) Å, b = 2.897(1) Å, c = 10.162(1) Å and β = 92.42(1)°. Only for the former phase, labeled cyanotrichite-98, a partial structure, corresponding to the [Cu4Al2(OH) 12 2+ ] cluster, was obtained ab initio by direct methods in space group C2/m on the basis of electron diffraction data. Geometric and charge-balance considerations allowed to reach the whole structure model for the cyanotrichite-98 phase. The sulfate group and water molecule result to be statistically disordered over two possible positions, but keeping the average structure consistent with the C-centering symmetry, in agreement with ADT results.

Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data.

The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (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 atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic 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 compositions.

Structural characterization of the of inorganic and organic hydrotalcites

Layered double hydroxides are versatile materials used for intercalating bioactive molecules, both in pharmaceutical and cosmetic fields, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability, and/or obtaining modified release properties. Hydrotalcite is commercially available in its carbonate form, which is usually transformed into the nitrate form and finally exchanged by organic anions to obtain or regulate bioactivity or photo-activity effects (1). In this study all the steps of these transformations were characterized from the structural viewpoints by X-ray powder diffraction (XRPD) and automated electron diffraction tomography (ADT). ADT allowed shedding light on the nitrate position and conformation inside LDH. XRPD demonstrated at first that the presence of carbonate impurities is able to drive the intercalation of organic molecules into LDH, since CO32- contaminated samples tend to assume d-spacings roughly multiple of LDH-CO3 d-spacing. Finally XRPD was employed at in situ conditions to unravel the structural transformation occurring during the substitution of carbonate by nitrate ion and of the nitrate ion by organic anions. The carbonate-nitrate substitutions resulted to be very rapid (only few seconds) and only the use of a fast area detector, coupled to synchrotron radiation, allowed obtaining reliable patterns to perform XRPD refinement of the disordered structure at the sub-second time resolution. The nitrate-organic substitution resulted slower and depending on the chemical properties of the organic molecules.

Quasicrystal approximants solved by Rotation Electron Diffraction (RED)

We have developed single crystal electron diffraction for powder-sized samples, i.e. &lt; 0.1μm in all dimensions. Complete 3D electron diffraction is collected by Rotation Electron Diffraction (RED) in about one hour. Data processing takes another hour. The crystal structures are solved by standard crystallographic techniques. X-ray crystallography requires crystals several micrometers big. For nanometer sized crystals, electron diffraction and electron microscopy (EM) are the only possibilities. Modern transmission EMs are equipped with the two things that are necessary for turning them into automatic single crystal diffractometers; they have CCD cameras and all lenses and the sample stage are computer-controlled. Two methods have been developed for collecting complete (except for a missing cone) 3D electron diffraction data; the Rotation Electron Diffraction (RED) [1] and Automated Electron Diffraction Tomography (ADT) by Kolb et al. [2]. Because of the very strong interaction between electrons and matter, an electron diffraction pattern with visible spots is obtained in one second from a submicron sized crystal in the EM. By collecting 1000-2000 electron diffraction patterns, a complete 3D data set is obtained. The geometry in RED is analogous to the rotation method in X-ray crystallography; the sample is rotated continuously along one rotation axis. The data processing results in a list of typically over 1000 reflections with h,k,l and Intensity. The unit cell is typically obtained correctly to within 1%. Space group determination is done as in X-ray crystallography from systematically absent reflections, but special care must be taken because occasionally multiple electron diffraction can give rise to very strong forbidden reflections. At +/-60° tilt with 0.1° steps, a complete data collection will be some 1200 frames. With one second exposures this takes about one hour. There is no need to align the crystal orientation. The reciprocal lattice can be rotated and displayed at any direction of view. Sections such as hk0, hk1, hk2, h0l and so on can easily be cut out and displayed. We have solved over 50 crystal structures by RED in one year. These include the most complex zeolites ever solved and quasicrystal approximants, such as the pseudo-decagonal approximants PD2 [3] and PD1 in AlCoNi. Observed and calculated sections of reciprocal space (cut at 1.0Å) are shown in Fig. 1. Notice the 10-fold symmetry of strong reflections.

Evidence of noncentrosymmetry of human tooth hydroxyapatite crystals.

Herein, we investigate human single hydroxyapatite crystals (enamel and dentine) by convergent-beam electron diffraction (CBED) and automated electron-diffraction tomography (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 experimental evidence is of prime importance for understanding the morphogenesis and the architectural organization of calcified tissues.

Structure solution of zeolites by automated electron diffraction tomography – Impact and treatment of preferential orientation

In this paper the reliability of structure solution of nano-crystalline porous compounds with preferred orientation based on automated electron diffraction tomography (ADT) is discussed. It will be shown that the limitations of the data acquisition geometry can be overcome by completing the missing diffraction data with additional diffraction information. Apart from different ways of sample preparation, data merging with either additional ADT data sets or intensities derived from X-ray powder diffraction comprise an effective way to improve the accuracy of the structure solution.

Automated electron diffraction tomography (ADT) and X-ray powder diffraction for structure characterization of layered materials

Automated electron diffraction tomography (ADT) and X-ray powder diffraction for structure characterization of layered materials