"Ab initio" structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique

Using a combination of our recently developed automated diffraction tomography (ADT) module with precession electron technique (PED), quasi-kinematical 3D diffraction data sets of an inorganic salt (BaSO(4)) were collected. The lattice cell parameters and their orientation within the data sets were found automatically. The extracted intensities were used for "ab initio" structure analysis by direct methods. The data set covered almost the complete set of possible symmetrically equivalent reflections for an orthorhombic structure. The structure solution in one step delivered all heavy (Ba, S) as well as light atoms (O). Results of the structure solution using direct methods, charge flipping …

Automated Diffraction Tomography: A New Era for Electron Crystallography

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

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

The new mineral sarrabusite Pb5CuCl4(SeO3)4 has been discovered in the Sardinian mine of Baccu Locci, near Villaputzu. It occurs as small lemon–yellow spherical aggregates of tabular crystals (< 10 µm) of less than 100 µm in diameter. The crystal structure has been solved from and refined against electron diffraction of a microcrystal. Data sets have been measured by both a manual and an automated version of the new electron-diffraction tomography 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 sha…

Microphase separation upon crystallization of small amphiphilic molecules: ‘low’ temperature form II of sodium benzoate (E 211)

A so far unknown low temperature polymorph (form II crystallized at 350 °C) of the common food preservative sodium benzoate (NaBz; E 211) could be crystallized by annealing (7 days) of the poorly crystalline technical material. Its crystal structure was solved by indexing a tiny single crystal by electron diffraction followed by structure solution and refinement applying powder X-ray diffraction (PXRD). The new polymorph shows many structural similarities to form I (crystallized at 420 °C). Both form I and II are the result of a microphase separation: the structures consist of pseudo-hexagonal packings of rod-shaped micelles where the core consists of sodium cations being coordinated by the…

Free-Standing Mono layer Two-Dimensional Supramolecular Organic Framework with Good Internal Order

Utilizing dynamic self-assembly and self-sorting to obtain large-area, molecularly precise monolayered structures represents a promising approach toward two-dimensional supramolecular organic frameworks (2D SOF) or 2D supramolecular polymers. So far, related approaches suffer from small domain sizes, fragility and weak long-range internal order. Here we report on the self-assembly of a host-guest enhanced donor-acceptor interaction, consisting of a tris(methoxynaphthyl)-substituted truxene spacer, and a naphthalene diimide substituted with N-methyl viologenyl moieties as donor and acceptor monomers, respectively, in combination with cucurbit[8]uril as host monomer toward monolayers of an un…

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

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

Structural insights into M2O-Al2O3-WO3 (M = Na, K) system by electron diffraction tomography.

TheM2O–Al2O3–WO3(M= alkaline metals) system has attracted the attention of the scientific community because some of its members showed potential applications as single crystalline media for tunable solid-state lasers. These materials behave as promising laser host materials due to their high and continuous transparency in the wide range of the near-IR region. A systematic investigation of these phases is nonetheless hampered because it is impossible to produce large crystals and only in a few cases a pure synthetic product can be achieved. Despite substantial advances in X-ray powder diffraction methods, structure investigation on nanoscale is still challenging, especially when the sample i…

Crystalline Non‐Equilibrium Phase of a Cobalt(II) Complex with Tridentate Ligands

In six-coordinate complexes, flexible tridentate ligands enable mer, cis-fac, and trans-fac stereoisomers. With labile metal ions of the first transition metal series, typically only the final thermodynamic product is available because of the rapid isomerization processes. Here we report on the structural characterization of a so far elusive kinetic intermediate of [Co(ddpd)2](BF4)2 (1; ddpd = N,N′-dimethyl-N,N′-dipyridine-2-yl-pyridine-2,6-diamine). Microcrystals of the cis-fac isomer of 1 were obtained by rapid precipitation. The solid-state structure of cis-fac-1 was determined from electron diffraction data.

Cover Picture: Nanostructuring with a Crosslinkable Discotic Material (Small 8/2007)

Supramolecular PEG-co-oligo(p-benzamide)s prepared on a peptide synthesizer.

An automated synthesis protocol has been developed for the preparation of oligo(p-benzamide)s on solid support using a commercial peptide synthesizer employing a variation of standard Fmoc chemistry. Bis(trichloromethyl carbonate) in NMP was used to activate the aromatic carboxylic acids for acylation of secondary aromatic amines on solid support. N-Protected hepta(p-benzamide) was automatically prepared on solid support and manually converted to a solid supported block co-oligomer by attaching a poly(ethylene glycol) chain. Cleavage from the support could be achieved with minimal loss of the p-methoxybenzyl N-protective group. While the N-protected block co-oligomer was molecularly dissolv…

Automated electron diffraction tomography - a new tool for nano crystal structure analysis

Automated electron Diffraction Tomography (ADT) comprises an upcoming method for “ab intio” structure analysis of nano crystals. 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 diameter down to 50 nm. For crystal tracking micro-probe STEM imaging is used. Full automation of the acquisition procedure allowed optimisation of the electron dose distribution and therefore analysis of highly beam sensitive samples. Cell parameters, space group and reflection intensitie…

ChemInform Abstract: Facile Synthesis and Characterization of Monocrystalline Cubic ZrO2Nanoparticles.

Abstract Crystalline ZrO2 nanoparticles were prepared from zirconium isopropoxide by slow hydrolysis and subsequent hydrothermal treatment of solutions containing various amounts of sodium hydroxide at 180 °C. Whereas moderately basic solutions lead to the formation of nanoparticles of monoclinic ZrO2 with plate-like morphology, and nanoparticles of the cubic ZrO2 high-temperature polymorph with diameters of approx. 5 nm were obtained from strongly basic solutions. The morphology, structure and properties of as-synthesized nanoparticles were characterized using HRTEM, XRD, Raman spectroscopy, UV–vis, PL spectroscopy and BET measurements. The formation of both, the monoclinic and the cubic p…

Electron Crystallography on Polymorphs

Structure analysis via electron diffraction in combination with x-ray powder diffraction and simulation methods has been performed on single crystals of small organic molecules which form polymorphs. For two different examples of pigments and non-linear optical active material data collection, cell parameter and space group determination, structure analysis and refinement are discussed.

Detecting Crystalline Nonequilibrium Phases on the Nanometer Scale

The use of Automated electron Diffraction Tomography (ADT) is presented as a novel approach for crystallization studies at the nanometer scale for nonequilibrium phases. Here, ADT was applied to elucidate the structural identity of the recently reported hexagonal morphology of caffeine crystals, which grow only on specific surfaces. Caffeine was crystallized from solution on a specially treated TEM carbon grid. The analysis of ADT data revealed that the lattice parameters of these hexagons match those of the high temperature α- form of caffeine. Furthermore, it was observed that in this hexagonal morphology, the α-form remained stable for a prolonged period of time. The stabilization of hex…

Solution Synthesis of a New Thermoelectric Zn1-xSb Nanophase and Its Structure Determination Using Automated Electron Diffraction Tomography

Engineering materials with specific physical 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 conductivity of the system. Low thermal conductivity is a prerequisite for effective thermoelectric materials, and the challenge is to limit the transport of heat by phonons, without simultaneously decreasing charge transport. A solution-phase technique was devised for synthesis of thermoelectric "Zn(4)Sb(3)" nanocrystals as a precursor for phase segregation into ZnSb and a new Zn-Sb intermetallic phase, Zn(1+delta)Sb, in a peritectoid reaction. Our …

The role of electron diffraction in zeolite structure determination

Because electron diffraction can sample individual microcrystals, it is clear that this single crystal method can facilitate, in at least two ways, structure determination for inorganic materials, such as zeolites, that are preferentially microcrystalline. First, in a qualitative application, three-dimensional tilts of individual small crystals, to map the reciprocal lattice, greatly facilitates unit cell and space group determination when powder diffraction indexing programs fail. If incoherent multiple scattering leads to violation of systematic absences, these absences can be restored by collection of precession diffraction patterns based on the Vincent-Midgley method [1], as demonstrate…

Solid-State Pyrolyses of Metal Phthalocyanines: A Simple Approach towards Nitrogen-Doped CNTs and Metal/Carbon Nanocables

Solid-state pyrolysis of organometallic precursors has emerged as an alternative method for preparing carbon nanostructures such as carbon nanotubes (CNT) and carbon anions. The morphology of the tubes can be controlled by the nature of the precursors and the pyrolysis procedures, and micrometer long nanotubes, composed of metal carbide wires encased in a graphitic sheath. Cobalt phthalocyanine (CoPc) as well as iron phthalocyanine were pyrolyzed at different temperatures to obtain CNTs. HRTEM and energy-dispersion X-Ray analysis disclosed that the core consisted of long, iron-containing single crystals and that the core was fully surrounded by crystallized graphic carbon. Iron-filled carbo…

Structure analysis of titanate nanorods by automated electron diffraction tomography

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, prepared as nanorods, was investigated by electron diffraction, X-ray powder diffraction, thermogravimetric analysis and high-resolution transmission electron microscopy. The structure was determined ab initio using electron diffraction data collected by the recently developed automated diffraction tomography 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 crystallization. The nanorods are typically …

Structure solution with automated electron diffraction tomography data: different instrumental approaches

Summary Over the past few years automated electron diffraction tomography has become an established technique for structure solution of nano-crystalline material. The intentional choice of an arbitrary tilt axis and thus, the use of nonoriented diffraction patterns (off-zone acquisition) together with fine equidistant sampling of the reciprocal space result in high quality intensity data sets. Coupling automated electron diffraction tomography with electron beam precession (Vincent & Midgley, 1994) enables sampling of intensities between the static slices of reciprocal space and therefore enhances the quality of intensity data further; relatively complex structures have been solved using 3D…

Artificial granularity in two-dimensional arrays of nanodots fabricated by focused-electron-beam-induced deposition.

We have prepared 2D arrays of nanodots embedded in an insulating matrix by means of focused-electron-beam-induced deposition using the W(CO)(6) precursor. By varying the deposition parameters, i.e. the electron beam current and energy and the raster constant, we obtain an artificial granular material with tunable electrical properties. The analysis of the temperature dependence of the conductivity and of the current-voltage characteristic suggests that the transport mechanism is governed by electron tunneling between artificial grains. In order to understand the nature of the granularity and thus the microstructural origin of the electronic transport behavior, we perform TEM and micro-Raman…

Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data.

Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of 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 hydrogen-bonding scheme is realised; the hydrogen-bonding scheme is, however, in perfect agreement with solid-state NMR data.

Structural Characterization of Organics Using Manual and Automated Electron Diffraction

In the last decade the importance of transmission electron microscopic studies has become increasingly important with respect to the characterization of organic materials, ranging from small organic molecules to polymers and biological macromolecules. This review will focus on the use of transmission electron microscope to perform electron crystallography experiments, detailing the approaches in acquiring electron crystallographic data. The traditional selected area approach and the recently developed method of automated diffraction tomography (ADT) will be discussed with special attention paid to the handling of electron beam sensitive organic materials.

Towards automated diffraction tomography: Part I—Data acquisition

Abstract The ultimate aim of electron diffraction data collection for structure analysis is to sample the reciprocal space as accurately as possible to obtain a high-quality data set for crystal structure determination. Besides a more precise lattice parameter determination, fine sampling is expected to deliver superior data on reflection intensities, which is crucial for subsequent structure analysis. Traditionally, three-dimensional (3D) diffraction data are collected by manually tilting a crystal around a selected crystallographic axis and recording a set of diffraction patterns (a tilt series) at various crystallographic zones. In a second step, diffraction data from these zones are com…

Using Electron Diffraction to Solve the Crystal Structure of a Laked Azo Pigment

The structure of the ζ phase of Pigment Red 53:2 was solved using electron diffraction data. The unit cell determination appeared to be more complicated due to twinning of the crystals. A series of...

The crystallisation of copper(ii) phenylphosphonates

The crystal structures and syntheses of four different copper(II) phenylphosphonates, the monophenylphosphonates α-, β-, and γ-Cu(O3PC6H5)·H2O (α-CuPhPmH (1) β-CuPhPmH (2) and γ-CuPhPmH (3)), and the diphosphonate Cu(HO3PC6H5)2·H2O (CuPhP2mH (4)), are presented. The compounds were synthesized from solution at room temperature, at elevated temperature, under hydrothermal conditions, and mechanochemical conditions. The structures of α-CuPhPmH (1) and CuPhP2mH (4) were solved from powder X-ray diffraction data. The structure of β-CuPhPmH (2) was solved by single crystal X-ray analysis. The structures were validated by extended X-ray absorption fine structure (EXAFS) and DTA analyses. Disorder …

H-bonding schemes of di- and tri-p-benzamides assessed by a combination of electron diffraction, X-ray powder diffraction and solid-state NMR

The crystal structures of di- and tri-p-benzamides are solved by a combination of single crystal, electron and powder X-ray diffraction. Different hydrogen-bonding schemes observed in the two structures are described and classified. The hydrogen-bonding networks are correlated to complementary data obtained from multinuclear solid-state NMR.

“Ab-initio” structure solution of nano-crystalline minerals and synthetic materials by automated electron tomography

Most of the newly discovered mineral phases, as well as many new synthesized industrial materials, appear only in the form of nano crystals, with a size not sufficient for single-crystal x-ray structure analysis. The development of techniques able to investigate the structure of nano crystalline materials is therefore one of the most important frontiers of crystallography. The most widespread technique providing relatively fast and well consolidated routes for structure analysis of bulk materials is x-ray powder diffraction (XRPD). Nevertheless, XRPD suffers from intrinsic 1-dimension reduction of information that greatly limits its applicability in presence of peak broadening and overlappi…

Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C23H21N5O9.

The crystal structure of the nanocrystalline alpha phase of Pigment Yellow 213 (P.Y. 213) was solved by a combination of single-crystal electron diffraction and X-ray powder diffraction, despite the poor crystallinity of the material. The molecules form an efficient dense packing, which explains the observed insolubility and weather fastness of the pigment. The pair-distribution function (PDF) of the alpha phase is consistent with the determined crystal structure. The beta phase of P.Y. 213 shows even lower crystal quality, so extracting any structural information directly from the diffraction data is not possible. PDF analysis indicates the beta phase to have a columnar structure with a si…

Advances in automated diffraction tomography

Crystal structure solution by means of electron diffraction or investigation of special structural features needs high quality data acquisition followed by data processing which delivers cell parameters, space group and in the end a 3D data set. The final step is the structure analysis itself including structure solution and subsequent refinement.

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

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

Small Organic Molecules and Higher Homologs

ChemInform Abstract: Hydrate Networks under Mechanical Stress - A Case Study for Co3(PO4)2·8H2O.

The mechanochemically (ball milling) induced loss of bound H2O in Co3(PO4)2·8H2O is investigated together with an associated phase transition and its kinetics by powder synchrotron XRD and quantitative IR spectroscopy.

Towards automated diffraction tomography. Part II--Cell parameter determination.

Automated diffraction tomography (ADT) allows the collection of three-dimensional (3d) diffraction data sets from crystals down to a size of only few nanometres. 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 determination from the collected 3d diffraction data. Cell parameter determination is done via extraction of peak positions from a recorded data set (called the data reduction path) followed by subsequent cluster analysis of difference vectors. The procedure of lattice parameter determination is presented in detail f…

Total-scattering pair-distribution function of organic material from powder electron diffraction data.

AbstractThis paper shows that pair-distribution function (PDF) analyses can be carried out on organic and organometallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction and nanodiffraction in transmission electron microscopy or nanodiffraction in scanning transmission electron microscopy modes. The methods were demonstrated on organometallic complexes (chlorinated and unchlorinated copper phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrat…

ChemInform Abstract: Solution Synthesis of a New Thermoelectric Zn1+xSb Nanophase and Its Structure Determination Using Automated Electron Diffraction Tomography.

Thermoelectric nanoparticles of the nominal composition Zn4Sb3 are prepared by heating Sb nanoparticles with a 9-fold excess of Zn particles (synthesized by reaction of SbCl3 or ZnCl2 with Li[Et3BH] in THF at room temperature, and about 65 °C, respectively) in trioctylamine at about 300 °C for 225 min.

Crystal structure of disordered nanocrystalline $\alpha^{II}$-quinacridone determined by electron diffraction

CrystEngComm 18(4), 529 - 535(2016). doi:10.1039/C5CE01855B

Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters.

A new approach to determining the unit-cell vectors from single-crystal diffraction data based on clustering analysis is proposed. The method uses the density-based clustering algorithm DBSCAN. Unit-cell determination through the clustering procedure is particularly useful for limited tilt sequences and noisy data, and therefore is optimal for single-crystal electron-diffraction automated diffraction tomography (ADT) data. The unit-cell determination of various materials from ADT data as well as single-crystal X-ray data is demonstrated.

Automated diffraction tomography combined with electron precession: a new tool forab initionanostructure analysis

AbstractThree-dimensional electron diffraction data was collected with our recently developed module for automated diffraction tomography and used to solve inorganic as well as organic crystal structuresab initio. The diffraction data, which covers nearly the full relevant reciprocal space, was collected in the standard nano electron diffraction mode as well as in combination with the precession technique and was subsequently processed with a newly developed automated diffraction analysis and processing software package. Non-precessed data turned out to be sufficient forab initiostructure solution by direct methods for simple crystal structures only, while precessed data allowed structure s…

Introduction to ADT/ADT3D

ADT approach was successfully used within the last years to solve crystal structure of nanocrystalline material ab-inito using programs initially written for X-ray diffraction data. The methodology of ADT data analysis including data extraction in a format suitable for established structure solution programs was developed. A collection of processing routines was implemented into dedicated software ADT3D. Here the main steps of ADT data processing are explained, and the complete sequence of steps from importing raw data to saving the hklI file is demonstrated.

Reactive Polymers: A Versatile Toolbox for the Immobilization of Functional Molecules on TiO2 Nanoparticles

Facile synthesis and characterization of monocrystalline cubic ZrO2 nanoparticles

Abstract Crystalline ZrO2 nanoparticles were prepared from zirconium isopropoxide by slow hydrolysis and subsequent hydrothermal treatment of solutions containing various amounts of sodium hydroxide at 180 °C. Whereas moderately basic solutions lead to the formation of nanoparticles of monoclinic ZrO2 with plate-like morphology, and nanoparticles of the cubic ZrO2 high-temperature polymorph with diameters of approx. 5 nm were obtained from strongly basic solutions. The morphology, structure and properties of as-synthesized nanoparticles were characterized using HRTEM, XRD, Raman spectroscopy, UV–vis, PL spectroscopy and BET measurements. The formation of both, the monoclinic and the cubic p…

Nanostructuring with a crosslinkable discotic material.

A high-yielding synthesis afforded a hexa-peri-hexabenzocoronene carrying acrylate units at the end of six attached alkyl spacers. The polymerization of these acrylate moieties could be initiated with thermal energy and through direct photoactivation without the addition of a photoinitiator. This allowed the organization of the liquid-crystalline material to be fixed in either the crystalline state or the mesophase, which preserved the organization in the respective phase. The use of a focused synchrotron beam permitted selected regions of a thin film to be rendered insoluble. After "developing" the film in this lithographic process by dissolving the soluble, unpolymerized material, defined…

Pd@Fe2O3 Superparticles with Enhanced Peroxidase Activity by Solution Phase Epitaxial Growth

Compared to conventional deposition techniques for the epitaxial growth of metal oxide structures on a bulk metal substrate, wet-chemical synthesis based on a dispersible template offers advantages such as low cost, high throughput, and the capability to prepare metal/metal oxide nanostructures with controllable size and morphology. However, the synthesis of such organized multicomponent architectures is difficult because the size and morphology of the components are dictated by the interplay of interfacial strain and facet-specific reactivity. Here we show that solution-processable two-dimensional Pd nanotetrahedra and nanoplates can be used to direct the epitaxial growth of γ-Fe2O3 nanoro…

Haloperoxidase Mimicry by CeO2−xNanorods Combats Biofouling

CeO2-x nanorods are functional mimics of natural haloperoxidases. They catalyze the oxidative bromination of phenol red to bromophenol blue and of natural signaling molecules involved in bacterial quorum sensing. Laboratory and field tests with paint formulations containing 2 wt% of CeO2-x nanorods show a reduction in biofouling comparable to Cu2 O, the most typical biocidal pigment.

Hydrate Networks under Mechanical Stress – A Case Study for Co 3 (PO 4 ) 2 ·8H 2 O

The nature of the bound water in solids with hydrogen-bonded networks depends not only on temperature and pressure but also on the nature of the constituents. The collapse and reorientation of these network structures determines the stability of hydrated solids and transitions to other crystalline or amorphous phases. Here, we study the mechanochemically induced loss of bound water in Co₃(PO₄)₂·8H₂O and compare this process to the behavior under hydrostatic pressure. The associated phase transition and its kinetics were monitored by X-ray powder diffraction with Synchrotron radiation and quantitative IR spectroscopy. High shearing forces are responsible for the degradation of the hydrogen-b…