scholarly journals Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

Diffraction by crystals

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Three Dimensional ◽  
Incident Beam ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Angle Of Incidence ◽  
X Ray ◽  
Max Von Laue ◽  
The Fourier Transform

In Chapter 4 many two-dimensional examples were shown, in which a diffraction pattern represents the Fourier transform of the scattering object. When a diffracting object is three-dimensional, a new effect arises. In diffraction by a repetitive object, rays are scattered in many directions. Each unit of the lattice scatters, but a diffracted beam arises only if the scattered rays from each unit are all in phase. Otherwise the scattering from one unit is cancelled out by another. In two dimensions, there is always a direction where the scattered rays are in phase for any order of diffraction (just as shown for a one-dimensional scatterer in Fig. 4.1). In three dimensions, it is only possible for all the points of a lattice to scatter in phase if the crystal is correctly oriented in the incident beam. The amplitudes and phases of all the scattered beams from a three-dimensional crystal still provide the Fourier transform of the three-dimensional structure. But when a crystal is at a particular angular orientation to the X-ray beam, the scattering of a monochromatic beam provides only a tiny sample of the total Fourier transform of its structure. In the next section, we are going to find what is needed to allow a diffracted beam to be generated. We shall follow a treatment invented by Lawrence Bragg in 1913. Max von Laue, who discovered X-ray diffraction in 1912, used a different scheme of analysis; and Paul Ewald introduced a new way of looking at it in 1921. These three methods are referred to as the Laue equations, Bragg’s law and the Ewald construction, and they give identical results. All three are described in many crystallographic text books. Bragg’s method is straightforward, understandable, and suffices for present needs. I had heard J.J. Thomson lecture about…X-rays as very short pulses of radiation. I worked out that such pulses…should be reflected at any angle of incidence by the sheets of atoms in the crystal as if these sheets were mirrors.…It remained to explain why certain of the atomic mirrors in the zinc blende [ZnS] crystal reflected more powerfully than others.

Three-dimensional morphology of anatase nanocrystals obtained from supercritical flow synthesis with industrial grade TiOSO4 precursor

2019 ◽  
Vol 75 (6) ◽  
pp. 1086-1095 ◽  
Author(s):  
Jinlong Yu ◽  
Frederik Søndergaard-Pedersen ◽  
Aref Mamakhel ◽  
Paolo Lamagni ◽  
Bo Brummerstedt Iversen
Keyword(s):  
Three Dimensional ◽  
High Specific Surface Area ◽  
X Ray Diffraction ◽  
Titanyl Sulfate ◽  
Supercritical Flow ◽  
Price Expectation ◽  
X Ray ◽  
Industrial Grade ◽  
Transmission Electron ◽  
Dimensional Reconstruction

Anatase TiO2 (a-TiO2) nanocrystals are vital in catalytic applications both as catalysts (e.g. photodegradation) and as a carrier material (e.g. NOx removal from exhaust). The synthesis of a-TiO2 nanocrystals and their properties have been heavily scrutinized, but there exists a clear gap between the scientific literature, and the scale and price expectation of industrial application. Here it is demonstrated that the industrially most attractive Ti precursor, titanyl sulfate (TiOSO4), can be combined with the green, scalable and fast supercritical flow method to produce phase pure and highly crystalline a-TiO2 nanoparticles with high specific surface area. Control of the nanocrystal morphology is important since it is known that certain facets substantially promote catalytic activity. It is, however, in itself challenging to determine nanocrystal morphology to provide a rational basis for the synthesis control. Here we advocate the use of advanced Rietveld refinement of powder X-ray diffraction data including anisotropic size broadening models in aiding to establish the sample three-dimensional morphology. This relatively quick and robust method assists in overcoming the often encountered ambiguity inherent in two-dimensional to three-dimensional reconstruction of selected particle morphologies with transmission electron microscopy and tomography techniques.

Study on Novel Structure of Potassium Borate Hydrate: K(H4B5O10)·2(H2O)

2012 ◽  
Vol 531-532 ◽  
pp. 409-412
Author(s):  
Hai Xing Liu ◽  
Fang Fang Jian ◽  
Jing Wang ◽  
Guang Zeng ◽  
Hui Juan Yue ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Potassium Borate ◽  
Polyhydroxy Compounds ◽  
Novel Structure ◽  
Solution Reaction

Numerous stable complexes of boric acid with polyhydroxy compounds, including tartaric, salicylic, citric, malic, and other acids, are known. The structure of some compounds contains polyanion. In this paper, a novel potassium borate hydrate [K(H4B5O10) •2(H2O)] has been synthesized from a solution reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. Orthorhombic, Aba2. a = 11.0781(14) Å b = 11.1780(15) Å c = 9.0508(11) Å α=β=γ=90°. V= 1120.8(2) Å3. Z=4. Rgt = 0.0244, wRref = 0.0623. T= 298 K. The crystal packing is stabilized by O-H...O hydrogen bonds interaction and three dimensional framwork structure is formed. The work is originality and has a new crystallographic structure shape.

scholarly journals Structure of catalase determined by MicroED

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Brent L Nannenga ◽  
Dan Shi ◽  
Johan Hattne ◽  
Francis E Reyes ◽  
Tamir Gonen
Keyword(s):  
Structure Determination ◽  
Three Dimensional ◽  
Bovine Liver ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Continuous Rotation ◽  
Bovine Liver Catalase ◽  
Diffraction Patterns ◽  
Atomic Analysis

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (<xref ref-type="bibr" rid="bib26">Shi et al., 2013</xref>). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

Three-dimensional grain resolved strain mapping using laboratory X-ray diffraction contrast tomography: theoretical analysis

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Adam Lindkvist ◽  
Yubin Zhang
Keyword(s):  
Near Field ◽  
Three Dimensional ◽  
Simulated Data ◽  
Three Dimensions ◽  
X Ray Diffraction ◽  
Strain Mapping ◽  
X Ray ◽  
Microstructural Parameters ◽  
Diffraction Contrast ◽  
Sample Distance

Laboratory diffraction contrast tomography (LabDCT) is a recently developed technique to map crystallographic orientations of polycrystalline samples in three dimensions non-destructively using a laboratory X-ray source. In this work, a new theoretical procedure, named LabXRS, expanding LabDCT to include mapping of the deviatoric strain tensors on the grain scale, is proposed and validated using simulated data. For the validation, the geometries investigated include a typical near-field LabDCT setup utilizing Laue focusing with equal source-to-sample and sample-to-detector distances of 14 mm, a magnified setup where the sample-to-detector distance is increased to 200 mm, a far-field Laue focusing setup where the source-to-sample distance is also increased to 200 mm, and a near-field setup with a source-to-sample distance of 200 mm. The strain resolution is found to be in the range of 1–5 × 10−4, depending on the geometry of the experiment. The effects of other experimental parameters, including pixel binning, number of projections and imaging noise, as well as microstructural parameters, including grain position, grain size and grain orientation, on the strain resolution are examined. The dependencies of these parameters, as well as the implications for practical experiments, are discussed.

Three-Dimensional Reconstruction of Atoms in Surface X-Ray Diffraction

2003 ◽  
Vol 42 (Part 2, No. 2B) ◽  
pp. L189-L191 ◽  
Author(s):  
Kazushi Sumitani ◽  
Toshio Takahashi ◽  
Shinichiro Nakatani ◽  
Akinobu Nojima ◽  
Osami Sakata ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Three Dimensional Reconstruction ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimensional Reconstruction
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