scholarly journals Atomic structure of a single large biomolecule from diffraction patterns of random orientations

2012 ◽  
Vol 179 (1) ◽  
pp. 41-45 ◽  
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Atomic Structure ◽  
Large Biomolecule ◽  
Diffraction Patterns

scholarly journals Local atomic structure determination using focused electron beams

2014 ◽  
Vol 70 (a1) ◽  
pp. C26-C26
Author(s):  
Joanne Etheridge
Keyword(s):  
Quantum Wells ◽  
Atomic Structure ◽  
Structural Information ◽  
Electron Beams ◽  
Focal Point ◽  
Local Atomic Structure ◽  
Atomic Scale ◽  
Chemical Information ◽  
Diffraction Patterns

This talk will give an overview of methods for solving the atomic structure of nanostructured materials using focused electron beams. It will illustrate these methods with a range of applications, such as the determination of the atomic structure and stability of nanoparticle facets [1]; the local atomic structure of "chessboard' nanostructures in lithium-based titanate perovskites; and the measurement of local polarity, dopant concentration and atomic-scale morphology in semiconducting nanowire quantum wells. These methods take advantage of the fact that electron wavefields can be brought to a focal point smaller than an Ångström in diameter, enabling small volumes of matter to be probed and characterized. The wealth of information contained in the resulting diffraction patterns can be interrogated selectively to isolate and `image' specific structural information. Several methods using small focused electron beams will be described in this talk, including; (i) An approach for the determination of centrosymmetric structures from the direct observation of structure factor phases by inspection of features in convergent beam electron diffraction patterns [2]. The method can achieve high resolution from just a few phase observations and no intensity measurements or iterative refinements are required; (ii) Methods for the quantitative interpretation of the intensity in atomic resolution imaging and diffraction data for the measurement of local atomic and electronic structure; (iii) Pseudo-confocal scanning transmission electron microscopy methods for obtaining depth and chemical information which record the scattered intensity in a plane conjugate to the specimen (as opposed to the diffraction plane) [3].

scholarly journals Direct refinement of the atomic structure of MoS2layered compounds from PXRD

2014 ◽  
Vol 70 (a1) ◽  
pp. C511-C511
Author(s):  
Ivan Bushmarinov ◽  
Alexander Goloveshkin ◽  
Alexandre Golub
Keyword(s):  
Atomic Structure ◽  
Stoichiometric Composition ◽  
Intercalation Compounds ◽  
Layered Compounds ◽  
Organic Layer ◽  
Published Data ◽  
X Ray Diffraction ◽  
Cell Content ◽  
X Ray ◽  
Diffraction Patterns

The graphene analog MoS2can be exfoliated into single-layer dispersion of MoS2crystals by reduction of starting material to LiMoS2followed by detachment of its layers in aqueous solvents. This dispersion reacts with organic salts in solution, producing precipitates of layered MoS2intercalated with their cations [1]. Most of these compounds have distinct chemical composition and powder X-ray diffraction (PXRD) patterns. The analysis of published data, however, indicates that these diffraction patterns were used only for fingerprinting and estimation of cation size and orientation by checking the positions of the basal (00l) reflections. The low-intensity hkl zone of the diffraction patterns was effectively ignored. In the current work, we report that the diffraction patterns of MoS2intercalation compounds contain enough information to refine their atomic structure directly. We found that the patterns of (NR4)x MoS2(R=alkyl, H) compounds correspond to turbostratic disorder of MoS2-organic layers. The patterns were indexed with a common orthorhombic cell. The cell content was Rietveld refined using a modification of a "supercell approach" [2,3] developed for full-pattern modeling of disordered clays. We determined that the Mo atoms in MoS2layers in the intercalation compounds change the coordination from prismatic to octahedral and that the S atoms form "nanorunnels" containing organic cations. The geometry of the Mo-Mo chains forming in the layer was consistent with the EXAFS data. The ordering of the organic layer depended on the nature of the cation, with (NEt4)x MoS2notably ordered enough to have specific stoichiometric composition (x=1/6) defined by the intralayer packing. The PW-DFT-d calculations based on our model confirmed our results. The developed approach allows determination of previously inaccessible atomic structures of a wide class of MoS2-based layered compounds using commercially available software and laboratory X-ray diffraction data.

More features, more tools, moreCrysTBox

2017 ◽  
Vol 50 (4) ◽  
pp. 1226-1234 ◽  
Author(s):  
Miloslav Klinger
Keyword(s):  
Atomic Structure ◽  
Automated Analysis ◽  
Inverse Pole Figure ◽  
Input Image ◽  
Accurate Analysis ◽  
Transmission Electron ◽  
High Resolution Tem ◽  
Diffraction Patterns ◽  
Crystallographic Planes ◽  
Convergent Beam

A new release of theCrysTBoxsoftware is introduced. The original toolbox allows for an automated analysis of transmission electron microscope (TEM) images and for crystallographic visualization. The existing tools, which are capable of highly precise analyses of high-resolution TEM images, as well as spot, disc and ring diffraction patterns, are extended to include a tool for automatically measuring TEM sample thickness using convergent beam electron diffraction in a two-beam approximation. An implementation of geometric phase analysis is newly available, employing one of the existing tools to identify parameters and indices of crystallographic planes depicted in the input image and allowing easier and more accurate analysis. The crystallographic visualization capabilities are extended as well. Along with the simulated diffraction pattern and atomic structure, a stereographic projection and inverse pole figure tool is newly offered. A new tool able to visualize the atomic structure of two different phases and their interface is also introduced.

Light Optical Diffraction Studies of Macromolecular Ultrastructure

1970 ◽  
Vol 28 ◽  
pp. 258-259
Author(s):  
Glen B. Haydon
Keyword(s):  
High Resolution ◽  
Diffraction Analysis ◽  
Diffraction Pattern ◽  
Electron Micrographs ◽  
Optical Diffraction ◽  
Electron Micrograph ◽  
Its Analysis ◽  
Resolution Electron ◽  
Diffraction Patterns

Analysis of light optical diffraction patterns produced by electron micrographs can easily lead to much nonsense. Such diffraction patterns are referred to as optical transforms and are compared with transforms produced by a variety of mathematical manipulations. In the use of light optical diffraction patterns to study periodicities in macromolecular ultrastructures, a number of potential pitfalls have been rediscovered. The limitations apply to the formation of the electron micrograph as well as its analysis.(1) The high resolution electron micrograph is itself a complex diffraction pattern resulting from the specimen, its stain, and its supporting substrate. Cowley and Moodie (Proc. Phys. Soc. B, LXX 497, 1957) demonstrated changing image patterns with changes in focus. Similar defocus images have been subjected to further light optical diffraction analysis.

Electron microscopy and diffraction studies of polyimides

1983 ◽  
Vol 41 ◽  
pp. 28-29
Author(s):  
O.C. de Hodgins ◽  
K. R. Lawless ◽  
R. Anderson
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Structural Features ◽  
Inert Atmosphere ◽  
Polyimide Films ◽  
Resolution Electron ◽  
The Matrix ◽  
High Resolution Electron Microscope ◽  
Diffraction Patterns ◽  
Polymeric Samples

Commercial polyimide films have shown to be homogeneous on a scale of 5 to 200 nm. The observation of Skybond (SKB) 705 and PI5878 was carried out by using a Philips 400, 120 KeV STEM. The objective was to elucidate the structural features of the polymeric samples. The specimens were spun and cured at stepped temperatures in an inert atmosphere and cooled slowly for eight hours. TEM micrographs showed heterogeneities (or nodular structures) generally on a scale of 100 nm for PI5878 and approximately 40 nm for SKB 705, present in large volume fractions of both specimens. See Figures 1 and 2. It is possible that the nodulus observed may be associated with surface effects and the structure of the polymers be regarded as random amorphous arrays. Diffraction patterns of the matrix and the nodular areas showed different amorphous ring patterns in both materials. The specimens were viewed in both bright and dark fields using a high resolution electron microscope which provided magnifications of 100,000X or more on the photographic plates if desired.

Two Investigations into Grain Boundary Structure

1977 ◽  
Vol 35 ◽  
pp. 688-691
Author(s):  
P. Humble
Keyword(s):  
Grain Boundary ◽  
Dark Field ◽  
Boundary Structure ◽  
Boundary Dislocation ◽  
Bright Field ◽  
Intrinsic Structure ◽  
Weak Beam ◽  
Grain Boundary Structure ◽  
Independent Information ◽  
Diffraction Patterns

There has been sustained interest over the last few years into both the intrinsic (primary and secondary) structure of grain boundaries and the extrinsic structure e.g. the interaction of matrix dislocations with the boundary. Most of the investigations carried out by electron microscopy have involved only the use of information contained in the transmitted image (bright field, dark field, weak beam etc.). Whilst these imaging modes are appropriate to the cases of relatively coarse intrinsic or extrinsic grain boundary dislocation structures, it is apparent that in principle (and indeed in practice, e.g. (1)-(3)) the diffraction patterns from the boundary can give extra independent information about the fine scale periodic intrinsic structure of the boundary.In this paper I shall describe one investigation into each type of structure using the appropriate method of obtaining the necessary information which has been carried out recently at Tribophysics.

Disappearance Voltage Determinations Using a Convergent Beam

1971 ◽  
Vol 29 ◽  
pp. 184-185
Author(s):  
W. L. Bell
Keyword(s):  
Second Order ◽  
Objective Method ◽  
Uniform Thickness ◽  
Rocking Curve ◽  
Crystal Perfection ◽  
Kikuchi Line ◽  
Central Maximum ◽  
Diffraction Patterns ◽  
Convergent Beam ◽  
Beam Technique

Disappearance voltages for second order reflections can be determined experimentally in a variety of ways. The more subjective methods, such as Kikuchi line disappearance and bend contour imaging, involve comparing a series of diffraction patterns or micrographs taken at intervals throughout the disappearance range and selecting that voltage which gives the strongest disappearance effect. The estimated accuracies of these methods are both to within 10 kV, or about 2-4%, of the true disappearance voltage, which is quite sufficient for using these voltages in further calculations. However, it is the necessity of determining this information by comparisons of exposed plates rather than while operating the microscope that detracts from the immediate usefulness of these methods if there is reason to perform experiments at an unknown disappearance voltage.The convergent beam technique for determining the disappearance voltage has been found to be a highly objective method when it is applicable, i.e. when reasonable crystal perfection exists and an area of uniform thickness can be found. The criterion for determining this voltage is that the central maximum disappear from the rocking curve for the second order spot.

Electronic Cone Illumination with the Conventional Transmission Electron Microscope

1977 ◽  
Vol 35 ◽  
pp. 72-73
Author(s):  
William Krakow
Keyword(s):  
Electronic Device ◽  
Chromatic Aberration ◽  
Objective Lens ◽  
Hollow Cone ◽  
Transmission Electron ◽  
Lissajous Figures ◽  
High Resolution Images ◽  
Imaging Mode ◽  
Diffraction Patterns ◽  
Transmission Microscope

An electronic device has been constructed which manipulates the primary beam in the conventional transmission microscope to illuminate a specimen under a variety of virtual condenser aperture conditions. The device uses the existing tilt coils of the microscope, and modulates the D.C. signals to both x and y tilt directions simultaneously with various waveforms to produce Lissajous figures in the back-focal plane of the objective lens. Electron diffraction patterns can be recorded which reflect the manner in which the direct beam is tilted during exposure of a micrograph. The device has been utilized mainly for the hollow cone imaging mode where the device provides a microscope transfer function without zeros in all spatial directions and has produced high resolution images which are also free from the effect of chromatic aberration. A standard second condenser aperture is employed and the width of the cone annulus is readily controlled by defocusing the second condenser lens.

Computer Indexing of Electron Diffraction Patterns Including the Effects of Lattice Symmetry

1977 ◽  
Vol 35 ◽  
pp. 22-23
Author(s):  
J. S. Lally ◽  
R. J. Lee
Keyword(s):  
Electron Diffraction ◽  
Zone Axis ◽  
Crystal Thickness ◽  
Double Diffraction ◽  
Automated Method ◽  
Lattice Symmetry ◽  
Intensity Calculations ◽  
Unknown Structure ◽  
Diffraction Patterns ◽  
Orientation Parameters

In the 50 year period since the discovery of electron diffraction from crystals there has been much theoretical effort devoted to the calculation of diffracted intensities as a function of crystal thickness, orientation, and structure. However, in many applications of electron diffraction what is required is a simple identification of an unknown structure when some of the shape and orientation parameters required for intensity calculations are not known. In these circumstances an automated method is needed to solve diffraction patterns obtained near crystal zone axis directions that includes the effects of systematic absences of reflections due to lattice symmetry effects and additional reflections due to double diffraction processes.Two programs have been developed to enable relatively inexperienced microscopists to identify unknown crystals from diffraction patterns. Before indexing any given electron diffraction pattern, a set of possible crystal structures must be selected for comparison against the unknown.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

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