HRTEM of antigorite: The structure as a polysomatic series

1988 ◽  
Vol 46 ◽  
pp. 566-567
Author(s):  
Gerard E. Spinnler ◽  
Max T. Otten
Keyword(s):  
Crystal Structures ◽  
Structural Information ◽  
Structure Refinement ◽  
Structural Data ◽  
Structural Disorder ◽  
Fourier Synthesis ◽  
Flat Plates ◽  
Serpentine Minerals ◽  
Transmission Electron ◽  
Approximate Composition

Antigorite is one of the serpentine minerals, a group of 1:1 layer silicates with the approximate composition of Mg3Si2O5(OH)4. These minerals display an unusual variety of crystal structures even though they are almost identical in composition; chrysotile has an elongated-tube structure, lizardite occurs as flat plates, and antigorite has corrugates layers.The details of the crystal structures of the serpentine minerals are not completely known. Threedimensional structure refinements only exist for one- and two- layer lizardite. For antigorite, the only direct structural information consists of a two-dimensional Fourier synthesis of hOI diffractions. The lack of detailed structural data on these minerals arises from the complexity of the structures as well as the paucity of sufficiently large, well-formed single crystals. In addition, structural disorder is common in these minerals, making structure refinement difficult.High resolution transmission electron microscopy (HRTEM) has been used to study antigorite in order to discriminate among various structural models of antigorite and to characterize its microstructures

Lattice-Fringe Fingerprinting: Structural identification of nanocrystals by HRTEM

2007 ◽  
Vol 1026 ◽  
Author(s):  
Moeck Peter ◽  
Ruben Bjorge
Keyword(s):  
Structural Information ◽  
Reciprocal Lattice ◽  
Chemical Information ◽  
Fourier Synthesis ◽  
Transmission Electron ◽  
Structure Factors ◽  
Lattice Geometry ◽  
Group A ◽  
Experimental Side ◽  
Novel Method

AbstractA novel method for the structurally identification of a nanocrystal from a single high resolution (HR) transmission electron microscopy (TEM) micrograph is described. Components of this method are demonstrated on both experimental and simulated HRTEM images. On the experimental side, the structural information that can be extracted from a HRTEM image is the projected reciprocal lattice geometry, the plane symmetry group, a few structure factor amplitudes and phases, and an outline of the projected atomic structure to the limited resolution of the HRTEM (via a Fourier synthesis of the structure factors). Searching for this information in a comprehensive database and matching it with high figures of merit to that of candidate structures should allow for highly discriminatory identifications of nanocrystals, even without additional chemical information as obtainable in analytical TEMs.

Crystal structures of cubic nitroprussides: M[Fe(CN)5NO]·xH2O(M=Fe, Co, Ni). Obtaining structural information from the background

2007 ◽  
Vol 22 (1) ◽  
pp. 27-34 ◽  
Author(s):  
A. Gómez ◽  
J. Rodríguez-Hernández ◽  
E. Reguera
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Model ◽  
Structural Information ◽  
Structural Disorder ◽  
Crystal Water ◽  
Metal Centers ◽  
Charge Delocalization ◽  
Positional Disorder ◽  
Local Environments

A new structural model is proposed for cubic nitroprussides and the crystal structure for the complex salts of Fe(2+), Co(2+), and Ni(2+) refined in that model. In cubic nitroprussides the building unit, [Fe(CN)5NO]2−, and the assembling metal (M=Fe2+, Co2+, Ni2+), have ¾ occupancy with three formula units per cell (Z=3). This leads to certain structural disorder and to different local environments for the outer metal. The crystallographic results are supported by the Mössbauer and infrared data. The XRD powder patterns, index in a cubic cell (Fm3m space group), show a sinuous background because of diffuse scattering from positional disorder of the metal centers. Because of this, the crystal structures were refined allowing the metal centers to move from the (0,0,0) and (0,0,1/2) positions (away from positional symmetry restrictions). The refinement under these conditions leads to excellent agreement factors (Rwp, Rp, S), good pattern background fitting, and produced a refined structural model consistent with the crystal chemistry of nitroprussides. The studied materials are obtained as hydrates. On heating, the crystal water evolves, and below 100°C an anhydrous phase is obtained, preserving the framework of the original hydrates. The loss of the crystal water leads to cell contraction that represents around 2% of cell volume reduction. On cooling down from room temperature to 77 and 12 K, a slight expansion for the -M-N≡C-Fe-C≡N-M- chain length is observed, suggesting that at low temperature and reduction in the metals charge delocalization on the CN bridges takes place. For M=Fe and Co the crystal structure was also refined for the anhydrous phase at 12, 77, and 300 K.

Measurement and Reduction of Radiation Damage in Frozen Hydrated Crystalline Specimens

1978 ◽  
Vol 36 (3) ◽  
pp. 70-77 ◽  
Author(s):  
R.M. Glaeser ◽  
S.B. Hayward
Keyword(s):  
Diffraction Pattern ◽  
Structural Information ◽  
Structural Disorder ◽  
Structural Features ◽  
Biological Macromolecules ◽  
Diffraction Intensity ◽  
Object Structure ◽  
Specimen Material ◽  
Unit Cells ◽  
Identical Unit

Highly ordered or crystalline biological macromolecules become severely damaged and structurally disordered after a brief electron exposure. Evidence that damage and structural disorder are occurring is clearly given by the fading and eventual disappearance of the specimen's electron diffraction pattern. The fading and disappearance of sharp diffraction spots implies a corresponding disappearance of periodic structural features in the specimen. By the same token, there is a oneto- one correspondence between the disappearance of the crystalline diffraction pattern and the disappearance of reproducible structural information that can be observed in the images of identical unit cells of the object structure. The electron exposures that result in a significant decrease in the diffraction intensity will depend somewhat upon the resolution (Bragg spacing) involved, and can vary considerably with the chemical makeup and composition of the specimen material.

Transmission electron microscope studies in special ceramics

1978 ◽  
Vol 36 (1) ◽  
pp. 268-269
Author(s):  
A. Zangvil ◽  
L.J. Gauckler ◽  
G. Schneider ◽  
M. Rühle
Keyword(s):  
Phase Diagrams ◽  
Crystal Structures ◽  
Thin Foil ◽  
Limited Extent ◽  
Complex Materials ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Electron Microscopes ◽  
Lattice Resolution

The use of high temperature special ceramics which are usually complex materials based on oxides, nitrides, carbides and borides of silicon and aluminum, is critically dependent on their thermomechanical and other physical properties. The investigations of the phase diagrams, crystal structures and microstructural features are essential for better understanding of the macro-properties. Phase diagrams and crystal structures have been studied mainly by X-ray diffraction (XRD). Transmission electron microscopy (TEM) has contributed to this field to a very limited extent; it has been used more extensively in the study of microstructure, phase transformations and lattice defects. Often only TEM can give solutions to numerous problems in the above fields, since the various phases exist in extremely fine grains and subgrain structures; single crystals of appreciable size are often not available. Examples with some of our experimental results from two multicomponent systems are presented here. The standard ion thinning technique was used for the preparation of thin foil samples, which were then investigated with JEOL 200A and Siemens ELMISKOP 102 (for the lattice resolution work) electron microscopes.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

Structural studies of small amorphous volumes by electron diffraction

1990 ◽  
Vol 48 (4) ◽  
pp. 122-123
Author(s):  
Pierre Moine
Keyword(s):  
Electron Diffraction ◽  
Born Approximation ◽  
Structural Information ◽  
Fundamental Relation ◽  
X Rays ◽  
Structural Studies ◽  
Diffraction Experiment ◽  
Transmission Electron ◽  
Amorphous Structures ◽  
Diffraction Patterns

Qualitatively, amorphous structures can be easily revealed and differentiated from crystalline phases by their Transmission Electron Microscopy (TEM) images and their diffraction patterns (fig.1 and 2) but, for quantitative structural information, electron diffraction pattern intensity analyses are necessary. The parameters describing the structure of an amorphous specimen have been introduced in the context of scattering experiments which have been, so far, the most used techniques to obtain structural information in the form of statistical averages. When only small amorphous volumes (< 1/μm in size or thickness) are available, the much higher scattering of electrons (compared to neutrons or x rays) makes, despite its drawbacks, electron diffraction extremely valuable and often the only feasible technique.In a diffraction experiment, the intensity IN (Q) of a radiation, elastically scattered by N atoms of a sample, is measured and related to the atomic structure, using the fundamental relation (Born approximation) : IN(Q) = |FT[U(r)]|.

HRTEM study of valleriite, a hydroxide-bearing copper sulfide

1990 ◽  
Vol 48 (4) ◽  
pp. 462-463
Author(s):  
S. Wang ◽  
P. R. Buseck
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Copper Sulfide ◽  
Carbonaceous Chondrite ◽  
Structural Data ◽  
Basic Structure ◽  
Long Period ◽  
Selected Area Electron Diffraction ◽  
Transmission Electron ◽  
Wavy Structure

Valleriite is an unusual mineral, consisting of intergrowths of sulfide layers (corresponding in structure to the mineral smythite - Fe9S11) and hydroxide layers (corresponding to brucite - Mg(OH2)). It has a composition of approximately 1.526[Mg.68Al.32(OH)2].[Fe1.07Cu.93S2] and consists of two interpenetrating lattices, each of which retains its individual structural and diffraction characteristics parallel to the layering. The valleriite structure is related to that of tochilinite, an unusual iron-rich mineral that is of considerable interest for the origin of certain carbonaceous chondrite meteorites and to those of franckeite and cylindrite, two minerals that are of interest because of their unique morphological and crystallographic properties, e.g., the distinctive curved form of cylindrite and the perfect mica-like cleavage with unusual striations and the long-period wavy structure of franckeite.Our selected-area electron diffraction (SAED) patterns and high-resolution transmission electron microscope (HRTEM) images of valleriite provide new structural data. A basic structure and a new superstructure have been observed.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

scholarly journals Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

2020 ◽  
Vol 48 (22) ◽  
pp. 12604-12617
Author(s):  
Pengpeng Long ◽  
Lu Zhang ◽  
Bin Huang ◽  
Quan Chen ◽  
Haiyan Liu
Keyword(s):  
Genome Sequence ◽  
Energy Function ◽  
Structural Information ◽  
Structural Data ◽  
P Values ◽  
A Genome ◽  
Z Scores ◽  
Transcription Regulators ◽  
Dna Specificity ◽  
Tetracycline Repressor

Abstract We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.

Mesoscopic characterization of the optical property of antiphase boundaries in CuPt-ordered GaInP2

1999 ◽  
Vol 588 ◽  
Author(s):  
Y. Ohno ◽  
S. Takeda
Keyword(s):  
Optical Property ◽  
Light Emission ◽  
Polarized Light ◽  
Structural Data ◽  
Luminescence Spectra ◽  
Antiphase Boundaries ◽  
Transmission Electron ◽  
Tem Method ◽  
Low Dimensional ◽  
First Time

AbstractWe have developed an apparatus for polarized cathodoluminescence (CL) spectroscopy combined with transmission electron microscopy (TEM), that enables us to obtain simultaneously structural data in higher spatial resolution by TEM and polarized luminescence spectra by CL of the same microscopic area. The polarized-CL/TEM method is very useful to study the optical properties of low-dimensional microstructures in semiconducting materials. We have applied the method to examine the optical property of antiphase boundaries in CuPt-ordered GaInP2 and found, for the first time, the polarized light emission from the APBs whose habit planes are parallel to the (T11) and (1T0) atomic planes.

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