Structural analysis and potential extraction from diffraction data of disordered systems by least-biased feature matching

2021 ◽  
Vol 155 (23) ◽  
pp. 234501
Author(s):  
Yuansheng Zhao
Keyword(s):  
Structural Analysis ◽  
Diffraction Data ◽  
Disordered Systems ◽  
Feature Matching

Turbostratic Disorder in [(Bi2Te3)x(TiTe2)y] Superlattices

2003 ◽  
Vol 793 ◽  
Author(s):  
Fred R. Harris ◽  
Stacey Standridge ◽  
Carolyn Feik ◽  
David C. Johnson
Keyword(s):  
Structural Analysis ◽  
Diffraction Data ◽  
Two Dimensional ◽  
Superlattice Structure ◽  
Number Of Layers ◽  
Turbostratic Disorder ◽  
Diffraction Peaks ◽  
Superlattice Structures ◽  
Modulated Elemental Reactant ◽  
Type Of Behavior

ABSTRACTA family of metastable [(Bi2Te3)x(TiTe2)y] superlattices (where × and y denote the number of layers of each of the two components) was prepared by annealing modulated elemental reactant precursors at temperatures below 280°C. Structural analysis by traditional XRD shows the superlattice structures are highly aligned to the substrate with many orders of diffraction peaks from the c direction of the superlattice. Off-axis diffraction techniques presented in this paper suggest that the order between the layers in the a-b direction of these superlattice structures is turbostratic. In this type of behavior, the quasi two-dimensional crystals of Bi2Te3 and TiTe2 that comprise the superlattice structure lie like a deck of cards thrown in disarray on a surface. An analysis of the diffraction data leading to this conclusion is given.

scholarly journals PyMDA: microcrystal data assembly using Python

2020 ◽  
Vol 53 (1) ◽  
pp. 277-281
Author(s):  
Lina Takemaru ◽  
Gongrui Guo ◽  
Ping Zhu ◽  
Wayne A. Hendrickson ◽  
Sean McSweeney ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Data Quality ◽  
Diffraction Data ◽  
Incomplete Data ◽  
Unit Cell ◽  
Data Sets ◽  
X Ray ◽  
Assembly Method ◽  
Multi Stage ◽  
Recent Developments

The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.

scholarly journals Crystallization, preliminary X-ray diffraction analysis and Patterson search of oxyhaemoglobin I from the wolf (Chrysocyon brachiurus)

1999 ◽  
Vol 55 (9) ◽  
pp. 1618-1619 ◽  
Author(s):  
A. L. S. Smarra ◽  
V. Fadel ◽  
M. Dellamano ◽  
J. R. Olivieri ◽  
W. F. de Azevedo ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Structural Analysis ◽  
Synchrotron Radiation ◽  
Diffraction Data ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Comparative Biochemistry ◽  
X Ray ◽  
Patterson Search

Oxyhaemoglobin I isolated from the Brazilian wolf Chrysocyon brachiurus has been crystallized and X-ray diffraction data has been collected to 2.06 Å resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P212121 and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit. The structure was determined using standard molecular-replacement techniques and is currently being refined using maximum-likelihood protocols. This is the first haemoglobin isolated from a member of the Canidae family to be crystallized and it will provide further insights in the comparative biochemistry of vertebrate haemoglobins.

scholarly journals Constraints and restraints in crystal structure analysis

2009 ◽  
Vol 42 (2) ◽  
pp. 362-364 ◽  
Author(s):  
Attilio Immirzi
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Structure Analysis ◽  
Diffraction Data ◽  
Crystal Structure Analysis ◽  
Internal Coordinates

The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed.

X-ray absorption spectroscopy principles and practical use in materials analysis

2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Wolfgang Grünert ◽  
Konstantin Klementiev
Keyword(s):  
Fine Structure ◽  
Structural Analysis ◽  
Disordered Systems ◽  
Structural Information ◽  
Research Strategies ◽  
Edge Structure ◽  
X Ray ◽  
Absorption Fine ◽  
Wide Range ◽  
X Ray Absorption

AbstractThe X-ray Absorption Fine Structure (XAFS) with its subregions X-ray Absorption Near-edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) is a powerful tool for the structural analysis of materials, which is nowadays a standard component of research strategies in many fields. This review covers a wide range of topics related to its measurement and use: the origin of the fine structure, its analytical potential, derived from the physical basis, the environment for measuring XAFS at synchrotrons, including different measurement geometries, detection modes, and sample environments, e. g. for in-situ and operando work, the principles of data reduction, analysis, and interpretation, and a perspective on new methods for structure analysis combining X-ray absorption with X-ray emission. Examples for the application of XAFS have been selected from work with heterogeneous catalysts with the intention to demonstrate the strength of the method providing structural information about highly disperse and disordered systems, to illustrate pitfalls in the interpretation of results (e. g. by neglecting the averaged character of the information obtained) and to show how its merits can be further enhanced by combination with other methods of structural analysis and/or spectroscopy.

scholarly journals Recovery of data from perfectly twinned virus crystals revisited

2016 ◽  
Vol 72 (6) ◽  
pp. 817-822 ◽  
Author(s):  
Helen Mary Ginn ◽  
David Ian Stuart
Keyword(s):  
Structural Analysis ◽  
Iterative Method ◽  
Test Data ◽  
Diffraction Data ◽  
Poor Quality ◽  
Real Problem ◽  
Special Classes

Perfect merohedral twinning of crystals is not uncommon and complicates structural analysis. An iterative method for the deconvolution of data from perfectly merohedrally twinned crystals in the presence of noncrystallographic symmetry (NCS) has been reimplemented. It is shown that the method recovers the data effectively using test data, and an independent metric of success, based on special classes of reflections that are unaffected by the twin operator, is now provided. The method was applied to a real problem with fivefold NCS and rather poor-quality diffraction data, and it was found that even in these circumstances the method appears to recover most of the information. The software has been made available in a form that can be applied to other crystal systems.

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