LauePt, a graphical-user-interface program for simulating and analyzing white-beam X-ray diffraction Laue patterns

2010 ◽  
Vol 43 (4) ◽  
pp. 926-928 ◽  
Author(s):  
X. R. Huang
Keyword(s):  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
White Beam ◽  
Diffraction Geometry ◽  
Wide Range ◽  
User Friendly ◽  
Beam Diffraction ◽  
Laue Method

LauePtis a robust and extremely easy-to-use Windows application for accurately simulating, indexing and analyzing white-beam X-ray diffraction Laue patterns of any crystals under arbitrary diffraction geometry. This program has a user-friendly graphic interface and can be conveniently used by nonspecialists with little X-ray diffraction or crystallography knowledge. Its wide range of applications include (1) determination of single-crystal orientation with the Laue method, (2) white-beam topography, (3) white-beam microdiffraction, (4) X-ray studies of twinning, domains and heterostructures, (5) verification or determination of crystal structures from white-beam diffraction, and (6) teaching of X-ray crystallography.

scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

The petrology of the Mount Padbury mesosiderite and its achondrite enclaves

1966 ◽  
Vol 36 (276) ◽  
pp. 1029-1060 ◽  
Author(s):  
G. J. H. McCall
Keyword(s):  
Microscopic Analysis ◽  
Host Material ◽  
Refractive Indices ◽  
X Ray Diffraction ◽  
Thin Sections ◽  
X Ray ◽  
Wide Range ◽  
Varied Range ◽  
Optical Determination

SummaryThe petrography of the Mount Padbury meteorite, previously briefly recorded, is described in some detail. Both the metalliferous host material of the mesosiderite and the varied range of silicate-rich, virtually metal-free enclaves (including both familiar achondrite material and unfamiliar achondrite material) are described. Eucrite, brecciated eucrite, and a peculiar ‘shocked’ form of eucrite (resembling some terrestrial flaser-gabbros) are the calcium-rich achondrite types represented; hypersthene achondrite (including typical diogenite material and unfamiliar material) and olivine achondrite (granular aggregates of olivine not entirely similar to the unique chassignite and single crystals up to 4 in. in length) are the calcium-poor achondrite types represented. The eucrite displays more or less uniform mineralogy, but the mineral constituents are present in varying proportions, and there is a wide range of textural variations recognized. The silicate grain fragments enclosed in the metallic reticulation to form the mesosiderite host material are, significantly, entirely of minerals seen within the achondrite enclaves—plagioclase, hypersthene, pigeonite, olivine, and tridymite.These results include microscopic analysis of thin sections and polished sections, X-ray diffraction studies, optical determination of refractive indices using mineral grain mounts, and chemical analyses.The wider implications of this new and unique meteorite find are briefly considered.

scholarly journals RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction

2020 ◽  
Vol 53 (2) ◽  
pp. 587-593
Author(s):  
A. Boulle ◽  
V. Mergnac
Keyword(s):  
Web Application ◽  
The Internet ◽  
Programming Environment ◽  
X Ray Diffraction ◽  
Web Browser ◽  
Web Based ◽  
X Ray ◽  
Depth Profiles ◽  
User Friendly

RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.

Quantitative X-Ray Structure Determination of Superlattices and Interfaces

1991 ◽  
Vol 229 ◽  
Author(s):  
Ivan K. Schuller ◽  
Eric E. Fullerton ◽  
H. Vanderstraeten ◽  
Y. Bruynseraede
Keyword(s):  
General Procedure ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Diffraction Profile ◽  
X Ray ◽  
Superlattice Structure ◽  
Wide Range ◽  
Fitting Algorithm ◽  
Superlattice Structures

AbstractWe present a general procedure for quantitative structural refinement of superlattice structures. To analyze a wide range of superlattices, we have derived a general kinematical diffraction formula that includes random, continuous and discrete fluctuations from the average structure. By implementing a non-linear fitting algorithm to fit the entire x-ray diffraction profile, refined parameters that describe the average superlattice structure, and deviations from this average are obtained. The structural refinement procedure is applied to a crystalline/crystalline Mo/Ni superlattices and crystalline/amorphous Pb/Ge superlattices. Roughness introduced artificially during growth in Mo/Ni superlattices is shown to be accurately reproduced by the refinement.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

2010 ◽  
Vol 66 (5) ◽  
pp. 558-567 ◽  
Author(s):  
Anna S. Gardberg ◽  
Alexis Rae Del Castillo ◽  
Kevin L. Weiss ◽  
Flora Meilleur ◽  
Matthew P. Blakeley ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Electron Density ◽  
Pyrococcus Furiosus ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Improved Model

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3-protonated perdeuterated crystals ofPyrococcus furiosusrubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high-confidence positions for D atoms than 1.1 Å resolution X-ray data at 100 K or RT. At or above the 1.0σ level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0σ level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

scholarly journals A simple pressure-assisted method for MicroED specimen preparation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jingjing Zhao ◽  
Hongyi Xu ◽  
Hugo Lebrette ◽  
Marta Carroni ◽  
Helena Taberman ◽  
...  
Keyword(s):  
High Viscosity ◽  
Specimen Preparation ◽  
Universal Method ◽  
X Ray Diffraction ◽  
Simple Method ◽  
X Ray ◽  
Wide Range ◽  
Major Bottleneck ◽  
Crystal Electron

AbstractMicro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.

scholarly journals RaDMaX: a graphical program for the determination of strain and damage profiles in irradiated crystals

2016 ◽  
Vol 49 (1) ◽  
pp. 311-316 ◽  
Author(s):  
M. Souilah ◽  
A. Boulle ◽  
A. Debelle
Keyword(s):  
Spline Functions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Depth Profiles ◽  
Diffraction Model ◽  
Calculated Curve ◽  
Fitting Procedures ◽  
Damage Depth ◽  
User Friendly

RaDMaX(radiation damage in materials analysed with X-ray diffraction) is a user-friendly graphical program that allows the determination of strain and damage depth profiles in ion-irradiated crystals. This task is achieved by fitting experimental X-ray diffraction data, recorded in symmetrical θ–2θ geometry, with a dynamical diffraction model parametrized with variable strain and damage profiles based onB-spline functions. The strain and damage profiles can be graphically manipulated so as to fit the calculated curve to the experimental data. Automatic fitting procedures (generalized simulated annealing and conventional least squares) are also implemented.RaDMaXis free and open source (CeCILL licence) and can be downloaded from http://aboulle.github.io/RaDMaX.

scholarly journals History of protein crystallography in China

2007 ◽  
Vol 362 (1482) ◽  
pp. 1035-1042 ◽  
Author(s):  
Zihe Rao
Keyword(s):  
Protein Crystallography ◽  
Three Dimensional ◽  
Porcine Insulin ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Subsequent Determination ◽  
History Of

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

scholarly journals FXD-CSD-GUI: a graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions

2019 ◽  
Vol 52 (6) ◽  
pp. 1437-1439
Author(s):  
Sigmund H. Neher ◽  
Helmut Klein ◽  
Werner F. Kuhs
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Crystal Size ◽  
Data Handling ◽  
Size Distributions ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
User Friendly

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

Diffraction Contrast Tomography - A Synchrotron Radiation Technique for Mapping Polycrystalline Microstructures in 3D

2008 ◽  
Vol 571-572 ◽  
pp. 207-212 ◽  
Author(s):  
Andrew King ◽  
Greg Johnson ◽  
Wolfgang Ludwig
Keyword(s):  
X Ray Diffraction ◽  
Transmitted Beam ◽  
X Ray ◽  
Diffraction Contrast ◽  
Diffraction Geometry ◽  
Radiation Technique ◽  
Non Destructive ◽  
Diffraction Microscopy

In this paper the authors describe a technique based on synchrotron x-ray diffraction which has been used to produce full 3D grain maps (both grain shapes and orientations) in annealed aluminium alloy and stainless steel samples containing around 500 grains. The procedure is termed diffraction contrast tomography (DCT), reflecting its similarities with conventional absorption contrast tomography. It is an extension of the 3D X-ray diffraction microscopy (3DXRD) concept, and has been developed in collaboration with its inventors. The specimen is illuminated using a monochromatic synchrotron x-ray beam, and grains imaged using the extinction contrast that appears in the transmitted beam when grains are aligned in the diffraction condition during rotation of the sample. The beams of radiation diffracted by the grains are captured simultaneously on the same detector as the direct beam image. The combination of diffraction and extinction information aids the grain indexing operation, in which pairs of diffraction and extinction images are assigned to grain sets. 3D grain shapes are determined by algebraic reconstruction from the limited number of extinction projections, while crystallographic orientation is found from the diffraction geometry. The non-destructive nature of the technique allows for in-situ studies of mapped samples. Research is in progress to extend the technique to allow the determination of the elastic strain and stress tensors on a grain-by-grain basis.

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