A compact superconducting ring as a radiation source for X-ray crystallography

1998 ◽  
Vol 5 (3) ◽  
pp. 333-335 ◽  
Author(s):  
H. Iwasaki ◽  
N. Kurosawa ◽  
S. Masui ◽  
S. Fujita ◽  
T. Yurugi ◽  
...  
Keyword(s):  
Large Scale ◽  
Beam Current ◽  
Imaging Plate ◽  
Anomalous Scattering ◽  
Organic Crystals ◽  
X Ray ◽  
X Ray Crystallography ◽  
Superconducting Ring ◽  
Electron Orbit ◽  
Diffraction Patterns

A compact superconducting storage ring installed at Ritsumeikan University is operated at an electron-beam energy of 0.575 GeV and an initial beam current of 300 mA. The radius of the circular electron orbit is as small as 0.5 m, suggesting that the radiation emitted contains short-wavelength components. With an imaging plate as a detector, X-ray precession diffraction patterns were recorded for organic single crystals within a reasonable period of time using radiation of wavelength 0.155 nm (8 keV) to 0.248 nm (5 keV). The use of the radiation in the structural study of organic crystals containing 3d metal atoms using the phenomena of anomalous scattering is described. If appropriately planned, X-ray diffraction and/or scattering experiments can be made at the compact ring without recourse to a large-scale ring.

scholarly journals Cover art

2016 ◽  
Vol 85 (1) ◽  
Author(s):  
Rakesh Gudimella
Keyword(s):  
Large Scale ◽  
Molecular Model ◽  
Essential Medicines ◽  
Chemical Formula ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chemical Structures ◽  
Diffraction Patterns ◽  
Cover Art

Cover art by Rakesh Gudimella. In 1964, Dorothy Hodgkin won the Nobel Prize for the discovery of the structure of penicillin using the emerging technique of x-ray crystallography. The original x-ray diffraction patterns and the subsequent molecular model she created is shown in the foreground. Although the chemical formula of penicillin was known, its structure was not, making it difficult to produce on a large scale. Her discovery set us on the path to understanding antibiotic mechanisms and opened the door for the synthesis of cephalosporins and other important medications. The background shows the chemical structures of several lifesaving and influential drugs on the WHO List of Essential Medicines.

Reminiscences and discoveries: Dorothy Hodgkin and the Indian connection

1996 ◽  
Vol 50 (1) ◽  
pp. 115-127 ◽  
Keyword(s):  
Large Angle ◽  
Direct Methods ◽  
Statistical Fluctuation ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Scattering ◽  
Molecular Sizes ◽  
Indian Institute Of Science

Dorothy Hodgkin - as crystallographer, scientist and human being - far surpasses most, and so it is not easy to write about her many-splendoured personality. Instead, my aim here will he to discuss her influence on the growth of X-ray crystallography in India, directly through those who worked with her and indirectly by her travelling all over this country. In such an account, one must be pardoned for some personal element creeping in. In the twenties, India had developed a fairly strong tradition in X-ray physics. The six-week visit of C.V. Raman to Europe in 1921 greatly changed his research interests. On seeing the blue of the Mediterranean he started his researches on the scattering of light in liquids which finally culminated in the discovery of what is now called the Raman Effect. His encounter with Sir William Bragg and his work on naphthalene structure started three lines of research in India. First, Raman fabricated an X-ray tube and was amongst the earliest to use X-ray diffraction as a structural tool to study liquids. He showed that while in large-angle scattering the haloes reflected specific molecular sizes and packing shapes, small-angle scattering was directly related to the statistical fluctuation of density in a liquid. Second, Raman knew that Bragg’s first structure of naphthalene was not consistent with its birefringence, while the second one was. With this as cue he and his school launched extensive studies on the optical and magnetic anisotropy of organic crystals to get vital information on the arrangements of molecules in the crystalline state. Third, one of his students, Kedareshwar Bannerjee, was amongst the earliest to probe into the problem of phase determination by direct methods and for this he used Bragg’s data on naphthalene. Unfortunately, in spite of this early lead, it was not until 1951 that the first crystal structure was solved in India using Fourier methods by Gopinath Kartha. The Indian Institute of Science (IISc) had great hopes of starting a powerful school of X-ray crystallography when G.N. Ramachandran came back from Cambridge. But he went over to Madras, and there he established one of the most renowned Schools of Biophysics. With Gopinath Kartha he solved the structure of collagen.

scholarly journals Advances in Synchrotron X-ray Polycrystalline Diffraction

1988 ◽  
Vol 41 (2) ◽  
pp. 101 ◽  
Author(s):  
William Parrish
Keyword(s):  
High Resolution ◽  
Grazing Angle ◽  
Anomalous Scattering ◽  
Wavelength Selection ◽  
High Count ◽  
Instrument Function ◽  
X Ray ◽  
Depth Analysis ◽  
Diffraction Patterns ◽  
New Applications

The advantages of synchrotron radiation for X-ray polycrystalline diffraction are illustrated by a number of examples. The plane wave parallel-beam X-ray optics uses a Si(lll) channel monochromator for easy wavelength selection and a set of long parallel slits to define the diffracted beam. The constant simple instrument function and the high resolution symmetrical profiles (FWHM 0.05") greatly simplify the data analysis and add a new dimension to profile broadening studies. The geometry permits uncoupling the 6-26 sample-detector relationship without changing the profile shape and makes possible new applications such as grazing angle incidence depth analysis of thin films. The same instrumentation is used for high resolution energy dispersive diffraction (BOD) by step-scanning the monochromator. The resolution is two orders of magnitude better than conventional BOD and can be used at high count rates. The easy wavelength selection yields diffraction patterns with the highest PI B and permits anomalous scattering studies.

scholarly journals Structures of pseudo-decagonal approximants in Al−Co−Ni

2012 ◽  
Vol 370 (1969) ◽  
pp. 2949-2959 ◽  
Author(s):  
Sven Hovmöller ◽  
Linus Hovmöller Zou ◽  
Xiaodong Zou ◽  
Benjamin Grushko
Keyword(s):  
High Resolution Electron Microscopy ◽  
Limited Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Cell Dimensions ◽  
Diffraction Patterns ◽  
Quasi Crystals ◽  
Unit Cell Dimensions ◽  
Microscopy Images

Quasi-crystals shocked the crystallographic world when they were reported in 1984. We now know that they are not a rare exception, and can be found in many alloy systems. One of the richer systems for quasi-crystals and their approximants is Al−Co−Ni. A large series of pseudo-decagonal (PD) approximants have been found. Only two of them, PD4 and PD8, have been solved by X-ray crystallography. We report here the structures of PD1, PD2, PD3 and PD5, solved from the limited information that is provided by electron diffraction patterns, unit cell dimensions and high-resolution electron microscopy images.

Update in a Rietveld analysis program for x-ray powder spectro-diffractometry

2003 ◽  
Vol 18 (1) ◽  
pp. 32-35 ◽  
Author(s):  
Yanan Xiao ◽  
Fujio Izumi ◽  
Timothy Graber ◽  
P. James Viccaro ◽  
Dale E. Wittmer
Keyword(s):  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Anomalous Scattering ◽  
Analysis Program ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Synchrotron Light ◽  
Diffraction Patterns

A computer program for refining anomalous scattering factors using x-ray powder diffraction data was revised on the basis of the latest version of a versatile pattern-fitting system, RIETAN-2000. The effectiveness of the resulting program was confirmed by applying it to simulated and measured powder-diffraction patterns of Mn3O4 taken at a synchrotron light source.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

2018 ◽  
Vol 25 (3) ◽  
pp. 748-756 ◽  
Author(s):  
M. X. Tang ◽  
Y. Y. Zhang ◽  
J. C. E ◽  
S. N. Luo
Keyword(s):  
Single Crystal ◽  
Large Scale ◽  
Incident Beam ◽  
Wave Structure ◽  
X Ray Diffraction ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Case Transmission ◽  
Dynamics Simulations

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

scholarly journals xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

2014 ◽  
Vol 70 (9) ◽  
pp. 2344-2355 ◽  
Author(s):  
Ryan McGreevy ◽  
Abhishek Singharoy ◽  
Qufei Li ◽  
Jingfen Zhang ◽  
Dong Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Protein Structures ◽  
Data Bank ◽  
Real Space ◽  
Low Resolution ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Electron Density Map

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally,viasystematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

A Rietveld-analysis program for X-ray powder spectro-diffractometry

1999 ◽  
Vol 14 (2) ◽  
pp. 106-110 ◽  
Author(s):  
Yanan Xiao ◽  
Shinjiro Hayakawa ◽  
Yohichi Gohshi ◽  
Masaharu Oshima ◽  
Fujio Izumi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Absorption Edge ◽  
Rietveld Method ◽  
Rietveld Analysis ◽  
Anomalous Scattering ◽  
Analysis Program ◽  
X Ray ◽  
Diffraction Patterns ◽  
X Ray Absorption

In order to exploit X-ray powder spectro-diffractometry, the program RIETAN-97ß for refining crystal structure and lattice parameters by the Rietveld method was modified extensively. The resulting software can be used to refine anomalous scattering factors, fr and fi, for specified crystallographic sites near the X-ray absorption edge of a particular element. The effectiveness of the modified software was tested by using powder diffraction patterns simulated by the original RIETAN-97ß software and a series of measured powder diffraction patterns of Fe3O4 with incident X-ray energies near the absorption edge of iron.

scholarly journals Identifying dynamic, partially occupied residues using anomalous scattering

2019 ◽  
Author(s):  
Serena Rocchio ◽  
Ramona Duman ◽  
Kamel El Omari ◽  
Vitaliy Mykhaylyk ◽  
Zhen Yan ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Structural Changes ◽  
Structural Data ◽  
Anomalous Scattering ◽  
Long Wavelength ◽  
X Ray Crystallography ◽  
Structural Ensembles ◽  
Analysis Strategy ◽  
Chain Conformations

AbstractX-ray crystallography is generally used to take single snapshots of a protein’s conformation. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes Residual Anomalous and Electron Density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data collection and analysis strategy for partially occupied iodine anomalous signals. Using the long wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with as low as ~12% occupancy is demonstrated. The number and position of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly dynamic sections of crystal structures.SynopsisStructural studies on partially occupied, dynamic protein systems by crystallography are difficult. We present methods here for detecting these states in crystals.

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