scholarly journals Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

2017 ◽  
Vol 114 (28) ◽  
pp. 7222-7227 ◽  
Author(s):  
Jeffrey J. Donatelli ◽  
James A. Sethian ◽  
Peter H. Zwart
Keyword(s):  
Diffraction Data ◽  
Single Particle ◽  
Structural Information ◽  
Real Space ◽  
Underlying Structure ◽  
X Ray Diffraction ◽  
Single Particles ◽  
State Orientation ◽  
Diffraction Patterns

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithm to reconstruct structural information from single-particle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.

scholarly journals Born out of Fire and Ice: Polymorph Studies of the Antiviral Famciclovir

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 129
Author(s):  
Liana Vella-Zarb ◽  
Ulrich Baisch
Keyword(s):  
Variable Temperature ◽  
Chemical Properties ◽  
Crystal Form ◽  
X Ray Diffraction ◽  
Crystal Forms ◽  
X Ray ◽  
Physical Chemical ◽  
Diffraction Patterns ◽  
Crystalline Forms

There is much interest and focus on solid forms of famciclovir. However, in spite of the abundance of reported differences in oral bioavailability, compressibility, and other physical–chemical properties of the various crystal forms of this drug, very little precise structural analysis is available in the literature to date. The form used in the commercial formulation is the anhydrous form I. Patents and patent applications report three different anhydrous crystalline forms on the basis of unindexed powder diffraction patterns. Single-crystal and variable-temperature X-ray diffraction experiments using the commercially available anhydrous form of famciclovir were carried out and led not only to the crystal structure determination of the anhydrous form I, but also to discovery of a new crystal form of anhydrous famciclovir from powder data.

scholarly journals Crystallization and X-ray diffraction data analysis of human deoxyhaemoglobin A0 fully stripped of any anions

1999 ◽  
Vol 55 (11) ◽  
pp. 1914-1916 ◽  
Author(s):  
F. A. V. Seixas ◽  
W. F. de Azevedo ◽  
M. F. Colombo
Keyword(s):  
Diffraction Data ◽  
Oxygen Affinity ◽  
X Ray Diffraction ◽  
Structural Explanation ◽  
Human Haemoglobin ◽  
X Ray ◽  
High Resolution Structure ◽  
Allosteric Properties

In this work, initial crystallographic studies of human haemoglobin (Hb) crystallized in isoionic and oxygen-free PEG solution are presented. Under these conditions, functional measurements of the O2-linked binding of water molecules and release of protons have evidenced that Hb assumes an unforeseen new allosteric conformation. The determination of the high-resolution structure of the crystal of human deoxy-Hb fully stripped of anions may provide a structural explanation for the role of anions in the allosteric properties of Hb and, particularly, for the influence of chloride on the Bohr effect, the mechanism by which Hb oxygen affinity is regulated by pH. X-ray diffraction data were collected to 1.87 Å resolution using a synchrotron-radiation source. Crystals belong to the space group P21212 and preliminary analysis revealed the presence of one tetramer in the asymmetric unit. The structure is currently being refined using maximum-likelihood protocols.

Determining the C60 molecular arrangement in thin films by means of X-ray diffraction

2011 ◽  
Vol 44 (5) ◽  
pp. 983-990 ◽  
Author(s):  
Chris Elschner ◽  
Alexandr A. Levin ◽  
Lutz Wilde ◽  
Jörg Grenzer ◽  
Christian Schroer ◽  
...  
Keyword(s):  
Thin Films ◽  
Structural Information ◽  
Grazing Incidence ◽  
Test Material ◽  
C60 Fullerene ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Molecular Arrangement ◽  
Diffraction Patterns

The electrical and optical properties of molecular thin films are widely used, for instance in organic electronics, and depend strongly on the molecular arrangement of the organic layers. It is shown here how atomic structural information can be obtained from molecular films without further knowledge of the single-crystal structure. C60 fullerene was chosen as a representative test material. A 250 nm C60 film was investigated by grazing-incidence X-ray diffraction and the data compared with a Bragg–Brentano X-ray diffraction measurement of the corresponding C60 powder. The diffraction patterns of both powder and film were used to calculate the pair distribution function (PDF), which allowed an investigation of the short-range order of the structures. With the help of the PDF, a structure model for the C60 molecular arrangement was determined for both C60 powder and thin film. The results agree very well with a classical whole-pattern fitting approach for the C60 diffraction patterns.

NanoPDF64: software package for theoretical calculation and quantitative real-space analysis of powder diffraction data of nanocrystals

2017 ◽  
Vol 50 (6) ◽  
pp. 1821-1829 ◽  
Author(s):  
Kazimierz Skrobas ◽  
Svitlana Stelmakh ◽  
Stanislaw Gierlotka ◽  
Bogdan F. Palosz
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Analytical Formula ◽  
Real Space ◽  
Distribution Functions ◽  
Powder Diffraction Data ◽  
Space Analysis ◽  
Atomic Vibrations ◽  
Hexagonal Close Packed Structure ◽  
Diffraction Patterns

NanoPDF64is a tool designed for structural analysis of nanocrystals based on examination of powder diffraction data with application of real-space analysis. The program allows for fast building of models of nanocrystals consisting of up to several hundred thousand atoms with either cubic or hexagonal close packed structure. The nanocrystal structure may be modified by introducing stacking faults, density modulation waves (i.e.the core–shell model) and thermal atomic vibrations. The program calculates diffraction patterns and, by Fourier transform, the reduced pair distribution functionsG(r) for the models. ExperimentalG(r)s may be quantitatively analyzed by least-squares fitting with an analytical formula.

scholarly journals Rubidium tetrafluoridobromate(III): redetermination of the crystal structure from single-crystal X-ray diffraction data

IUCrData ◽  
2019 ◽  
Vol 4 (11) ◽  
Author(s):  
Artem V. Malin ◽  
Sergei I. Ivlev ◽  
Roman V. Ostvald ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Single Crystals ◽  
Diffraction Data ◽  
Structure Type ◽  
X Ray Diffraction ◽  
X Ray ◽  
Square Planar ◽  
Atomic Coordinates

Single crystals of rubidium tetrafluoridobromate(III), RbBrF4, were grown by melting and recrystallizing RbBrF4 from its melt. This is the first determination of the crystal structure of RbBrF4 using single-crystal X-ray diffraction data. We confirmed that the structure contains square-planar [BrF4]− anions and rubidium cations that are coordinated by F atoms in a square-antiprismatic manner. The compound crystallizes in the KBrF4 structure type. Atomic coordinates and bond lengths and angles were determined with higher precision than in a previous report based on powder X-ray diffraction data [Ivlev et al. (2015). Z. Anorg. Allg. Chem. 641, 2593–2598].

2D real space visualization of d values in polycrystalline bulk materials of different hardness

2021 ◽  
Vol 54 (2) ◽  
pp. 597-603
Author(s):  
Mari Mizusawa ◽  
Kenji Sakurai
Keyword(s):  
Lattice Distortion ◽  
Structural Information ◽  
Hardness Test ◽  
Real Space ◽  
Polycrystalline Materials ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
D Values

Conventional X-ray diffraction measurements provide some average structural information, mainly on the crystal structure of the whole area of the given specimen, which might not be very uniform and may include different crystal structures, such as co-existing crystal phases and/or lattice distortion. The way in which the lattice plane changes due to strain also might depend on the position in the sample, and the average information might have some limits. Therefore, it is important to analyse the sample with good lateral spatial resolution in real space. Although various techniques for diffraction topography have been developed for single crystals, it has not always been easy to image polycrystalline materials. Since the late 1990s, imaging technology for fluorescent X-rays and X-ray absorption fine structure has been developed via a method that does not scan either a sample or an X-ray beam. X-ray diffraction imaging can be performed when this technique is applied to a synchrotron radiation beamline with a variable wavelength. The present paper reports the application of X-ray diffraction imaging to bulk steel materials with varying hardness. In this study, the distribution of lattice distortion of hardness test blocks with different hardness was examined. Via this 2D visualization method, the grains of the crystals with low hardness are large enough to be observed by X-ray diffraction contrast in real space. The change of the d value in the vicinity of the Vickers mark has also been quantitatively evaluated.

IDATENandG-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA

2014 ◽  
Vol 21 (6) ◽  
pp. 1378-1383 ◽  
Author(s):  
Yuki Sekiguchi ◽  
Masaki Yamamoto ◽  
Tomotaka Oroguchi ◽  
Yuki Takayama ◽  
Shigeyuki Suzuki ◽  
...  
Keyword(s):  
User Interfaces ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Custom Made ◽  
Sample Position ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
User Friendly ◽  
Ccd Detectors

Using our custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors, cryogenic coherent X-ray diffraction imaging experiments have been undertaken at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user-friendly graphical user interfaces have been developed. The first is a program suite namedIDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI-1, loading a flash-cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI-1, adjusting the sample position with respect to the X-ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X-ray pulses. NamedG-SITENNO, the other suite is an automated version of the originalSITENNOsuite, which was designed for processing diffraction data. These user-friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.

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