Influence of wavelength and pulse duration on single-shot x-ray diffraction patterns from nonspherical nanoparticles

The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested.

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Data processing software suiteSITENNOfor coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA

Journal of Synchrotron Radiation ◽

10.1107/s1600577514003439 ◽

2014 ◽

Vol 21 (3) ◽

pp. 600-612 ◽

Cited By ~ 25

Author(s):

Yuki Sekiguchi ◽

Tomotaka Oroguchi ◽

Yuki Takayama ◽

Masayoshi Nakasako

Keyword(s):

Data Processing ◽

Free Electron ◽

Free Electron Laser ◽

Single Shot ◽

X Ray Diffraction ◽

X Ray ◽

Custom Made ◽

Diffraction Imaging ◽

Diffraction Patterns ◽

Ccd Detectors

Coherent X-ray diffraction imaging is a promising technique for visualizing the structures of non-crystalline particles with dimensions of micrometers to sub-micrometers. Recently, X-ray free-electron laser sources have enabled efficient experiments in the `diffraction before destruction' scheme. Diffraction experiments have been conducted at SPring-8 Angstrom Compact free-electron LAser (SACLA) using the custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors. In the experiments, ten thousands of single-shot diffraction patterns can be collected within several hours. Then, diffraction patterns with significant levels of intensity suitable for structural analysis must be found, direct-beam positions in diffraction patterns determined, diffraction patterns from the two CCD detectors merged, and phase-retrieval calculations for structural analyses performed. A software suite namedSITENNOhas been developed to semi-automatically apply the four-step processing to a huge number of diffraction data. Here, details of the algorithm used in the suite are described and the performance for approximately 9000 diffraction patterns collected from cuboid-shaped copper oxide particles reported. Using theSITENNOsuite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles.

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Improved crystal orientation and physical properties from single-shot XFEL stills

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714024134 ◽

2014 ◽

Vol 70 (12) ◽

pp. 3299-3309 ◽

Cited By ~ 32

Author(s):

Nicholas K. Sauter ◽

Johan Hattne ◽

Aaron S. Brewster ◽

Nathaniel Echols ◽

Petrus H. Zwart ◽

...

Keyword(s):

Crystal Orientation ◽

Degrees Of Freedom ◽

Reciprocal Lattice ◽

Single Shot ◽

X Ray Diffraction ◽

Reciprocal Lattice Point ◽

X Ray ◽

Structure Factors ◽

Rotational Degrees Of Freedom ◽

Diffraction Patterns

X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model the diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg's law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographicRfactors and sharpening anomalous differences that are near the level of the noise.

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Single-shot full strain tensor determination with microbeam X-ray Laue diffraction and a two-dimensional energy-dispersive detector

Journal of Applied Crystallography ◽

10.1107/s1600576717005581 ◽

2017 ◽

Vol 50 (3) ◽

pp. 901-908 ◽

Cited By ~ 9

Author(s):

A. Abboud ◽

C. Kirchlechner ◽

J. Keckes ◽

T. Conka Nurdan ◽

S. Send ◽

...

Keyword(s):

Elastic Strain ◽

Strain Tensor ◽

Energy Dispersive ◽

Single Shot ◽

Two Dimensional ◽

X Ray Diffraction ◽

Laue Diffraction ◽

Experimental Procedure ◽

X Ray ◽

Diffraction Patterns

The full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section). Taking advantage of a two-dimensional energy-dispersive X-ray detector (pnCCD), the position and energy of the collected Laue spots were measured for multiple positions on the sample, allowing the measurement of variations in the local microstructure. At the same time, both the deviatoric and hydrostatic components of the elastic strain and stress tensors were calculated.

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Characterizing crystalline defects in single nanoparticles from angular correlations of single-shot diffracted X-rays

IUCrJ ◽

10.1107/s205225252000144x ◽

2020 ◽

Vol 7 (2) ◽

pp. 276-286 ◽

Cited By ~ 1

Author(s):

Akinobu Niozu ◽

Yoshiaki Kumagai ◽

Toshiyuki Nishiyama ◽

Hironobu Fukuzawa ◽

Koji Motomura ◽

...

Keyword(s):

Free Electron ◽

Structural Information ◽

Single Shot ◽

X Ray Diffraction ◽

X Ray ◽

Angular Correlations ◽

Crystalline Defects ◽

X Ray Scattering ◽

Diffraction Patterns ◽

Ray Scattering

Characterizing and controlling the uniformity of nanoparticles is crucial for their application in science and technology because crystalline defects in the nanoparticles strongly affect their unique properties. Recently, ultra-short and ultra-bright X-ray pulses provided by X-ray free-electron lasers (XFELs) opened up the possibility of structure determination of nanometre-scale matter with Å spatial resolution. However, it is often difficult to reconstruct the 3D structural information from single-shot X-ray diffraction patterns owing to the random orientation of the particles. This report proposes an analysis approach for characterizing defects in nanoparticles using wide-angle X-ray scattering (WAXS) data from free-flying single nanoparticles. The analysis method is based on the concept of correlated X-ray scattering, in which correlations of scattered X-ray are used to recover detailed structural information. WAXS experiments of xenon nanoparticles, or clusters, were conducted at an XFEL facility in Japan by using the SPring-8 Ångstrom compact free-electron laser (SACLA). Bragg spots in the recorded single-shot X-ray diffraction patterns showed clear angular correlations, which offered significant structural information on the nanoparticles. The experimental angular correlations were reproduced by numerical simulation in which kinematical theory of diffraction was combined with geometric calculations. We also explain the diffuse scattering intensity as being due to the stacking faults in the xenon clusters.

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Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100079176 ◽

1977 ◽

Vol 35 ◽

pp. 330-333

Author(s):

T. Gulik-Krzywicki ◽

M.J. Costello

Keyword(s):

Biological Materials ◽

Molecular Organization ◽

X Ray Diffraction ◽

Glass Capillary ◽

X Ray ◽

Rate Dependent ◽

Before And After ◽

Freeze Etching ◽

Diffraction Patterns ◽

Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

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Examination of Rabbit Fc Crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100100445 ◽

1968 ◽

Vol 26 ◽

pp. 140-141

Author(s):

J. P. Robinson ◽

P. G. Lenhert

Keyword(s):

Molecular Weight ◽

Flat Plate ◽

Phosphate Buffer ◽

Asymmetric Unit ◽

X Ray Diffraction ◽

X Ray ◽

Neutral Ph ◽

Small Crystals ◽

Carbon Coated ◽

Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

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Control of the phase composition of advanced calcium phosphates using an x-ray diffractometer with a curved position-sensitive detector

Industrial laboratory Diagnostics of materials ◽

10.26896/1028-6861-2020-86-6-29-35 ◽

2020 ◽

Vol 86 (6) ◽

pp. 29-35

Author(s):

V. P. Sirotinkin ◽

O. V. Baranov ◽

A. Yu. Fedotov ◽

S. M. Barinov

Keyword(s):

Phase Composition ◽

Calcium Phosphates ◽

Position Sensitive Detector ◽

Sensitive Detector ◽

X Ray Diffraction ◽

X Ray ◽

Impurity Phases ◽

Position Sensitive ◽

Diffraction Peaks ◽

Diffraction Patterns

The results of studying the phase composition of advanced calcium phosphates Ca10(PO4)6(OH)2, β-Ca3(PO4)2, α-Ca3(PO4)2, CaHPO4 · 2H2O, Ca8(HPO4)2(PO4)4 · 5H2O using an x-ray diffractometer with a curved position-sensitive detector are presented. Optimal experimental conditions (angular positions of the x-ray tube and detector, size of the slits, exposure time) were determined with allowance for possible formation of the impurity phases during synthesis. The construction features of diffractometers with a position-sensitive detector affecting the profile characteristics of x-ray diffraction peaks are considered. The composition for calibration of the diffractometer (a mixture of sodium acetate and yttrium oxide) was determined. Theoretical x-ray diffraction patterns for corresponding calcium phosphates are constructed on the basis of the literature data. These x-ray diffraction patterns were used to determine the phase composition of the advanced calcium phosphates. The features of advanced calcium phosphates, which should be taken into account during the phase analysis, are indicated. The powder of high-temperature form of tricalcium phosphate strongly adsorbs water from the environment. A strong texture is observed on the x-ray diffraction spectra of dicalcium phosphate dihydrate. A rather specific x-ray diffraction pattern of octacalcium phosphate pentahydrate revealed the only one strong peak at small angles. In all cases, significant deviations are observed for the recorded angular positions and relative intensity of the diffraction peaks. The results of the study of experimentally obtained mixtures of calcium phosphate are presented. It is shown that the graphic comparison of experimental x-ray diffraction spectra and pre-recorded spectra of the reference calcium phosphates and possible impurity phases is the most effective method. In this case, there is no need for calibration. When using this method, the total time for analysis of one sample is no more than 10 min.

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Infrared spectroscopic study of the YPO4-YCrO4 system

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19852139 ◽

1985 ◽

Vol 50 (10) ◽

pp. 2139-2145

Author(s):

Alexander Muck ◽

Eva Šantavá ◽

Bohumil Hájek

Keyword(s):

Spectroscopic Study ◽

Infrared Spectra ◽

Point Of View ◽

Mixed Crystals ◽

Crystal Symmetry ◽

Infrared Spectroscopic Study ◽

X Ray Diffraction ◽

X Ray ◽

Infrared Spectroscopic ◽

Diffraction Patterns

The infrared spectra and powder X-ray diffraction patterns of polycrystalline YPO4-YCrO4 samples are studied from the point of view of their crystal symmetry. Mixed crystals of the D4h19 symmetry are formed over the region of 0-30 mol.% YPO4 in YCrO4. The Td → D2d → D2 or C2v(GS eff) correlation is appropriate for both PO43- and CrO43- anions.

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Deep learning for visualization and novelty detection in large X-ray diffraction datasets

npj Computational Materials ◽

10.1038/s41524-021-00575-9 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Lars Banko ◽

Phillip M. Maffettone ◽

Dennis Naujoks ◽

Daniel Olds ◽

Alfred Ludwig

Keyword(s):

Thin Film ◽

Crystal Structure ◽

Artificial Intelligence ◽

Deep Learning ◽

Novelty Detection ◽

Structural Similarity ◽

X Ray Diffraction ◽

X Ray ◽

Diffraction Patterns ◽

Post Hoc

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.

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