scholarly journals In-situ diffraction experiments at the Photon Factory MX beamlines

2014 ◽  
Vol 70 (a1) ◽  
pp. C500-C500
Author(s):  
Yusuke Yamada ◽  
Naohiro Matsugaki ◽  
Masahiko Hiraki ◽  
Ryuichi Kato ◽  
Toshiya Senda
Keyword(s):  
Gas Flow ◽  
Active Area ◽  
Array Detector ◽  
Data Sets ◽  
Diffraction Experiment ◽  
X Ray ◽  
Photon Factory ◽  
Large Active Area ◽  
In Situ Diffraction

Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography. Once a crystal appears in a certain crystallization condition, the crystal is typically harvested from the crystallization drop, soaked into a cryoprotection buffer, flash-cooled with a liquid nitrogen or cold gas flow and finally evaluated its diffraction quality by an X-ray beam. During these long process, crystal may be damaged and the result from the diffraction experiment does not necessarily reflect a nature of the crystal. On in-situ diffraction experiment, where a crystal in a crystallization drop is directly irradiated to an X-ray beam, a diffraction image from a crystal without any external factors such as harvesting and cryoprotection and, as a result, a nature of crystal can be evaluated quickly. In the Photon Factory, a new table-top diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, on-axis viewing system with a large numeric aperture and a plate rack where ten crystallization plates can be placed. These components sit on a common plate and it is placed on the existing diffractometer table in the beamline endstation. The CCD detector with a large active area and a pixel array detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and user interface were also developed. Since 2014, user operation of the new diffractometer was started and in-situ diffraction experiments were mainly performed for evaluations of crystallization plates from a large crystallization screening project in our facility. BL-17A [1], one of micro-focus beamlines at the Photon Factory, is planned to be upgraded in March 2015. With this upgrade, a new diffractometer, which has a capability to handle a crystallization plate, will be installed so that diffraction data sets from crystals in crystallization drop can be collected.

100 years in situ diffraction

2017 ◽  
Vol 232 (12) ◽  
Author(s):  
Holger Kohlmann
Keyword(s):  
Diffraction Experiment ◽  
X Ray Diffraction ◽  
X Ray ◽  
In Situ Diffraction

AbstractThe X-ray diffraction experiment of iron at temperatures up to 1000°C, which Albert Hull conducted 100 years ago, in 1917, may be regarded as the first

SGTools: a suite of tools for processing and analyzing large data sets from in situ X-ray scattering experiments

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Nie Zhao ◽  
Chunming Yang ◽  
Fenggang Bian ◽  
Daoyou Guo ◽  
Xiaoping Ouyang
Keyword(s):  
Data Processing ◽  
Small Angle ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
X Ray ◽  
Intensity Mapping ◽  
X Ray Scattering ◽  
Ray Scattering

In situ synchrotron small-angle X-ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets generated from in situ X-ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing-incidence small-angle X-ray scattering (GISAXS). This article presents an open-source software suite (SGTools) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X-ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools. The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.

In situ time-resolved X-ray diffraction of tobermorite formation process under hydrothermal condition: Influence of reactive al compound

2011 ◽  
Vol 26 (2) ◽  
pp. 134-137 ◽  
Author(s):  
K. Matsui ◽  
A. Ogawa ◽  
J. Kikuma ◽  
M. Tsunashima ◽  
T. Ishikawa ◽  
...  
Keyword(s):  
Hydrothermal Reaction ◽  
High Energy ◽  
Saturated Steam ◽  
Array Detector ◽  
Time Interval ◽  
X Rays ◽  
X Ray Diffraction ◽  
Formation Reaction ◽  
X Ray

Hydrothermal formation reaction of tobermorite in the autoclaved aerated concrete (AAC) process has been investigated by in situ X-ray diffraction. High-energy X-rays from a synchrotron radiation source in combination with a newly developed autoclave cell and a photon-counting pixel array detector were used. XRD measurements were conducted in a temperature range 100–190°C throughout 12 h of reaction time with a time interval of 4.25 min under a saturated steam pressure. To clarify the tobermorite formation mechanism in the AAC process, the effect of Al addition on the tobermorite formation reaction was studied. As intermediate phases, non-crystalline calcium silicate hydrate (C-S-H), hydroxylellestadite (HE), and katoite (KA) were clearly observed. Consequently, it was confirmed that there were two reaction pathways via C-S-H and KA in the tobermorite formation reaction of Al containing system. In addition, detailed information on the structural changes during the hydrothermal reaction was obtained.

Inflexible stoichiometry in bulk pyrite FeS2 as viewed by in situ and high-resolution X-ray diffraction

2018 ◽  
Vol 74 (5) ◽  
pp. 436-444 ◽  
Author(s):  
Rebecca D. McAuliffe ◽  
Daniel P. Shoemaker
Keyword(s):  
Gas Flow ◽  
Lattice Parameter ◽  
Iron Pyrite ◽  
X Ray Diffraction ◽  
Intrinsic Defects ◽  
X Ray ◽  
Solubility Range ◽  
Absorber Material ◽  
Line Compound

Non-stoichiometry is considered to be one of the main problems limiting iron pyrite, FeS2, as a photovoltaic absorber material. Although some historical diffraction experiments have implied a large solubility range of FeS2−δ with δ up to 0.25, the current consensus based on calculated formation energies of intrinsic defects has lent support to line-compound behavior. Here it is shown that pyrite stoichiometry is relatively inflexible in both reductive conditions and in autogenous sulfur partial pressure, which produces samples with precise stoichiometry of FeS2 even at different Fe/S ratios. By properly standardizing in situ gas-flow X-ray diffraction measurements, no significant changes in the lattice parameter of FeS2 can be resolved, which portrays iron pyrite as prone to forming sulfur-deficient compounds, but not intrinsic defects in the manner of NiS2−δ.

scholarly journals A Novel Method to Maintain the Sample Position and Pressure in Differentially Pumped Systems Below the Resolution Limit of Optical Microscopy Techniques

2020 ◽  
pp. 000370282094279
Author(s):  
Christopher M. Goodwin ◽  
John D. Alexander ◽  
Matthew Weston ◽  
David Degerman ◽  
Mikhail Shipilin ◽  
...  
Keyword(s):  
Optical Microscopy ◽  
Photoelectron Spectroscopy ◽  
Gas Flow ◽  
Feedback System ◽  
Resolution Limit ◽  
X Ray ◽  
System Pressure ◽  
Sample Position ◽  
Microscopy Techniques

We present a new method to maintain constant gas pressure over a sample during in situ measurements. The example shown here is a differentially pumped high-pressure X-ray photoelectron spectroscopy system, but this technique could be applied to many in situ instruments. By using the pressure of the differential stage as a feedback source to change the sample position, a new level of consistency has been achieved. Depending on the absolute value of the sample-to-aperture distance, this technique allows one to maintain the distance within several hundred nanometers, which is below the limit of typical optical microscopy systems. We show that this method is well suited to compensate for thermal drift. Thus, X-ray photoelectron spectroscopy data can be acquired continuously while the sample is heated and maintaining constant pressure over the sample. By implementing a precise manipulator feedback system, pressure variations of less than 5% were reached while the temperature was varied by 400 ℃. The system is also shown to be highly stable under significant changes in gas flow. After changing the flow by a factor of two, the pressure returned to the set value within 60 s.

In Situ Diffraction Studies: Thermal Decomposition of a Natural Plumbojarosite and the Development of Rietveld-Based Data Analysis Techniques

2010 ◽  
Vol 651 ◽  
pp. 37-64 ◽  
Author(s):  
Ian C. Madsen ◽  
Ian E. Grey ◽  
Stuart J. Mills
Keyword(s):  
Thermal Decomposition ◽  
Amorphous Material ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Analysis Techniques ◽  
Path Lengths ◽  
Instrument Configuration

A study of the thermal decomposition sequence of a sample of natural arsenian plumbojarosite has been undertaken using in situ X-ray diffraction. The sample was heated to 900°C using an Anton-Paar heating stage fitted to an INEL CPS120 diffractometer. The data were analysed using a whole-pattern, Rietveld based approach for the extraction of quantitative phase abundances. The instrument configuration used required the development and application of algorithms to correct for aberrations in the (i) peak intensities due to differing path lengths of incident and diffracted beams in the sample and (ii) peak positions due to sample displacement. Details of the structural models used were refined at selected steps in the pattern and then fixed for subsequent analysis. The data sequence consists of some 110 individual data sets which were analysed sequentially with the output of each run forming the input for analysis of the next data set. The results of the analysis show a complex breakdown and recrystallisation sequence including the formation of a major amount of amorphous material after initial breakdown of the plumbojarosite.

The effect of iron content on dehydration kinetics of talc

2020 ◽  
Author(s):  
Li Yi ◽  
Ruixin Zhang ◽  
Siyu Yang
Keyword(s):  
Subduction Zone ◽  
Iron Content ◽  
Diffraction Experiment ◽  
Dehydration Reaction ◽  
X Ray Diffraction ◽  
Hydrous Mineral ◽  
Hydrous Minerals ◽  
X Ray ◽  
Kinetics Of

<p>    Subduction zone is a distinct activity structure of hypocenter distribution of earthquakes. Hydrous minerals are involved in the chemical and physical activities in subduction zones. As a widely distributed hydrous mineral in shallow depths, talc has potential significance in various fault activities, and its dehydration reaction may be an important cause of the earthquake. Iron is a main element of the earth's crust, and the iron contents of hydrous minerals have a large impact on melting point, the rheological strength physical and chemical properties of the rocks. As a common hydrous mineral, the iron content of talc is not uniform; therefore, it is very important to study the dehydration kinetics of talc with different iron content.</p><p>    The dehydration reaction of three different iron contents talc was studied by means of synchronous thermal analysis, high temperature and high pressure differential thermal experiment and in-situ synchrotron X-ray diffraction experiment. Data of synchronous thermal analysis was calculated by Flynn-Wall-Ozawa (FWO). The activation energies of different iron content talc were calculated as 359.8 kJ/mol（FeO：0.4wt%），368.2.0 kJ/mol（FeO：2.0wt％），belonging to the second-order reaction. Data of in-situ synchrotron X-ray diffraction experiment was fitted by Avrami equation, E=350 kJ/mol（FeO：2.0wt％），n=1.67. The dehydration of talc followed random nucleation and growth mechanism. High content of iron obviously resulted in lower dehydration temperature.</p><p>  The release rate of talc dehydration fluid was 2.3E-05 to 6.1E-06 obtained by in-situ synchrotron X-ray diffraction experiment，it could lead to local overpressure induced rock brittle fracture. The supercritical fluid produced by the dehydration of talc in the subduction zone further attenuates the rock, resulting in local overpressure, which eventually leads to rock failure. The results suggested that the dehydration of different iron contents of talc may occur at the different depth around hundreds of kilometers, so the study was significant to our understanding of the genetic mechanism of earthquakes in the subduction zone.</p>

An in situ x-ray absorption spectroscopic cell for high temperature gas-flow measurements

1998 ◽  
Vol 69 (7) ◽  
pp. 2618-2621 ◽  
Author(s):  
George Meitzner ◽  
Simon R. Bare ◽  
Deborah Parker ◽  
Hyung Woo ◽  
Daniel A. Fischer
Keyword(s):  
High Temperature ◽  
Gas Flow ◽  
Flow Measurements ◽  
X Ray ◽  
X Ray Absorption ◽  
High Temperature Gas

scholarly journals Structural and In Situ X-ray Diffraction Study of Hydrogenation of CaxMg1−xNi2 (0 ≤ x ≤ 1)

Crystals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 47
Author(s):  
Zia Ur Rehman ◽  
Mohsan Nawaz ◽  
Hameed Ullah ◽  
Pervaiz Ahmad ◽  
Mayeen Uddin Khandaker ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Powder Diffraction ◽  
Gas Flow ◽  
Hydrogen Gas ◽  
Laves Phase ◽  
X Ray Diffraction ◽  
X Ray ◽  
Phase Type ◽  
Diffraction Patterns

In the quasi-binary system CaNi2-MgNi2 solid-solutions CaxMg1−xNi2 (0 ≤ x ≤ 1) were prepared from the elements. They crystallize in the hexagonal Laves phase type (MgNi2, C36) for x ≤ 0.33 (P63/mmc, a = 482.51(7) pm, c = 1582.1(3) pm for x = 0, a = 482.59 (3), c = 1583.1(1) for x = 0.33) and in the cubic Laves phase type (MgCu2, C15) for 0.33 < x (Fd−3m, a = 697.12(3) pm for x = 0.5, a = 705.11(2) pm for x = 0.67, a = 724.80(2) pm for x = 1). After hydrogenation in an autoclave the X-ray diffraction patterns changed completely. Reflections assigned to CaNiH3, and Ni and Rietveld refinement confirmed this. The hydrogenation properties of CaxMg1−xNi2 (0 ≤ x ≤ 1) compounds were also studied in situ by X-ray powder diffraction. In situ X-ray powder diffraction of CaxMg1−xNi2 (0 ≤ x ≤ 1) compounds under 0.3 MPa hydrogen gas flow (15 sccm), data collected on a Rigaku SmartLab diffractometer in an Anton Paar XRK 900 Reactor Chamber using Cu-Kα1 radiation. Scanning electron microscopy and EDX spectroscopy confirmed the entitled materials and elemental composition, respectively. From the Transmission electron microscopy and Selected area electron diffraction concluded that the CaxMg1−xNi2 (0 ≤ x ≤ 1) compounds were crystalline.

scholarly journals Structure determination from in situ diffraction with the Rigaku PlateMate

2014 ◽  
Vol 70 (a1) ◽  
pp. C1152-C1152
Author(s):  
Pierre Le Magueres ◽  
Angela Criswell ◽  
Joseph Ferrara
Keyword(s):  
Room Temperature ◽  
Data Set ◽  
X Ray ◽  
The Past ◽  
Large Numbers ◽  
Structure Solution ◽  
Crystal Properties ◽  
Manual Handling ◽  
In Situ Diffraction

As crystallographers face increasing problems with crystallizing new proteins, in-situ screening in crystallization trays at room temperature is experiencing a renaissance. It saves a lot of time when screening large numbers of crystallization hits and it helps avoid crystal damage caused by human manipulation error (harsh manual handling, bad freezing) or changes in crystal properties (dehydration, wrong cryo-conditions). In certain cases, it is also possible to go beyond screening and collect enough data for structure solution, especially on an X-ray home source where a less intense beam helps minimize the devastations of radiation damage occurring at room temperature. The Rigaku PlateMate has proved itself as an efficient and easy-to-use in-situ screening tool on the field for the past two years. It is as easily mounted on a goniometer as a regular goniometer head and thanks to a plate adapter with SBS footprints, it accommodates most 96-wells plate types, from sitting and hanging drop to LCP plates. In addition, thanks to its narrow dimensions and aided by software to prevent collisions with the detector and the crystal viewing camera, the PlateMate can be used to easily collect data from crystals in situ. In this work, we present structure solution results obtained from data collected with the PlateMate on crystals from various proteins (native crystals or containing gold or iodine) and using one or multiple crystals to make up a complete data set.

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