The site occupancy of Mg in the brownmillerite structure and its effect on hydration properties: an X-ray/neutron diffraction and EXAFS study

2001 ◽  
Vol 34 (1) ◽  
pp. 55-61 ◽  
Author(s):  
A. C. Jupe ◽  
J. K. Cockcroft ◽  
P. Barnes ◽  
S. L. Colston ◽  
G. Sankar ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Site Occupancy ◽  
Pure Form ◽  
Site Preference ◽  
Data Sets ◽  
Hydration Properties ◽  
Time Resolved ◽  
X Ray ◽  
Mg Doping

Samples of pure (Ca2FeAlO5) and lightly doped (Ca2Fe0.95Al0.95Mg0.05Si0.05O5) brownmillerite have been synthesized. Synchrotron X-ray and neutron diffraction data have been collected so that the structures can be refined using, simultaneously, both diffraction data sets and known compositional information; this overcomes the problem of under-determinacy resulting from multi-occupation of the tetrahedrally and octahedrally coordinated sites in the structure. For the pure form, a 2.7:1 iron/aluminium preference for octahedral/tetrahedral (respectively) occupation is obtained. This trend is reflected also in the doped brownmillerite, though, because of the low level of Mg doping, the occupancy of Mg is only resolved through the additional use of Mg EXAFS (extended X-ray absorption fine structure) data, which shows that Mg displays a distinct octahedral site preference rather than a disordered occupation between the octahedral/tetrahedral sites. The consequences of Mg doping are then examined using time-resolved multi-angle energy-dispersive powder X-ray diffraction studies of the mineral undergoing hydration; this shows that the pure form is more active than the doped form.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

scholarly journals Lower resolution Laue neutron data yield correct nanocluster formulations

2014 ◽  
Vol 70 (a1) ◽  
pp. C187-C187
Author(s):  
Alison Edwards
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Diffraction Pattern ◽  
Precise Determination ◽  
Data Sets ◽  
X Rays ◽  
Low Resolution ◽  
Neutron Data ◽  
X Ray ◽  
Product Formulation

"The renaissance in Laue studies - at neutron sources - provides us with access to single crystal neutron diffraction data for synthetic compounds without requiring synthesis of prohibitively large amounts of compound or improbably large crystals. Such neutron diffraction studies provide vital data where proof of the presence or absence of hydrogen in particular locations is required and which cannot validly be proved by X-ray studies. Since the commissioning of KOALA at OPAL in 2009[1] we have obtained numerous data sets which demonstrate the vital importance of measuring data even where the extent of the diffraction pattern is at relatively low resolution - especially when compared to that obtainable for the same compound with X-rays. In the Laue experiment performed with a fixed radius detector, data reduction is only feasible for crystals in the ""goldilocks"" zone – where the unit cell is relatively large for the detector, a correspondingly low resolution diffraction pattern in which adjacent spots are less affected by overlap will yield more data against which a structure can be refined than a pattern of higher resolution – one where neighbouring spots overlap rendering both unusable (in our current methodology). Analogous application of powder neutron diffraction in such determinations is also considered. Single crystal neutron diffraction studies of several important compounds (up to 5KDa see figure below)[2] in which precise determination of hydride content by neutron diffraction was pivotal to the final formulation will be presented. The neutron data sets typically possess 20% or fewer unique data at substantially "lower resolution" than the corresponding X-ray data sets. Careful refinement clearly reveals chemical detail which is typically unexplored in related X-ray diffraction studies reporting high profile chemistry despite the synthetic route being one which hydride ought to be considered/excluded in product formulation."

scholarly journals Accurate H-atom parameters for the two polymorphs of L-histidine at 5, 105 and 295 K

2021 ◽  
Vol 77 (5) ◽  
pp. 785-800
Author(s):  
Giulia Novelli ◽  
Charles J. McMonagle ◽  
Florian Kleemiss ◽  
Michael Probert ◽  
Horst Puschmann ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Crystal Packing ◽  
Basis Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Refinement Method ◽  
Primary Amino ◽  
Precision And Accuracy

The crystal structure of the monoclinic polymorph of the primary amino acid L-histidine has been determined for the first time by single-crystal neutron diffraction, while that of the orthorhombic polymorph has been reinvestigated with an untwinned crystal, improving the experimental precision and accuracy. For each polymorph, neutron diffraction data were collected at 5, 105 and 295 K. Single-crystal X-ray diffraction experiments were also performed at the same temperatures. The two polymorphs, whose crystal packing is interpreted by intermolecular interaction energies calculated using the Pixel method, show differences in the energy and geometry of the hydrogen bond formed along the c direction. Taking advantage of the X-ray diffraction data collected at 5 K, the precision and accuracy of the new Hirshfeld atom refinement method implemented in NoSpherA2 were probed choosing various settings of the functionals and basis sets, together with the use of explicit clusters of molecules and enhanced rigid-body restraints for H atoms. Equivalent atomic coordinates and anisotropic displacement parameters were compared and found to agree well with those obtained from the corresponding neutron structural models.

H-bonding scheme in allactite: a combined single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, FTIR and EPMA-WDS study

2016 ◽  
Vol 80 (5) ◽  
pp. 719-732 ◽  
Author(s):  
G. Diego Gatta ◽  
Ferdinando Bosi ◽  
Maria Teresa Fernandez Diaz ◽  
Ulf Hålenius
Keyword(s):  
Neutron Diffraction ◽  
Optical Absorption ◽  
Single Crystal ◽  
Absorption Spectroscopy ◽  
Structure Refinement ◽  
Site Occupancy ◽  
Optical Absorption Spectroscopy ◽  
Hydroxyl Groups ◽  
X Ray ◽  
Bonding Scheme

AbsatractThe crystal chemistry of allactite from Långban, Värmland (Sweden) was investigated by single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, Fourier-transform infra-red spectroscopy (FTIR) and electron microprobe analysis by wavelength-dispersive spectroscopy (EPMA-WDS). The optical spectra indicate the presence of Mn in valence state 2+ only. Assuming 16 O atoms per formula unit, arsenic as As5+and the (OH) content calculated by charge balance, the resulting formula based on the EPMA-WDS data is (Mn2+6.73Ca0.13Mg0.12Zn0.02)∑7.00(As5+)2.00O16H8, very close to the ideal composition Mn7(AsO4)2(OH)8. In the unpolarized FTIR spectrum of allactite, fundamental (OH)-stretching bands are observed at 3236, 3288, 3387, 3446, 3484, 3562 and 3570 cm–1, suggesting that a number of OH environments, with different hydrogen bond strengths, occur in the structure. The neutron structure refinement shows that four independent H sites occur in allactite with full site occupancy, all as members of hydroxyl groups. The complex hydrogen-bonding scheme in the allactite structure is now well defined, with at least nine hydrogen bonds energetically favourable with mono-, bi- and trifurcated configurations.

scholarly journals AUSPEX: a graphical tool for X-ray diffraction data analysis

2017 ◽  
Vol 73 (9) ◽  
pp. 729-737 ◽  
Author(s):  
Andrea Thorn ◽  
James Parkhurst ◽  
Paul Emsley ◽  
Robert A. Nicholls ◽  
Melanie Vollmar ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Software Tool ◽  
Data Conversion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pixel Detectors ◽  
Graphical Tool ◽  
Data Acquisition And Processing

In this paper,AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated howAUSPEXcan be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected byAUSPEX.

X-ray powder diffraction study of K2MSiO4, M=Mg, Zn, Co, Cd

1996 ◽  
Vol 11 (1) ◽  
pp. 51-55 ◽  
Author(s):  
W. A. Dollase
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Method ◽  
Site Occupancy ◽  
Cubic Phase ◽  
Variable Degree ◽  
Cubic Symmetry ◽  
X Ray ◽  
Constrained Model ◽  
Diffraction Patterns

The title materials are stuffed cristobalites possessing moderate to extreme pseudosymmetry. On the bases of their X-ray powder diffraction patterns, the Mg, Zn, and Cd compounds had been previously reported as cubic and, more recently, the Zn phase as orthorhombic. Newly measured X-ray powder diffraction data demonstrate that all (including the hitherto unknown Co analog) have the Pca21 structure of Na2BeSiO4 at room temperature, but with a widely variable degree of cubic pseudosymmetry. Observed X-ray diffraction data are in good agreement with those calculated by the Rietveld method using a constrained model with Pca21 M2+/Si site occupancy and pseudocentrosymmetric Pcab atom locations. For the most nearly cubic phase, the Cd compound, there is too little deviation in the pattern from cubic symmetry to support atom coordinate refinement even with the constrained model. In these derivatives of the stuffed cristobalite structure family, M2+ and Si atoms form an ordered tetrahedral array which avoids M2+–O–M2+ connections. Potassium atoms fill all of the intervening large cavity sites.

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