INTEGRATION OF SINGLE CRYSTAL NEUTRON DATA USING A P.S.D : A CASE OF LARGE, WEAK AND OFTEN OVERLAPPING REFLECTIONS

1986 ◽  
Vol 47 (C5) ◽  
pp. C5-27-C5-34
Author(s):  
M. ROTH ◽  
A. LEWIT-BENTLEY
Keyword(s):  
Single Crystal ◽  
Neutron Data

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 Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras

2019 ◽  
Vol 75 (2) ◽  
pp. 111-115 ◽  
Author(s):  
Ryan Knihtila ◽  
Alicia Y. Volmar ◽  
Flora Meilleur ◽  
Carla Mattos
Keyword(s):  
Single Crystal ◽  
Radiation Damage ◽  
Communication Networks ◽  
Active Site ◽  
Small Gtpase ◽  
Data Sets ◽  
Neutron Data ◽  
Major Drawback ◽  
X Ray ◽  
Ionizable Groups

Neutron protein crystallography (NPC) reveals the three-dimensional structures of proteins, including the positions of H atoms. The technique is particularly suited to elucidate ambiguous catalytic steps in complex biochemical reactions. While NPC uniquely complements biochemical assays and X-ray structural analyses by revealing the protonation states of ionizable groups at and around the active site of enzymes, the technique suffers from a major drawback: large single crystals must be grown to compensate for the relatively low flux of neutron beams. However, in addition to revealing the positions of hydrogens involved in enzyme catalysis, NPC has the advantage over X-ray crystallography that the crystals do not suffer radiation damage. The lack of radiation damage can be exploited to conduct in crystallo parametric studies. Here, the use of a single crystal of the small GTPase Ras to collect three neutron data sets at pD 8.4, 9.0 and 9.4 is reported, enabling an in crystallo titration study using NPC. In addition to revealing the behavior of titratable groups in the active site, the data sets will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks, Tyr32, Tyr96 and Tyr137, with pK a values expected to be in the range sampled in our experiments.

Investigation into the Crystal Structure of the Perovskite Lead Hafnate, PbHfO3

1998 ◽  
Vol 54 (1) ◽  
pp. 18-28 ◽  
Author(s):  
D. L. Corker ◽  
A. M. Glazer ◽  
W. Kaminsky ◽  
R. W. Whatmore ◽  
J. Dec ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Room Temperature ◽  
Lead Zirconate ◽  
Crystal Structure Analysis ◽  
Temperature Structure ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray

The room-temperature crystal structure of the perovskite lead hafnate PbHfO3 is investigated using both low-temperature single crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 Å) and polycrystalline neutron diffraction (D1A instrument, ILL, λ = 1.90788 Å). Single crystal X-ray data at 100 K: space group Pbam, a = 5.856 (1), b = 11.729 (3), c = 8.212 (2) Å, V = 564.04 Å3 with Z = 8, μ = 97.2 mm−1, F(000) = 1424, final R = 0.038, wR = 0.045 over 439 reflections with F >1.4σ(F). Polycrystalline neutron data at 383 K: a = 5.8582 (3), b = 11.7224 (5), c = 8.2246 (3) Å, V = 564.80 Å3 with χ2 = 1.62. Although lead hafnate has been thought to be isostructural with lead zirconate, no complete structure determination has been reported, as crystal structure analysis in both these materials is not straightforward. One of the main difficulties encountered is the determination of the oxygen positions, as necessary information lies in extremely weak l = 2n + 1 X-ray reflections. To maximize the intensity of these reflections the X-ray data are collected at 100 K with unusually long scans, a procedure which had previously been found successful with lead zirconate. In order to establish that no phase transitions exist between room temperature and 100 K, and hence that the collected X-ray data are relevant to the room-temperature structure, birefringence measurements for both PbZrO3 and PbHfO3 are also reported.

scholarly journals Rietveld refinement round robin. I. Analysis of standard X-ray and neutron data for PbSO4

1992 ◽  
Vol 25 (5) ◽  
pp. 589-610 ◽  
Author(s):  
R. J. Hill
Keyword(s):  
Single Crystal ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Data Sets ◽  
X Rays ◽  
Neutron Data ◽  
X Ray ◽  
Atomic Coordinates

The Commission on Powder Diffraction of the International Union of Crystallography has undertaken an intercomparison of Rietveld refinements performed with two `standard' PbSO4 powder diffraction patterns: a conventional (two-wavelength) X-ray pattern collected on a Bragg–Brentano diffractometer with Cu Kα radiation and a constant-wavelength neutron pattern collected on the D1A diffractometer at the Institut Laue–Langevin. The aims of this project were: (i) to evaluate a cross section of currently used Rietveld refinement software; (ii) to examine the range and effect of various strategies of Rietveld refinement; (iii) to assess the precision and accuracy (spread) of the parameters derived by Rietveld analysis. 23 participants provided 18 refinements with the X-ray data and 20 refinements with the neutron data, using 11 different Rietveld-analysis programs. Analysis of the submitted results shows that refinement strategies play a large part in determining the detailed outcome of a Rietveld refinement. The wide variation in the values of the agreement indices obtained in these studies of the same data sets highlights the need for standardization both of the refinement procedures and of the type of data included in the algorithms used for assessing the fit. The major factors limiting the accuracy of the derived PbSO4 crystal structure parameters were: (i) use of insufficiently flexible peak shape and/or background functions; (ii) elimination of the high-angle diffraction data from the refinement; (iii) inclusion of an insufficiently wide range of diffraction angles on either side of the centroid of each peak during the step intensity calculation; and, additionally for X-rays, (iv) simultaneous release of the O-atom site-occupancy and displacement parameters. Rietveld analysis of the PbSO4 X-ray powder diffraction data provided atomic coordinates and isotropic displacement parameters for the Pb and S atoms that are precise (i.e. have small e.s.d.s) and are in reasonable agreement with the values derived from a single crystal study (viz the spread of coordinates is over the range 0.007–0.042 Å). On the other hand, the `light' O-atom parameters show relatively poor precision and have a disconcertingly wide spread of values about the weighted mean (viz 0.12–0.19 Å for the coordinates). Despite the much lower intrinsic resolution of the neutron data (i.e. peak widths some four times those of the X-ray data), the coordinates and anisotropic displacement parameters obtained for the Pb and O atoms are very precise and have a relatively narrow distribution about the single-crystal results, namely 0.004–0.020 Å for the coordinates. The range of coordinates determined from the neutron data for the relatively `light' S atom is correspondingly larger, namely 0.024–0.043 Å, about equivalent to that obtained from the X-ray data. In general, and as expected, the e.s.d.s from the Rietveld analyses are substantially smaller than the observed inter-refinement variation of the unit-cell dimensions, atomic coordinates and isotropic displacement parameters by factors of up to, respectively, 17, 5 and 22 for X-rays, and 25, 3 and 5 for neutrons. This investigation indicates that results of possibly high precision but low accuracy are not uncommon in Rietveld analysis. The disparity between individual refinements can be expected to increase further when, unlike here, the analyses are undertaken using data sets collected under diverse experimental conditions.

The Crystal and Molecular Structure of Chloro-mer-Tris(dimethylphenylphosphine)-cis-dihydridoiridium(III) by X-Ray and Neutron Diffraction

1988 ◽  
Vol 41 (5) ◽  
pp. 641 ◽  
Author(s):  
GB Robertson ◽  
PA Tucker
Keyword(s):  
Molecular Structure ◽  
Neutron Diffraction ◽  
Single Crystal ◽  
Least Squares ◽  
Crystal And Molecular Structure ◽  
Monoclinic Space Group ◽  
Neutron Data ◽  
Full Matrix ◽  
Space Group ◽  
X Ray

The structure of mer-(Pme2Ph)3Cl-cis-H2IrIII (1) has been determined by single-crystal X-ray and neutron diffraction analyses. Crystals are monoclinic, space group P21, with a 11.476(4), b 14.069(5), c 8.286(3)Ǻ, β 92.45(1)° and Z 2. Full-matrix least-squares analyses converged 0.022 for 7773 X-ray data and R(F2) = 0.062 for 1538 neutron data. Ir -H [1.557(11)Ǻ trans to Cl, 1.603(10) Ǻ trans to P] and Ir -P distances [2.292(1)Ǻ trans to P, 2.328(1)Ǻ trans to H] both exhibit trans lengthening effects. Consistent with the increased hydride content the Ir -P distances in (1) are c. 0.04 Ǻ shorter than for the corresponding bonds in its dichloro monohydrido analogues and c. 0.08 Ǻ shorter than those in the trichloride . In contrast Ir-Cl [2.505(1)Ǻ] is not significantly different to the corresponding distance (2.504 Ǻ av.) in mer -(PMe2Ph)3-cis-Cl2HIrIII.

scholarly journals Use of a miniature diamond-anvil cell in a joint X-ray and neutron high-pressure study on copper sulfate pentahydrate

IUCrJ ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Giulia Novelli ◽  
Konstantin V. Kamenev ◽  
Helen E. Maynard-Casely ◽  
Simon Parsons ◽  
Garry J. McIntyre
Keyword(s):  
High Pressure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Diamond Anvil Cell ◽  
Structural Parameters ◽  
Structure Refinement ◽  
Neutron Data ◽  
X Ray ◽  
Sulfate Pentahydrate ◽  
Diamond Anvil

Single-crystal X-ray and neutron diffraction data are usually collected using separate samples. This is a disadvantage when the sample is studied at high pressure because it is very difficult to achieve exactly the same pressure in two separate experiments, especially if the neutron data are collected using Laue methods where precise absolute values of the unit-cell dimensions cannot be measured to check how close the pressures are. In this study, diffraction data have been collected under the same conditions on the same sample of copper(II) sulfate pentahydrate, using a conventional laboratory diffractometer and source for the X-ray measurements and the Koala single-crystal Laue diffractometer at the ANSTO facility for the neutron measurements. The sample, of dimensions 0.40 × 0.22 × 0.20 mm3 and held at a pressure of 0.71 GPa, was contained in a miniature Merrill–Bassett diamond-anvil cell. The highly penetrating diffracted neutron beams passing through the metal body of the miniature cell as well as through the diamonds yielded data suitable for structure refinement, and compensated for the low completeness of the X-ray measurements, which was only 24% on account of the triclinic symmetry of the sample and the shading of reciprocal space by the cell. The two data-sets were combined in a single `XN' structure refinement in which all atoms, including H atoms, were refined with anisotropic displacement parameters. The precision of the structural parameters was improved by a factor of up to 50% in the XN refinement compared with refinements using the X-ray or neutron data separately.

scholarly journals Application of Charge & Band-flipping to Time-of-Flight Neutron Diffraction Data

2014 ◽  
Vol 70 (a1) ◽  
pp. C188-C188 ◽  
Author(s):  
Pamela Whitfield ◽  
Alan Coehlo ◽  
Ashfia Huq ◽  
Christina Hoffmann ◽  
Xiaoping Wang
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Time Of Flight ◽  
Easy Access ◽  
Neutron Diffraction Data ◽  
Crystal Data ◽  
Powder Diffraction Data ◽  
Neutron Data

Charge-flipping has become a popular approach to ab-initio structure solution from X-ray powder diffraction data in particular due to its speed and need for minimal input other than lattice parameters. Given the appetite of charge-flipping for low d-spacing reflections, time-of-flight (TOF) neutron data should be a good match from a resolution standpoint, with easy access to high Q and lack of form-factor drop-off. One obvious issue with neutron data is the presence of elements with negative scattering lengths, where the inherent assumption of atoms always having positive `density' in the algorithm breaks down. This means that portions of the structure can be effectively invisible. Given that some of these elements (e.g. H and Mn) are commonly found in samples of interest the issue is more than simple academic curiosity. Of course such atoms can be found by difference maps, but the issue has also been addressed within the charge-flipping algorithm with the `band-flipping' modification [1]. Although Oszlányi & Sütö demonstrated the approach was viable with simulated neutron single crystal data [1], to the authors' knowledge it hasn't been used previously with experimental single crystal or powder neutron diffraction data. Powder diffraction data from POWGEN and wavelength-resolved TOF Laue single crystal data from TOPAZ at the Spallation Neutron Source have been used to probe the relative ease of charge-flipping with different TOF data using the TOPAS software package [2]. In addition the effectiveness of different customized band-flipping approaches has been tested to extract positions for positive and negative scattering elements simultaneously.

A Preparation of High Resolution Standards for Electron Microscopy. Part II

1971 ◽  
Vol 29 ◽  
pp. 160-161
Author(s):  
Akira Tanaka ◽  
David F. Harling
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Carbon Black ◽  
Single Crystal ◽  
Dark Field ◽  
Graphitized Carbon Black ◽  
Graphitized Carbon ◽  
Dark Field Imaging ◽  
Crystal Films ◽  
Micro Holes

In the previous paper, the author reported on a technique for preparing vapor-deposited single crystal films as high resolution standards for electron microscopy. The present paper is intended to describe the preparation of several high resolution standards for dark field microscopy and also to mention some results obtained from these studies. Three preparations were used initially: 1.) Graphitized carbon black, 2.) Epitaxially grown particles of different metals prepared by vapor deposition, and 3.) Particles grown epitaxially on the edge of micro-holes formed in a gold single crystal film.The authors successfully obtained dark field micrographs demonstrating the 3.4Å lattice spacing of graphitized carbon black and the Au single crystal (111) lattice of 2.35Å. The latter spacing is especially suitable for dark field imaging because of its preparation, as in 3.), above. After the deposited film of Au (001) orientation is prepared at 400°C the substrate temperature is raised, resulting in the formation of many square micro-holes caused by partial evaporation of the Au film.

Structure of Palladium Single-Crystal Films Prepared by Flash Evaporation onto (001) NaCl Substrates

1970 ◽  
Vol 28 ◽  
pp. 456-457
Author(s):  
L. E. Murr ◽  
G. Wong
Keyword(s):  
Single Crystal ◽  
High Vacuum ◽  
Ultra High Vacuum ◽  
High Rate ◽  
Flash Evaporation ◽  
Optimum Load ◽  
Single Crystal Films ◽  
Crystal Films ◽  
A Current

Palladium single-crystal films have been prepared by Matthews in ultra-high vacuum by evaporation onto (001) NaCl substrates cleaved in-situ, and maintained at ∼ 350° C. Murr has also produced large-grained and single-crystal Pd films by high-rate evaporation onto (001) NaCl air-cleaved substrates at 350°C. In the present work, very large (∼ 3cm2), continuous single-crystal films of Pd have been prepared by flash evaporation onto air-cleaved (001) NaCl substrates at temperatures at or below 250°C. Evaporation rates estimated to be ≧ 2000 Å/sec, were obtained by effectively short-circuiting 1 mil tungsten evaporation boats in a self-regulating system which maintained an optimum load current of approximately 90 amperes; corresponding to a current density through the boat of ∼ 4 × 104 amperes/cm2.

Dislocations, Ordering and Antiferromagnetic Domains in MnO

1970 ◽  
Vol 28 ◽  
pp. 522-523
Author(s):  
D. J. Barber ◽  
R. G. Evans
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Optical Microscopy ◽  
Defect Chemistry ◽  
Magnetic Structures ◽  
Optically Transparent ◽  
Magnetic Features ◽  
Antiferromagnetic Domains

Manganese (II) oxide, MnO, in common with CoO, NiO and FeO, possesses the NaCl structure and shows antiferromagnetism below its Neel point, Tn∼ 122 K. However, the defect chemistry of the four oxides is different and the magnetic structures are not identical. The non-stoichiometry in MnO2 small (∼2%) and below the Tn the spins lie in (111) planes. Previous work reported observations of magnetic features in CoO and NiO. The aim of our work was to find explanations for certain resonance results on antiferromagnetic MnO.Foils of single crystal MnO were prepared from shaped discs by dissolution in a mixture of HCl and HNO3. Optical microscopy revealed that the etch-pitted foils contained cruciform-shaped precipitates, often thick and proud of the surface but red-colored when optically transparent (MnO is green). Electron diffraction and probe microanalysis indicated that the precipitates were Mn2O3, in contrast with recent findings of Co3O4 in CoO.

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