Lower resolution Laue neutron data yield correct nanocluster formulations

"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."

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

Journal of Applied Crystallography ◽

10.1107/s0021889892003649 ◽

1992 ◽

Vol 25 (5) ◽

pp. 589-610 ◽

Cited By ~ 59

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.

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Constraint-induced direct phasing method

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273316013875 ◽

2017 ◽

Vol 73 (1) ◽

pp. 54-60

Author(s):

Hongliang Xu

Keyword(s):

Single Crystal ◽

Diffraction Pattern ◽

Powder Diffraction ◽

Diffraction Data ◽

Structural Information ◽

Initial Structure ◽

X Rays ◽

Structural Refinement ◽

Low Resolution ◽

Crystallization Experiments

The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimetre in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented microcrystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Although single-crystal diffraction data consist of discrete spots or X-ray reflections, the diffraction of microcrystals in a powder forms rings so that the reflections overlap. Thus, the analysis is more challenging due to unavoidable errors in the structure-factor amplitudes and the low-resolution data available for structure determination. This paper introduces a constraint-induced phasing method that (i) improves structure solutions measured by success rate, quality of solutions and various figures of merit, and (ii) extends low-resolution powder diffraction data to atomic resolution by adding unmeasured reflections. Application results have shown clearly that the constraint-induced phasing method is an effective way to produce initial structure models that are suitable for further structural refinement and completion.

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A Re-investigation of the Crystal Structure of the Perovskite PbZrO3 by X-ray and Neutron Diffraction

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768196012414 ◽

1997 ◽

Vol 53 (1) ◽

pp. 135-142 ◽

Cited By ~ 86

Author(s):

D. L. Corker ◽

A. M. Glazer ◽

J. Dec ◽

K. Roleder ◽

R. W. Whatmore

Keyword(s):

Crystal Structure ◽

Low Temperature ◽

Neutron Diffraction ◽

Single Crystal ◽

Lead Zirconate ◽

Conclusive Evidence ◽

X Rays ◽

X Ray Diffraction ◽

X Ray ◽

Structure Investigations

The crystal structure of the perovskite lead zirconate PbZrO3 has been redetermined using single-crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 Å). Single-crystal data at 100 K: space group. Pbam, a = 5.884 (1), b = 11.787 (3), c = 8.231 (2) Å, V = 570.85 Å3 with Z = 8, μ = 612.6 cm−1, D x = 8.06 Mg m−3, F(000) = 1168, final R = 0.033, wR = 0.061 over 555 reflections with I > 2σ(I). An investigation is made into previous contradicting reports of a possible disorder in the O atoms and their origin by examining the crystal pseudo-symmetry. Information distinguishing an ordered and disordered oxygen substructure is shown to reside in weak l odd reflections. Because of their extremely low intensities these reflections have not contributed sufficiently in previous X-ray structure investigations and hence, to date, conclusive evidence differentiating between ordered and disordered models has not been possible. By collecting single-crystal X-ray data at low temperature and by using exceptionally long scans on selected hkl, l odd, reflections, a new accurate structure determination is presented and discussed, showing the true ordered oxygen positions. Because of the large difference in scattering factors between lead and oxygen when using X-rays, a neutron diffraction Rietveld refinement using polycrystalline samples (D1A instrument, ILL, λ = 1.90788 Å) is also reported as further evidence to support the true ordered oxygen structure revealed by the low-temperature X-ray analysis.

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

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18018125 ◽

2019 ◽

Vol 75 (2) ◽

pp. 111-115 ◽

Cited By ~ 2

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.

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

Australian Journal of Chemistry ◽

10.1071/ch9880641 ◽

1988 ◽

Vol 41 (5) ◽

pp. 641 ◽

Cited By ~ 6

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.

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Detailed single crystal studies on silicates using neutron diffraction

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314088895 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1110-C1110

Author(s):

Martin Meven ◽

G. Gatta

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Room Temperature ◽

Structural Features ◽

X Rays ◽

X Ray Diffraction ◽

X Ray ◽

Order And Disorder ◽

Structural Details ◽

Displacement Regime

Up to now minerals of the silicate family are an interesting and versatile topic of research. Different members of the epidote, lithium tourmaline and beryl groups with very different structural features were studied on the single crystal diffractometer HEIDI at the hot source of the Heinz Maier-Leibnitz Zentrum in Garching (MLZ) in the recent past. The combination of neutron and X-ray diffraction in combination with other methods revealed for each of the studied minerals valuable information about their structural details. Epidote, an important mineral for metamorphic or magmatic petrology was studied with neutrons at room temperature and at 1070 K. The results confirm the high structural stability with no dehydration and only slight thermal expansion [1]. A combined study with x-ray and neutron diffraction on the complex boro-cyclo-silicate elbaite give insight to the displacement regime and H and O order and disorder respectively [2]. Combined single crystal diffraction with x-rays at room temperature and with neutrons at 2.3 K on pezzottaite, an obverse/reverse twin of the beryl family reveals a complex displacement regime with possible partial H2O replacement [3].

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Electron Microscopy of Shock Loaded Polycrystalline Beryllium

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052547 ◽

1974 ◽

Vol 32 ◽

pp. 506-507 ◽

Cited By ~ 1

Author(s):

J. M. Galbraith ◽

L. E. Murr ◽

A. L. Stevens

Keyword(s):

Electron Microscopy ◽

Wave Propagation ◽

Structural Change ◽

Single Crystal ◽

Diffraction Pattern ◽

Shock Loading ◽

Slip Systems ◽

Compression Tests ◽

X Ray Diffraction ◽

X Ray

Uniaxial compression tests and hydrostatic tests at pressures up to 27 kbars have been performed to determine operating slip systems in single crystal and polycrystal1ine beryllium. A recent study has been made of wave propagation in single crystal beryllium by shock loading to selectively activate various slip systems, and this has been followed by a study of wave propagation and spallation in textured, polycrystal1ine beryllium. An alteration in the X-ray diffraction pattern has been noted after shock loading, but this alteration has not yet been correlated with any structural change occurring during shock loading of polycrystal1ine beryllium.This study is being conducted in an effort to characterize the effects of shock loading on textured, polycrystal1ine beryllium. Samples were fabricated from a billet of Kawecki-Berylco hot pressed HP-10 beryllium.

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