scholarly journals Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin

2012 ◽  
Vol 68 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Zoë Fisher ◽  
Andrey Y. Kovalevsky ◽  
Marat Mustyakimov ◽  
B. Leif Hanson ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
Resolution Time ◽  
X Ray ◽  
Two Temperatures ◽  
Atomic Displacement Parameters

The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

Structure and phase transition of the Se-rich variety of antimonpearceite, [(Ag,Cu)6(Sb,As)2(S,Se)7][Ag9Cu(S,Se)2Se2]

2006 ◽  
Vol 62 (5) ◽  
pp. 768-774 ◽  
Author(s):  
Michel Evain ◽  
Luca Bindi ◽  
Silvio Menchetti
Keyword(s):  
Phase Transition ◽  
Room Temperature ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimensional Diffusion ◽  
Ionic Conducting ◽  
Local Arrangement ◽  
Diffusion Paths ◽  
Linear Coordination

The crystal structure of a Se-rich antimonpearceite has been solved and refined by means of X-ray diffraction data collected at temperatures above (room temperature) and below (120 K) an ionic conductivity-induced phase transition. Both structure arrangements consist of the stacking of [(Ag,Cu)6(Sb,As)2(S,Se)7]2− A (A′) and [Ag9Cu(S,Se)2Se2]2+ B (B′) module layers in which Sb forms isolated SbS3 pyramids typically occurring in sulfosalts; copper links two S atoms in a linear coordination, and silver occupies sites with coordination ranging from quasi-linear to almost tetrahedral. In the ionic-conducting form, at room temperature, the silver d 10 ions are found in the B (B′) module layer along two-dimensional diffusion paths and their electron densities described by means of a combination of a Gram–Charlier development of the atomic displacement factors and a split-atom model. The structure resembles that of pearceite, except for the presence of both specific (Se) and mixed (S, Se) sites. In the low-temperature `ordered' phase at 120 K the silver d 10 ions of the B (B′) module layer are located in well defined sites with mixed S—Se coordination ranging from quasi-linear to almost tetrahedral. The structure is then similar to that of 222-pearceite but with major differences, specifically its cell metric, symmetry and local arrangement in the B (B′) module layer.

scholarly journals Single-crystal neutron and X-ray diffraction study of garnet-type solid-state electrolyte Li6La3ZrTaO12: an in situ temperature-dependence investigation (2.5 ≤ T ≤ 873 K)

2021 ◽  
Vol 77 (1) ◽  
pp. 123-130
Author(s):  
Günther J. Redhammer ◽  
Martin Meven ◽  
Steffen Ganschow ◽  
Gerold Tippelt ◽  
Daniel Rettenwander
Keyword(s):  
Solid State ◽  
Single Crystal ◽  
Czochralski Method ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Solid State Electrolyte ◽  
Cubic Symmetry ◽  
X Ray ◽  
Site Occupation ◽  
Atomic Displacement Parameters

Large single crystals of garnet-type Li6La3ZrTaO12 (LLZTO) were grown by the Czochralski method and analysed using neutron diffraction between 2.5 and 873 K in order to fully characterize the Li atom distribution, and possible Li ion mobility in this class of potential candidates for solid-state electrolyte battery material. LLZTO retains its cubic symmetry (space group Ia 3 d) over the complete temperature range. When compared to other sites, the octahedral sites behave as the most rigid unit and show the smallest increase in atomic displacement parameters and bond length. The La and Li sites show similar thermal expansion in their bond lengths with temperature, and the anisotropic and equivalent atomic displacement parameters exhibit a distinctly larger increase at temperatures above 400 K. Detailed inspection of nuclear densities at the Li1 site reveal a small but significant displacement from the 24d position to the typical 96h position, which cannot, however, be resolved from the single-crystal X-ray diffraction data. The site occupation of LiI ions on Li1 and Li2 sites remains constant, so there is no change in site occupation with temperature.

scholarly journals MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models

2018 ◽  
Vol 74 (7) ◽  
pp. 606-620 ◽  
Author(s):  
Jouko J. Virtanen ◽  
Yang Zhang
Keyword(s):  
Protein Structures ◽  
Target Position ◽  
Protein Crystal ◽  
Conformational Search ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Homologous Proteins ◽  
X Ray ◽  
Replica Exchange Monte Carlo ◽  
Protein Models

Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r.m.s.d. of below 2 Å to the target position, which is 10% higher than was obtained by Phaser. However, cases studies show that many of the models for which Phaser failed and MR-REX succeeded can be solved by Phaser by pruning them and using nondefault parameters. The factors effecting success and the parts of the methodology which lead to success are studied. The results demonstrate a new avenue for molecular replacement which outperforms (and has results that are complementary to) the state-of-the-art MR methods, in particular for distantly homologous proteins.

Polymorphism of naphthazarin and its relation to solid-state proton transfer. Neutron and X-ray diffraction studies on naphthazarin C

1985 ◽  
Vol 399 (1817) ◽  
pp. 295-319 ◽  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Neutron Diffraction ◽  
Room Temperature ◽  
Model Comparison ◽  
Molecular Model ◽  
Molecular Formula ◽  
X Ray Diffraction ◽  
X Ray

The crystal structure of naphthazarin C has been determined by neutron diffraction at 60 and 300 K (λ ═ 0.895 Å; 1 Å ═ 10 -10 m ═ 10 -1 nm) and X-ray diffraction at 300 K. The space group is Pc at 60 K, but P 2 1 /c at 300 K. There are small but significant differences in cell dimensions at the two temperatures: a ═ 7.664 (7.915), b ═ 7.304 (7.262), c ═ 15.16 (15.284) Å; β ═ 114.60 (114.20)°; Z ═ 4; U ═ 771.6 (801.3) Å 3 (values at 300 K in parentheses). Neutron diffraction shows that the Pc and P 2 1 /c structures are related by an order-disorder transition at 110±1 K. Structure analysis (1771 reflections; R F ═ 0.035; R W ═ 0.036) showed that the hydroxyl hydrogens are largely ordered at 60 K, the appropriate molecular formula being 5, 8-dihydroxy-1, 4-naphthadione. Neutron diffraction measurements at 300 K (1769 reflections; R F ═ 0.052) indicated a disordered molecular model with one-half of an hydrogen atom attached to each oxygen. X -ray diffraction measurements on naphthazarin C at 300 K (two independent sets of intensity measurements, one with CuKα and the other with MoKα) support this disordered model. The molecular dimensions for naphthazarin A and B also fit this model. Comparison of the crystal structure of naphthazarin C with those of the A and B polymorphs shows that only the former has intermolecular O─H • • • O hydrogen bonding. The diffraction results combined with the available solid-state n. m. r. data show that there is at room temperature a rapid intramolecular exchange of hydroxylic protons between each pair of oxygen atoms in all three naphthazarin polymorphs. Many 1, 3-diketones exist in an enol form in the solid. These enol forms have been reported to be disordered for about twenty molecules at room temperature (this total includes one molecule studied at 108 K, and four amino-imino systems) and ordered systems have been reported for about fifteen molecules. Intermolecular hydrogen bonding occurs only in a few of these crystals.

scholarly journals Detailed single crystal studies on silicates using neutron diffraction

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].

scholarly journals Origin of forbidden reflections in multiferroic Ba2CoGe2O7 by neutron diffraction: symmetry lowering or Renninger effect?

2016 ◽  
Vol 49 (2) ◽  
pp. 556-560 ◽  
Author(s):  
Andrew Sazonov ◽  
Martin Meven ◽  
Georg Roth ◽  
Robert Georgii ◽  
István Kézsmárki ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Structural Model ◽  
Structural Parameters ◽  
Theoretical Description ◽  
Orthorhombic Symmetry ◽  
X Ray Diffraction ◽  
Multiple Diffraction ◽  
X Ray ◽  
Precise Knowledge

For a symmetry-consistent theoretical description of the multiferroic phase of Ba2CoGe2O7 a precise knowledge of its crystal structure is a prerequisite. In a previous synchrotron X-ray diffraction experiment on multiferroic Ba2CoGe2O7 at room temperature, forbidden reflections were found that favour the tetragonal-to-orthorhombic symmetry lowering of the compound [Hutanu, Sazonov, Murakawa, Tokura, Náfrádi & Chernyshov (2011), Phys. Rev. B, 84, 212101]. Here, the results are reported of room-temperature single-crystal diffraction studies with both hot and cold neutrons to differentiate between genuine symmetry lowering and multiple diffraction (the Renninger effect). A comparison of the experimental multiple diffraction patterns with simulated ones rules out symmetry lowering. Thus, the structural model based on the tetragonal space group P\overline{4}2_{1}m was selected to describe the Ba2CoGe2O7 symmetry at room temperature. The precise structural parameters from neutron diffraction at 300 K are presented and compared with the previous X-ray diffraction results.

Neutron and X-ray single-crystal diffraction from protein microcrystalsviamagnetically oriented microcrystal arrays in gels

2016 ◽  
Vol 72 (7) ◽  
pp. 823-829 ◽  
Author(s):  
Shu Tsukui ◽  
Fumiko Kimura ◽  
Katsuhiro Kusaka ◽  
Seiki Baba ◽  
Nobuhiro Mizuno ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Structure Determination ◽  
Room Temperature ◽  
X Ray Diffraction ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Diffraction Structure ◽  
First Time ◽  
Magnetically Aligned

Protein microcrystals magnetically aligned in D2O hydrogels were subjected to neutron diffraction measurements, and reflections were observed for the first time to a resolution of 3.4 Å from lysozyme microcrystals (∼10 × 10 × 50 µm). This result demonstrated the possibility that magnetically oriented microcrystals consolidated in D2O gels may provide a promising means to obtain single-crystal neutron diffraction from proteins that do not crystallize at the sizes required for neutron diffraction structure determination. In addition, lysozyme microcrystals aligned in H2O hydrogels allowed structure determination at a resolution of 1.76 Å at room temperature by X-ray diffraction. The use of gels has advantages since the microcrystals are measured under hydrated conditions.

X-ray diffraction study for one-dimensional ionic conductors K x (Ga1 − y Aly)2 + x Ti2 − x O7 (x ≃ 0.14, y ≃ 0.10, 0.23, 0.39)

2005 ◽  
Vol 61 (6) ◽  
pp. 608-615
Author(s):  
Yuichi Michiue ◽  
Shinzo Yoshikado
Keyword(s):  
Atomic Displacement ◽  
Ionic Conductors ◽  
X Ray Diffraction ◽  
Conduction Path ◽  
Coordination Polyhedra ◽  
Bottleneck Effect ◽  
One Dimensional ◽  
X Ray ◽  
Al Content ◽  
Atomic Displacement Parameters

The structures of one-dimensional ionic conductors K x (Ga1 − y Al y )2 + x Ti2 − x O7 (x ≃ 0.14, y ≃ 0.10, 0.23, 0.39) were refined by single-crystal X-ray diffraction. A one-dimensional tunnel-like space with a large cross section is formed by the linkage of coordination polyhedra of the metal and oxygen ions; K ions are distributed in the tunnel. Significant differences were seen in structures with different Al content; these differences could be explained by considerations in crystal chemistry. The probability density functions (PDFs) of the K ion were obtained using up to fourth-order terms of the atomic displacement parameters. The joint PDFs for the K ion have clarified that a K conduction path deviates slightly from the central axis of the tunnel in all the samples. In contrast with the usual one-dimensional ionic conductors, no distinct bottleneck effect was observed from the joint-PDFs and one-particle potentials.

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