Two-dimensional incommensurately modulated structure of (Sr0.13Ca0.87)2CoSi2O7 crystals

The incommensurate structure of (Sr0.13Ca0.87)2CoSi2O7 at room temperature has been determined from single-crystal X-ray diffraction data. The compound has a non-centrosymmetric tetragonal basic cell of a = 7.8743 (4) and c = 5.0417 (2) Å with the space group P4¯21 m. The refinements of the basic structure converged to R = 0.038 for 757 main reflections. The two-dimensional incommensurate structure is characterized by the wavevectors q 1 = 0.286 (3)(a* + b*) and q 2 = 0.286 (3)(−a* + b*), where a*, b* are the reciprocal lattice vectors of the basic structure. With the (3 + 2)-dimensional superspace group P p4mg P4¯21 m , the refinements converged to R = 0.071 for 1697 observed reflections (757 main and 940 satellite reflections). The structure is described in terms of displacement of the atoms, rotation, distortion of CoO4 and SiO4 tetrahedra, and the partial ordering of the Sr and Ca atoms accompanied with the modulation. Correlated evolution of these features throughout the crystal gives rise to various oxygen coordination around Ca/Sr. Comparison of the derived modulated structure to that of Ca2CoSi2O7 clarified that the partial substitution of Ca by large alkaline-earth atoms such as Sr should decrease the distortion of the polyhedra around the cations.

Download Full-text

X-RAY DIFFRACTION STUDY OF THE MODULATED STRUCTURE IN SUPERCONDUCTING SINGLE-CRYSTAL Bi2Sr2CaCu2Oy

Modern Physics Letters B ◽

10.1142/s0217984988000795 ◽

1988 ◽

Vol 02 (08) ◽

pp. 985-991 ◽

Cited By ~ 3

Author(s):

X. CHU ◽

Z.H. MAI ◽

Y.F. YAN ◽

J.H. WANG ◽

D.N. ZHENG ◽

...

Keyword(s):

Experimental Data ◽

Single Crystal ◽

Diffraction Study ◽

Basic Structure ◽

X Ray Diffraction ◽

Modulated Structure ◽

Space Group ◽

One Dimensional ◽

X Ray ◽

Average Structure

X-ray precession technique1 has been utilized to study the reciprocal space of the superconducting single crystal Bi 2 Sr 2 CaCu 2 O y. An average structure with space group of Pnnn and a real structure with the superspace group of [Formula: see text] or [Formula: see text] have been found for this one dimensional modulated incommensurate material. As well, a basic structure with the space group of Fmmm is derived from the experimental data.

Download Full-text

Applications of dynamical theory of X-ray diffraction by perfect crystals to reciprocal space mapping

Journal of Applied Crystallography ◽

10.1107/s1600576717010123 ◽

2017 ◽

Vol 50 (5) ◽

pp. 1256-1266 ◽

Cited By ~ 12

Author(s):

Vasily I. Punegov ◽

Konstantin M. Pavlov ◽

Andrey V. Karpov ◽

Nikolai N. Faleev

Keyword(s):

Reciprocal Lattice ◽

Dynamical Theory ◽

Two Dimensional ◽

Instrumental Function ◽

X Ray Diffraction ◽

Reciprocal Space Mapping ◽

Lattice Vector ◽

Reflected Waves ◽

X Ray ◽

Special Case

The classical dynamical theory of X-ray diffraction is expanded to the special case of transversely restricted wavefronts of the incident and reflected waves. This approach allows one to simulate the two-dimensional coherently scattered intensity distribution centred around a particular reciprocal lattice vector in the so-called triple-crystal diffraction scheme. The effect of the diffractometer's instrumental function on X-ray diffraction data was studied.

Download Full-text

BINoculars: data reduction and analysis software for two-dimensional detectors in surface X-ray diffraction

Journal of Applied Crystallography ◽

10.1107/s1600576715009607 ◽

2015 ◽

Vol 48 (4) ◽

pp. 1324-1329 ◽

Cited By ~ 25

Author(s):

Sander Roobol ◽

Willem Onderwaater ◽

Jakub Drnec ◽

Roberto Felici ◽

Joost Frenken

Keyword(s):

Data Reduction ◽

Modular Design ◽

Reciprocal Lattice ◽

Measurement Techniques ◽

Three Dimensional ◽

Two Dimensional ◽

X Ray Diffraction ◽

Data Set ◽

High Resolution Data ◽

X Ray

BINocularsis a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques. This paper covers the design and the underlying methods employed in this software package and explains howBINocularscan be used to improve the workflow of surface X-ray diffraction measurements and analysis.

Download Full-text

Two-dimensionally modulated structure of the rare-earth polysulfide GdS2−x (x = 0.18 ≃ 13/72)

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768103022213 ◽

2003 ◽

Vol 59 (6) ◽

pp. 709-719 ◽

Cited By ~ 17

Author(s):

Rafael Tamazyan ◽

Sander van Smaalen ◽

Inga Grigorevna Vasilyeva ◽

Heinrich Arnold

Keyword(s):

Basic Structure ◽

Structure Type ◽

Structure Model ◽

X Ray Diffraction ◽

Modulated Structure ◽

X Ray ◽

Experimental Resolution ◽

Quality Of Fit ◽

True Structure

The crystal structure of GdS2−x is determined by single-crystal X-ray diffraction as a 144-fold superstructure of the ZrSSi structure type. The superstructure is described as a two-dimensional, commensurately modulated structure with the superspace group P4/n(αβ½)(00)(ss) and with α = 1/4 and β = 1/3. Structure refinements within the classical approach, employing the 144-fold supercell, fail because most of the superlattice reflections have zero intensities within the experimental resolution. Within the superspace approach the absent superlattice reflections are systematically classified as higher-order satellite reflections. Accordingly, the superspace approach has been used to refine the structure model comprising the basic structure positions and the amplitudes of the modulation functions of the three crystallographically independent atoms. The quality of fit to the diffraction data and the values of the refined parameters are independent of the assumption on the true symmetry (incommensurate or a 12 × 12 × 2, I-centred superlattice with different symmetries). Arguments of structural plausibility then suggest that the true structure is a superstructure with space group I\bar{4}, corresponding to sections of superspace given by (t 1, t 2) equal to [(4n − 1)/48, (4m − 3)/48] or [(4n − 3)/48, (4m − 1)/48] (n and m are integers). Analysis of the structure, employing both superspace techniques (t plots) and the supercell structure model all show that the superstructure corresponds to an ordering of vacancies and an orientational ordering of S_2^{2-} dimers within the square layers of the S2 atoms.

Download Full-text

Tubulin structure at intermediate resolution

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140634 ◽

1995 ◽

Vol 53 ◽

pp. 852-853

Author(s):

K. H. Downing ◽

S. G. Wolf ◽

E. Nogales

Keyword(s):

High Resolution ◽

Structural Data ◽

Therapeutic Drug ◽

Zinc Ions ◽

Two Dimensional ◽

X Ray Diffraction ◽

X Ray ◽

Negative Stain ◽

Functional Mechanisms ◽

Tubulin Structure

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.

Download Full-text

Microstructure and crystal symmetry of Pb2Sr2(Y/Ca)Cu3O9−δ

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100173455 ◽

1990 ◽

Vol 48 (4) ◽

pp. 64-65

Author(s):

Y. P. Lin ◽

J. S. Xue ◽

J. E. Greedan

Keyword(s):

Electron Diffraction ◽

High Temperature Superconductors ◽

Carbon Film ◽

Basic Structure ◽

Crystal Symmetry ◽

X Ray Diffraction ◽

X Ray ◽

Space Groups ◽

New Family ◽

Convergent Beam

A new family of high temperature superconductors based on Pb2Sr2YCu3O9−δ has recently been reported. One method of improving Tc has been to replace Y partially with Ca. Although the basic structure of this type of superconductors is known, the detailed structure is still unclear, and various space groups has been proposed. In our work, crystals of Pb2Sr2YCu3O9−δ with dimensions up to 1 × 1 × 0.25.mm and with Tc of 84 K have been grown and their superconducting properties described. The defects and crystal symmetry have been investigated using electron microscopy performed on crushed crystals supported on a holey carbon film.Electron diffraction confirmed x-ray diffraction results which showed that the crystals are primitive orthorhombic with a=0.5383, b=0.5423 and c=1.5765 nm. Convergent Beam Electron Diffraction (CBED) patterns for the and axes are shown in Figs. 1 and 2 respectively.

Download Full-text

Xenon Trioxide Adducts of O-Donor Ligands; [(CH3)2CO]3XeO3, [(CH3)2SO]3(XeO3)2, (C5H5NO)3(XeO3)2, and [(C6H5)3PO]2XeO3

10.26434/chemrxiv.7092263.v1 ◽

2018 ◽

Author(s):

Katherine Marczenko ◽

James Goettel ◽

Gary Schrobilgen

Keyword(s):

Room Temperature ◽

Triphenylphosphine Oxide ◽

Donor Ligands ◽

Mechanical Shock ◽

X Ray Diffraction ◽

X Ray ◽

Oxygen Coordination ◽

Xenon Trioxide ◽

Distorted Octahedra ◽

Coordination Spheres

Oxygen coordination to the Xe(VI) atom of XeO3 was observed in its adducts with triphenylphosphine oxide, dimethylsulfoxide, pyridine-N-oxide, and acetone. The crystalline adducts were characterized by low-temperature, single-crystal X-ray diffraction and Raman spectroscopy. Unlike solid XeO3, which detonates when mechanically or thermally shocked, the solid [(C6H5)3PO]2XeO3, [(CH3)2SO]3(XeO3)2, and (C5H5NO)3(XeO3)2 adducts are insensitive to mechanical shock, but undergo rapid deflagration when ignited by a flame. Both [(C6H5)3PO]2XeO3 and (C5H5NO)3(XeO3)2 are air-stable whereas [(CH3)2SO]3(XeO3)2 slowly decomposes over several days and [(CH3)2CO]3XeO3 undergoes adduct dissociation at room temperature. The xenon coordination sphere of [(C6H5)3PO]2XeO3 is a distorted square pyramid which provides the first example of a five-coordinate XeO3 adduct. The xenon coordination spheres of the remaining adducts are distorted octahedra comprised of three Xe---O secondary contacts that are approximately trans to the primary Xe–O bonds of XeO3. Quantum-chemical calculations were used to assess the Xe---O adduct bonds, which are predominantly electrostatic σ-hole bonds between the nucleophilic oxygen atoms of the bases and the σ-holes of the xenon atoms.

Download Full-text

Synthesis and Structure of a Clathrated Two-Dimensional Metal-Organic Framework: [Cd(4,4'-bpy)2(H2O)2](ClO4)2·(L)2·H2O (L = Bis(1-pyrazinylethylidene)hydrazine)

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20080024 ◽

2008 ◽

Vol 73 (1) ◽

pp. 24-31

Author(s):

Dayu Wu ◽

Genhua Wu ◽

Wei Huang ◽

Zhuqing Wang

Keyword(s):

Metal Organic Framework ◽

Channel Structure ◽

Two Dimensional ◽

X Ray Diffraction ◽

Guest Molecules ◽

X Ray ◽

Square Planar ◽

Metal Organic ◽

Aqueous Meoh ◽

Organic Framework

The compound [Cd(4,4'-bpy)2(H2O)2](ClO4)2·(L)2 was obtained by the reaction of Cd(ClO4)2, bis(1-pyrazinylethylidene)hydrazine (L) and 4,4'-bipyridine in aqueous MeOH. Single-crystal X-ray diffraction has revealed its two-dimensional metal-organic framework. The 2-D layers superpose on each other, giving a channel structure. The square planar grids consist of two pairs of shared edges with Cd(II) ion and a 4,4'-bipyridine molecule each vertex and side, respectively. The square cavity has a dimension of 11.817 × 11.781 Å. Two guest molecules of bis(1-pyrazinylethylidene)hydrazine are clathrated in every hydrophobic host cavity, being further stabilized by π-π stacking and hydrogen bonding. The results suggest that the hydrazine molecules present in the network serve as structure-directing templates in the formation of crystal structures.

Download Full-text

New mixed-valent alkali chain sulfido ferrates A1+x[FeS2] (A = K, Rb, Cs; x = 0.333–0.787)

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1515/zkri-2020-0023 ◽

2020 ◽

Vol 235 (8-9) ◽

pp. 275-290

Author(s):

Michael Schwarz ◽

Pirmin Stüble ◽

Katharina Köhler ◽

Caroline Röhr

Keyword(s):

Alkali Metal ◽

General Structure ◽

Variable Number ◽

Monoclinic Space Group ◽

X Ray Diffraction ◽

Modulated Structure ◽

Space Group ◽

X Ray ◽

Local Coordination ◽

Natural Pyrite

AbstractFour new mixed-valent chain alkali metal (A) sulfido ferrates of the general structure family ${A}_{1+x}\left[{\text{Fe}}_{x}^{\text{II}}{\text{Fe}}_{1-x}^{\text{III}}{\text{S}}_{2}\right]$ were synthesized in the form of tiny green-metallic needles from nearly stoichiometric melts reacting elemental potassium with natural pyrite (A = K) or previously prepared Rb2S/Cs2S2 with elemental iron and sulfur (A = Rb/Cs). The crystal structures of the compounds were determined by means of single crystal X-ray diffraction: In the (3+1)D modulated structure of K7.15[FeS2]4 (space group Ccce(00σ3)0s0, a = 1363.87(5), b = 2487.23(13), c = 583.47(3) pm, q = 0,0,0.444, R1 = 0.055/0.148, x = 0.787), a position modulation of the two crystallographically different undulated ${}_{\infty }{}^{1}\left[{\text{FeS}}_{4/2}\right]$ tetrahedra chains and the surrounding K cations is associated with an occupation modulation of one of the three potassium sites. In the case of the new monoclinic rubidium ferrate Rb4[FeS2]3 (x = $\frac{1}{3}$; space group P21/c, a = 1640.49(12), b = 1191.94(9), c = 743.33(6) pm, β = 94.759(4)°, Z = 4, R1 = 0.1184) the undulation of the tetrahedra chain is commensurate, the repetition unit consists of six tetrahedra. In the second new Rb ferrate, Rb7[FeS2]5 (x = 0.4; monoclinic, space group C2/c, K7[FeS2]5-type; a = 2833.9(2), b = 1197.36(9), c = 744.63(6) pm, β = 103.233(4)°, Z = 4, R1 = 0.1474) and its isotypic mixed Rb/Cs-analog Rb3.6Cs3.4[FeS2]5 (a = 2843.57(5), b = 1226.47(2), c = 759.890(10) pm, β = 103.7170(9)°, R1 = 0.0376) the chain buckling leads to a further increased repetition unit of 10 tetrahedra. For all mixed-valent ferrates, the Fe–S bond lengths continuously increase with the amount (x) of Fe(II). The buckling of the chains is controlled through the local coordination of the S atoms by the variable number of A cations of different sizes.

Download Full-text