An elementary introduction to superspace crystallography

Author(s):  
Sander van Smaalen

AbstractAperiodic crystals are defined as a crystalline state of matter, that has atomic structures with long-range order but without translational symmetry. Experimentally, they are characterized by sharp Bragg reflections in the X-ray diffraction, that can be indexed by integers, if four or more reciprocal basis vectors are used. An introduction is given to the basic concepts of the superspace theory for structural analysis of incommensurately modulated crystals and incommensurate composite crystals [De Wolff, Janner and Janssen, Acta Crystallogr.

2010 ◽  
Vol 43 (2) ◽  
pp. 227-236 ◽  
Author(s):  
Leandro M. Acuña ◽  
Diego G. Lamas ◽  
Rodolfo O. Fuentes ◽  
Ismael O. Fábregas ◽  
Márcia C. A. Fantini ◽  
...  

The local atomic structures around the Zr atom of pure (undoped) ZrO2nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr—O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye–Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to thezdirection; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.


Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 273 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.


1985 ◽  
Vol 22 (2) ◽  
pp. 545-553 ◽  
Author(s):  
M. J. Musmar ◽  
Gary E. Martin ◽  
Robert T. Gampe ◽  
Vincent M. Lynch ◽  
Stanley H. Simonsen ◽  
...  

Author(s):  
Yuliya V. Butina ◽  
Elena A. Danilova ◽  
Maxim V. Dmitriev ◽  
Aleksey V. Solomonov

For citation:Butina Yu.V., Danilova E.A., Dmitriev M.V., Solomonov А.V. Crystal structure of bis[1-(diaminomethylene)-thiouron-1-ium] sulfate. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 1. P. 45-49. In this work crystal data of bis[1-(diaminomethylene)-thiouron-1-ium] sulfate is shown. This compound was characterized by IR spectroscopy and elemental analysis. The monocrystal of this compound was obtained and the structure was confirmed by single X-ray analysis. Moreover, the work describes potential application of synthesized compound. Comparative characteristics of thiourea and its known salts are demonstrated. It is known, that derivatives of thiourea have several tautomeric forms, which can be different in crystalline state or in solution. Therefore, changed scheme of the synthesis of 2-imino-4-thiobiuret is proposed. Elemental cell of crystal consists of two 1-(diaminomethylene)thiouron-1-ium cations and one sulfat anion. A full set of X-ray diffraction data was deposited in the Cambridge Structural Database (deposit CCDC 1421710) and it can be gotten from the site www.ccdc.cam.ac.uk/data_request/cif.


Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.


2020 ◽  
Vol 10 (24) ◽  
pp. 8776
Author(s):  
Sheng-Fang Huang ◽  
Yen-Cheng Chang ◽  
Po-Liang Liu

A new ternary compound Cu2SnTi3 has been synthesized by vacuum sintering at 900 °C. The atomic structures of CaCu5- and InNi2-like Cu2SnTi3 are calculated using density functional theory methods. The X-ray diffraction (XRD) analysis and selected area diffraction (SAD) patterns of the new ternary compound Cu2SnTi3 are considered to verify the atomic structures of CaCu5- and InNi2-like Cu2SnTi3. The results reveal that the InNi2-like Cu2SnTi3 model has the lowest total energy of −35.239 eV, representing the trigonal crystal structure. The orthorhombic crystal structure of the CaCu5-like Cu2SnTi3 model has the second lowest total energy of −33.926 eV. Our theoretical X-ray diffraction peak profiles of InNi2-like (CaCu5-like) Cu2SnTi3 are nearly identical to experimental one, leading to an error below 2.0% (3.0%). In addition, the hexagonal crystal structure of the CaCu5-like Cu2SnTi3 model has the highest total energy of −33.094 eV. The stability of the Cu2SnTi3 in terms of energy follows the order: the trigonal, orthorhombic, and hexagonal crystal structure.


Minerals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 181 ◽  
Author(s):  
Peter Paufler ◽  
Stanislav K. Filatov

At the dawn of crystal structure analysis, the close personal contact between researchers in Russia and Germany, well documented in the “Zeitschrift für Krystallographie und Mineralogie”, contributed significantly to the evolution of our present knowledge of the crystalline state. The impact of the Russian crystallographer E. S. Fedorov upon German scientists such as A. Schoenflies and P. Groth and the effect of these contacts for Fedorov are highlighted hundred years after the death of the latter. A creative exchange of ideas paved the way for the analysis of crystal structures with the aid of X-ray diffraction.


2008 ◽  
Vol 41 (3) ◽  
pp. 600-605 ◽  
Author(s):  
Jeffrey J. Lovelace ◽  
Cameron R. Murphy ◽  
Lee Daniels ◽  
Kartik Narayan ◽  
Clarence E. Schutt ◽  
...  

For a normal periodic crystal, the X-ray diffraction pattern can be described by an orientation matrix and a set of three integers that indicate the reciprocal lattice points. Those integers determine the spacing along the reciprocal lattice directions. In aperiodic crystals, the diffraction pattern is modulated and the standard periodic main reflections are surrounded by satellite reflections. The successful indexing and refinement of the main unit cell andqvector usingTWINSOLVE, developed by Svensson [(2003). Lund University, Sweden], are reported here for an incommensurately modulated, aperiodic crystal of a profilin:actin complex. The indexing showed that the modulation is along thebdirection in the crystal, which corresponds to an `actin ribbon' formed by the crystal lattice. Interestingly, the transition to the aperiodic state was shown to be reversible and the diffraction pattern returned to the periodic state during data collection. It is likely that the protein underwent a conformational change that affected the neighbouring profilin:actin molecules in such a way as to produce the observed modulation in the diffraction pattern. Future work will aim to trap the incommensurately modulated crystal state, for example using cryocooling or chemical crosslinking, thus allowing complete X-ray data to be collected.


1988 ◽  
Vol 41 (12) ◽  
pp. 1977 ◽  
Author(s):  
HD Becker ◽  
BW Skelton ◽  
AB Turner ◽  
AH White

Oxidation of 10-methyl-9-anthraldehyde with hydrogen peroxide in acetic acid in the presence of sulfuric acid gives 9-formyloxy-10-methylanthracene which dimerizes in solution upon exposure to light. The head-to-tail structure of the 4π+4π photodimer was established by a single-crystal X-ray diffraction study. In the crystalline state, the molecular structure is centrosymmetric, and the length of the photochemically formed bonds 1.646(4)Ǻ. Crystals are monoclinic, P21/c, a 7.980(5), b 16.143(7), c 9.571(3)Ǻ, β 114.38(3)°, Z=2 dimers; R was 0.041 for 1362 'observed' diffractometer reflections.


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