Superspace description of the crystal structures of Ca n (Nb,Ti) n O3n + 2 (n = 5 and 6)

2007 ◽  
Vol 63 (2) ◽  
pp. 183-189 ◽  
Author(s):  
Jonathan Guevarra ◽  
Andreas Schönleber ◽  
Sander van Smaalen ◽  
Frank Lichtenberg
Keyword(s):  
Crystal Structures ◽  
Homologous Series ◽  
Three Dimensional ◽  
Natural Explanation ◽  
Modulated Structures ◽  
Superspace Formalism ◽  
Superspace Description

The crystal structures of two members of the homologous series Ca n (Nb,Ti) n O3n + 2, with n = 5 and 6, are presented within the superspace formalism. A common (3 + 1)-dimensional superspace model is used to describe the crystal structures of both compositions within a particular homologous series, where the primary modulation wavevector and the width of the atomic domains vary systematically with composition. The two crystal structures are characterized as commensurately modulated structures consisting of discontinuous atomic domains described by occupational crenel functions. The displacive modulation functions for the two compounds exhibit similarities, but they also show that the idea of a unified superspace model does not extend toward the precise atomic positions. For n = 6, the centrosymmetric (3 + 1)-dimensional superspace symmetry provides a natural explanation for the pseudo-symmetries that are present in the non-centrosymmetric (three-dimensional) superstructure of this compound. The efficiency of the superspace approach is demonstrated by structure refinements in (3 + 1)-dimensional superspace and by comparing these results with the refinements in their three-dimensional superstructures.

Modular crystals as modulated structures: the case of the lillianite homologous series

2008 ◽  
Vol 64 (6) ◽  
pp. 684-701 ◽  
Author(s):  
Luis Elcoro ◽  
J. M. Perez-Mato ◽  
Karen Friese ◽  
Václav Petříček ◽  
Tonči Balić-Žunić ◽  
...  
Keyword(s):  
Homologous Series ◽  
Robust Method ◽  
Composite Approach ◽  
Modulated Structures ◽  
Superspace Formalism ◽  
Study Case ◽  
Starting Model ◽  
Modular Structures ◽  
Composite Description

The use of the superspace formalism is extended to the description and refinement of the homologous series of modular structures with two symmetry-related modules with different orientations. The lillianite homologous series has been taken as a study case. Starting from a commensurate modulated composite description with two basic subsystems corresponding to the two different modules, it is shown how a more efficient description can be achieved using so-called zigzag modulation functions. These linear zigzag modulations, newly implemented in the program JANA2006, have very large fixed amplitudes and introduce in the starting model the two orientations of the underlying module sublattices. We show that a composite approach with this type of function, which treats the cations and anions as two separate subsystems forming a misfit compound, is the most appropriate and robust method for the refinements.

Structure of (Ga2O3)2(ZnO)13 and a unified description of the homologous series (Ga2O3)2(ZnO)2 n + 1

2012 ◽  
Vol 68 (3) ◽  
pp. 250-260 ◽  
Author(s):  
Yuichi Michiue ◽  
Noboru Kimizuka ◽  
Yasushi Kanke ◽  
Takao Mori
Keyword(s):  
Homologous Series ◽  
Unit Cell ◽  
Dimensional Model ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Modulated Structures ◽  
Superspace Formalism ◽  
Complex Phenomena ◽  
Unified Description

The structure of (Ga2O3)2(ZnO)13 has been determined by a single-crystal X-ray diffraction technique. In the monoclinic structure of the space group C2/m with cell parameters a = 19.66 (4), b = 3.2487 (5), c = 27.31 (2) Å, and β = 105.9 (1)°, a unit cell is constructed by combining the halves of the unit cell of Ga2O3(ZnO)6 and Ga2O3(ZnO)7 in the homologous series Ga2O3(ZnO) m . The homologous series (Ga2O3)2(ZnO)2n + 1 is derived and a unified description for structures in the series is presented using the (3+1)-dimensional superspace formalism. The phases are treated as compositely modulated structures consisting of two subsystems. One is constructed by metal ions and another is by O ions. In the (3 + 1)-dimensional model, displacive modulations of ions are described by the asymmetric zigzag function with large amplitudes, which was replaced by a combination of the sawtooth function in refinements. Similarities and differences between the two homologous series (Ga2O3)2(ZnO)2n + 1 and Ga2O3(ZnO) m are clarified in (3 + 1)-dimensional superspace. The validity of the (3 + 1)-dimensional model is confirmed by the refinements of (Ga2O3)2(ZnO)13, while a few complex phenomena in the real structure are taken into account by modifying the model.

Superspace description of the homologous series Ga2O3(ZnO) m

2010 ◽  
Vol 66 (2) ◽  
pp. 117-129 ◽  
Author(s):  
Yuichi Michiue ◽  
Noboru Kimizuka
Keyword(s):  
Homologous Series ◽  
Ideal Model ◽  
Modulated Structure ◽  
Superspace Formalism ◽  
Alternative Settings ◽  
Complex Phenomena ◽  
Modular Structures ◽  
Unified Description ◽  
Superspace Description ◽  
The Ideal

A unified description for the structures of the homologous series Ga2O3(ZnO) m , gallium zinc oxide, is presented using the superspace formalism. The structures were treated as a compositely modulated structure consisting of two subsystems. One is constructed with metal ions and the other with O ions. The ideal model is given, in which the displacive modulations of ions are well described by the zigzag function with large amplitudes. Alternative settings are also proposed which are analogous to the so-called modular structures. The validity of the model has been confirmed by refinements for phases with m = 6 and m = 9 in the homologous series. A few complex phenomena in real structures are taken into account by modifying the ideal model.

scholarly journals Crystal structures of [Mn(bdc)(Hspar)2(H2O)0.25]·2H2O containing MnO6+1capped trigonal prisms and [Cu(Hspar)2](bdc)·2H2O containing CuO4squares (Hspar = sparfloxacin and bdc = benzene-1,4-dicarboxylate)

2016 ◽  
Vol 72 (1) ◽  
pp. 96-101
Author(s):  
Zhe An ◽  
Jing Gao ◽  
William T. A. Harrison
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Crystal Structures ◽  
Metal Ion ◽  
Three Dimensional ◽  
Trigonal Prism ◽  
Planar Geometry ◽  
Cationic Complex ◽  
Counter Ion ◽  
Square Planar

The syntheses and crystal structures of 0.25-aqua(benzene-1,4-dicarboxylato-κ2O,O′)bis(sparfloxacin-κ2O,O′)manganese(II) dihydrate, [Mn(C8H4O4)(C19H22F2N4O3)2(H2O)0.25]·2H2O or [Mn(bdc)(Hspar)2(H2O)0.25]·2H2O, (I), and bis(sparfloxacin-κ2O,O′)copper(II) benzene-1,4-dicarboxylate dihydrate, [Cu(C19H22F2N4O3)2](C8H4O4)·2H2O or [Cu(Hspar)2](bdc)·2H2O, (II), are reported (Hspar = sparfloxacin and bdc = benzene-1,4-dicarboxylate). The Mn2+ion in (I) is coordinated by twoO,O′-bidentate Hspar neutral molecules (which exist as zwitterions) and anO,O′-bidentate bdc dianion to generate a distorted MnO6trigonal prism. A very long bond [2.580 (12) Å] from the Mn2+ion to a 0.25-occupied water molecule projects through a square face of the prism. In (II), the Cu2+ion lies on a crystallographic inversion centre and a CuO4square-planar geometry arises from its coordination by twoO,O′-bidentate Hspar molecules. The bdc dianion acts as a counter-ion to the cationic complex and does not bond to the metal ion. The Hspar ligands in both (I) and (II) feature intramolecular N—H...O hydrogen bonds, which closeS(6) rings. In the crystals of both (I) and (II), the components are linked by N—H...O, O—H...O and C—H...O hydrogen bonds, generating three-dimensional networks.

scholarly journals Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis

2017 ◽  
Vol 91 (6) ◽  
Author(s):  
Suresh Banjara ◽  
Sofia Caria ◽  
Linda K. Dixon ◽  
Mark G. Hinds ◽  
Marc Kvansakul
Keyword(s):  
Crystal Structures ◽  
African Swine Fever Virus ◽  
Three Dimensional ◽  
African Swine Fever ◽  
Fever Virus ◽  
Structural Basis ◽  
Dna Virus ◽  
Content Type ◽  
Antiapoptotic Proteins ◽  
Apoptosis Inhibition

ABSTRACT Programmed cell death is a tightly controlled process critical for the removal of damaged or infected cells. Pro- and antiapoptotic proteins of the Bcl-2 family are pivotal mediators of this process. African swine fever virus (ASFV) is a large DNA virus, the only member of the Asfarviridae family, and harbors A179L, a putative Bcl-2 like protein. A179L has been shown to bind to several proapoptotic Bcl-2 proteins; however, the hierarchy of binding and the structural basis for apoptosis inhibition are currently not understood. We systematically evaluated the ability of A179L to bind proapoptotic Bcl-2 family members and show that A179L is the first antiapoptotic Bcl-2 protein to bind to all major death-inducing mammalian Bcl-2 proteins. We then defined the structural basis for apoptosis inhibition of A179L by determining the crystal structures of A179L bound to both Bid and Bax BH3 motifs. Our findings provide a mechanistic understanding for the potent antiapoptotic activity of A179L by identifying it as the first panprodeath Bcl-2 binder and serve as a platform for more-detailed investigations into the role of A179L during ASFV infection. IMPORTANCE Numerous viruses have acquired strategies to subvert apoptosis by encoding proteins capable of sequestering proapoptotic host proteins. African swine fever virus (ASFV), a large DNA virus and the only member of the Asfarviridae family, encodes the protein A179L, which functions to prevent apoptosis. We show that A179L is unusual among antiapoptotic Bcl-2 proteins in being able to physically bind to all core death-inducing mammalian Bcl-2 proteins. Currently, little is known regarding the molecular interactions between A179L and the proapoptotic Bcl-2 members. Using the crystal structures of A179L bound to two of the identified proapoptotic Bcl-2 proteins, Bid and Bax, we now provide a three-dimensional (3D) view of how A179L sequesters host proapoptotic proteins, which is crucial for subverting premature host cell apoptosis.

Crystal structures of tricalcium citrates

2018 ◽  
Vol 33 (2) ◽  
pp. 98-107 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Crystal Structures ◽  
Density Functional ◽  
Three Dimensional ◽  
Water Molecules ◽  
Calcium Citrate ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Calcium Supplements ◽  
Dimensional Network

The crystal structures of calcium citrate hexahydrate, calcium citrate tetrahydrate, and anhydrous calcium citrate have been solved using laboratory and synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Both the hexahydrate and tetrahydrate structures are characterized by layers of edge-sharing Ca coordination polyhedra, including triply chelated Ca. An additional isolated Ca is coordinated by water molecules, and two uncoordinated water molecules occur in the hexahydrate structure. The previously reported polymorph of the tetrahydrate contains the same layers, but only two H2O coordinated to the isolated Ca and two uncoordinated water molecules. Anhydrous calcium citrate has a three-dimensional network structure of Ca coordination polyhedra. The new polymorph of calcium citrate tetrahydrate is the major crystalline phase in several commercial calcium supplements.

Phosphate tungsten bronze series: crystallographic and structural properties of low-dimensional conductors

2001 ◽  
Vol 57 (5) ◽  
pp. 603-632 ◽  
Author(s):  
P. Roussel ◽  
O. Pérez ◽  
Ph. Labbé
Keyword(s):  
Crystal Structures ◽  
Structural Properties ◽  
Tungsten Bronze ◽  
Structural Description ◽  
X Ray ◽  
X Ray Scattering ◽  
Modulated Structures ◽  
Low Dimensionality ◽  
Low Dimensional ◽  
Thickness Function

Phosphate tungsten bronzes have been shown to be conductors of low dimensionality. A review of the crystallographic and structural properties of this huge series of compounds is given here, corresponding to the present knowledge of the different X-ray studies and electron microscopy investigations. Three main families are described, monophosphate tungsten bronzes, Ax (PO2)4(WO3)2m , either with pentagonal tunnels (MPTBp) or with hexagonal tunnels (MPTBh), and diphosphate tungsten bronzes, Ax (P2O4)2(WO3)2m , mainly with hexagonal tunnels (DPTBh). The general aspect of these crystal structures may be described as a building of polyhedra sharing oxygen corners made of regular stacking of WO3-type slabs with a thickness function of m, joined by slices of tetrahedral PO4 phosphate or P2O7 diphosphate groups. The relations of the different slabs with respect to the basic perovskite structure are mentioned. The structural description is focused on the tilt phenomenon of the WO6 octahedra inside a slab of WO3-type. In this respect, a comparison with the different phases of the WO3 crystal structures is established. The various modes of tilting and the different possible connections between two adjacent WO3-type slabs involve a great variety of structures with different symmetries, as well as the existence of numerous twins in MPTBp's. Several phase transitions, with the appearance of diffuse scattering and modulation phenomena, were analysed by X-ray scattering measurements and through the temperature dependence of various physical properties for the MPTBp's. The role of the W displacements within the WO3-type slabs, in two modulated structures (m = 4 and m = 10), already solved, is discussed. Finally, the complexity of the structural aspects of DPTBh's is explained on the basis of the average structures which are the only ones solved.

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