Crystal structure refinements of tetragonal (OH,F)-rich spessartine and henritermierite garnets

2018 ◽  
Vol 74 (1) ◽  
pp. 104-114 ◽  
Author(s):  
Sytle M. Antao ◽  
Laura A. Cruickshank
Keyword(s):  
Large Deviation ◽  
Scattered Electron ◽  
Cubic Symmetry ◽  
Oh Groups ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
Jahn Teller ◽  
Homogeneous Composition ◽  
Cation Sites

Cubic garnet (space group Ia\overline 3 d) has the general formula X 3 Y 2 Z 3O12, where X, Y and Z are cation sites. In the tetragonal garnet (space group I41/acd), the corresponding cation sites are X1 and X2, Y, and Z1 and Z2. In both space groups only the Y site is the same. The crystal chemistry of a tetragonal (OH,F)-rich spessartine sample from Tongbei, near Yunxiao, Fujian Province, China, with composition X (Mn2.82Fe^{2+}_{0.14}Ca0.04)Σ3 Y {Al1.95Fe^{3+}_{0.05}}Σ2 Z [(SiO4)2.61(O4H4)0.28(F4)0.11]Σ3 (Sps94Alm5Grs1) was studied with single-crystal X-ray diffraction and space group I41/acd. The deviation of the unit-cell parameters from cubic symmetry is small [a = 11.64463 (1), c = 11.65481 (2) Å, c/a = 1.0009]. Point analyses and back-scattered electron images, obtained by electron-probe microanalysis, indicate a homogeneous composition. The Z2 site is fully occupied, but the Z1 site contains vacancies. The occupied Z1 and Z2 sites with Si atoms are surrounded by four O atoms, as in anhydrous cubic garnets. Pairs of split sites are O1 with F11 and O2 with O22. When the Z1 site is vacant, a larger [(O2H2)F2] tetrahedron is formed by two OH and two F anions in the O22 and F11 sites, respectively. This [(O2H2)F2] tetrahedron is similar to the O4H4 tetrahedron in hydrogarnets. These results indicate ^{X}{{\rm Mn}^ {2+}_{3}}\,^{Y}{\rm Al}_{2}^{Z}[({\rm SiO}_{4})_{2}({\rm O}_{2}{\rm H}_{2})_{0.5}({\rm F}_{2})_{0.5}]_{\Sigma3} as a possible end member, which is yet unknown. The H atom that is bonded to the O22 site is not located because of the small number of OH groups. In contrast, tetragonal henritermierite, ideally ^{X}{\rm Ca}_{3}\,^{Y}{\rm Mn}^{3+}_{2}\,^{Z}[({\rm SiO}_{4})_{2}({\rm O}_{4}{\rm H}_{4})_1]_{\Sigma3}, has a vacant Z2 site that contains the O4H4 tetrahedron. The H atom is bonded to an O3 atom [O3—H3 = 0.73 (2) Å]. Because of O2—Mn3+—O2 Jahn–Teller elongation of the Mn3+O6 octahedron, a weak hydrogen bond is formed to the under-bonded O2 atom. This causes a large deviation from cubic symmetry (c/a = 0.9534).

Intergrowth polytypoids as modulated structures: a superspace description of the Sr n (Nb,Ti) n O3n + 2 compound series

2001 ◽  
Vol 57 (4) ◽  
pp. 471-484 ◽  
Author(s):  
L. Elcoro ◽  
J. M. Perez-Mato ◽  
R. L. Withers
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Separation Distance ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
Average Structure ◽  
Layer Stacking ◽  
Compound Series ◽  
Three Dimensional Space

A new, unified superspace approach to the structural characterization of the perovskite-related Sr n (Nb,Ti) n O3n + 2 compound series, strontium niobium/titanium oxide, is presented. To a first approximation, the structure of any member of this compound series can be described in terms of the stacking of (110)-bounded perovskite slabs, the number of atomic layers in a single perovskite slab varying systematically with composition. The various composition-dependent layer-stacking sequences can be interpreted in terms of the structural modulation of a common underlying average structure. The average interlayer separation distance is directly related to the average structure periodicity along the layer stacking direction, while an inherent modulation thereof is produced by the presence of different types of layers (particularly vacant layers) along this stacking direction. The fundamental atomic modulation is therefore occupational and can be described by means of crenel (step-like) functions which define occupational atomic domains in the superspace, similarly to what occurs for quasicrystals. While in a standard crystallographic approach, one must describe each structure (in particular the space group and cell parameters) separately for each composition, the proposed superspace model is essentially common to the whole compound series. The superspace symmetry group is unique, while the primary modulation wavevector and the width of some occupation domains vary linearly with composition. For each rational composition, the corresponding conventional three-dimensional space group can be derived from the common superspace group. The resultant possible three-dimensional space groups are in agreement with all the symmetries reported for members of the series. The symmetry-breaking phase transitions with temperature observed in many compounds can be explained in terms of a change in superspace group, again in common for the whole compound series. Inclusion of the incommensurate phases, present in many compounds of the series, lifts the analysis into a five-dimensional superspace. The various four-dimensional superspace groups reported for this incommensurate phase at different compositions are shown to be predictable from a proposed five-dimensional superspace group apparently common to the whole compound series. A comparison with the scarce number of refined structures in this system and the homologous (Nb,Ca)6Ti6O20 compound demonstrates the suitability of the proposed formalism.

Structures and Phase Transitions of the A 7PSe6 (A = Ag, Cu) Argyrodite-Type Ionic Conductors. I. Ag7PSe6

1998 ◽  
Vol 54 (4) ◽  
pp. 376-383 ◽  
Author(s):  
M. Evain ◽  
E. Gaudin ◽  
F. Boucher ◽  
V. Petricek ◽  
F. Taulelle
Keyword(s):  
Phase Transition ◽  
Atomic Displacement ◽  
Ionic Conductors ◽  
Reliability Factor ◽  
Conducting Phase ◽  
Cubic Symmetry ◽  
Space Group ◽  
Ionic Conducting ◽  
Jahn Teller ◽  
Diffusion Paths

The crystal structures of the two polymorphic forms of the argyrodite Ag7PSe6 compound are analysed by means of single-crystal X-ray diffraction. Above the phase transition at 453 K leading to the ionic conducting phase, γ-Ag7PSe6 crystallizes in cubic symmetry, space group F4¯3m, with a = 10.838 (3) Å, V = 1273.1 (12) Å3 and Z = 4 at 473 K. The refinement of the 473 K structure leads to a reliability factor of R = 0.0326 for 192 independent reflections and 33 variables. Diffusion paths for silver d 10 ions are evidenced by means of a combination of a Gram–Charlier development of the atomic displacement factors and a split model. Below the phase transition β-Ag7PSe6 crystallizes again in cubic symmetry, but with the space group P213 and a = 10.772 (2) Å, V = 1250.1 (6) Å3 and Z = 4 at room temperature. The refinement of the 293 K structure leads to a reliability factor of R = 0.0267 for 1125 independent reflections and 68 variables. In the β-Ag7PSe6 ordered phase the silver cations are found in various sites corresponding to the most pronounced probability density locations of the high-temperature diffusion paths. Those positions correspond to low coordination (2, 3 and 4) sites, in agreement with the silver preference for such environments. In addition, the Ag atoms are found slightly displaced from the true linear, triangular or tetrahedral coordination, as expected from second-order Jahn–Teller effects.

scholarly journals Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites

2015 ◽  
Vol 71 (9) ◽  
pp. 1161-1168 ◽  
Author(s):  
Christopher T. Jurgenson ◽  
Thomas D. Pollard
Keyword(s):  
Binding Site ◽  
Structural Information ◽  
Unit Cell ◽  
Molecular Structures ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
New Space

Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space groupP212121contained one complex per asymmetric unit, with unit-cell parametersa= 105.48,b= 156.71,c= 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space groupP41contained two complexes per asymmetric unit, with unit-cell parametersa=b= 149.93,c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.

Determination of the Space Group of Ceramic BaO.Pr2O3.4TiO2 by Electron Diffraction

1995 ◽  
Vol 28 (5) ◽  
pp. 577-581 ◽  
Author(s):  
F. Azough ◽  
P. E. Champness ◽  
R. Freer
Keyword(s):  
Phase Transition ◽  
Electron Diffraction ◽  
Mixed Oxide ◽  
Displacement Vector ◽  
Orthorhombic Symmetry ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
Antiphase Domains

Ceramic specimens of BaO.Pr203 .4TiO2 (Ba4.5Pr9Ti18O54) were prepared by the mixed-oxide route. Electron diffraction indicated that the compound has orthorhombic symmetry with cell parameters a ≃ 22.2, b ≃ 12.2 and c ≃ 7.6 Å. The space group was identified as Pnam, one of the two possible space groups previously identified for Ba3.75Ln9.5Ti18O54, where Ln = Nd, La or Sm. The fact that Pnam is a subgroup of the 2c superlattice of Pbam and the existence of antiphase domains with a displacement vector c/2 in BaO.Pr2O3 .4TiO2 suggests that it underwent a phase transition during cooling from Pbam to Pnam in which the c axis doubled.

X-ray powder diffraction data for three red azo pigments: sodium, barium, and ammonium lithol salts

2017 ◽  
Vol 32 (3) ◽  
pp. 187-192 ◽  
Author(s):  
Alicja Rafalska-Łasocha ◽  
Marta Grzesiak-Nowak ◽  
Piotr Goszczycki ◽  
Katarzyna Ostrowska ◽  
Wiesław Łasocha
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Space Group ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
Synthesis Procedure ◽  
Diffraction Patterns

Lithol reds belong to the group of azo pigments, which were popular artists’ colouring materials in the first half of the twentieth century. These pigments were also used in many branches of industry. Here, we report X-ray powder diffraction data, unit-cell parameters, and space groups for three compounds from this group: sodium (E)-2-((2-hydroxynaphthalen-1-yl)diazenyl)naphthalene-1-sulphonate monohydrate (Na lithol red), monoclinic, space group C2/c, with cell parameters a = 33.343(7), b = 6.667(2), c = 16.397(4) Å, β = 90.83°, V = 3644.51 Å3, Z = 8; barium (E)-2-[(2-hydroxynaphthalen-1-yl)diazenyl]naphthalene-1-sulphonate trihydrate (Ba lithol red), monoclinic, space group P21/m, with cell parameters a = 17.758(9), b = 6.209(4), c = 16.857(8) Å, β = 92.07°, V = 1857.39 Å3, Z = 2; and ammonium (E)-2-[(2-hydroxynaphthalen-1-yl)diazenyl]naphthalene-1-sulphonate monohydrate (NH4 lithol red), monoclinic, space group P2/c, with cell parameters a = 17.721(5), b = 6.428(3), c = 16.911(5) Å, β = 100.31(3)°, V = 1895.31 Å3, and Z = 4. In the first and third cases we synthesised the pigments in their monohydrate form, performed X-ray powder diffraction measurements, and indexed all of the obtained diffraction maxima. In the case of the barium compound, despite many efforts in the course of the synthesis procedure, the powder diffraction patterns of the obtained samples were not of the best quality. Nevertheless, we indexed the best one and found a reliable space group and cell parameters.

X-ray powder diffraction data for the N-acylamino acids: ortho, meta, and para-methyl hippuric acids

2016 ◽  
Vol 31 (3) ◽  
pp. 242-247
Author(s):  
Gerzon E. Delgado ◽  
Marilia Guillén ◽  
Jeans W. Ramírez ◽  
Asiloé J. Mora ◽  
Jines E. Contreras ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
Methylhippuric Acid ◽  
Diffraction Peaks

N-acylamino acid isomers: ortho, meta, and para-methylhippuric acids, are specific xylene metabolites. Here, we report X-ray powder diffraction data, unit-cell parameters, and space groups for the three isomer (C10H11NO3), [ortho-methylhippuric acid 2 mHA, monoclinic P21/n cell, a = 8.522(1), b = 10.443(1), c = 10.734(1) Å, β = 92.43(1)°, V = 954.5(1) Å3; meta-methylhippuric acid 3 mHA, monoclinic C2/c cell a = 20.0951(2), b = 10.485(1), c = 10.074(2) Å, β = 119.08(1)°, V = 1933.9(1) Å3; para-methylhippuric acid 4 mHA, orthorhombic P212121 cell, a = 5.1794(7), b = 8.279(1), c = 22.276(2) Å, V = 955.2(2) Å3], space group. In each case, all measured diffraction peaks were indexed and are consistent with the corresponding space group.

The crystal structure of khinite and polytypism in khinite and parakhinite

2008 ◽  
Vol 72 (3) ◽  
pp. 763-770 ◽  
Author(s):  
M. A. Cooper ◽  
F. C. Hawthorne ◽  
M. E. Back
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Oh Groups ◽  
Space Group ◽  
Jahn Teller

AbstractThe crystal structure of khinite, Pb2+Cu2+3Te6+O6(OH)2, orthorhombic, a = 5.7491(10), b = 10.0176(14), c = 24.022(3) Å, V = 1383.6(4) Å3, space group Fdd2, Z = 8, Dcalc = 6.29 g/cm3, from the Empire mine, Tombstone, Arizona, USA, has been solved by direct methods and refined to R1 = 3.2% on the basis of 636 unique observed reflections. There is one distinct Te site occupied by Te and coordinated by six O atoms in an octahedral arrangement with a <Te–O> distance of 1.962 Å. typical of Te6+. There are three octahedrally-coordinated Cu sites, each of which is occupied by Cu2+ with <Cu–O> distances of 2.132, 2.151 and 2.308 Å, respectively. Each Cu octahedron shows four short meridional bonds (~1.95 Å) and two long apical bonds (2.46–2.99 Å) characteristic of Jahn-Teller-distorted Cu2+ octahedra. There is one distinct Pb site occupied by Pb and coordinated by six O atoms and two (OH) groups with a <Pb–O, OH> distance of 2.690 Å. TeF6 and CuΦ6 octahedra share edges and corners to form an [MΦ2] (where Φ = O, OH) layer of composition [TeCu3Φ8]. These layers stack along the c axis at 6 A intervals with Pb atoms between the layers. Identical layers occur in the structure of parakhinite, Pb2+Cu2+Te6+O6(OH)2, hexagonal, a = 5.765(2), c = 18.001(9) Å, V =518.0(4) Å3, space group P32, Z = 3, Dcalc = 6.30 g/cm3. It is only the relative stacking of the TeCu3Φ8 layers in the c direction that distinguishes the two structures, and hence khinite and parakhinite are polytypes.

scholarly journals Crystallization and X-ray analysis of all of the players in the autoregulation of theataRTtoxin–antitoxin system

2018 ◽  
Vol 74 (7) ◽  
pp. 391-401 ◽  
Author(s):  
Dukas Jurėnas ◽  
Laurence Van Melderen ◽  
Abel Garcia-Pino
Keyword(s):  
Molecular Mechanisms ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
High Resolution Data ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
Intrinsically Disordered ◽  
Resolution Analysis ◽  
New Type

TheataRToperon from enteropathogenicEscherichia coliencodes a toxin–antitoxin (TA) module with a recently discovered novel toxin activity. This new type II TA module targets translation initiation for cell-growth arrest. Virtually nothing is known regarding the molecular mechanisms of neutralization, toxin catalytic action or translation autoregulation. Here, the production, biochemical analysis and crystallization of the intrinsically disordered antitoxin AtaR, the toxin AtaT, the AtaR–AtaT complex and the complex of AtaR–AtaT with a double-stranded DNA fragment of the operator region of the promoter are reported. Because they contain large regions that are intrinsically disordered, TA antitoxins are notoriously difficult to crystallize. AtaR forms a homodimer in solution and crystallizes in space groupP6122, with unit-cell parametersa = b = 56.3,c= 160.8 Å. The crystals are likely to contain an AtaR monomer in the asymmetric unit and diffracted to 3.8 Å resolution. The Y144F catalytic mutant of AtaT (AtaTY144F) bound to the cofactor acetyl coenzyme A (AcCoA) and the C-terminal neutralization domain of AtaR (AtaR44–86) were also crystallized. The crystals of the AtaTY144F–AcCoA complex diffracted to 2.5 Å resolution and the crystals of AtaR44–86diffracted to 2.2 Å resolution. Analysis of these structures should reveal the full scope of the neutralization of the toxin AtaT by AtaR. The crystals belonged to space groupsP6522 andP3121, with unit-cell parametersa=b= 58.1,c= 216.7 Å anda=b= 87.6,c = 125.5 Å, respectively. The AtaR–AtaT–DNA complex contains a 22 bp DNA duplex that was optimized to obtain high-resolution data based on the sequence of two inverted repeats detected in the operator region. It crystallizes in space groupC2221, with unit-cell parametersa= 75.6,b= 87.9,c= 190.5 Å. These crystals diffracted to 3.5 Å resolution.

scholarly journals Structure and H position of tetragonal hydrogarnet derived from CaGeO3garnet

2014 ◽  
Vol 70 (a1) ◽  
pp. C1112-C1112
Author(s):  
Akihiko Nakatsuka ◽  
Hiroki Matsutomi ◽  
Keiko Fujiwara ◽  
Noriaki Nakayama ◽  
Osamu Ohtaka ◽  
...  
Keyword(s):  
Single Crystal ◽  
Structure Refinement ◽  
Partial Replacement ◽  
Site Preference ◽  
Present Sample ◽  
Cubic Symmetry ◽  
Oh Groups ◽  
Space Group ◽  
Residual Electron Density ◽  
Low Symmetry

Hydrogarnets, represented by hydrogrossular, are produced by the replacement of (ZO4)4- in garnets by (H4O4)4- (Z: tetrahedral cation) and the vacancies of tetrahedral cations are created by this replacement. Most of reported hydrogarnets crystallizes with cubic symmetry (space group Ia-3d). To our knowledge, Ca3Mn2[SiO4]2.07[H4O4]0.93 with space group I41/acd (tetragonal) [1] has been only reported as a low-symmetry hydrogarnet. In the cubic hydrogarnets, all O atoms are crystallographically equivalent, whereas in low-symmetric one, they can be located at non-equivalent sites. Therefore, the investigation of low-symmetry hydrogarnes is important to gain knowledge of the site preference of H atoms. Recently, we have successfully synthesized the single crystal of a new low-symmetry hydrogarnet CaGe0.924O3H0.304 (= Ca3(CaGe)[GeO4]2.696[H4O4]0.304) with tetragonal space group I41/a, at 3 GPa and 1273 K under the presence of H2O component. This tetragonal hydrogarnet is produced by the partial replacement of (GeO4)4- in high-pressure CaGeO3 garnet, Ca3(CaGe)[GeO4]3, by (H4O4)4-. In the present study, we report the single crystal X-ray diffraction study of this hydrogarnet at 98 and 298 K. In the structure refinement at 298 K, the occupancy parameters resulted in 0.393(2) for tetrahedral Z2(Ge) site, coordinated only by O6 atoms, and showed no significant deviation from 1.0 for the remaining cation sites. The bond valence sums of each atom except O6 atom agree with the valences of occupied atoms, whereas that of O6 atom are 1.50, deviating largely from oxygen valence. Thus, the substitution of OH groups for O atoms in the present sample occurs only at O6 site, which indicates that O6 is the most preferential site for the OH substitution. The position of H atom will be examined from the residual electron density distributions at a low temperature of 98 K, and the hydrogen bonding in the crystal structure will be discussed.

Symmetrieverwandtschaften bei Varianten des Perowskit-Typs

2002 ◽  
Vol 58 (4) ◽  
pp. 594-606 ◽  
Author(s):  
Oliver Bock ◽  
Ulrich Müller
Keyword(s):  
Phase Transitions ◽  
Group Symmetry ◽  
Site Symmetry ◽  
Temperature Dependent ◽  
Space Group Symmetry ◽  
Space Group ◽  
Space Groups ◽  
Symmetry Reductions ◽  
Jahn Teller ◽  
Perovskite Type

The relationships among the huge number of derivative structures of the perovskite type are rationalized in a concise manner using group–subgroup relations between space groups. One family tree of such relations is given for perovskites having tilted coordination octahedra. Further group–subgroup relations are concerned with distortions of the octahedra, such as Jahn–Teller distortions or with atoms shifted from the octahedron centres. In these cases, the space-group symmetry reductions must allow site symmetry reductions of the occupied sites in the perovskite structure. On the other hand, subgroups in which the perovskite sites split into different independent sites are necessary for derivative structures with atom substitutions, such as in the elpasolites A 2 EMX 6. In addition, substitutions and distortions can be combined in adequate subgroups. Substitutions may also involve the occupation of atom sites of perovskite by molecular groups such as N(CH3)4 + or other organic cations, or by molecules like acetonitrile. If they are ordered, their molecular symmetry requires further space-group symmetry reductions. The anions can be replaced by cyanide ions or by NO2 − ions; space-group symmetry then depends on the temperature-dependent degree of order. The relationships can be used to predict if and what kind of twinning may occur in phase transitions and whether second-order phase transitions are possible.

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