The incommensurately modulated crystal structure of roshchinite, Cu0.09Ag1.04Pb0.65Sb2.82As0.37S6.08

2018 ◽  
Vol 233 (3-4) ◽  
pp. 255-267 ◽  
Author(s):  
Emil Makovicky ◽  
Berthold Stöger ◽  
Dan Topa
Keyword(s):  
Crystal Structure ◽  
Crystal Lattice ◽  
Second Order ◽  
Unit Cell ◽  
Orthorhombic Crystal ◽  
Probable Reason ◽  
Structure Solution ◽  
Compositional Changes ◽  
Parallel Configuration ◽  
The One

AbstractThe Pb–Ag–Sb sulfide roshchinite, Cu0.09Ag1.04Pb0.65Sb2.82As0.37S6.08, is a lillianite homologue N=4 with a complex incommensurate superstructure in the 8.46 Å direction of the orthorhombic crystal lattice witha19.0804(1) Å,b8.4591(2) Å andc12.9451(3) Å, superspace groupPbcn(0σ20)00s,q=0.41458(3)b*. A structure solution and refinement in (3+1) superspace, based on 10,019 observed reflections and 437 refined parameters was terminated at Robs(wR) equal to 7.27 (8.07)% using satellites up to second order; Robsis 4.82 for main reflections only. The Pb atoms in trigonal coordination prisms on planes of unit-cell twinning are semiperiodically replaced by antimony. The marginal columns of (311)PbSslabs of the Sb–Ag based structure which is based on PbS-like topology contain Sb, Ag(Cu) and mixed Ag/Sb sites in a complicated sequence. Central portions of the slabs are occupied by Sb–S crankshaft chains, best exposed on the (100)PbSplanes, which run diagonally across the slabs. In these planes, in their majority the chains display Sb3S4form and two opposing orientations, zig-zagging along the [010] direction. Every six chains, a parallel configuration of two chains occurs, but occasionally this interval is reduced to five chains. This, together with related compositional changes in the Pb– and Ag–Sb column, explains the one-dimensionally incommensurate character of roshchinite. Modestly elevated contents of As replacing Sb are the probable reason of modulation and non-commensurability in roshchinite.

Crystal structure of the (REE)-uranyl carbonate mineral kamotoite-(Y)

2017 ◽  
Vol 81 (3) ◽  
pp. 653-660 ◽  
Author(s):  
Jakub Plášil ◽  
Václav Petříček
Keyword(s):  
Crystal Structure ◽  
Cell Transformation ◽  
Unit Cell ◽  
Original Structure ◽  
Carbonate Mineral ◽  
X Ray Diffraction ◽  
X Ray ◽  
Uranyl Carbonate ◽  
Structure Solution ◽  
Super Cell

AbstractKamotoite-(Y) is a rare supergene product of uraninite hydration–oxidation weathering and its structure is unknown. Based on single-crystal X-ray diffraction data collected with high-redundancy using a microfocus source, kamotoite-(Y) is monoclinic, has space group P21/n,with a = 12.3525(5), b = 12.9432(5), c = 19.4409(7) Å, β = 99.857(3)°, V = 3069.8(2) Å3 and Z = 4. Crystals are pervasively twinned (two-fold rotation around [0.75 0 0.75]), giving a strongly pseudo-orthorhombic diffractionpattern. The pseudoorthorhombic pattern can be described with an orthorhombic super-cell (transformation matrix 0,1,0/1,0,1/3,0,1), approximately four times larger in volume then a true monoclinic unit cell. This unit-cell is the same as the cell given elsewhere for the structure of bijvoetite-(Y),another (REE)-containing uranyl carbonate. The successful structure solution and refinement (R = 0.044 for 6294 unique observed reflections), carried out using our choice of unit cell, as well as the superstructure refinement and comparison of the original structure data forbijvoetite-(Y) reveal that these two crystal structures are identical. The crystal structure of kamotoite-(Y) consists of electroneutral sheets of the bijvoetite-(Y) uranylanion topology and an interlayer with H2O molecules not-coordinated directly to any metal cation. Despite determinationof the kamotoite-(Y) structure and demonstration that bijvoetite-(Y) has the same structure, the identity of these two minerals cannot be proved without additional study of the holotype material.

scholarly journals Crystal structure of 7,8,15,16,17-pentathiadispiro[5.2.59.36]heptadecane

2019 ◽  
Vol 75 (6) ◽  
pp. 888-891 ◽  
Author(s):  
Robert Hofstetter ◽  
Benedict J. Elvers ◽  
Felix Potlitz ◽  
Andreas Link ◽  
Carola Schulzke
Keyword(s):  
Crystal Structure ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Related Molecule ◽  
One Dimensional ◽  
Compound C ◽  
The One ◽  
Parallel Fashion ◽  
Cyclohexyl Group

The title compound, C12H20S5, crystallizes in the monoclinic space group P21/c with four molecules in the unit cell. In the crystal, the asymmetric unit comprises the entire molecule with the three cyclic moieties arranged in a line. The molecules in the unit cell pack in a parallel fashion, with their longitudinal axes arranged along a uniform direction. The packing is stabilized by the one-dimensional propagation of non-classical hydrogen-bonding contacts between the central sulfur atom of the S3 fragment and the C—H of a cyclohexyl group from a glide-related molecule [C...S = 3.787 (2) Å].

scholarly journals Polder maps: improving OMIT maps by excluding bulk solvent

2017 ◽  
Vol 73 (2) ◽  
pp. 148-157 ◽  
Author(s):  
Dorothee Liebschner ◽  
Pavel V. Afonine ◽  
Nigel W. Moriarty ◽  
Billy K. Poon ◽  
Oleg V. Sobolev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Volume ◽  
Electron Density ◽  
Unit Cell Volume ◽  
Model Building ◽  
Unit Cell ◽  
Structure Factors ◽  
Structure Solution ◽  
Solvent Model ◽  
Solvent Molecules

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available inPHENIX.

scholarly journals Structural study of decrespignyite-(Y), a complex yttrium rare earth copper carbonate chloride, by three-dimensional electron and synchrotron powder diffraction

2020 ◽  
Vol 32 (5) ◽  
pp. 545-555
Author(s):  
Jordi Rius ◽  
Fernando Colombo ◽  
Oriol Vallcorba ◽  
Xavier Torrelles ◽  
Mauro Gemmi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rare Earth ◽  
Three Dimensional ◽  
South Australia ◽  
Direct Methods ◽  
Unit Cell ◽  
Synchrotron Powder Diffraction ◽  
Structure Solution ◽  
Hexanuclear Clusters ◽  
Metal Layers

Abstract. The crystal structure of the mineral decrespignyite-(Y) from the Paratoo copper mine (South Australia) has been obtained by applying δ recycling direct methods to 3D electron diffraction (ED) data followed by Rietveld refinements of synchrotron data. The unit cell is a= 8.5462(2), c= 22.731(2) Å and V= 1437.8(2) Å3, and the chemical formula for Z=1 is (Y10.35REE1.43Ca0.52Cu5.31)Σ17.61(CO3)14Cl2.21(OH)16.79⋅18.35H2O (REE: rare earth elements). The ED data are compatible with the trigonal P3‾m1 space group (no. 164) used for the structure solution (due to the disorder affecting part of the structure, the possibility of a monoclinic unit cell cannot completely be ruled out). The structure shows metal layers perpendicular to [001], with six independent positions for Y, REE and Cu (sites M1 to M4 are full, and sites M5 and M6 are partially vacant), and two other sites, Cu1 and Cu2, partially occupied by Cu. One characteristic of decrespignyite is the existence of hexanuclear (octahedral) oxo-hydroxo yttrium clusters [Y6(μ6-O)(μ3-OH)8O24] (site M1) with the 24 bridging O atoms belonging to two sets of symmetry-independent (CO3)2− ions, with the first set (2×) along a ternary axis giving rise to a layer of hexanuclear clusters and the second set (6×) tilted and connecting the hexanuclear clusters with hetero-tetranuclear ones hosting Cu, Y and REE (M2 and M3 sites). The rest of the crystal structure consists of two consecutive M3 + M4 layers containing the partially occupied M5, M6, and Cu2 sites and additional carbonate anions in between. The resulting structure model is compatible with the chemical analysis of the type material which is poorer in Cu and richer in (REE, Y) than the above-described material.

scholarly journals The structure of kaliophilite KAlSiO4, a long-lasting crystallographic problem

IUCrJ ◽  
2020 ◽  
Vol 7 (6) ◽  
pp. 1070-1083 ◽  
Author(s):  
Enrico Mugnaioli ◽  
Elena Bonaccorsi ◽  
Arianna E. Lanza ◽  
Erik Elkaim ◽  
Virginia Diez-Gómez ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rietveld Method ◽  
Structural Features ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Channel System ◽  
X Ray ◽  
Cell Parameters ◽  
Peak Broadening ◽  
Structure Solution

Kaliophilite is a feldspathoid mineral found in two Italian magmatic provinces and represents one of the 12 known phases with composition close to KAlSiO4. Despite its apparently simple formula, the structure of this mineral revealed extremely complex and resisted structure solution for more than a century. Samples from the Vesuvius–Monte Somma and Alban Hills volcanic areas were analyzed through a multi-technique approach, and finally the crystal structure of kaliophilite was solved using 3D electron diffraction and refined against X-ray diffraction data of a twinned crystal. Results were also ascertained by the Rietveld method using synchrotron powder intensities. It was found that kaliophilite crystallizes in space group P3 with unit-cell parameters a = 27.0597 (16), c = 8.5587 (6) Å, V = 5427.3 (7) Å3 and Z = 54. The kaliophilite framework is a variant of the tridymite topology, with alternating SiO4 and AlO4 tetrahedra forming sheets of six-membered rings (63 nets), which are connected along [001] by sharing the apical oxygen atoms. Considering the up (U) and down (D) orientations of the linking vertex, kaliophilite is the first framework that contains three different ring topologies: nine (1-3-5) (UDUDUD) rings, six (1-2-3) (UUUDDD) rings and twelve (1-2-4) (UUDUDD) rings. This results in a relatively open (19.9 tetrahedra nm−3) channel system with multiple connections between the double six-ring cavities. Such a framework requires a surprisingly large unit cell, 27 times larger than the cell of kalsilite, the simplest phase with the same composition. The occurrence of some Na for K substitution (3–10%) may be related to the characteristic structural features of kaliophilite. Micro-twinning, pseudo-symmetries and anisotropic hkl-dependent peak broadening were also detected, and they may account for the elusive character of the kaliophilite crystal structure.

The crystal structure of 1-azoniatricyclo[4.4.4.01,6]tetradecane and 1-azoniatricyclo[4.4.3.01,6]tridecane bromides

1982 ◽  
Vol 60 (9) ◽  
pp. 1073-1077 ◽  
Author(s):  
John M. McIntosh ◽  
Masood A. Khan ◽  
Louis T. J. Delbaere
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Nmr Spectra ◽  
Membered Ring ◽  
Unit Cell ◽  
Space Group ◽  
The One

The crystal structures of 1-azoniatricyclo[4.4.4.01,6]tetradecane bromide (1) and 1-azoniatricyclo[4.4.3.01,6]tridecane bromide (2) are reported. Compound 1, C13H24NBr, crystallizes in space group P63/mmc with a = 8.383(2) Å, c = 10.092 Å, γ = 120°, Z = 2. Compound 2, C12H22NBr, crystallizes in space group P63/mmc with a = 8.283(2) Å, c = 10.046(2) Å, γ = 120°, Z = 2. The crystal structures of 1 and 2 are statistically disordered with both enantiomers occurring in the unit cell. Compound 2 is further disordered with the one five-membered ring and the two six-membered rings of the cation being averaged over the same site in the unit cell.The structures confirm the previously reported conclusions based on the 400 MHz nmr spectra of 1.

Liquids and Solids

2021 ◽  
pp. 152-176
Author(s):  
Christopher O. Oriakhi
Keyword(s):  
Crystal Structure ◽  
Crystal Lattice ◽  
Vapour Pressure ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Covalent Bonds ◽  
Chemical Structures ◽  
Structures And Properties ◽  
Ratio Rule ◽  
Unit Cell Dimensions

Liquids and Solids introduce basic physical properties of liquids and solids. An overview of the liquid state is presented, with reference to polar covalent bonds and dipole moment. The effects of temperature on the vapour pressure of a liquid are described, including the Clausius-Clapeyron equation, which can be used to calculate the vapour pressure of a liquid at various temperatures. The chapter reviews the types of solids including their chemical structures and properties. The crystal lattice system and the unit cell relationships for the seven types of crystal lattice structures and the four substructures are examined. Guidelines for determining the number of atoms in a unit cell, including calculations involving unit cell dimensions, are explained. The ionic crystal structure, radius ratio rule for the ionic compounds and determination of crystal structure by X-ray diffraction and Bragg’s equation are covered.

Structure and thermal expansion of sulfuric acid octahydrate

2012 ◽  
Vol 45 (6) ◽  
pp. 1198-1207 ◽  
Author(s):  
Helen E. Maynard-Casely ◽  
Helen E. A. Brand ◽  
Kia S. Wallwork
Keyword(s):  
Crystal Structure ◽  
Thermal Expansion ◽  
Sulfuric Acid ◽  
Powder Diffraction ◽  
Unit Cell ◽  
Acid Solutions ◽  
X Ray ◽  
Structure Solution ◽  
Sulfuric Acid Solutions

Synchrotron X-ray powder diffraction has been used to structurally characterize crystallization products from 37.8 and 40.5 wt% aqueous sulfuric acid solutions. It is confirmed that, despite speculation in the literature, the structure that predominately crystallized from these solutions is sulfuric acid octahydrate (SAO). The existence of an uncharacterized phase is also noted. It was found that existing models proposed for the crystal structure of SAO did not satisfactorily fit to the data acquired here, and hence a new structure solution was sought. It is reported here that the structure of SAO is contained within a unit cell withI2 symmetry witha= 7.44247 (11),b= 7.4450 (1),c= 26.1168 (3) Å, β = 125.0428 (7)°,V= 1184.78 (3) Å3at 80 K. Data were collected at temperatures between 80 and 198 K, which enabled determination of the thermal expansion of SAO.

scholarly journals Crystal structure solution from experimentally determined atomic pair distribution functions

2010 ◽  
Vol 43 (3) ◽  
pp. 623-629 ◽  
Author(s):  
P. Juhás ◽  
L. Granlund ◽  
S. R. Gujarathi ◽  
P. M. Duxbury ◽  
S. J. L. Billinge
Keyword(s):  
Crystal Structure ◽  
Distribution Functions ◽  
Unit Cell ◽  
Second Step ◽  
X Ray ◽  
Atomic Pair ◽  
Structure Solution ◽  
Pair Distribution Functions ◽  
Atomic Radii ◽  
Periodic Crystal

An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

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