Site-occupancy Factors Research Articles

Crystal chemistry of synthetic Ti-Mg-bearing hibonites: A single-crystal X-ray study

Hibonite single crystals were synthesized using two different techniques: hot-pressing of polycrystalline hibonite by means of piston-cylinder apparatus and solid state reaction using citrate-based sol-gel precursors. Chemical analyses, UV/Vis spectroscopy, and single-crystal X-ray characterization were performed on four sets of Ti-Mg-bearing hibonites to investigate the substitution mechanism of Ti3+, Ti4+, and Mg2+, relevant for hibonites found in calcium-aluminum-rich inclusions in meteorites. The unit-cell volume of hibonite depends linearly on the concentration of Ti and Mg: V = 8.21(3)·(Titot + Mg)apfu + 586.06(1). Structural refinements, carried out in the space group P63/mmc, demonstrate that Ti occupies two sites: M2, a trigonal bipyramid, and M4, a distorted octahedron occurring in facesharing pairs. The Ti occupancy factor was refined at both sites. Due to the repulsion of neighboring Ti cations the bond distance M4-O3 increases with increasing Ti content and the cations are displaced from the central position of the polyhedron. The displacement factors (U33)M2 and the site occupancy factor for Ti in the M2 site positively correlate for the samples, which have more than 0.3-0.4 Tiapfu, while (U33)M2 remains that of pure hibonite for small Ti occupancies at the M2 site. This plateau of displacement factor reflects the local strain fields around the substituted Ti atoms and its magnitude indicates that these strain fields begin to overlap at a Ti-Ti separation of about 1-2 unit cells. For a sample synthesized at low oxygen fugacity we detected Ti3+ by means of UV/Vis absorption spectroscopy. The presence of Ti3+ has a clear effect on the M4-M4 distance, which deviates from the linear trend described by samples containing mainly Ti4+. The average bond length M3-O depends linearly on the Mg content of these synthetic hibonites clearly indicating that Mg occupies this site.

Synthesis and Crystal Structure of InFeO3(ZnO)4

AbstractInFeO3(ZnO)4 was prepared from binary oxides as starting materials at 1350 °C in sealed platinum tubes as an earth brown powder. Single crystals were grown from a K2MoO4 flux in sealed Pt‐tubes using cooling rates of –0.1 K min–1. The structure of InFeO3(ZnO)4 was refined in space group P63/mmc; No. 194 (a = 3.211(6) Å; c = 33.032(6) Å; Z = 2; R1 = 3.68 %) from XRD data and revealed a build‐up from alternate stacking of layers of edge‐sharing InO6 octahedra and 5 layers of corner‐sharing (Zn/Fe)O4 tetrahedra. Inversions of the (Zn/Fe)O4 tetrahedra occurs (i) at the InO6 octahedral layer and (ii) halfway in the wurtzite type region where the inversion boundary is built by cations in 4+1 trigonal bipyramidal coordination. The position of the cations in their oxygen surrounding is described by a factor t which quantifies the displacement of the cation from the center of a trigonal bipyramid towards one of the constituting tetrahedra. Refining the site occupation factors of the cations in the (Zn/Fe)O4 tetrahedra results in a clear and reasonable gradient for the distribution of iron. Refinement of the oxygen position reveals split positions for the oxygen atoms at the second inversion boundary in the center of the wurtzite type region which shows similarities to inversion domain boundaries at fivefold coordinated cations in the wurtzite type region of compounds of type ARO3(ZnO)m with m > 15. Thus, it is more likely to describe InFeO3(ZnO)4 as a closest‐packed structure of cations with oxygen filling the interstices.

Crystal structure of 2-ethyl-3-(4-fluoro-phenyl-sulfin-yl)-5,7-dimethyl-1-benzo-furan.

In the title compound, C18H17FO2S, the dihedral angle between the planes of the benzo­furan ring system (r.m.s. deviation = 0.004 Å) and the 4-fluoro­phenyl ring is 86.38 (6)°. The terminal C atom of the ethyl substituent is displaced by 1.444 (3) Å from the benzo­furan ring system to the same side of the mol­ecule as the 4-fluoro­phenyl ring. In the crystal, mol­ecules are linked via pairs of C—H⋯π inter­actions into inversion-related dimers. These dimers are further linked by π–π inter­actions between the benzene rings of neighbouring mol­ecules [centroid–centroid distance = 3.715 (3) Å] and between the furan rings of neighbouring mol­ecules [centroid–centroid distance = 3.598 (3) Å]. The mol­ecules are stacked along the a-axis direction. In the sulfinyl group, the S and O atoms are disordered over two sets of sites, with site-occupancy factors of 0.797 (3) and 0.213 (3).

Crystal structure of N-[4-amino-5-cyano-6-(methyl-sulfan-yl)pyridin-2-yl]-2-(cyclo-hexyl-sulfan-yl)acetamide.

In the title mol­ecule, C15H20N4OS2, the acetamido fragment is nearly coplanar with the pyridyl ring [C—N—C—C torsion angle = −4.1 (2)°], while the cyclo­hexyl­sulfanyl portion protrudes from this plane [N—C—C—S torsion angle = −40.8 (6)°]. In the crystal, alternating pairwise N—H⋯O and N—H⋯N hydrogen bonds across inversion centres form chains along [101], which are associated into stepped layers via offset π–π stacking between pyridyl rings [centroid–centroid distance = 3.566 (1) Å]. The cyclo­hexyl group and the two atoms of the S—C bond attached to it are disordered over two sets of sites with site-occupancy factors of 0.8845 (18) and 0.1155 (18).

Crystal structure of 7-bromo-2-(3-fluoro-phen-yl)-1-(methyl-sulfin-yl)naphtho[2,1-b]furan.

In the title compound, C19H11BrFO2S, the dihedral angle between the plane of the naphtho­furan ring system [r.m.s. deviation = 0.043 (2) Å] and that of the 3-fluoro­benzene ring is 39.32 (8)°. In the crystal, mol­ecules are linked by C—H⋯O and C—Br⋯π [3.835 (1) Å] inter­actions into stacks along the c axis, forming a three-dimensional network. The F atom is disordered over two positions, with site-occupancy factors of 0.851 (3) and 0.149 (3).

Similarities and peculiarities between the crystal structures of the hydrates of sodium sulfate and selenate.

The crystal structures of the two hydrates Na2SeO4·10H2O and Na2SeO4·7.5H2O are studied for the first time. The structures of Na2SO4·10H2O and Na2SO4·7H2O are reinvestigated as a function of temperature with respect to the degree of disorder of the O atoms of SO4(2-) in the decahydrate and the O atom of water in the heptahydrate. For Na2SO4·10H2O, the unit site occupancy factor (SOF) of O atoms of SO4(2-) was determined at 120 K. After the temperature dependence of the lattice parameters was studied from 120 to 260 K, it was shown that SOF decreased from 1.0 at 120 K to 0.247 at room temperature. The interesting fact that two salts with different chemical compositions and different crystal structures (Na2SO4·7H2O, tetragonal, space group P4(1)2(1)2 and Na2SeO4·7.5H2O, monoclinic, space group C2/c) can act mutually as a crystal nucleus is accounted for by similarities in certain fragments of their crystal structures. This phenomenon is attributed to similarities between particular elements of their structures.

Polymorphism of 2,5-[(diphenylphosphanyl)methyl]-1,1,2,4,4,5-hexaphenyl-1,4-diphospha-2,5-diboracyclohexane.

2,5-[(Diphenylphosphanyl)methyl]-1,1,2,4,4,5-hexaphenyl-1,4-diphospha-2,5-diboracyclohexane shows polymorphism as two tetrahydrofuran (THF) disolvates [C64H58B2P4·2C4H8O, (Ia) and (Ib)] and pseudo-polymorphism as its toluene monosolvate [C64H58B2P4·C7H8, (Ic)]. In each of polymorphs (Ia) and (Ib), the diphosphadiboracyclohexane molecule is located on a centre of inversion. The THF molecule of (Ib) is disordered over two sites, with a site-occupation factor of 0.612 (8) for the major-occupied site. Both structures crystallize in the same space group (P21/n), but they display a different crystal packing. For pseudo-polymorph (Ic), although the space group is P21/c, which is just a different setting of the P21/n space group of (Ia) and (Ib), the crystal packing is completely different. Although the crystal packing in these three structures is significantly different, their molecular conformations are surprisingly the same.

Crystal and Molecular Structure of Methyl 12-(3-bromophenyl)-9-[(4-methylbenzene)sulfonyl]-22-oxo-13,21-dioxa-9-azapentacyclo[12.8.0.02,11.03,8.015,20]docosa-1(14),3,5,7,15(20),16,18-heptaene-11-carboxylate

The crystal structure of the title compounds with both coumarin and sulfonamide moieties were examined. These two groups have very special for their pharmaceutical and medicinal properties have been determined from single crystal X-ray diffraction data. In the title compound crystallizes in the monoclinic space group C2/c with unit cell dimension a = 28.633(3) <TEX>${\AA}$</TEX>, b= 9.3215(7) <TEX>${\AA}$</TEX> and c= 24.590(2) <TEX>${\AA}$</TEX> [alpha & gamma=<TEX>$90^{\circ}$</TEX> beta= <TEX>$115.976(3)^{\circ}$</TEX>]. In the structure The S1 atom shows a distorted tetrahedral geometry, with O1-S1-O2 [119.74 <TEX>$(2)^{\circ}$</TEX>] and N1-S1-C5 [<TEX>$105.57(1)^{\circ}$</TEX>] angles deviating from ideal tetrahedral values are attributed to the Thrope-Ingold effect. The sum of bond angles around N1 (<TEX>$316.2(1)^{\circ}$</TEX>) indicates that N1 is in sp2 hybridization. The Pyridine ring adopts boat conformation and pyran rings adopt a sofa conformation. The carboxylate group of atoms were disordered over two positions with site occupancy factors 0.598 (9):0.402 (9). Crystal structure and packing is stabilized by <TEX>$C-H{\ldots}O$</TEX> intra and inter molecular hydrogen bond interactions.

Schorlomite and morimotoite: what's in a name?

The crystal structure of an isotropic, single phase, Ti-rich schorlomite garnet, ideally Ca3Ti4+2(Fe3+2Si)O12, from Magnet Cove, Arkansas was refined with the Rietveld method, space group $Ia\overline 3 d$, and monochromatic synchrotron high-resolution powder X-ray diffraction data. Electron-microprobe analysis gave an average composition {Ca2.92Na0.04Mn2+0.03Mg0.01}Σ3[Ti1.04Fe3+0.46Mg0.18Fe2+0.16Zr4+0.13V3+0.04]Σ2(Si2.21Fe3+0.71Al0.07)Σ3O12, and corresponds to the general garnet formula of [8]X3[6]Y2[4]Z3[4]O12. Schorlomite is the dominant component, but the composition contains significant amounts (&gt;15 mol.%) of andradite, Ca3(Fe3+2)Si3O12, morimotoite, Ca3(Ti4+Fe2+)Si3O12, and morimotoite-(Mg), Ca3(Ti4+Mg)Si3O12. The crystal structure model was refined well using isotropic and anisotropic displacement parameters. Using isotropic displacement parameters, the χ2 and R (F2) Rietveld refinement values are 1.148 and 0.0742, respectively. The unit-cell parameter, a = 12.18599(1) (Å), is large for a natural schorlomite for which complete structural data are available. The bond distances are average &lt;Ca–O&gt; = 2.4461, Ti–O = 2.0085(5), Si–O = 1.7022(5) Å, and site occupancy factors (sofs) for Ca(sof) = 0.963(1), Ti(sof) = 1.045(1), and Si(sof) = 1.150(2). Comparison of schorlomite data from the type locality in Magnet Cove with morimotoite from Ice River, Canada and the type locality in Japan show that they are quite similar and cast doubts as to morimotoite being different from schorlomite.

Crystal structure of morimotoite from Ice River, Canada

The crystal structure of a morimotoite garnet, ideally Ca3(Ti4+Fe2+)Si3O12, from the Ice River alkaline complex, British Columbia, Canada was refined by the Rietveld method, space group $Ia\overline 3 d$, and monochromatic synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Electron-microprobe analysis indicates a homogeneous sample with a formula {Ca2.91Mg0.05Mn2+0.03}Σ3[Ti1.09Fe3+0.46Fe2+0.37Mg0.08]Σ2(Si2.36Fe3+0.51Al0.14)Σ3O12. The HRPXRD data show a two-phase intergrowth. The reduced χ2 and overall R(F2) Rietveld refinement values are 1.572 and 0.0544, respectively. The weight percentage, unit-cell parameter (Å), distances (Å), and site occupancy factors (sofs) for phase-1 are as follows: 76.5(1)%, a = 12.156 98(1) Å, average &lt;Ca–O&gt; = 2.4383, Ti–O = 2.011(1), Si–O = 1.693(1) Å, Ca(sof) = 0.943(2), Ti(sof) = 0.966(2), and Si(sof) = 1.095(3). The corresponding values for phase-2 are 23.5(1)%, a = 12.160 67(2) Å, average &lt;Ca–O&gt; = 2.452, Ti–O = 1.988(3), Si–O = 1.704(3) Å, Ca(sof) = 1.063(7), Ti(sof) = 1.187(7), and Si(sof) = 1.220(8). The two phases cause strain that arises from structural mismatch and gives rise to low optical anisotropy. Because the two phases are structurally quite similar, a refinement using a single-phase model with anisotropic displacement parameters shows no unusual displacement ellipsoid for the O atom that requires a “split O-atom position”, as was done in previous studies.

4-tert-Butyl-pyridinium chloride-4,4'-(propane-2,2-di-yl)bis-(2,6-di-methyl-phenol)-toluene (2/2/1).

In the title solvated salt, C9H14N+·Cl−·C19H24O2·0.5C7H7, two mol­ecules of 4,4′-(propane-2,2-di­yl)bis­(2,6-di­methyl­phenol) are linked via O—H⋯Cl hydrogen bonds to two chloride ions, each of which is also engaged in N—H⋯Cl hydrogen bonding to a 4-tert-butyl­pyridinium cation, giving a cyclic hydrogen-bonded entity centred at 1/2, 1/2, 1/2. The toluene solvent mol­ecule resides in the lattice and resides on an inversion centre; the disorder of the methyl group requires it to have a site-occupancy factor of 0.5. No crystal packing channels are observed.

Crystal structure of 5-bromo-2,3-bis(2',5'-dimethylthiophene-3-yl)- thiophene, C16H15BrS3

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Element Misidentification in X-ray Crystallography: A Reassessment of the [MCl2(diazadiene)] (M = Cr, Mo, W) Series

A series of reports describing the syntheses and structures of [MCl2(diazadiene)] (M = Cr, Mo, W) complexes is reassessed in the context of known chemistry of low-valent Group VI metal complexes, crystallographic trends such as M-Cl bond lengths and unit cell volumes, and calculated metal-ligand bond lengths. Crystallographic data and computational results are inconsistent with any of these species being second or third row transition metal complexes. A review of the crystallographic information files accompanying the [MCl2(diazadiene)] (M = Mo, W) published structures reveals that the metal atoms were inappropriately treated with partial site occupancy factors (0.775 for Mo; 0.4005 and 0.417 for W), the effect of which was to manifest lighter-element behavior and better refinement in accord with the metal atoms' correct identity. A deliberate synthesis and characterization by X-ray diffraction of [ZnCl2((Mes)dad(Me))] ((Mes)dad(Me) = 1,4-bis(2,4,6-trimethylphenyl)-2,3-dimethyl-1,4-diaza-1,3-butadiene) are reported. Refinement of this structure with the same combination of second or third row metal and offsetting partial site occupancy is shown to provide final refinement statistics essentially the same as with the correct model employing M = Zn at site occupancy 1.00. Use of the published method for synthesis of [WCl2(diazadiene)] with (Mes)dad(Me) and [WBr4(MeCN)2] in lieu of [WCl4(MeCN)2] is shown to produce [ZnBr2((Mes)dad(Me))], which has also been characterized by X-ray diffraction. It is concluded that the unusual putative 12-electron [MCl2(diazadiene)] (M = Cr, Mo, W) complexes are in all cases the corresponding [ZnCl2(diazadiene)] complexes, Zn having been commonly employed as reducing agent in their synthesis.

In Search of the True Structure of the Sodium Chromium Alum II: Crystal Growth and Structure of the Double Salt NaCr(SO4)2(H2O)6·(CH3OH)0.6(2)· (H2O)1.5(5)

Attempts to crystallize the sodium chromium alum, NaCr(SO4)2(H2O)12, from water=methanol solutions at temperatures around 281 K yielded crystals of the title compound instead. Their monoclinic structure can be described as a centered rectangular array of linear {1 ∞}[Na(SO4)2]3- rods aligned parallel to [001] with vicinal rods held together by columns of isolated [Cr(H2O)6]3+ complexes. The structure forms channels parallel to [001] which are occupied by methanol and water molecules with atomic site occupancy factors of 1/5 and less. Various attempts to crystallize the compound or the sodium chromium alum from purely aqueous solutions remained unsuccessful

Crystal structure of 4-[benzylideneamino]-3-thiophen-2-yl-methyl-4,5-dihydro-1H-[1,2,4]triazole-5-one

The crystal structure of the title compound C14H12N4OS was determined by the X-ray diffraction method. The compound crystallizes in the triclinic space group \(P\bar 1\) with Z = 2. The molecule is not planar: the dihedral angle between the triazole and thiophene rings is 73.98(2)°, and that between the triazole and benzene rings is 4.05(2)°. The thiophene ring is disordered over two positions, which are approximately parallel and oppositely oriented. The major component refined to a site-occupancy factor of 0.573(3). An intramolecular C-H...O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked together by two pairs of N-H...O interactions (to the same O atom as acceptor), forming inversion dimers. The crystal packing is also stabilized by π-π interactions [centroid-centroid distance is 3.978 A].

(-)-Benzyl 2,3-dide-oxy-β-d-erythro-hex-2-eno-pyran-oside.

In the title compound, C13H16O4, the six-membered ring of the sugar moiety shows a half-chair conformation. In the crystal, mol­ecules are connected via O—H⋯O hydrogen bonds, forming columns around twofold screw axes along the b-axis direction. There is a disorder of the benz­yloxy group, which has two possible orientations with the phenyl group lying on a common plane [site-occupancy factors = 0.589 (9) and 0.411 (9)].

2-[(Ferrocen-1-yl)(hydroxy)methyl]prop-2-enenitrile

In the title ferrocene derivative, [Fe(C5H5)(C9H8NO)], the dihedral angle between the ene­nitrile group and the substituted cyclo­penta­dienyl ring is 71.2 (1)°. The cyclopentadienyl rings of the ferrocene moiety are arranged in an eclipsed conformation. The hy­droxy group, and the corresponding methine H atom, are disordered over two sets of sites with site-occupancy factors of 0.744 (4) and 0.256 (4). An intra­molecular C—H⋯O close contact is observed. In the crystal, O—H⋯N hydrogen bonds form a C(6) chain along [100].

Crystal structure of a birefringent andradite–grossular from Crowsnest Pass, Alberta, Canada

The structure of a birefringent andradite–grossular sample was refined using single-crystal X-ray diffraction (SCD) and synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Electron-microprobe results indicate a homogeneous composition of {Ca2.88Mn2+0.06Mg0.04Fe2+0.03}Σ3[Fe3+1.29Al0.49Ti4+0.17Fe2+0.06]Σ2(Si2.89Al0.11)Σ3O12. The Rietveld refinement reducedχ2 = 1.384 and overallR(F2) = 0.0315. The HRPXRD data show that the sample contains three phases. For phase-1, the weight %, unit-cell parameter (Å), distances (Å), and site occupancy factor (sof) are 62.85(7)%,a = 12.000 06(2), average &lt;Ca–O&gt; = 2.4196, Fe–O = 1.9882(5), Si–O = 1.6542(6) Å, Ca(sof) = 0.970(2), Fe(sof) = 0.763(1), and Si(sof) = 0.954(2). The corresponding data for phase-2 are 19.14(9)%,a = 12.049 51(2), average &lt;Ca–O&gt; = 2.427, Fe–O = 1.999(1), Si–O = 1.665(1) Å, Ca(sof) = 0.928(4), Fe(sof) = 0.825(3), and Si(sof) = 0.964(4). The corresponding data for phase-3 are 18.01(9)%,a = 12.019 68(3), average &lt;Ca–O&gt; = 2.424, Fe–O = 1.992(2), Si–O = 1.658(2) Å, Ca(sof) = 0.896(5), Fe(sof) = 0.754(4), and Si(sof) = 0.936(5). The fine-scale coexistence of the three phases causes strain that arises from the unit-cell and bond distances differences, and gives rise to strain-induced birefringence. The results from the SCD are similar to the dominant phase-1 obtained by the HRPXRD, but the SCD misses the minor phases.

Di-μ-acetato-κ4O:O′-bis[(1,10-phenanthroline-κ2N,N′)(trifluoromethanesulfonato-κO)copper(II)

The complete molecule of the title compound, [Cu2(C2H3O2)2(CF3O3S)2(C12H8N2)2], is completed by the application of a twofold rotation and comprises two CuII ions, each of which is penta­coordinated by two N atoms from a bidentate 1,10-phenanthroline (phen) ligand, two O atoms from acetate ligands and an O atom from a tri­fluoro­methane­sulfonate anion, forming a (4 + 1) distorted square-pyramidal coordination geometry. The CuII ions are connected by two acetate bridges in a syn–syn configuration. The F atoms of the tri­fluoro­methane­sulfonate ligands are disordered, with site-occupation factors of 70 and 30. The molecular structure is stabilized by intra­molecular face-to-face π–π inter­actions with centroid–centroid distances in the range 3.5654 (12)–3.8775(12) Å. The crystal structure is stabilized by C—H⋯O interactions, leading to a three-dimensional lattice structure.

μ-3,3′-Bis(trihydroboryl)[3]ferrocenophane]bis(chloridozirconocene)

The title compound, [FeZr2(C5H5)4Cl2(C13H18B2)], is a heteronuclear complex that consists of a [3]ferrocenophane moiety substituted at each cyclo­penta­dienyl (Cp) ring by a BH3 group; the BH3 group is bonded via two H atoms to the Zr atom of the zirconocene chloride moiety in a bidentate fashion. The two Cp rings of the [3]ferrocenophane moiety are aligned at a dihedral angle of 8.9 (4)° arising from the strain of the propane-1,3-diyl bridge linking the two Cp rings. [One methyl­ene group is disordered over two positions with a site-occupation factor of 0.552 (18) for the major occupied site.] The dihedral angles between the Cp rings at the two Zr atoms are 50.0 (3) and 51.7 (3)°. The bonding Zr⋯H distances are in the range 1.89 (7)–2.14 (7) Å. As the two Cp rings of the ferrocene unit are connected by an ansa bridge, the two Zr atoms approach each other at 6.485 (1) Å. The crystal packing features C—H⋯Cl inter­actions.