Michal Dušek

Crystallographic Computing System JANA2006: General features

Abstract JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

Refinement of modulated structures against X-ray powder diffraction data with JANA2000

JANA is a computer program for the refinement and analysis of periodic and aperiodic (incommensurately modulated structures and composite crystals) crystal structures. Here a new module is introduced that allows Rietveld refinements against powder diffraction data. It is shown that JANA2000 provides a state-of-the-art description of the peak profiles. A re-analysis of the low-temperature structure of (CO)xC60 showed that the application of icosahedral symmetry restrictions to the C60 molecule leads to a better description of the electron density and to a corrected position of the CO molecule as compared with a rigid-body refinement. The incommensurately modulated structure of NbTe4 has been successfully refined against X-ray powder diffraction data. The structural parameters are equal to, but less accurate, than the parameters obtained from a single-crystal study.

Bambus[n]urils: a new family of macrocyclic anion receptors.

A recently discovered anion receptor is jointed by three related macrocycles differing in the number of glycoluril units and type of substitution. The synthesis is carried out in nonpolar solvents compared to aqueous media used in the case of the original macrocycle. The size of macrocycle is controlled by a template. A hexameric macrocycle with benzyl substitution binds halide anions with an affinity exceeding 10(9) M(-1) while a tetrameric analog does not bind any of the investigated anions.

Anion-Free Bambus[6]uril and Its Supramolecular Properties

Methods for the preparation of anion-free bambus[6]uril (BU6) are presented. They are based on the oxidation of iodide anion, which is bound inside the macrocycle, utilizing dark oxidation by hydrogen peroxide or photooxidation in the presence of titanium dioxide. Anion-free BU6 was found to be insoluble in any of the investigated solvents; however, it dissolves in methanol/chloroform (1:1) or acetonitrile/water (1:1) mixtures in the presence of the tetrabutylammonium salt of a suitable anion. The association constants with halide ions, BF(4)(-), NO(3)(-), and CN(-), were measured by (1)H NMR spectroscopy. The highest association constant (8.9×10(5) M(-1)) was found for the 1:1 complex of BU6 with I(-) in acetonitrile/water mixture. A number of crystal structures of BU6 complexes with various anions were obtained. The influence of the anion size on the macrocycle diameter is discussed together with an unusual arrangement of the macrocycles into separate layers.

The modulated structure of Ba0.39Sr0.61Nb2O6. I. Harmonic solution

The structure of a crystal of Sr(0.61)Ba(0.39)Nb(2)O(6) has been solved and refined as an incommensurate structure in five-dimensional superspace. The structure is tetragonal, superspace group P4bm(pp1/2,p - p1/2), unit-cell parameters a = 12.4566 (9), c = 7.8698 (6) A, modulation vectors q(1) = 0.3075 (6) (a* + b*), q(2) = 0.3075 (6) (a* - b*). The data collection was performed on a KUMA-CCD diffractometer and allowed the integration of weak first-order satellite reflections. The structure was refined from 2569 reflections to a final value of R = 0.0479. The modulation affects mainly the positions of the O atoms, which are displaced by as much as 0.5 A, and the site 4c that is occupied by Sr and Ba atoms. Only a simplified model, in which this atomic position is occupied by an effective atom Sr/Ba, could be refined from the data set. The modulation of displacement parameters has been used to account for the modulated distribution of Sr and Ba. The whole refinement uses only first-order modulation waves, but there are strong indications that for a complete solution the use of higher-order satellites and a more complicated model is necessary.

Five-dimensional structure refinement of natural melilite, (Ca1.89Sr0.01Na0.08K0.02)(Mg0.92Al0.08)(Si1.98Al0.02)O7

The structure of a crystal of natural melilite from San Venanzo, Umbria (Italy) of the general formula X2T1(T2)2O7, where X = Ca0.945Sr0.005Na0.04K0.01, T1 = Mg0.92Al0.08 and T2 = Si0.99Al0.01, has been solved and refined as an incommensurate structure in five-dimensional superspace. The structure is tetragonal, superspace group P\bar 421m:p4mg, cell parameters a = 7.860 (1), c = 5.024 (1) A, modulation vectors q1 = 0.2815 (3)(a* + b*), q2 = 0.2815 (3)(−a* + b*). The data collection was performed on a KumaCCD diffractometer. The structure was refined from 7606 reflections to final R = 0.0481. A special modification of the refinement program Jana2000 was necessary to take into account overlapping of satellite reflections m × n = ±1, which could not be properly separated in the integration procedure. The final model includes modulations of the atomic positions as well as modulations of the thermal parameters. The latter are induced by strong differences in the neighbourhood of the actual modulated positions. The occupational modulation was neither significant for X nor for T1 sites and the sites were supposed to be occupied only by Ca and Mg, respectively. As a consequence of the Ca and O positional modulations six-, seven- and eightfold Ca coordination occur throughout the structure and the thermal ellipsoid changes its shape correspondingly. The positional modulation of the atoms causes variations in the interatomic distances which, however, do not affect bond-valence sums considerably, but induce flattening and rotation in T1 and T2 tetrahedra, respectively.

Hexagonal close-packed c60

CeO crystals were grown from purified powder material with a multiple sublimation technique. In addition to crystals with a cubic close-packed (ccp ) arrangement, crystals were found with a hexagonal close-packed (hcp ) structure. Detailed crystallographic evidence is given, including complete refinements, of the room-temperature structures of both polytypes. The radius of the CsO molecule was determined as 3.54 1 ( 1) A, and was found to be equal for both ccp and hcp crystals.

LOW-TEMPERATURE STRUCTURE OF SOLID C-70

The structure of the low-temperature phase of hexagonal close-packed (hcp) grown C70 is determined from single-crystal X-ray diffraction at 220 K and 100 K. An ordering of the molecules is found on the orthohexagonal supercell of a hcp structure with symmetry Pbnm. It involves alignment of the molecules with their long axis parallel to the original hexagonal axis, and a shift out of the original hcp positions. Intermolecular contacts are shown to be different from those found in C60. The crystal is determined to contain stacking faults resulting in the presence of AC and BC deformed hcp arrangements in addition to the original AB stacking. The stacking disorder is shown to be independent of the phase transitions, and presumably is an intrinsic property of hexagonal C70 crystals.

Determination of the modulated structure of Sr14/11CoO3 through a (3 + 1)-dimensional space description and using non-harmonic ADPs.

Sr(14/11)CoO(3) (i.e. Sr(14)Co(11)O(33), tetradecastrontium undecacobalt tritriacontaoxide), a new phase in the hexagonal perovskite Sr(x)CoO(3) system, has been prepared and its structure solved from single-crystal X-ray data within the (3 + 1)-dimensional formalism. Sr(14/11)CoO(3) crystallizes in the trigonal symmetry, R3;m(00gamma)0s superspace group with the following lattice parameters: a(s) = 9.508 (2), c(s) = 2.5343 (7) Å, q = 0.63646 (11)c(*) and V(s) = 198.40 (13) Å(3). With the commensurate versus incommensurate test not being conclusive, the structure was considered as commensurate (P32 three-dimensional space group), but refined within the (3 + 1)-dimensional formalism to a residual factor R = 0.0351 for 47 parameters and 1169 independent reflections. Crenel functions were used for the oxygen and cobalt description and a Gram-Charlier expansion up to the third order of the atomic displacement parameter was employed for one Co atom. The structure is similar to that of Sr(6/5)CoO(3), but with a different sequence of the octahedra and trigonal prism polyhedra along the [CoO(3)] chains. An interesting feature evidenced by the non-harmonic expansion is the displacement of the prismatic Co atoms from the site center, towards the prism rectangular faces.

Sejkoraite-(Y), a new member of the zippeite group containing trivalent cations from Jáchymov (St. Joachimsthal), Czech Republic: Description and crystal structure refinement

Abstract Sejkoraite-(Y), the triclinic (Y1.98Dy0.24)Σ2.22H+ 0.34[(UO2)8O88O7OH(SO4)4](OH)(H2O)26, is a new member of the zippeite group from the Červená vein, Jáchymov (Street Joachimsthal) ore district, Western Bohemia, Czech Republic. It grows on altered surface of relics of primary minerals: uraninite, chalcopyrite, and tennantite, and is associated with pseudojohannite, rabejacite, uranopilite, zippeite, and gypsum. Sejkoraite-(Y) forms crystalline aggregates consisting of yellow-orange to orange crystals, rarely up to 1 mm in diameter. The crystals have a strong vitreous luster and a pale yellow-to-yellow streak. The crystals are very brittle with perfect {100} cleavage and uneven fracture. The Mohs hardness is about 2. The mineral is not fluorescent either in short- or long-wavelength UV radiation. Sejkoraite-(Y) is yellow, with no visible pleochroism, biaxial negative with α′ = 1.62(2), β′ = 1.662(3), γ′ = 1.73(1), 2Vcalc = 79°. The empirical chemical formula (mean of 8 electron microprobe point analyses) was calculated on the basis of 12 (S + U) atoms: (Y1.49Dy0.17Gd0.11Er0.07Yb0.05Sm0.02)Σ1.90H+ 0.54 [(UO2)8.19O7OH(SO4)3.81](H2O)26.00. Sejkoraite-(Y) is triclinic, space group P1̄, a = 14.0743(6), b = 17.4174(7), c = 17.7062(8) Å, α = 75.933(4), β = 128.001(5), γ = 74.419(4)°, V = 2777.00(19) Å3, Z = 2, Dcalc = 4.04 g/cm3. The seven strongest reflections in the X-ray powder diffraction pattern are [dobs in Å (I) (hkl)]: 9.28 (100) (100), 4.64 (39) (200), 3.631 (6) (1̄42), 3.451 (13) (1̄44), 3.385 (10) (2̅4̅2), 3.292 (9) (044), 3.904(7) (300), 2.984 (10) (1̄4̅2). The crystal structure of sejkoraite-(Y) has been solved by the charge flipping method from single-crystal X-ray diffraction data and refined to Robs = 0.060 with GOFobs = 2.38, based on 6511 observed reflections. The crystal structure consists of uranyl sulfate sheets of zippeite anion topology, which alternate with an interlayer containing Y3+(H2O)n polyhedra and uncoordinated H2O groups. Two yttrium atoms are linked to the sheet directly via uranyl oxygen atom, and the remaining one is bonded by hydrogen bonds only. In the Raman and infrared spectrum of sejkoraite-(Y) there are dominating stretching vibrations of SO4 tetrahedra (-1200-1100 cm-1), UO22+ stretching vibrations (-900-800 cm-1), and O-H stretching (-3500-3200 cm-1) and H-O-H bending modes (-1640 cm-1). The new mineral is named to honor Jiří Sejkora, a Czech mineralogist of the National Museum in Prague.