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Crystal Structure of Vanadinite: Refinement of Anisotropic Displacement Parameters

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Crystal Structure of Vanadinite: Refinement of Anisotropic Displacement Parameters Journal of the Czech Geological Society 51/34(2006) 271 Crystal structure of vanadinite: Refinement of anisotropic displacement parameters Krystalová struktura vanadinitu: zpøesnìní anizotropních teplotních parametrù (2 figs, 5 tabs) FRANTIEK LAUFEK1 ROMAN SKÁLA2 JAKUB HALODA1 IVANA CÍSAØOVÁ3 1 Czech Geological Survey, Geologická 6, Praha 5, CZ-152 00 Czech Republic 2 Institute of Geology, Academy of Sciences of the Czech Republic, Rozvojová 135, Praha 6, CZ-165 02 Czech Republic 3 Faculty of Science, Charles University, Hlavova 8, Praha 2, CZ-128 43 Czech Republic The structure of vanadinite, Pb (VO ) Cl, from Mibladén, Morocco, was refined from single-crystal X-ray data. The full anisotropic struc- 5 4 3 tural refinement was carried out in the hexagonal space group P6 /m, unit cell parameters a = 10.2990(2), c = 7.3080(1) Å, 3 V = 671.30(2) Å3, Z = 2, with an R factor of 0.0197. The full anisotropic crystal structure refinement results in smaller departures of bond valence sums for cations from the ideal value than the isotropic one. Key words: vanadinite; crystal structure; anisotropic displacement parameter; single-crystal X-ray refinement Introduction Mineralization at Mibladén is comparable to other car- bonate-hosted lead-zinc deposits, sharing numerous char- Vanadinite, Pb (VO ) Cl, is an end member in the terna- acteristics with the Mississippi Valley type deposits 5 4 3 ry system pyromorphite-vanadinite-mimetite. It belongs (Jébrak et al. 1998). The lead ore at Mibladén is restricted to the apatite-group (Mandarino Back 2004). By anal- to the Mesozoic units near the present outcrop limit of ogy with the other apatite-group minerals that crystallize the formation, where the thickness of the sediments is in space group P6 /m, vanadinite was presumed to be minimal. Most of the lead ore is hosted by Domerian 3 hexagonal (Hendricks et al. 1932). Thirty years after the (=Midle Lias) dolomitic to carbonaceous formations (Fe- first description of the vanadinite structure, Trotter lenc Lenoble 1965). Barnes (1958) studied the three-dimensional atomic ar- At Mibladén, vanadinite occurs as an alteration prod- rangement in the phase. They refined the vanadinite struc- uct of galena in close association with barite, cerussite ture to R = 12 % using visual estimates of intensities from and anglesite. The crystals are characterized by their re- precession photographs. More recently, single crystal markable size (commonly up to 1 cm in length), a deep X-ray refinement of vanadinite was reported (Dai red colour and adamantine lustre. The crystals are short Hughes 1989). In their refinement, the displacement pa- hexagonal prisms terminated by a basal pinacoid. This rameters for cations were refined as anisotropic whereas makes them different from the barrel-shaped crystals oxygen atoms were refined as isotropic only. Despite the common to the apatite group minerals. abundance of museum-quality specimens, full anisotro- pic structural refinement of vanadinite is still lacking. Crystallographic data and chemical composition Partly to blame are some serious experimental difficul- ties: the X-ray scattering is dominated by highly-absorb- Data for crystal structure refinement were acquired ing lead atoms, and vanadium interaction with neutrons using 4-circle single-crystal diffractometer Nonius is negligible. The aim of this work was to perform full KappaCCD at the Centre of Molecular Structures at the anisotropic structure refinement and evaluate the effects Faculty of Science, Charles University, Prague. The pro- of anisotropic displacement parameters refinement on the gram COLLECT (Nonius 19972000), was used for data crystal structure of vanadinite. collection. Unit-cell refinement and data reduction was carried with program HKL-SCALEPACK (Otwinovski Locality and properties Minor 1997). After correction the data for absorption (Spek 2001), the structure was solved applying Sir92 Since 1979, Morocco has been an important source of su- (Altomare et al. 1994) and subsequent refinement was perb large vanadinite crystals or aggregates thereof (White carried out with SHELX97 program (Sheldrick 1997). 1984). One of the major vanadinite localities in Morocco The programs of the SHELX97 suite were operated is carbonate-hosted stratabound lead deposit in Mibladén, through WinGX graphical interface (Farrugia 1999). Two upper-Moulouya district (32°46N, 4°38W; Fig. 1). This refinements of the structure were carried out. In the first, locality also provided the sample studied. The sample that we refined all the atoms anisotropically. In the second contains vanadinite was purchased at a mineral fair in 2004 one, only heavy atoms were refined anisotropically, from a Czech mineral dealer. The sample was labelled va- whereas oxygen displacement parameters isotropically. nadinite from Mibladén, Morocco. Other refined parameters were the same in both refine- 272 Journal of the Czech Geological Society 51/34(2006) Microspec WDX-3PC. The following conditions were used: operating voltage 15 kV, beam current 16 nA, with Phi(rho ×Z) correction procedure and the standards vanadium (V) and lead (Pb). Results of six analyses, when averaged and recalculated on the basis of twelve oxygen atoms, yielded the following chemical formula: Pb V O Cl ; isomorphous elements like P and As 5.00 2.99 12.00 1.00 were below the detection limits. Infrared spectroscopic analysis, performed with FTIR spectrometer Magna 760 Nicolet using KBr pellet with- in the 4004000 cm-1 range, rules out the presence of OH- groups. Interpretation of results The full anisotropic refinement of the vanadinite struc- Fig. 1 Sketch map showing the geographic location of the Mibladén ture is in agreement with the atomic arrangement deter- locality. mined for this mineral by Dai Hughes (1989). Conse- quently, the reader is referred to the papers of Trotter ments and included scale factor, positional parameters, Barnes (1958) and Dai Hughes (1989) for a thorough and an isotropic extinction factor. Neutral atomic scat- description of the vanadinite structure. tering factors, including terms for anomalous dispersion, In order to show the effect of refinement of anisotro- were used in the refinement. The graphical representa- pic displacement parameters, we calculated effective co- tion of the structure was prepared with DIAMOND ordination numbers (ECoN) (Hoppe 1979) for cations as (Crystal Impact 2004) program and is shown in Fig. 2. Pb and V and bond valence sums. The effective coordi- Experimental details and crystal data are listed in Table 1, nation numbers were calculated by means of the program atomic positions and anisotropic temperature parameters of Rieder (1993), the bond valence calculations were car- are listed in Tables 2 and 3, respectively. ried out according to Brese OKeeffe (1991) using the The quantitative chemical composition of the exam- program Ivton (Baliæ-uniæ Vickoviæ 1996). Compar- ined crystal was measured with a scanning electron mi- ison between the calculated bond valence sums (BVS) croprobe CamScan 4 with a wave-dispersive analyser and effective coordination numbers (ECoN) (Hoppe Fig. 2 Perspective di- agrams for Pb1, Pb2 and V polyhedra in vanadinite. For each polyhedron, the c axis is vertical and a axis is approximately per- pendicular to the plane of the drawing. Journal of the Czech Geological Society 51/34(2006) 273 Table 1 Crystal data of vanadinite and structure refinement details. 1979) derived from the data of Dai Hughes (1989) and those from this study is shown in Table 4. The Space group P6 /m (No. 176) 3 full anisotropic refinement results in smaller depar- Unit cell dimensions (Å) a = 10.2990(2), c = 7.3080(1) tures of BVS from the ideal value. 3 Volume (Å ) 671.30(2) Bond lengths resulting from our refinement dis- Z, Calculated density (g.cm-3) 2, 7.006 play slight differences when compared to those of Absorption coefficient (mm-1) 64.7 Dai Hughes (1989) (Table 5). These discrepancies, F(000) 1184 however, might theoretically be attributed to differ- Absorption correction procedure empirical ent size of the unit cells. To assess the differenc- Wavelength (Å) 0.71073 es observed and to quantify the amplitude of de- Crystal size (mm) 0.19 x 0.16 x 0.07 viations in bond lengths and angles, respectively, È range for data collection (°) 3.60 to 30.02 we applied an approach of the so-called distor- Index ranges -14 ≤ h ≤ 14, -14 ≤ k ≤ 14, -10 ≤ l ≤ 10 tion parameters. Such distortion indicators as Reflection collected 23247 bond angle variance and bond length distortion Independent reflections 706 are commonly used to characterize the departure Refinement method Full-matrix least squares on F2 of an irregular polyhedron from ideal regular ge- Data/restrains/parameters 706/0/40 ometry. Probably the most common distortion Goodness-of-fit on F2 1.225 parameter that is suitable to characterize the dis- Final R indices [I > 2σ] R = 0.0197, wR = 0.0458 tortion of a polyhedron is the bond angle vari- R indices (all data) R = 0.0209, wR = 0.0470 ance, ó2, which was introduced by Robinson and n 2 2 Weighting scheme w-1 = [σ2(F 2) + (aP)2 + bP) co-workers (1971) ó as = Σ (è è ) / (n 1) where o i=1 i 0 where P is [F 2 + 2F ]/3 è is the ideal bond angle for a regular polyhe- o c 0 Goodness-of-fit = {Σ[w(F 2 - F 2)]/(n - p)}1/2 dron (e.g. 90° for an octahedron, 109.47° for a o c R = Σ||F |-|F ||/|F | tetrahedron), n is the number of bond angles in o c o the coordination polyhedron, and è are indi- wR = {Σ[w(F 2 - F 2)2/Σ[w(F 2)2]}1/2 i o c o vidual bond angles. The bond length distortion Table 2 Atomic coordinates and equivalent isotropic displacement Table 3 Anisotropic displacement parameters U (Å2 x 103) for ij parameters of vanadinite from Mibladén, Morocco.
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