Hostname: page-component-586b7cd67f-r5fsc Total loading time: 0 Render date: 2024-11-24T10:50:20.609Z Has data issue: false hasContentIssue false
  • English
  • Français

Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography

Published online by Cambridge University Press:  02 January 2018

Fernando Colombo ,
Enrico Mugnaioli ,
Oriol Vallcorba ,
Alberto García ,
Alejandro R. Goñi  and
Jordi Rius
Fernando Colombo*
Affiliation:
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra, Catalonia, Spain
Enrico Mugnaioli
Affiliation:
Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente. Università degli Studi di Siena. Via Laterino 8, 53100, Siena, Italy Centre for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127, Pisa, Italy
Oriol Vallcorba
Affiliation:
Experiments Division - MSPD Beamline (BL04. ALBA Synchrotron Light Source – CELLS. Crta BP 1413 Km 3.3, 08290 Cerdanyola del Vallès, Barcelona, Spain
Alberto García
Affiliation:
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra, Catalonia, Spain
Alejandro R. Goñi
Affiliation:
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra, Catalonia, Spain ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
Jordi Rius
Affiliation:
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra, Catalonia, Spain
*
*E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.

The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

Keywords

karibibitestructurearseniteelectron diffraction tomographylone electron pairdensity functional theory calculationsUrucum mine
Type
Research Article
Information
Mineralogical Magazine , Volume 81 , Issue 5 , October 2017 , pp. 1191 - 1202
Copyright
Copyright © The Mineralogical Society of Great Britain and Ireland 2017

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

§

Permanent address: CICTERRA-CONICET. FCEFyN – Universidad Nacional de Córdoba. Av. Vélez Sarsfield 1611 (X5016GCA) Córdoba, Argentina

References

Allmann, R. (1975) Beziehungen zwischen Bindungslängen und Bindungsstärken in Oxidstrukturen. Monatshefte für Chemie, 106, 779–793.CrossRefGoogle Scholar
Araki, T., Moore, P.B. and Brunton, G.D. (1980) The crystal structure of paulmooreite, Pb2[As2O5]; dimeric arsenite groups. American Mineralogist, 65, 340–345.Google Scholar
Bérar, J.-F. and Lelann, P. (1991) E.S.D.s and estimated probable error obtained in Rietveld refinements with local correlations. Journal of Applied Crystallography, 24, 1–5.CrossRefGoogle Scholar
Bowell, R.B., Alpers, C.N., Jamieson, H.E., Nordstrom, D.K. and Majzlan, J. (2014) The environmental geochemistry of arsenic: an overview. Pp. 1–16in: Arsenic: Environmental Geochemistry, Mineralogy and Microbiology (Bowell, R.B., Alpers, C.N., Jamieson, H.E., Nordstrom, D.K. and Majzlan, J., editors). Reviews in Mineralogy and Geochemistry, 79. Mineralogical Society of America, Chantilly, Virginia, USA.Google Scholar
Burla, M.C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Cuocci, C., Giacovazzo, C., Mallamo, M., Mazzone, A. and Polidori, G. (2015) Crystal structure determination and refinement via SIR2014. Journal of Applied Crystallography, 48, 306–309.CrossRefGoogle Scholar
Calvo, M. (2015) Minerales y Minas de España. Volumen VII. Fosfatos, Arseniatos y Vanadatos. Escuela Técnica Superior de Ingenieros de Minas de Madrid, Fundación Gómez Pardo.Google Scholar
Capitani, G.C., Mugnaioli, E., Rius, J., Gentile, P., Catelani, T., Lucotti, A. and Kolb, U. (2014) The Bi sulfates from the Alfenza Mine, Crodo, Italy: an automatic electron diffraction tomography (ADT) study. American Mineralogist, 99, 500–510.CrossRefGoogle Scholar
Craw, D. and Bowell, R.J. (2014) The characterization of arsenic in mine waste. Pp. 473–506 in: Arsenic: Environmental Geochemistry, Mineralogy and Microbiology (Bowell, R.B., Alpers, C.N., Jamieson, H.E., Nordstrom, D.K. and Majzlan, J., editors). Reviews in Mineralogy and Geochemistry, 79. Mineralogical Society of America, Chantilly, Virginia, USA.Google Scholar
Doyle, P.A. and Turner, P.S. (1968) Relativistic Hartree- Fock X-ray and electron scattering factors. Acta Crystallographica, A24, 390–397.CrossRefGoogle Scholar
Favreau, G. and Dietrich, J. E. (2006) Die Mineralien von Bou Azzer. Lapis, 31, 27–68.Google Scholar
Ghose, S., Sen Gupta, P.K. and Schlemper, E.O. (1987) Leiteite, ZnAs2O4: a novel type of tetrahedral layer structure with arsenite chains. American Mineralogist, 72, 629–632.Google Scholar
Graeser, S., Schwander, H., Demartin, F., Gramaccioli, C. M., Pilati, T. and Reusser, E. (1994) Fetiasite (Fe2+, Fe3+, Ti)3O2[As2O5], a new arsenite mineral: its description and crystal structure determination. American Mineralogist, 79, 996–1002.Google Scholar
Hawthorne, F.C. (1976) The hydrogen positions in scorodite. Acta Crystallographica, B32, 2891–2892.CrossRefGoogle Scholar
Hawthorne, F.C. (1985) Schneiderhöhnite, Fe2+ Fe3 3+ As5 3+O13, a densely packed arsenite structure. The Canadian Mineralogist, 23, 675–679.Google Scholar
Kampf, A.R., Mills, S.J., Housley, R.M., Rossman, G.R., Nash, B.P., Dini, M. and Jenkins, R.A. (2013) Joteite, Ca2CuAl[AsO4][AsO3(OH)]2(OH)2·5H2O, a new arsenate with a sheet structure and unconnected acid arsenate groups. Mineralogical Magazine, 77, 2811–2823.CrossRefGoogle Scholar
Kaur, N., Singh, B., Kennedy, B.J. and Gräfe, M. (2009) The preparation and characterization of vanadiumsubstituted goethite: the importance of temperature. Geochimica et Cosmochimica Acta, 73, 582–593.CrossRefGoogle Scholar
Klaska, R. and Gebert, W. (1982) Polytypie und Struktur von Gebhardit – Pb8 OCl6(As2O5)2 . Zeitschrift für Kristallographie, 159, 75–76.Google Scholar
Kolb, U., Gorelik, T., Kübel, C., Otten, M.T. and Hubert, D. (2007) Towards automated diffraction tomography: Part I – data acquisition. Ultramicroscopy, 107, 507–513.CrossRefGoogle ScholarPubMed
Larsen, A.O. (2013) Contributions to the mineralogy of the syenite pegmatites in the Larvik Plutonic Complex. Norsk Bergverksmuseum Skrift, 50, 101–109.Google Scholar
Lutz, H.D., Jung, M. and Waeschenbach, G. (1987) Kristallstrukturen des Löllingits FeAs2 und des Pyrits RuTe2 . Zeitschrift für Anorganische und Allgemeine Chemie, 554, 87–91.CrossRefGoogle Scholar
Majzlan, J., Palatinus, L. and Plášil, J. (2016) Crystal structure of Fe2(AsO4)(HAsO4)(OH)(H2O)3, a dehydration product of kaňkite. European Journal of Mineralogy, 28, 63–70.CrossRefGoogle Scholar
Mitchell, V.L. (2014) Health risks associated with chronic exposures to arsenic in the environment. Pp. 435–450 in: Arsenic: Environmental Geochemistry, Mineralogy and Microbiology (Bowell, R.B., Alpers, C.N., Jamieson, H.E., Nordstrom, D.K. and Majzlan, J., editors). Reviews in Mineralogy and Geochemistry, 79. Mineralogical Society of America, Chantilly, Virginia, USA.Google Scholar
Mugnaioli, E. (2015a) Single nano crystal analysis using automated electron diffraction tomography. Rendiconti Fisici dell’Accademia dei Lincei, 26, 211–223.CrossRefGoogle Scholar
Mugnaioli, E. (2015b) Closing the gap between electron and X-ray crystallography. Acta Crystallographica, B71, 737–739.Google Scholar
Mugnaioli, E., Gorelik, T. and Kolb, U. (2009) “Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. Ultramicroscopy, 109, 758–765.CrossRefGoogle ScholarPubMed
Norby, P. (1997) Synchrotron powder diffraction using imaging plates: crystal structure determination and Rietveld refinement. Journal of Applied Crystallography, 30, 21–30.CrossRefGoogle Scholar
O’Day, P. (2006) Chemistry and mineralogy of arsenic. Elements, 2, 77–83.CrossRefGoogle Scholar
Ohnishi, M., Shimobayashi, N., Kishi, S., Tanabe, M. and Kobayashi, S. (2013) Talmessite from the Uriya deposit at the Kiura mining area, Oita Prefecture, Japan. Journal of Mineralogical and Petrological Sciences, 108, 116–120.CrossRefGoogle Scholar
Ondruš, P., Skála, R., Císařova, I. Veselovský, F., Frýda, J. and Čejka, J. (2002) Description and crystal structure of vajdakite, [(Mo6+O2)2(H2O)2As2 3+ O5]·H2O – a new mineral from Jáchymov, Czech Republic. American Mineralogist, 87, 983–990.CrossRefGoogle Scholar
Pertlik, F. (1975) Verfeinerung der Kristallstrucktur von synthetischem Trippkeit, CuAs2O4 . Tschermaks mineralogische und petrographische Mitteilungen, 22, 211–217.CrossRefGoogle Scholar
Rius, J. (2012) Patterson function and delta-recycling: derivation of the phasing equations. Acta Crystallographica, A68, 399–400. Software downloaded from http://departments.icmab.es/crystallography/software/XLENS_P5 CrossRefGoogle Scholar
Rius, J. and Plana, F. (1982) Una nueva función que relaciona la longitud del enlace iónico con la valencia electrostática del catión. Anales de Química, 80, 147–149.Google Scholar
Rodríguez-Carvajal, J. (2001) Recent developments of the program FULLPROF. Commission on Powder Diffraction (IUCr) Newsletter, 26, 12–19.Google Scholar
Rozhdestvenskaya, I., Mugnaioli, E., Czank, M., Depmeier, W., Kolb, U., Reinholdt, A. and Weirich, T. (2010) The structure of charoite, (K,Sr,Ba,Mn)15-16 (Ca,Na)32[(Si70(O,OH)180)](OH,F)4.0·nH2O, solved by conventional and automated electron diffraction. Mineralogical Magazine, 74, 159–177.CrossRefGoogle Scholar
Sheldrick, G.M. (2008) A short history of SHELX. Acta Crystallographica, A64, 112–122.CrossRefGoogle Scholar
Soler, J.M., Artacho, E., Gale, J.D., García, A., Junquera, J., Ordejón, P. and Sánchez-Portal, D. (2002) The SIESTA method for ab initio order-N materials simulation. Journal of Physics:CondensedMatter, 14, 2745–2779.Google Scholar
Vaughan, D.J. (2006) Arsenic. Elements, 2, 71–75.CrossRefGoogle Scholar
Vincent, R. and Midgley, P.A. (1994) Double conical beam-rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy, 53, 271–282.CrossRefGoogle Scholar
Voloshin, A.V., Pakhomovsky, Y.A. and Bakhchisaraitsev, A.Y. (1989) On karibibite and schneiderhöhnite from pegmatites of Eastern Kazakhstan. Novye Dannye o Mineralakh, 36, 129–135 [in Rusian].Google Scholar
von Knorring, O., Sahama, T.G. and Rehtijärvi, P. (1973) Karibibite, a new FeAs mineral from South West Africa. Lithos, 6, 265–272.CrossRefGoogle Scholar