Hostname: page-component-cd9895bd7-hc48f Total loading time: 0 Render date: 2024-12-26T03:56:00.273Z Has data issue: false hasContentIssue false
  • English
  • Français

First accurate location of two proton sites in tourmaline: A single-crystal neutron diffraction study of oxy-dravite

Published online by Cambridge University Press:  05 July 2018

G. D. Gatta ,
F. Bosi ,
G. J. McIntyre  and
H. Skogby
G. D. Gatta*
Affiliation:
Dipartimento di Scienze della Terra, Universitá degli Studi di Milano, Via Botticelli 23, I-20133 Milan, Italy
F. Bosi
Affiliation:
Dipartimento di Scienze della Terra, Sapienza Universitá di Roma, Piazzale Aldo Moro 5, I-00185 Rome, Italy Department of Geosciences, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden
G. J. McIntyre
Affiliation:
Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC NSW 2232, Australia
H. Skogby
Affiliation:
Department of Geosciences, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden
*
E-mail: diego.gatta@unimi.it
Get access Rights & Permissions [Opens in a new window]

Abstract

A single-crystal neutron diffraction study of oxy-dravite from Osarara (Narok district, Kenya) was performed. Intensity data were collected in Laue geometry at 10 K and anisotropic-structure refinement was undertaken. For the first time, two independent H sites were refined unambiguously for a mineral belonging to the tourmaline supergroup and located at 0.26, 0.13, 0.38 (labelled as H3, site occupancy ∼98%) and at 0, 0, 0.9 (labelled as H1, site occupancy ∼25%). The H-bonding scheme can thus be defined as follows: (1) the O at the O3 site acts as a ‘donor’ and the O at the O5 site as ‘acceptor’, the refined O3–H3 bond distance is 0.972(2) Å (and 0.9946 Å corrected for “riding motion”), H3⋯O5 = 2.263(2) Å, O3⋯O5 = 3.179(1) Å and O3–H3⋯O5 = 156.6(1)°; (2) the oxygen at the O1 site acts as a ‘donor’ and the O atoms at O4 and O5 as ‘acceptors’, the refined O1–H1 bond distance is 0.958(8) Å (and 0.9833 Å corrected for “riding motion”), H1⋯O4 = 2.858(6) Å, O1⋯O4 = 3.378(1) Å and O1–H1⋯O4 = 115.12(1)°, whereas H1⋯O5 = 2.886(6) Å, O1⋯O5 = 3.444(1) Å and O1–H1⋯O5 = 118.23(1)°. A further test refinement was performed with the H1 site out of the three-fold axis (at 0.02, 0.01, 0.90); this leads to O1–H1 = 0.995(8) Å (and 1.0112 Å corrected for “riding motion”), H1⋯O4 = 2.747(6) Å and O1–H1⋯O4 = 121.7(4)°, whereas H1⋯O5 = 2.654(9) Å and O1–H1⋯O5 = 136.5(6)°. Bond-valence analysis shows that the H-bonding strength involving O3 is stronger than that involving O1: ∼0.11 and <0.05 valence units, respectively.

The refined angle between the O3–H3 vector and [0001] is 3.40(9)°. Such a small angle is in line with a pleochroic scheme for the OH-stretching absorption bands measured by infrared spectroscopy.

Keywords

oxy-dravitetourmalinecrystal chemistryneutron Laue diffractioninfrared spectroscopyhydrogen bonding
Type
Research Article
Information
Mineralogical Magazine , Volume 78 , Issue 3 , June 2014 , pp. 681 - 692
Copyright
Copyright © The Mineralogical Society of Great Britain and Ireland 2014

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.)

References

Agrosí, G., Bosi, F., Lucchesi, S., Melchiorre, G. and Scandale, E. (2006) Mn-tourmaline crystals from island of Elba (Italy): Growth history and growth marks. American Mineralogist, 91, 944–952.CrossRefGoogle Scholar
Bačík, P., Cempírek, J., Uher, P., Novák, M., Ozdín, D., Filip, J., Škoda, R., Breiter, K., Klementová, M. and Ďud’a R. (2013) Oxy-schorl, Na(Fe2 2+Al)Al6Si6O18 (BO3)3(OH)3O, a new mineral from Zlatá Idka, Slovak Republic and Přibyslavice, Czech Republic. American Mineralogist, 98, 485–492.CrossRefGoogle Scholar
Bosi, F. (2010) Octahedrally coordinated vacancies in tourmaline: a theoretical approach. Mineralogical Magazine, 74, 1037–1044.CrossRefGoogle Scholar
Bosi, F. (2011) Stereochemical constraints in tourmaline: from a short-range to a long-range structure. The Canadian Mineralogist, 49, 17–27.CrossRefGoogle Scholar
Bosi, F. (2013) Bond-valence constraints around the O1 site of tourmaline. Mineralogical Magazine, 77, 343–351.CrossRefGoogle Scholar
Bosi, F., Andreozzi, G.B., Federico, M., Graziani, G. and Lucchesi, S. (2005) Crystal chemistry of the elbaite-schorl series. American Mineralogist, 90, 1784–1792.CrossRefGoogle Scholar
Bosi, F. and Skogby, H. (2013) Oxy-dravite, Na(Al2Mg)(Al5Mg)(Si6O18)(BO3)3(OH)3O, a new mineral species of the tourmaline supergroup. American Mineralogist, 98, 1442–1448.CrossRefGoogle Scholar
Bosi, F., Balić-Žunić, T. and Surour, A.A. (2010) Crystal structure analysis of four tourmalines from the Cleopatra’s Mines (Egypt) and Jabal Zalm (Saudi Arabia) and the role of Al in the tourmaline group. American Mineralogist, 95, 510–518.CrossRefGoogle Scholar
Bosi, F., Skogby, H., Agrosí, G. and Scandale, E. (2012) Tsilaisite, NaMn3Al6(Si6O18)(BO3)3(OH)3OH, a new mineral species of the tourmaline supergroup from Grotta d’Oggi, San Pietro in Campo, island of Elba, Italy. American Mineralogist, 97, 989–994.CrossRefGoogle Scholar
Bosi, F., Skogby, H., Hålenius, U. and Reznitskii, L. (2013) Crystallographic and spectroscopic characterization of Fe-bearing chromo-alumino-povondraite and its relations with oxy-chromium-dravite and oxy-dravite. American Mineralogist, 98, 1557–1564.CrossRefGoogle Scholar
Brown, I.D. (2002) The chemical bond in inorganic chemistry: the bond valence model. Series: International Union of Crystallography Monographs on Crystallography, 12, Oxford University Press, UK, 288 pp.Google Scholar
Busing, W.R. and Levy, H.A. (1964) The effect of thermal motion on the estimation of bond lengths from diffraction measurements. Act a Crystallographica, 17, 142–146.CrossRefGoogle Scholar
Campbell, J.W. (1995) LAUEGEN, an X-windowsbased program for the processing of Laue diffraction data. Journal of Applied Crystallography, 28, 228–236.CrossRefGoogle Scholar
Campbell, J.W., Hao, Q., Harding, M.M., Nguti, N.D. and Wilkinson, C. (1998) LAUEGEN version 6.0 and INTLDM. Journal of Applied Crystallography, 31, 496–502.CrossRefGoogle Scholar
Cempírek, J., Houzar, S., Novák, M., Groat, L.A., Selway, J.B. and Šrein, V. (2013) Crystal structure and compositional evolution of vanadium-rich oxydravite from graphite quartzite at Bítovánky, Czech Republic. Journal of Geosciences, 58, 149–162.CrossRefGoogle Scholar
Dutrow, B.L. and Henry, D.J. (2011) Tourmaline: A geologic DVD. Elements, 7, 301–306.CrossRefGoogle Scholar
Farrugia, L.J. (1999) WinGX suite for small-molecule single-crystal crystallography. Journal of Applied Crystallography, 32, 837–838.CrossRefGoogle Scholar
Filip, J., Bosi, F., Novák, M., Skogby, H., Tuček, J., Čuda, J. and Wildner, M. (2012) Redox processes of iron in the tourmaline structure: example of the hightemperature treatment of Fe3+-rich schorl. Geochimica et Cosmochimica Acta, 86, 239–256.CrossRefGoogle Scholar
Gatta, G.D., Danisi, R.M., Adamo, I., Meven, M. and Diella, V. (2012) A single-crystal neutron and X-ray diffraction study of elbaite. Physics and Chemistry of Minerals, 39, 577–588.CrossRefGoogle Scholar
Gatta, G.D., Merlini, M., Valdrè, G., Liermann, H.-P., Nénert, G., Rothkirch, A., Kahlenberg, V. and Pavese, A. (2013) On the crystal structure and compressional behaviour of talc: a mineral of interest in petrology and material science. Physics and Chemistry of Minerals, 40, 145–156.CrossRefGoogle Scholar
Gonzales-Carreño, T., Fernández, M. and Sanz, J. (1988) Infrared and electron microprobe analysis of tourmaline. Physics and Chemistry of Minerals, 15, 452–460.CrossRefGoogle Scholar
Grice, J.D. and Ercit, T.S. (1993) Ordering of Fe and Mg in the tourmaline crystal structure: The correct formula. Neues Jahrbuch für Mineralogie – Abhandlungen, 165, 245–266.Google Scholar
Hawthorne, F.C. (1996) Structural mechanisms for lightelement variations in tourmaline. The Canadian Mineralogist, 34, 123–132.Google Scholar
Hawthorne, F.C. (2002) Bond-valence constraints on the chemical composition of tourmaline. The Canadian Mineralogist, 40, 789–797.CrossRefGoogle Scholar
Henry, D.J., Novak, M., Hawthorne, F.C., Ertl, A., Dutrow, B., Uher, P. and Pezzotta, F. (2011) Nomenclature of the tourmaline supergroup-minerals. American Mineralogist, 96, 895–913.CrossRefGoogle Scholar
Henry, D.J. and Dutrow, B.L. (2011) The incorporation of fluorine in tourmaline: Internal crystallographic controls or external environmental influences? The Canadian Mineralogist, 49, 41–56.Google Scholar
Larson, A.C. (1967) Inclusion of secondary extinction in least-squares calculations. Acta Crystallographica, 23, 664–665.CrossRefGoogle Scholar
Lussier, A.J., Hawthorne, F.C., Aguiar, P.M., Michaelis, V.K. and Kroeker, S. (2011) Elbaite-liddicoatite from Black Rapids glacier, Alaska. Periodico di Mineralogia, 80, 57–73.Google Scholar
McIntyre, G.J., Lemée-Cailleau, M.-H. and Wilkinson, C. (2006) High-Speed Neutron Laue Diffraction Comes of Age. Physica B, 385–386, 1055–1058.CrossRefGoogle Scholar
Novák, M., Povondra, P. and Selway, J.B. (2004) Schorl-oxy-schorl to dravite-oxy-dravite tourmaline from granitic pegmatites; examples from the Moldanubicum, Czech Republic. European Journal of Mineralogy, 16, 323–333.CrossRefGoogle Scholar
Novák, M., Škoda, P., Filip, J., Macek, I. and Vaculovič, T. (2011) Compositional trends in tourmaline from intragranitic NYF pegmatites of the TřebíčPluton, Czech Republic; electron microprobe, Mössbauer and LA-ICP-MS study. The Canadian Mineralogist, 49, 359–380.CrossRefGoogle Scholar
Piltz, R.O. (2011) Accurate data analysis for the Koala and VIVALDI neutron Laue diffractometers. Abstracts of the XXII IUCr Congress, Madrid (Spain) 22–30 August 2011. Act a Crystallographica, A67, C155.CrossRefGoogle Scholar
Sears, V.F. (1986) Neutron scattering lengths and crosssections. Pp. 521–550 in: Neutron Scattering, Methods of Experimental Physics (K. Sköld and D.L. Price, editors). Vol. 23A. Academic Press, New York.Google Scholar
Sheldrick, G.M. (2008) A short history of SHELX. Acta Crystallographica, A64, 112–122.CrossRefGoogle Scholar
Skogby, H., Bosi, F. and Lazor, P. (2012) Short-range order in tourmaline: a vibrational spectroscopic approach to elbaite. Physics and Chemistry of Minerals, 39, 811–816.CrossRefGoogle Scholar
Sidey, V. (2011) A simplified empirical model for approximation of the ‘bond valence–bond length’ correlation for H–O bonds. Acta Crystallographica, B67, 263–265.CrossRefGoogle Scholar
Taylor, M.C., Cooper, M.A. and Hawthorne, F.C. (1995) Local charge-compensation in hydroxy-deficient uvite. The Canadian Mineralogist, 33, 1215–1221.Google Scholar
Tippe, A. and Hamilton, W.C. (1971) A neutrondiffraction study of the ferric tourmaline, buergerite. American Mineralogist, 56, 101–113.Google Scholar
van Hinsberg, V.J., Henry, D.J. and Marschall, H.R. (2011) Tourmaline: an ideal indicator of its host environment. The Canadian Mineralogist, 49, 1–16.CrossRefGoogle Scholar
Wilkinson, C., Khamis, H.W., Stansfield, R.F.D. and McIntyre, G.J. (1988) Integration of single-crystal reflections using area multidetectors. Journal of Applied Crystallography, 21, 471–478.CrossRefGoogle Scholar
Supplementary material: File

Gatta et al. supplementary material

CIF 1

Download Gatta et al. supplementary material(File)
File 33.5 KB
Supplementary material: File

Gatta et al. supplementary material

CIF 2

Download Gatta et al. supplementary material(File)
File 33.8 KB