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Crystallography and Crystal Chemistry Laboratory

The crystallography and crystal chemistry laboratory is housed inside the UOS of the IGG of Pavia and deals with the study of crystalline solids.

The Laboratory

The international community recently celebrated the enormous impact the discovery of X-ray diffraction has had on much of modern science with the International Year of Crystallography (IYCr2014, UN A/RES/66/284). Since we have been able to determine and visualize the 3D structure of crystalline solids, we have been able to successfully address highly complex issues such as the relationships between structure and properties, between structure, crystal chemistry, and conditions of formation, and between structure and function in geological, biochemical, and technological processes. By understanding in detail the materials that form our environment and our very bodies, and that accompany our lives in every way, we can now optimize their properties for the most diverse and unexpected purposes. These goals are evident in every field, from chemistry to pharmacology, from biology to medicine, from earth sciences to materials sciences, to the knowledge and preservation of cultural heritage.

The Crystallography and Crystal Chemistry Laboratory in Pavia was founded in the 1970s as the CNR's Center for Structural Crystallography and for a long time served as a user center for various Italian groups working in Earth sciences. Over the years, it has been enriched with instrumentation (often modified in-house) and expertise, and especially with databases containing the crystal-chemical descriptions of rock minerals, which were then used for structural modeling, particularly in the case of amphiboles (for which the laboratory remains an international reference point). Another strength of the laboratory is the ability to monitor in situ the processes that occur at high temperatures in crystalline solids, such as structural rearrangements, phase transitions, and deprotonation processes.

Research topics are addressed in a multidisciplinary manner through internal and external collaborations at IGG, both in terms of the techniques used (including other diffraction techniques and various types of spectroscopy) and the issues involved (mineralogical, geochemical, petrological). The laboratory also provides external crystallographic data and structural resolution of crystalline materials through a third-party service.

Instruments

The laboratory is equipped with the following equipment:

  • A Bruker-AXS SMART-APEX diffractometer, co-owned by the Department of Earth and Environmental Sciences of the University of Pavia, which allows for the rapid collection of diffraction data at RT using a CCD area detector (Fig. 1a). The X-ray source is a 2kW sealed tube with a molybdenum anode.
  • Two Philips PW1100 automatic single-crystal diffractometers (Fig. 1b,c) managed by the FEBO control software (a complete rewrite of the original Philips software carried out in Pavia, allowing for the optimization of the diffractometric analysis and data collection procedures). The X-ray source is a 2 kW sealed tube with a molybdenum anode.
  • An in-house designed heating device for Philips PW1100 goniometers (Fig. 2) allows heat treatment and in situ diffraction analysis at temperatures up to 1000 °C and with angular resolution up to 2 theta = 58°.
  • It is also possible to use a powder diffractometer (owned by the Department of Earth and Environmental Sciences of the University of Pavia) to identify mineralogical phases, whether organic or inorganic, even in mixtures.

Staff and Contacts

The staff of the isotopic chemical laboratory is composed of:

  • Dr. Roberta Oberti (CNR Researcher – Laboratory Manager)
  • Roberto Gastoni (CNR Technician)

Collaboratori:

  • Giuseppe Toscani, (CNR Technician)
  • Dott.ssa Serena Tarantino, DISTA Pavia (Ricercatore Associato)
  • Dott. Michele Zema, DISTA Pavia (Ricercatore Associato)
  • Massimo Boiocchi, Large Instrument Center, Pavia (Technician)

Contacts:

  • Dr. Roberta Oberti: telephone: +39 0382 985885
  • email: roberta.oberti@igg.cnr.it

Methods and Applications

Whatever the sample to be analyzed, an unknown mineral to be identified, a crystal identified in a thin section and considered particularly interesting for reconstructing a petrogenetic process, a synthetic material whose structure and chemical composition one wishes to know, the procedure to follow is the same.

The best crystal (or crystals if, for example, chromatic variability is noted) is selected on the basis of its optical properties, and it is mounted on the goniometric head.

The diffracted intensities are collected, corrected, and processed in the most appropriate manner. The crystallographic structure is solved and a crystal-chemical model is refined (in which, in addition to the positions of the atoms, the atomic species present in different percentages in each structural site are defined). The electron density map is studied to verify the presence of neglected atoms, positional disorder, or other aspects useful for an accurate description. The three-dimensional model is visualized.

In the case of rock minerals, models derived from statistical investigations of databases are then used to obtain detailed information on composition, cationic ordering, and in some cases the quantity of light and volatile elements present.

Very often, the information obtained is integrated with that obtainable from different spectroscopic techniques (XAS, FTIR, FTIR imaging, Mössbauer), which provide information on oxidation states, local ordering, homogeneity and diffusion in the crystal (e.g. during high-T processes).

In this way, structural refinement becomes a true analytical tool at the atomic scale.

Applications:

  • Identification of crystalline phases (organic or inorganic, synthetic or natural) by measuring cell constants or structural analysis
  • Structural determinations at room temperature (theta max = 67°)
  • Detailed mineralogical and crystal-chemical systematics
  • Structural determinations at high temperatures (up to 1000 °C, theta max = 29°)
  • Study of thermal expansion, phase transitions and deprotonation processes performed in operando in the temperature and resolution ranges defined above

Other skills:

  • Phase identification (even in mixtures) and quality control by powder diffractometry
  • Preparation of single crystals used for structural refinement for EMP or SIMS analysis (embedded in epoxy resin and polished to the surface)

Scientific Projects and Interests

The laboratory is currently primarily engaged in the characterization of new minerals, in completing the systematics of the amphibole supergroup (with particular attention to the oxo component) and in crystal-chemical modeling (to develop simple, universally usable relationships linking the results of structural refinement with crystal-chemical composition and cationic ordering), and in the systematic study of deprotonation processes in amphiboles and other hydrous minerals.

Furthermore, it provides expertise and data of interest for projects more focused on geochemical and petrogenetic aspects, such as information on the ordering of major and trace elements and the OH content of amphiboles (which are a function of both chemical composition and crystallization conditions of P, T, and fO2). All of this is available on samples of minerals and natural (terrestrial and planetary) and synthetic materials.

The collaborations that underpin these projects involve numerous scientists in Italy and around the world.

Publications

  • CÁMARA F., OBERTI R., CHOPIN C., MEDENBACH O. (2006) The arrojadite enigma: I. A new formula and a new model for the arrojadite structure. Am. Mineral. 91, 1249-1259.
  • McCallum I.S., Domeneghetti M.C., Schwartz J.M., Mullen E.K., Zema M., CÁMARA F., McCammon C., Ganguly J. (2006) Cooling history of lunar Mg-suite gabbronorite 76255, troctolite 76535 and Stillwater pyroxenite SC-936: The record in exsolution and ordering in pyroxenes. Geochimica Cosmochimica Acta 70, 6068-6078.
  • OBERTI R., .QUARTIERI S., DALCONI M.C., BOSCHERINI F., IEZZI G., BOIOCCHI M. (2006) Distinct local environments for Ca along the non-ideal pyrope-grossular solid-solution: a new model based on crystallographic and EXAFS analysis. Chem. Geol. 335, 347-359.
  • Domeneghetti M.C., Fioretti A.M., CÁMARA F., Molin G., Tazzoli V. (2007) Thermal history of ALH 84001 meteorite by Fe2+-Mg ordering in orthopyroxene. Meteor. Planet. Sciences 42, 1703-1710.
  • HAWTHORNE F.C., OBERTI R. (2007) Amphiboles: Crystal-chemistry. In: Amphiboles: Crystal Chemistry, Occurrence and Health Issues edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G 67, 1-54.
  • HAWTHORNE F.C., OBERTI R. (2007) Classification of the amphiboles. In: Amphiboles: Crystal Chemistry, Occurrence and Health Issues edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G 67, 55-88.
  • OBERTI R., DELLA VENTURA G., CÁMARA F. (2007) New amphibole compositions: natural and synthetic. In: Amphiboles: Crystal Chemistry, Occurrence and Health Issues edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G 67, 89-124.
  • OBERTI R., HAWTHORNE F.C., CANNILLO E., CÁMARA F. (2007) Long-range order in amphiboles. In: Amphiboles: Crystal Chemistry, Occurrence and Health Issues edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G 67, 125-172.
  • TIEPOLO M., OBERTI R., ZANETTI A., VANNUCCI R., FOLEY S. (2007) Trace-Element Partitioning Between Amphiboles and Silicate Melts. In: Amphiboles: Crystal Chemistry, Occurrence and Human Health edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G 67, 417-452.
  • WELCH M.D., CAMARA F., DELLA VENTURA G., IEZZI G. (2007) Non-ambient in situ studies of amphiboles. In: Amphiboles: Crystal Chemistry, Occurrence and Health Issues, edito da F.C. Hawthorne, R. Oberti, G. Della Ventura e A. Mottana. RIM&G, 67, pp. 223–260.
  • CÁMARA F., OBERTI R., OTTOLINI L., DELLA VENTURA G., BELLATRECCIA F. (2008) The crystal-chemistry of Li in gadolinite: a multi-analytical approach. Am. Mineral. 93, 996-1004.
  • CÁMARA F., NESTOLA F., ANGEL, R.J., OHASHI H. (2009): Spontaneous strain variations through the low temperature displacive phase transition of LiGaSi2O6 clinopyroxene. Eur. J. Mineral. 21, 599-614.
  • Redhammer G.J., Cámara F., Alvaro M., Nestola F., Tippelt G., Prinz S., Simons J., Roth G., Amthauer G. (2010) Thermal expansion and high temperature P21/c-C2/c phase transition in clinopyroxene-type LiFeGe2O6 and comparison to NaFe(Si,Ge)2O6. Phys. Chem. Minerals, 37, 685-704.
  • HAWTHORNE F.C., OBERTI R. (co-chairs), HARLOW G.E., MARESCH W.V., MARTIN R.F., SCHUMACHER J.C., WELCH M.D. (2012) Nomenclature of the amphibole supergroup. Am. Mineral. 97, 2031-2048.
  • Nestola F., Pasqual D., Welch M.D., Oberti R. (2012) The effects of composition upon the high-pressure behaviour of amphiboles: compression of gedrite to 7 GPa and a comparison with anthophyllite and proto-amphibole. Min. Mag. 76, 987-995.
  • PERINELLI C., ANDREOZZI G.B. CONTE A.M., OBERTI R., ARMIENTI P. (2012) Redox state of subcontinental lithospheric mantle and metasomatism relationships: insights from spinel-peridotites from northern Victoria Land (Antarctica). Contrib. Mineral. Petrol.164, 1053-1067.
  • JENKINS D.M., DELLA VENTURA G., OBERTI R, BOZHILOV K. (2013) Synthesis and characterization of amphiboles along the tremolite-glaucophane join. Am. Mineral. 98, 588-600.
  • OBERTI R., BOIOCCHI M., HAWTHORNE F.C., BALL, N.A., HARLOW, G.E. (2015) Eckermannite revised. The new holotype from the Jade Mine Tract, Myanmar: crystal structure, mineral data and hints on the reasons for the rarity of eckermannite. Am. Mineral. 100, 909-914.
  • Dyar M.D., Breves E.A., Gunter M.E., Lanzirotti A., Tucker J.M., Carey C.J., Peel S., Brown E.B., OBERTI R., Lerotic M., Delaney J.S.(2016) Use of multivariate analysis for synchrotron micro-XANES analysis of iron valence state in amphiboles. Am. Mineral. 101, 1171-1189.
  • OBERTI R., DELLA VENTURA G., BOIOCCHI M., ZANETTI A., HAWTHORNE F.C. (2016) New data on the crystal-chemistry of oxo-mangani-leakeite and mangano-mangani-ungarettiite from the Hoskins mine and their impossible solid-solution – An XRD and FTIR study. Min. Mag., in press.