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Refikite from Krásno, Czech Republic: a crystal-and molecular-structure study

Published online by Cambridge University Press:  02 January 2018

Richard Pažout ,
Jiři´ Sejkora ,
Jaroslav Maixner ,
Michal Dušek  and
Jaromír Tvrdý
Richard Pažout*
Affiliation:
Central laboratories, Institute of Chemical Technology Prague, Technická 5, CZ-166 28, Prague 6, Czech Republic
Jiři´ Sejkora
Affiliation:
Department of Mineralogy and Petrology, National Museum, Cirkusová 1740, CZ-193 00, Prague 9, Czech Republic
Jaroslav Maixner
Affiliation:
Central laboratories, Institute of Chemical Technology Prague, Technická 5, CZ-166 28, Prague 6, Czech Republic
Michal Dušek
Affiliation:
Institute of Physics of the AS CR, na Slovance 2, CZ-182 21, Prague 8, Czech Republic
Jaromír Tvrdý
Affiliation:
Azalková 522, Liberec, CZ-460 15, Czech Republic
*
* E-mail: [email protected]
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Abstract

The crystal structure of the organic mineral refikite has been determined. The mineral was found in joints in bark and wood from pine trees in the 'V Borkách' peat deposit near the town of Krásno, Slavkovský les Mountains, western Bohemia, Czech Republic. It forms white to light-yellow polycrystalline crusts or randomly intergrown, transparent, colourless, very thin, acicular crystals up to 0.2–0.5 mm long. Sometimes, colourless-to-white elongated prismatic crystals up to 1–1.5 mm in size were encountered. The mineral is soft (Mohs hardness ∼1) and very brittle, with an uneven fracture. No visible cleavage was discerned. Crystals have a greasy-to-glassy lustre; fine crystal aggregates have a pearly lustre. Refikite, empirical formula C20H34O2 or C19H33COOH, is a derivative of abietic acid. It is orthorhombic, space group P21212, with a = 22.6520(7), b = 10.3328(3), c = 7.6711(2) Å, V = 1795.49(9) Å3, Z = 4. Refikite comprises two closely related compounds based on perhydrophenanthrene. The major component has two axial methyl groups, one terminal carboxylic group and one terminal propan-2-yl (isopropyl) group joined to the three fused rings in the same fashion as in abietic acid. However, the fused ring system is fully reduced (contains single bonds only). In the minor component, the terminal propan-2-yl group is replaced by a propen-2-yl (methylvinyl) group. The crystal structure is stabilized by strong O···H–O hydrogen bonds. High-resolution mass spectroscopy (HRMS) confirmed a molecular mass of 306 and the formula C20H34O2. Hydrogen-1 and carbon-13 nuclear magnetic resonance (NMR) spectroscopy showed the presence of four methyl groups in the major component; infrared (IR), Raman and NMR spectra are consistent with the structure. The HRMS, IR and Raman spectroscopy methods confirmed the presence of a minor component containing the propen-2-yl group replacing the propan-2-yl group. This is also reflected in a shortened C15–C17 single bond metric of 1.468(6) Å shown by single-crystal X-ray analysis. The trivial name of the major component of refikite is tetrahydroabietic acid or abietan-18-oic acid. This work represents the first proof of the existence of abietic acid derivatives as naturally occurring species.

Keywords

refikite1,4a-dimethyl-7-propan-2-yl-tetradecahydrophenanthrene-1-carboxylic acidabietic-type resin acidscrystal structuresingle-crystal X-ray diffractioninfrared spectroscopyRaman spectroscopyNMRhigh-resolution mass spectroscopy.
Type
Research Article
Information
Mineralogical Magazine , Volume 79 , Issue 1 , February 2015 , pp. 59 - 70
Copyright
Copyright © The Mineralogical Society of Great Britain and Ireland 2015

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References

Anthony, J.W., Bideaux, R.A., Bladh, K.W. and Nichols, M.C. (2003) Handbook of Mineralogy, V. Borates, Carbonates, Sulfates. Mineral Data Publishing, Tucson, USA.Google Scholar
Dana, E.S. (1892) Dana’s System of Mineralogy, 6th Edition. John Wiley, New York, pp. 1006-1007.Google Scholar
Echigo, T. and Kimata, M. (2010) Crystal chemistry and genesis of organic minerals: a review of oxalate and polycyclic aromatic hydrocarbon minerals. The Canadian Mineralogist 48, 1329-1358.CrossRefGoogle Scholar
Farrugia, L.J. (1997) ORTEP-3 for Windows – a version of ORTEP-III with a graphical user interface (GUI). Journal of Applied Crystallography 30, 565.CrossRefGoogle Scholar
Fiala, F. (1968) Granitoids of the Slavkovský (Císařský ) les Mountains. Sborník geologických veˇd, geologie 14, 93-160.Google Scholar
Dennington, R., Keith, T. and Millam, J. (2009) GaussView Version 5. Semichem Inc., Shawnee Mission, Kansas, USA.Google Scholar
Flack, H.D. (1983) On enantiomorph-polarity estimation. Acta Crystallographica, A39, 876-881.CrossRefGoogle Scholar
Hazen, R.M., Downs, R.T., Jones, A.P. and Kah, L. (2013) Carbon mineralogy and crystal chemistry. Pp. 7-46. in: Carbon in Earth (Hazen, R.M., Jones, A.P. and Baross, J.A., editors). Reviews in Mineralogy & Geochemistry, 75. Mineralogical Society of America and the Geochemical Society, Chantilly, Virginia, USA.Google Scholar
Hintze, C. (1933) Handbuch der Mineralogie. Walter de Gruyter, Berlin.Google Scholar
Hooft, R.W.W., Straver, L.H. and Spek, A.L. (2008) Determination of absolute structure using Bayesian statistics on Bijvoet differences. Journal of Applied Crystallography 41, 96-103.CrossRefGoogle ScholarPubMed
Karle, I.L. (1972) The crystal structure of levopimaric acid, C20H30O2 . Acta Crystallographica, B28, 2000-2007.CrossRefGoogle Scholar
Krása, P. (2013) Localities in the Carlsbad region important on the European scale. http://www.priroda-kv.cz/lokality/krasenske_raseliniste/index.php. [Accessed on December 28, 2013]Google Scholar
Legrand des Cloiseaux, A.L.O. (1874) Manuel de Minéralogie Tome Second. Dunod, Paris, pp. 58-59.Google Scholar
Leymerie, A. (1857) Cours de Minéralogie (Histoire Naturelle), Première Partie. Victor Masson, Paris.Google Scholar
Leymerie, A. (1859) Cours de Minéralogie (Histoire Naturelle), Deuxième Partie. Victor Masson, Paris [Réfikite, p. 400].Google Scholar
Mace, H.A. and Peterson, R.C. (1995) The crystal structure of fichtelite, a naturally occurring hydrocarbon. The Canadian Mineralogist 33, 7-11.Google Scholar
Macrae, C.F., Bruno, I.J., Chisholm, J.A., Edgington, P.R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. and Wood, P.A. (2008) Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures. Journal of Applied Crystallography 41, 466-470.CrossRefGoogle Scholar
Okada, K. and Takekuma, S. (1994) Crystal structure and conformational analysis of 7,13-abietadien-18- oic acid. Bulletin of the Chemical Society of Japan 67, 807-815.CrossRefGoogle Scholar
Palatinus, L. and Chapuis, G. (2007) SUPERFLIP – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. Journal of Applied Crystallography 40, 786-790.CrossRefGoogle Scholar
Parsons, S., Flack, H.D. and Wagner, T. (2013) Use of intensity quotients and differences in absolute structure refinement. Acta Crystallographica, B69, 249-259.Google Scholar
Pažout, R. and Sejkora, J. (2012) X-ray powder diffraction data for the mineral refikite. Powder Diffraction 27, 215-216.CrossRefGoogle Scholar
Petříček, V., Dušek, M. and Palatinus, L. (2006) JANA2006, Structure Determination Software Programs. Institute of Physics, Prague, Czech Republic.Google Scholar
Rao, X., Song, Z. and Shang, S. (2009) 7-Propan-2-yl- 1,4a-dimethyl-1,2,3,4,4a,-5,6,7,8,9,10,10a-dodecahydrophenanthrene- 1-carboxylic acid, Acta Crystallographica, E65, o2804.Google Scholar
Spek, A.L. (2003) Single-crystal structure validation with the program PLATON. Journal of Applied Crystallography 36, 7-13.CrossRefGoogle Scholar
Strunz, H. and Contag, B. (1965) Evenkit, Flagstaffit, Idrialin und Reficit. Neues Jahrbuch für Mineralogie, Monatshefte, 19-25.Google Scholar
Tesař, J. (2007) Complex analysis of a natural healing source of peloid C ˇ istá – Krásno (Probe OS-280807). Unpublished Report, Reference Laboratories of Natural Healing Sources of the Ministry of Health of the Czech Republic.Google Scholar