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X-ray powder diffraction data for the mineral refikite

Published online by Cambridge University Press:  17 August 2012

R. Pažout  and
J. Sejkora
R. Pažout*
Affiliation:
Central Laboratories, Institute of Chemical Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
J. Sejkora
Affiliation:
Department of Mineralogy and Petrology, National Museum, Cirkusová 1740, 193 00 Prague 9, Czech Republic
*
a)Author to whom correspondence should be addressed. Electronic mail: richard.pazout@vscht.cz
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Abstract

X-ray powder diffraction data, unit-cell parameters and space group for a rare natural organic mineral refikite, C20H32O2, abiet-13(15)-en-18-oic acid, are reported [a = 22.55(2) Å, b = 10.469(6) Å, c = 7.930(9) Å, unit-cell volume V = 1871.82 Å3, Z = 4 and space group P21212]. All measured lines were indexed and are consistent with the P21212 space group. No detectable impurities were observed.

Keywords

X-ray powder diffractionmineral refikiteabiet-13(15)-en-18-oic acid14a-dimethyl-7-(1-methylethylidene)-tetradecahydrophenanthrene-1-carboxylic acid
Type
New Diffraction Data
Information
Powder Diffraction , Volume 27 , Issue 3 , September 2012 , pp. 215 - 216
Copyright
Copyright © International Centre for Diffraction Data 2012

I. INTRODUCTION

The organic mineral refikite belongs to a rare group of natural hydrocarbons containing oxygen such as flagstaffite, hoelite and guanine, and was first described by Strunz and Contag (Reference Strunz and Contag1965) from Kolbermohr, Bavaria, Germany, as needle-like crystals in roots of fossil spruce in a swamp. Refikite, summary formula C20H32O2 or C19H31COOH, trivial name abiet-13(15)-en-18-oic acid, systematic name 1,4a-dimethyl-7-(1-methylethylidene)-tetradecahydrophenanthrene-1-carboxylic acid, belongs to abietic-type resin acids (Figure 1). The systematic name differs from the one given by Strunz and Contag (Reference Strunz and Contag1965) and was established on the basis of single-crystal structure of the mineral by the first author of this article.

Figure 1. Structural formula of the organic mineral refikite, abiet-13(15)-en-18-oic acid.

The original description of mineral (Strunz and Contag, Reference Strunz and Contag1965) included the correct determination of non-centrosymmetric space group P21212 from Weissenberg photographs, which was confirmed by single-crystal measurement.

II. EXPERIMENTAL

A. Sample preparation

The sample is formed by white to white-yellowish polycrystaline crusts and occasional transparent rare crystals growing on pine tree bark. The maximum size of crystals is about 1 mm, the coatings take several square centimetres. The samples were found at the locality V Borkách, near Krásno nad Teplou, Slavkovský les Mountains, western Bohemia, Czech Republic, Central Europe, under bark of peated wood. The natural sample was characterized by powder and single-crystal diffraction, as well as by nuclear magnetic resonance (NMR) and HR MS (negative electrospray, [M-H]- = 305.2481 Da).

B. Diffraction data collection and reduction

The diffraction pattern for the title compound was collected at room temperature using an X'Pert PRO θ–θ powder diffractometer with parafocusing Bragg–Brentano geometry and CuKα radiation (λ = 1.5418 Å, generator setting: 40 kV, 30 mA). Owing to a small amount of the sample, it was placed on the surface of a silicon zero-background sample holder. To gain intensities, the Soller slits used for the measurement were 0.04 rad instead of 0.02 rad used for collecting a standard ICDD pattern that results in slightly higher background intensities level.

An ultrafast X'Celerator detector was employed to collect XRD data over the angular range from 7° to 70° 2θ with a step size of 0.017° 2θ and a counting time of 40.64 s per step. Data evaluation was performed using the software package HighScore Plus V 3.0c PANalytical, Almelo, Netherlands.

Automatic indexing of the experimental XRD pattern was done using TREOR (Werner et al., Reference Werner, Erikson and Westdahl1985). Space group of the original card 00-028-2009 was established from Weissenberg photographs (Strunz and Contag, Reference Strunz and Contag1965) and was verified by single-crystal measurement.

III. RESULTS

The experimental powder diffraction pattern is depicted in Figure 2 up to 40° 2θ as no diffraction lines were observed at higher angles. Automatic indexing results obtained by TREOR show that the title compound is orthorhombic with space group P21212 and unit-cell parameters: a = 22.55(2) Å, b = 10.469(6) Å, c = 7.930(9) Å, unit-cell volume V = 1871.82 Å3 and Z = 4. The figures of merit are F 19 = 9(0.020001, 116) (Smith and Snyder, Reference Smith and Snyder1979) and M 19 = 6 (de Wolff, Reference de Wolff1968). All lines were indexed and are consistent with the P21212 space group.

Figure 2. X-ray powder diffraction pattern of the mineral refikite using CuKα 1 radiation (λ = 1.5406 Å).

Considering the quality of the natural organic sample and the scarcity of the mineral, the presented data of 19 diffraction lines (Table I) represent an improvement over the current card 00-028-200 that contains seven diffraction lines.

TABLE I. Indexed X-ray powder diffraction data for the organic mineral refikite, C20H32O2, abiet-13(15)-en-18-oic acid, are reported [a = 22.55(2)) Å, b = 10.469(6) Å, c = 7.930(9) Å, unit-cell volume V = 1871.82 Å3, Z = 4 and space group P21212]. All measured lines were indexed and are consistent with the P21212 space group.

ACKNOWLEDGMENTS

This work was financially supported by the grant GAČR 104/09/1497 of the Grant Agency of the Czech Republic and by the grant DKRVO MK-S 760/2012 OVV of the Ministry of Culture of the Czech Republic. The authors would like to thank Ian Madsen for helpful advice. We also thank Jaroslav Maixner and Radek Cibulka for consultations on the chemical name and to Jaroslav Tvrdý for providing the sample.

References

de Wolff, P. M. (1968). “A simplified criterion for the reliability of a powder pattern indexing,” J. Appl. Crystallogr 1, 108–113.CrossRefGoogle Scholar
Smith, G. S. and Snyder, R. L. (1979). “FN: A criterion for rating powder diffraction patterns and evaluating the reliability of powder indexing,” J. Appl. Crystallogr. 12, 60–65.CrossRefGoogle Scholar
Strunz, H. and Contag, B. (1965). “Evenkit, Flagstaffit, Idrialin und Reficit,” Neues Jahrb. Mineral., Monatsh., 19–25.Google Scholar
Werner, P. E., Erikson, L., and Westdahl, M. (1985). “Treor, a semi-exhaustive trial-and-error powder indexing program for all symmetries,” J. Appl. Cryst. 18, 367–370.CrossRefGoogle Scholar
Figure 0

Figure 1. Structural formula of the organic mineral refikite, abiet-13(15)-en-18-oic acid.

Figure 1

Figure 2. X-ray powder diffraction pattern of the mineral refikite using CuKα1 radiation (λ = 1.5406 Å).

Figure 2

TABLE I. Indexed X-ray powder diffraction data for the organic mineral refikite, C20H32O2, abiet-13(15)-en-18-oic acid, are reported [a = 22.55(2)) Å, b = 10.469(6) Å, c = 7.930(9) Å, unit-cell volume V = 1871.82 Å3, Z = 4 and space group P21212]. All measured lines were indexed and are consistent with the P21212 space group.