Experimental Details and Crystal Structure Refinement from

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1 Experimental Details and Crystal Structure Refinement from Long, J. M., J. Rakovan, J. A. Jaszczak, A. Sommer, and R. Anczkiewicz Fluorapatite from a remarkable occurrence of graphite and associated minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Single crystal X-ray diffraction (XRD) Experimental Methods Single crystal X-ray diffraction data were collected at Miami University. An 200 m fragment was taken from the apatite crystal pictured in Figure 2 in Long et al. (2013) and glued to a glass fiber for XRD data collection. The crystal fragment was mounted on a Bruker Apex CCD diffractometer equipped with graphite-monochromated MoK radiation. Data collection details, structure-refinement parameters, refined cell-parameters, and other crystal data are reported in Table 1. Data were collected for a full sphere of reciprocal space, and absorption corrections were applied using semi-empirical methods using the SADABS (Bruker AXS, Inc. 2003) program. Data were integrated as well as corrected for Lorentz and polarization factors using the program SAINTPLUS (Bruker AXS, Inc. 2003). The crystal structure was solved by direct methods and difference-fourier maps using the Bruker SHELXTL v (Bruker AXS, Inc. 2000) package of programs. Neutral-atom scattering factors and terms for anomalous dispersion were employed throughout the solution and refinement. The structure was refined on F 2 with anisotropic thermal parameters. Atom parameters are listed in Table 2, anisotropic thermal parameters are listed in Table 3, and selected interatomic distances are listed in Table 4. minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 1

2 Energy dispersive spectroscopy (EDS) X-ray fluorescence data were collected by EDS on a Zeiss Supra35 variable pressure scanning electron microscope (SEM) with a field emission source and an EDAX X-ray detector at Miami University. Data were collected on an uncoated crystal fragment placed on an aluminum sample mount with carbon tape, in high vacuum at 20 kv. A characteristic EDS spectra from Merelani fluorapatite with peak integration results is shown in Figure 1. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) A polished grain mount was made from several millimeter sized fragments taken from the apatite crystal pictured in figure 2 in Long et al. (2013). Trace element analyses by LA-ICP- MS were performed at the Institute of Geological Sciences, Polish Academy of Sciences, Kraków Research Centre using a 193 nm excimer laser-ablation system RESOlution M50 by Resonetics coupled with quadrupole ICP-MS XSeriesII by Thermo. Details of the RESOlution M50 performance are given in Müller et al. (2009). Ablation took place in pure He (flow rate of 0.9 L/min), to which Ar nebulizer gas (flow rate of L/min) was mixed downstream of the two volume LA cell, and after passing through a signal smoothing device, the analyte was delivered to the ICP source. A small addition of nitrogen ( L/min) was used to enhance sensitivity of the ICP-MS. Analyses were performed with spot size of μm, fluence of 5 J/cm 2 and at repetition rate of 5 Hz. Each 45 s ablation time was preceded by 20 s blank and followed by 20 s washout. Five replicate measurements were made at different spots on the Merelani apatite. Sample runs were bracketed by measurements of NIST 612 glass (Pearce et al.,1997; Jochum et al., 2011). The concentrations of S and Cl in the 612 glass were taken from Jochum et al. (2011). Calcium concentration was used as an internal standard. Data were processed using Glitter software of Macquarie University, Australia (Griffin et al., 2008). Tables 5 and 6 report the measured elemental concentrations and the associated one-sigma errors on the measurements respectively. Polarized Light Observations Images of crystals backlit by polarized light were made using liquid crystal display (LCD) computer monitors. LCDs are ideal sources of broad, even polarized light emission for the study of objects too large for typical microscopes. For best results the computer screens were made to emit bright white light (i.e. using a word processor or image rendering program bring up a blank page set to a white background and adjust the screen brightness and contrast). The polarization direction of the monitors was determined using a polarizing plate with known polarization direction. Alignment of the LCD polarization direction with crystallographic axes of samples was based on crystal morphology (fig. 2). Figure 3 was taken with nonpolarized front and side illumination of the specimen and a polarizing filter on the camera. Rotation of the filter also allows observation of pleochroism in the sample. A short movie clip showing a crystal while rotating the polarizing filter on the camera is also available on Rocks & Minerals Supplementary Materials webpage minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 2

3 Optical Absorption Spectroscopy (OAS) Orientation dependent polarized optical absorption spectra were collected, on all three crystals mentioned in Long et al. (2013) using an Ocean Optics S2000 spectrometer in the Molecular Microspectroscopy Laboratory, Department of Chemistry and Biochemistry, Miami University. Light from a fiber coupled tungsten halogen source was collimated to a beam diameter of approximately 5 millimeters and passed through an Edmund Scientific Polaroid sheet. This light was then directed through the absorption cell whose open path was approximately 75 millimeters in length. After passing through the cell, the light was focused onto a fiber optic which was coupled to the S2000 spectrometer. A variable aperture was placed in the cell to control the diameter of the collimated beam for 0.5 millimeters to 5 millimeters. The collimated beam diameter was controlled so as to allow light to be directed through regions of interest in the samples. Raman Spectroscopy Raman spectral analyses of inclusions in the apatite crystal pictured in figure 2 in Long et al. (2013) were conducted at Miami University and Michigan Technological University. In Molecular Microspectroscopy Laboratory, Department of Chemistry and Biochemistry at Miami University data were collected with a Renishaw InVia Raman microscope. The spectrometer interfaced to the microscope employed a 1800 groove/mm grating and a charge-coupled detector (CCD). The sample was excited using a HeNe laser (wavelength = nm) that was focused onto the sample using a 20 (0.40 N.A.) objective. The same objective was employed to collect the back-scattered Raman radiation. Spectra were collected at 4-wavenumber resolution over the range of 100 1,500 wavenumbers using an integration time of 30 seconds per point. Three individual spectra were averaged to produce the final Raman spectrum. Abscissa values of the Raman shift were calibrated using the phonon band of single-crystal silicon located at ± 0.3 wavenumbers. A series of spectra were taken for each inclusion feature at several different focal points to find the optimum signal. A Jobin-Yvon LabRAM HR800 Raman spectrometer equipped a high-precision x-y mapping stage was used in the Department of Physics at Michigan Technological University. Incident light from 17-mW linearly polarized HeNe laser was focused on the sample using an Olympus BX-41 microscope and a 100 objective lens, giving a laser spot size on the sample of approximately 1 μm. Back-scattered light was passed through the same objective lens into the spectrometer system's notch filter, 1800 gr/mm diffraction grating, and CCD. In order to better collect scattered light from a more localized region in the inclusions within the apatite crystal, a 150 m confocal hole was employed. To avoid undesirable heating effects from the incident laser, a neutral filter was used to decrease the incident laser intensity by a factor of 2. Abscissa values were calibrated using the phonon band of single-crystal silicon. Raman spectra were explored over Raman shifts ranging from 100 to 4,000 wavenumbers. Final spectra were collected with 1-wavenumber resolution using an integration time of 5 to 10 seconds per point, minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 3

4 averaged over 50 to 100 consecutive accumulation cycles. Sharp peaks due to cosmic rays were removed from the data during collection. References BrukRUKerR AXxS, IncC SHELXTL v.6.14 Software Package. Madison, Wisconsin, U.S.A. BrukRUKerR AXxS, IncC SaintPlus v.6.45 Software Package. Madison, Wisconsin, U.S.A. Dunitz, J. D., V. Schomaker, and K. N. Trueblood Interpretation of atomic displacement parameters from diffraction studies of crystals. The Journal of Physical Chemistry 92(4): Griffin, W. L., N. J. Pearson, E. A. Belousova, and A. Saeed GLITTER: data reduction software for laser ablation ICP-MS. In: Sylvester, P. (ed.) Mineralogical Association of 48 Canada Short Course Series Volume 40, Vancouver, B.C. Appendix 2, Jochum, K.P., U. Weis, B. Stoll, D. Kuzmin, D.E. Jacob, A. Stracke, K. Birbaum, D. Frick, D. Günther, and J. Enzweiler Determination of Reference Values for NIST SRM Glasses following ISO Guidelines. Geostandards and Geoanalytical Research 35: Long, J. M., J. Rakovan, J. A. Jaszczak, A. Sommer, and R. Anczkiewicz Fluorapatite from a remarkable occurrence of graphite and associated minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals X:XX Muller, W., M. Shelley, P. Miller, and S. Broude, Initial performance metrics of a new custom-designed ArF excimer LA-ICPMS system coupled to a two-volume laser ablation cell. Journal of Analytical Atomic Spectrometry 24: Pearce, N. J. G., W. T. Perkins, J. A. Westgate, M. P. Gorton, S. E. Jackson, C. R. Neal, and P. Chenery A Compilation of New and Published Major and Trace Element Data for NIST SRM 610 and NIST SRM 612 Glass Reference Materials. Geostandards Newsletter 21(1): Willis, B.T.M. and A. W. Pryor Thermal Vibrations in Crystallography. Cambridge: Cambridge University Press. 296p. minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 4

5 Table 1: Data collection details, structure-refinement parameters, refined cell-parameters, and other crystal data. Diffractometer : Bruker APEX X-ray radiation, power MoK (λ= Å), 45 kv, 35 ma Crystal size mm Structural formula Ca 10 (PO 4 ) 6 F 2 Space group P6 3 /m Unit-cell parameters a, b, c (Å) (3) (3) (5) ( o ) V (Å) Z 1 Frame width, scan time, 0.20, 15 s, 4500 number of frames: Values of h, k, l h - 12, k -12, -9 - l - 9 Temperature 20 o C Detector distance 5 cm R int (before, after SADABS absorption correction) Measured reflections, unique 7162, 477 reflections, full sphere Refined parameters 39, refined on F 2 R1 = for 477 Fo > 4sig(Fo) and for all 477 data wr2 = , GooF = S = Largest difference peaks: +0.47, e/å 3 Table 2: Fractional coordinates and equivalent isotropic displacement parameters (Ueq) (Willis & Pryor 1975) of atoms in the Merelani fluorapatite. Site x y z Ueq Ca (1) Ca (7) (8) P (8) (8) F O (24) (23) O (24) (24) O (17) (17) (22) minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 5

6 Table 3: Anisotropic thermal parameters (Dunitz et al. 1988) for atoms in the Merelani fluorapatite. Site U11 U22 U33 U23 U13 U12 Ca Ca P F O O O Table 4: Selected interatomic distances in the Merelani fluorapatite. Atom 1 Atom 2 Distance Atom 1 Atom 2 Distance Ca1 - O1(x3) (14) Ca2 - F (5) O2(x3) (15) O3(x2) (15) O3(x3) (15) O (20) O3(x2) 2.496(2) Mean = O (21) Mean = P - O3(x2) (15) O (19) O (20) Mean = minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 6

7 Table 5. Trace Element Concentrations in PPM. From NIST612 glass standard and Merelani apatite (specific isotope measured). Element NIST612 NIST612 apatite 1 apatite 2 apatite 3 apatite 4 apatite 5 NIST612 NIST612 apatite avg. NIST612 avg. Na(23) Mg(24) Si(29)* <47.26 <49.53 <49.68 <49.77 < n/a S(33) Cl(35) Cl(37) Ca(43) V(51) Cr(52) Fe(54)** Mn(55) Fe(57) Co(59) As(75) Sr(88) Y(89) La(139) Ce(140) Pr(141) Nd(146) Sm(147) Eu(153) Gd(157) Tb(159) Dy(163) Ho(165) Er(166) Tm(169) Yb(172) Lu(175) Hf(178) Pb(208) Th(232) U(238) * Concentrations in sample below minimum detection limit. ** Large error due to mass interference with ArO minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 7

8 Table 6. One-sigma error in the measurements reported in table 5. Element NIST612 NIST612 apatite 1 apatite 2 apatite 3 apatite 4 apatite 5 NIST612 NIST612 apatite avg. NIST612 avg. Na(23) Mg(24) Si(29) S(33) Cl(35) Cl(37) Ca(43) V(51) Cr(52) Fe(54)* Mn(55) Fe(57) Co(59) As(75) Sr(88) Y(89) La(139) Ce(140) Pr(141) Nd(146) Sm(147) Eu(153) Gd(157) Tb(159) Dy(163) Ho(165) Er(166) Tm(169) Yb(172) Lu(175) Hf(178) Pb(208) Th(232) U(238) minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 8

9 Figure 1. EDS spectra from Merelani fluorapatite (sample pictured in Figure 2 of Long et al. 2013) with peak integration results. minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 9

10 Figure 2. Observation of pleochroism in a Merelani fluorapatite crystal using a laptop LCD monitor as a source of polarized light. Left image, a-axis, [100] parallel to LCD polarization direction. Right image c-axis, [001] parallel to LCD polarization direction. The crystal measures 2.05 x 1.7 x 1.3 cm. Fine Mineral International specimen. John Rakovan photos. minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 10

11 Figure 3. Observation of pleochroism in Merelani fluorapatite crystals using a polarizing filter on the camera. Left image, filter polarization direction roughly parallel to c-axis, [001] of the crystals. Right image, filter polarization direction roughly parallel to a-axis, [100] of the crystals. Note that reflected light from the glass that the crystal is sitting on is highly polarized. The direction of this polarization is approximately parallel to the bottom edge of the photograph. When the filter polarization direction is vertical the reflected light is blocked (left image). Look for this reflection in the online video cited above. The crystal cluster measures 2.3 x 2.0 x 1.7 cm. John Rakovan specimen. John Jaszczak photos. minerals, Karo Pit, Block D, Merelani Hills, Arusha Region, Tanzania. Rocks & Minerals 88: Page 11