By Joseph Caleb Chappell Three Groups of Fluorapatite from the Mont

ABSTRACT

CHEMICAL AND STRUCTURAL CHARACTERIZATION OF FLUORAPATITE FROM THE POUDRETTE PEGMATITE, MONT SAINT-HILAIRE, QUEBEC, CANADA

by Joseph Caleb Chappell Three groups of fluorapatite from the Mont Saint-Hilaire igneous complex in Quebec, Canada have been analyzed with scanning electron microscopy (SEM), electron probe microanalyses (EPMA), single-crystal X-ray diffraction (SCXRD), Fourier transform infrared spectroscopy (FTIR), and magic angle spinning nuclear magnetic resonance (MAS-NMR) to fully characterize the chemical and structural details of fluorapatite from one of the most mineralogically diverse locales on Earth. SEM and EPMA revealed these fluorapatites to be enriched in Th, Y, and Na, while FTIR showed substantial concentrations of carbonate substituting for phosphate at the tetrahedral site. The Th contents observed in these fluorapatites are the highest ever observed for natural samples, and have implications for designing new solid nuclear waste forms. SCXRD refinements revealed the dissymetrization of two of the three groups from the classic P63/m space group to the P space group due to the elevated Y and Na contents. Lastly, the FTIR and NMR data show the presence of the long debated C-F bond the observation of which has important implications for the incorporation of carbonate groups into apatites, and is the first time this bond has been observed in any natural mineral.

CHEMICAL AND STRUCTURAL CHARACTERIZATION OF FLUORAPATITE FROM THE POUDRETTE PEGMATITE, MONT SAINT-HILAIRE, QUEBEC, CANADA

A Thesis

Submitted to the Faculty of Miami University In partial fulfillment of The requirements for the degree of Master of Science. Department of Geology and Environmental Earth Science. by Joseph Caleb Chappell Miami University Oxford, Ohio. 2019

Advisor: John Rakovan

Reader: Claire McLeod

Reader: Mark Krekeler

This thesis titled

CHEMICAL AND STRUCTURAL CHARACTERIZATION OF FLUORAPATITE FROM THE POUDRETTE PEGMATITE, MONT SAINT-HILAIRE, QUEBEC, CANADA

Joseph Caleb Chappell

has been approved for publication by

The College of Arts and Science

and

Department of Geology and Environmental Earth Science

______John Rakovan

______Claire McLeod

______Mark Krekeler

Table of Contents List of Tables…………………………………………………………………………………….iv List of Figures……………………………………………………………………………….……v Dedication……………………………………………………………………………...…….…..vi Acknowledgments……………………………………………………………...………...….….vii Introduction……………………………………………………………………………………....1 Occurrence…………………………………………………………….………………………….2 Analytical Methods………………………………………………………………………………3 Scanning Electron Microscopy……………...... 3 Electron Probe Microanalysis…………………………………………………………….3 Single Crystal X-ray Diffraction…………………………………………………………..3 Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy………………...4 Magic Angle Spinning-Nuclear Magnetic Resonance…………………………………….4 Results Scanning Electron Microscopy……………………………………………………………5 Electron Probe Microanalysis…………………………………………………………….5 Single Crystal X-ray Diffraction…………………………………………………………..6 Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy………………...6 Magic Angle Spinning-Nuclear Magnetic Resonance…………………………………….7 Discussion Sodium in the fluorapatite structure………………………………………………………7 Thorium in the fluorapatite structure……………………………………………………..8 Yttrium in the fluorapatite structure………………………………………………………9 Solid solution with belovite group minerals……………………………………………..10

3- Carbonate in the fluorapatite structure and evidence for the CO3F molecule…………10 Conclusions……………………………………………………………………………………...11 References……………………………………………………………………………………….12 Tables……………………………………………………………………………………………16 Figures……………………………………………………………………………………...... 20 Supplemental Data……………………………………………………………………………...32

iii

List of Tables Table 1. SCXRD Experimental Details from group 2………………….………………………..17 Table 2. Atomic positions, etc, for group 2……………………………………...………………18 Table 3. Selected mean bond lengths from group 2…………………………………….….…….18 Table 4. SCXRD Experimental Details from group 3…………………………….……….…….19 Table 5. Atomic positions, etc, for group 3…………………………………………….…..……20 Table 6. Selected mean bond lengths from group 3……………………………………….……..20

List of Figures

Figure 1. Geologic map of Mont Saint-Hilaire……………………………………………...…..21 Figure 2. Picture if the Poudrette pegmatite………………………………………………...…..22 Figure 3. XEDS spectrum of the Mont Saint-Hilaire fluorapatite………………………………23 Figure 4. SEM image of fluorapatite……………………………………………………………24 Figure 5. Mean EPMA analyses for all fluorapatites……………………………………………25 Figure 6. CIF of refined group 2 fluorapatite crystal structures…………………………...……26 Figure 7. CIF of refined group 3 fluorapatite crystal structures…………………………….…..27 Figure 8. ATR-FTIR spectrum of group 2 fluorapatite……………………………………...….28 Figure 9. ATR-FTIR spectrum of group 3 fluorapatite…………………………………...…….29 Figure 10. ATR-FTIR zoom of C-F signal region for group 2 fluorapatite……………………..30 Figure 11. ATR-FTIR zoom of C-F signal region for group 3 fluorapatite……………………..31 Figure 12. 19F MAS-NMR spectrum of group 3 fluorapatite……………………………….…...32

Dedication This body of work is dedicated to my wife Hillary and our two cats Halpert and Beesly who we adopted right as I was beginning this Master’s degree. Beesly unfortunately passed away quite suddenly, just days after the defending this thesis, but he will always hold a special place in our hearts.

Acknowledgments

This work would not have been possible without the mentoring of my adviser John Rakovan and his expertise in the field of apatite chemistry. The collection of the FTIR data by Andy Sommer in the Department of Chemistry at Miami University is greatly appreciated, as is the NMR data collection by Brian Phillips in the Department of Geoscience at Stony Brook University. Lázslo and Elsa Horváth originally provided the samples to be studied, and without them this entire project would not have begun.

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Introduction

Fluorapatite (Ca5(PO4)3F) is the most common phosphate mineral on Earth, and its accommodating crystal structure allows for nearly half the elements on the periodic table to substitute into one of 4 distinct sites (Hughes & Rakovan 2015). The M1 site is 9-fold coordinated and generally accommodates cations slightly larger than Ca, while the M2 site is 7-fold coordinated and generally incorporates cations slightly smaller than Ca, though this is not always the case (Fleet & Pan 1997). The tetrahedrally coordinated site, where P5+ sits in end member fluorapatite, can accommodate cations such as Si4+, C4+, , As5+, V5+, and S6+. And lastly the X site, or anion column site, is often occupied by more than one constituent with the most to least common being F, OH, Cl, and C.

Because of this flexible crystal structure and crystal chemistry, fluorapatite has been studied extensively for a variety of applications, including biomedical, environmental remediation, and multiple materials science applications (Rakovan & Pasteris 2015). Because of its ubiquity in rock forming environments, large stability field, and affinity for many trace elements including lanthanides and actinides, fluorapatite has long been used in geochronologic and petrogenetic studies (Piccoli & Candela 2002, Braund et al. 2017, Chakhmouradian et al. 2017). These same characteristics are reasons for interest in using apatite as a sequestration agent for heavy metals and as a solid nuclear waste form (Ewing & Wang 2002, Luo et al. 2011, Rigali et al. 2016, Li et al. 2017). Naturally occurring fluorapatite has been found with significant quantities of U and Th, up to 0.40wt %, and perhaps most notably Pu at the Oklo natural reactor in Gabon (Bros et al. 1996, Horie et al. 2004). Both studies concluded that fissiongenic LREE and nucleogenic Pu were selectively trapped in the fluorapatite grains while the reactor was at its peak and have remained in the crystal structure over the last ~2.0Ga years (Bros et al. 1996, Horie et al. 2004). The retention of these elements within the apatite grains is especially interesting when considering the dissolution of uraninite during this time span. Studies such as Rakovan and Hughes (2000), Rakovan et al. (2002), Luo et al. (2009), and Luo et al. (2011) have utilized single-crystal X-ray diffraction (SCXRD) and extended X-ray absorption fine structure (EXAFS) techniques to assess the site preference of fissiongenic elements such as U and Th in the apatite structure, and have yielded significant insight into the accommodation of these elements by the fluorapatite structure.

2- Substitution of the CO3 ion into apatite has also been of great interest and debate, mainly among those studying apatite for biomedical applications (Reigner et al. 1994, Fleet & Liu 2003, Fleet 2017). Because of the often-small size of natural and synthetic apatite crystals that are heavily 2- 2- substituted by the CO3 ion, samples which do contain significant CO3 content and have crystals of large enough size for single-crystal X-ray diffraction studies are of considerable interest to those studying this aspect of apatite crystal chemistry (Fleet 2014).

A suite of 12 apatite group minerals from the Poudrette Quarry in the Mont Saint-Hilaire igneous complex have been examined with electron probe microanalyses, single-crystal X-ray diffraction, Fourier transform infrared-spectroscopy, and magic-angle spinning nuclear magnetic resonance spectroscopy. From this suite, 3 different groups of samples displayed unusually high Na, Y, Th 2- and CO3 concentrations and are the focus of this study. While fluorapatite has received much attention related to its ability to sequester and retain many potentially harmful elements such as Pb, As, 90Sr, U, and Th, never have Th concentrations of this magnitude been observed and studied 2- in detail for natural fluorapatite, and the elevated concentrations of Na, Y, and CO3 bring

important crystal chemical complexities to be explored. While hundreds of minerals have been identified from Mont Saint-Hilaire, and several dozen new species described, no work has been undertaken involving a detailed examination of the more ubiquitous mineral fluorapatite. This study not only serves to further our understanding of the crystal chemistry of radionuclides in natural fluorapatite, but, may also provide insight into the complex geochemical processes occurring at Mont Saint-Hilaire.

Occurrence The unique and diverse mineralogy observed at the Poudrette Quarry in the Mont Saint-Hilaire igneous complex, Quebec, Canada, is only rivaled by localities such as Långban, Filipstad, Sweden, the Tsumeb Mine, Tsumeb, Namibia, or the Franklin and Sterling Hill Mines, NW, New Jersey. To date, over 400 distinct mineral species and 65 type minerals have been identified from this small quarry in southern Canada. Among these, fluorapatite is well known and is found in all lithologies except one (Horváth and Gault 1990). Igneous rocks comprising the pluton can be divided into three suites, known as the Sunrise, Pain de Sucre, and East Hill suites (Currie et al. 1986). The Sunrise suite exhibits well-defined igneous stratigraphy and is composed of medium-grained gabbroic rocks rich in clinopyroxene and calcic plagioclase but free of nepheline. While texturally like the Sunrise suite, the Pain de Sucre suite is characterized by nepheline and olivine bearing diorites and gabbros which intrude the Sunrise suite in the form of a thick ring dyke. The East Hill suite forming the eastern portion of the Mont Saint- Hilaire complex, is the youngest of the three suites, and contains gabbro and diorite autoliths of the Sunrise and Pain de Sucre groups. Volumetrically the East Hill group is dominantly composed of foid syenites, which can be further divided into i) fine-grained porphyritic foid syenites, ii) sodalite-rich foid syenites, iii) medium-grained foid syenites, and iv) coarse-grained foid syenites (Schilling et al. 2011). In the East Hill suite lies the Poudrette quarry, the most well-known locality in the Mont Saint- Hilaire complex that has produced most of the mineral diversity observed from the pluton (Fig. 1). The East Hill suite has been dated to ~122Ma by Currie et al. (1986) which is the youngest of the three major geologic groups. Within the Poudrette quarry lies the Poudrette pegmatite, the largest and most noteworthy pegmatite in Mont Saint-Hilaire. The Poudrette pegmatite has produced >170 distinct mineral species, 8 of which are new (McDonald et al. 2013). Three distinct zones comprise the pegmatite 1) a banded outer zone consisting of alternating hornfels and a fine-grained albite- rich component 2) a middle zone consisting of coarse grained microcline, eudialyte, nepheline, and pyroxene group minerals and 3) an inner zone which has undergone extensive hydrothermal alteration and contains various Fe-Mn and REE carbonates and zeolites (McDonald et al. 2013, Fig. 2). Notably, both LREE and Y+HREE carbonates have been described from this inner zone. Lastly, the Poudrette pegmatite is distinguished from all other pegmatites in the quarry by being hosted in a large hornfels xenolith. Fluorapatite samples from group 1 were collected from an unidentified pegmatite within the Poudrette quarry, group 2 samples came from the extensively altered core zone of the Poudrette pegmatite, and group 3 samples came from the banded outer zone of the Poudrette pegmatite. Within the outer zone of the Poudrette pegmatite fluorapatite is one of the more dominant minerals,

while in the core zone it is a less abundant mineral. Fluorapatite crystals from group 1 are approximately 150 μm x 50 μm x 50 μm, are colorless to a pale green in color, and number several hundred crystals covering a pebble 2 cm x 1 cm x 1 cm in size. Fluorapatite crystals from group 2 are approximately 70 μm x 40 μm x 25 μm in size, are colorless with no visible inclusions, and number several thousand crystals covering 4 different pebbles collected which are each approximately 2 cm x 1 cm x 1cm in size. Fluorapatite crystals from group 3 are hexagonal prisms approximately 250 μm x 80 μm x 80 μm in size, are colorless but often contain visible inclusions, and number in the several hundred covering a single pebble approximately 10 cm x 5 cm x 2 cm in size.

Analytical Methods Scanning Electron Microscopy (SEM) For this study, a Zeiss Supra 35 VP field emission scanning electron microscope was used. This SEM is equipped with an X-ray Energy Dispersive Bruker Espirit detector with a spectral resolution of 129eV and limit of detection for most elements of ~0.5 wt%. For X-ray Energy Dispersive Spectroscopy (XEDS) data collection, samples were analyzed under a 20kV voltage and samples were generally uncoated. An aperture of at least 60μm was used for XEDS collection and occasionally a 120μm aperture was used if particularly low counts were observed. Polished resin mounts of fluorapatite crystals were analyzed using backscatter electron detection (BSE). Samples were analyzed under a 20kV voltage with a 60μm aperture when in BSE mode. Uncoated samples were often analyzed under variable-pressure (VPSE) conditions to assess sub-micron scale details without generating excess charging on the samples.

Electron Probe Micro-Analysis (EPMA) To help mitigate halogen migration during analyses (Stormer et al. 1993) samples were prepared for EPMA by embedding crystals in resin such that their c-axes were parallel to the polished mount. This results in the electron beam striking perpendicular to c. All samples were oriented optically as the c-axis was elongate on all crystals examined. Crystals were then polished down with a 0.05 μm alumina paste and coated with ~10nm of amorphous carbon. Crystals from group 2 are too small to be mounted and polished in a resin without being completely polished away. Instead, clean crystals displaying well-defined prism faces were placed on a carbon sticky tab for EPMA. Analyses were performed on a Cameca SX-100 at the New Mexico Bureau of Geology and Mineral Resources Electron Microprobe Laboratory, equipped with 3 wavelength dispersive spectrometers. A 20nA beam current was used for measurement of Ca, Na, P, F, Cl, S, Si, Mn, and Fe, while a 200nA beam current was used for measurement of Sr, Y, La, Ce, Nd, Eu, Th, U, and Pb. The spot size was 10μm for all spots on the polished crystals and reduced to 5μm on the smaller unpolished crystals. Standards used were the Beeson apatite (Ca, Sr, P, F, Cl, S), kaersutite (Na, Mn, Fe, Si), monazite (U and Th), CePO4 (Ce), LaPO4 (La), NdPO4 (Nd), and YPO4 (Y). The data were reduced using a ZAF correction routine.

Single Crystal X-ray Diffraction (SCXRD) All single-crystal X-ray diffraction analyses were conducted on a Bruker D8 Quest single crystal X-ray diffractometer equipped with a PHOTON CMOS detector and MoKα radiation. Crystals were mounted on a Kapton loop with a small amount of paratone oil. Data were collected at ambient temperature (293K) and pressure (1atm). A full Ewald sphere of data to a resolution of 0.6 Å was collected for each crystal. A frame width of 0.2o was used for each scan, with 10 second exposures per frame, and resulted in the collection of ~7500 frames per crystal. The measured intensities were corrected for Lorentz polarization effects and absorption using the Bruker Apex3 package of programs.

Site occupancy refinements Because of the many elements detected in EPMA that substitute for Ca on the M sites, the program OccQP was utilized for accurate site occupancy refinements for use in the final single-crystal models. OccQP is a MATLAB based program which takes a quadratic programming approach to assigning correct site occupancies with minimal assumptions (Wright et al. 2000).

Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR) Samples were prepared in the same way as for the EPMA data collection but were left uncoated for FTIR data collection. Attenuated total internal reflection (ATR) images were collected with a Perkin-Elmer Spotlight 400 infrared microscope interfaced to a Perkin-Elmer Spectrum One Fourier transform infrared spectrometer (FTIR). The system employed a 16 X 1, liquid nitrogen cooled, mercury cadmium telluride (HgCdTe) array detector. Images were collected over an area of 400 X 400 micrometers using the ATR imaging accessory which was based on a germanium internal reflection element. Each spectrum in the image was collected using 8 cm-1 spectral resolution and represents the average of 4 individual scans. Spectra were collected every 6.25μm.

Solid State NMR. Solid-state magic angle spinning (MAS) NMR spectra were obtained on a Varian Infinity Plus 500 MHz (11.7 T) spectrometer operating at 470.179 MHz for 19F, using standard single-pulse (SP) techniques. 19F spectra were collected at a spinning rate of 15 kHz. A Varian-Chemagnetics T3- type HX probe configured for 4 mm rotors was used for all single-pulse experiments. Therotor 19 assembly consisted of ZrO2 sleeves and vespel tips and spacers. The F pulse width was 5 μs(π/2), and the relaxation delay was 600 s for full relaxation, determined by acquisition of fluorapatite spectra with relaxation delays between 5 and 800 s. After 600 s the signal intensity did not increase further, so these spectra are considered fully relaxed under these conditions. The number of transients varied between 4 and 148 owing to the varied concentration of fluorine. 19F chemical shifts were measured relative to CFCl3 (l) set to δF= 0 ppm. No signal was observed in background spectra for 19F collected using an empty 4 mm rotor.

Results SEM Data from XEDS first revealed a complex chemistry in all three groups of fluorapatite crystals, as noted by Figure 3. In addition to typical fluorapatite constituent’s multiple additional elements were noted. These included high concentrations of Na, and significant quantities Ce and La. The two peaks at 2.9 and 3.1 KeV situated between the Ca and P Kα emission lines correspond to two of the Th M fluorescence lines. BSE imaging revealed a complex concentric zoning pattern in the samples (Fig. 5 and 7). BSE examination did not show the presence of inclusions within the fluorapatite crystals. Uncoated single crystals mounted on carbon sticky tabs were also examined under VPSE imaging conditions to assess crystal habit. Many samples that appeared to be single crystals when examined with traditional light microscopy were shown to be aggregates of two or more slightly divergent crystals (Fig. 4).

EPMA Figure 5 shows the mean quantitative chemistry results from the EPMA analyses from the three distinct groups of samples. Consistent among all samples were the negligible concentrations observed for Cl, Si, and S. The elements Eu and U were initially analyzed for, but after multiple analyses showed these elements were below detection limit (bdl) they were excluded. Supplemental Figures 1-3 shows the analyzed spot on each crystal for each data point, and supplemental Tables 1-3 show the resulting analyses for each spot. For groups 2 and 3, totals significantly below 100% were observed and is the result of significant carbonate replacing phosphate in the structure, which is discussed further in the FTIR results section. Group 1

Mean values for all zones in all crystals from group 1 are ThO2 0.43 wt%, Y2O3 0.14 wt%, Na2O 1.75 wt%, CaO 49.76 wt%, P2O5 37.73 wt%, ƩLREE2O3 3.51 wt%, and F 3.85 wt%. Mean total values for all analyses is 97.98 wt%. From these analyses the following stoichiometric formula can be derived: Ca8.9 Na0.6 Th0.02 Y0.01 LREE0.2 (PO4)5.3 F2.04. Full results for all elements analyzed can be found in supplemental table 1. Group 2 Mean values for all zones in all crystals from group 2 are ThO2 2.29 wt%, Y2O3 5.08 wt%, Na2O 3.38 wt%, CaO 41.13 wt%, P2O5 35.08 wt%, ƩLREE2O3 3.57 wt%, and F 4.04 wt%. Mean total values for all analyses is 94.81 wt%. From these analyses the following stoichiometric formula can be derived: Ca7.78 Na1.16 Th0.09 Y0.48 LREE0.23 (PO4)5.25 F2.26. Full results for all elements analyzed can be found in supplemental table 2.

Group 3

Mean values for all zones in all crystals from group 3 are ThO2 0.67 wt%, Y2O3 4.85 wt%, Na2O 4.01 wt%, CaO 40.97 wt%, P2O5 33.90 wt%, ƩLREE2O3 3.51 wt%, and F 3.83 wt%. Mean total values for all analyses is 92.59 wt%. From these analyses the following

stoichiometric formula can be derived: Ca7.93 Na1.41 Th0.03 Y0.47 LREE0.23 (PO4)5.19 F2.20. Full results for all elements analyzed can be found in supplemental table 3.

SCXRD Crystal structures from groups 2 and 3 were solved and refined from SCXRD data to R1 values of 0.0238 and 0.0466 respectively where Fo>4σ(Fo) (table 1 and 4). The data from both groups were solved and refined in space groups P6/m, P, P63, P63/m, and P using the software SHELXT and SHELXL-2016 respectively (Sheldrick 2015a, Sheldrick 2015b). The best fit for both sets of data were solved and refined in the P space group. The P space group differs from the P63/m space group in that the four equivalent M1 sites per unit cell become two sets of two non-equivalent sites known as the M1 and M1’ sites, and the O3 site becomes the O3 and O4 sites. Additional aspects of the structure to note are the multiple OH- positions modeled in the anion column in addition to the main F- site, and the Ca2’ site modeled for the data from group 2 samples. For groups 2 and 3, tables 1 and 4 report SCXRD experimental details and cell parameters, tables 2 and 5 report the atomic positions, anisotropic thermal parameters, and site occupancy factors (sof), tables 3 and 6 report selected bond lengths, and Figures 6 and 7 display the crystallographic information files (CIFs) generated from the final SCXRD refinements. Final site occupancy refinements from OccQP are reported in supplementary Figure 9. SCXRD datasets collected on group 1 crystals did not provide suitable data for a crystal structure refinement due to the agglomeration like texture observed in Fig. 4, which prevented a suitable single crystal being isolated. A CIF containing observed and calculated structure factors has been deposited and is available from the Depository of Unpublished Data on the MAC website.

ATR-FTIR Figures 8 and 9 display the results of the ATR-FTIR spectra extracted from mapping conducted on the polished crystals from groups 2 and 3 respectively. These results confirm the presence of substantial carbonate replacing phosphate in the B-type substitution. The peak observed at 868 cm- 1 for groups 2 and 3 are attributable to the υ2 mode of the carbonate molecule, and peaks at 1412 and 1468 cm-1 for group 2, peaks at 1416 and 1460cm-1 are also signals from the carbonate molecule but correspond to the υ3 mode. Peaks at 960 in group 2 and 3 correspond to the υ1 mode of the phosphate tetrahedron, while peaks at 1000 and 1016 in groups 2 and 3 respectively correspond to the υ3 mode of the phosphate tetrahedron (Antonakos et al. 2007). In both group 2 and 3 a small but noticeable doublet is observed at ~1200 cm-1 and is within the known range of a C-F stretch. For group 2, peaks at 1182 and 1248cm-1 are contributions from the epoxy used to mount the crystals but are at distinctly different positions than the signals observed at 1192 and 1212cm-1, further evidence these signals originate from the sample itself and contain a C-F bond. Based on the presence of carbonate bending and stretching modes present in the FTIR spectra, the diminution of P content in the EPMA results with no other elements observed to replace P, and sof values significantly less than 1 for the P site in the SCXRD data, the carbonate values are estimated at 0.76 apfu for group 2, and 0.80 apfu for group 3, which translates to ~5.5 wt% for each group. This means in every 4 out of 5 unit cells, one phosphate molecule is completely replaced by a carbonate molecule.

MAS-NMR Figure 12 shows the results of 19F MAS-NMR for group 3 samples and confirms the presence of multiple F environments. The strongest signal at -103ppm corresponds to F in the anion column, while the signal at -88ppm corresponds to an F defect site first observed by Mason et al. 2009 and formerly described and defined by Yi et al. 2013. The last signal at -68ppm has not been observed in any previous study examining any apatite via NMR and thus not attributable to another known F site in the apatite structure. However, this signal is firmly within the range for F-C interactions for fluoropolymers. After this signal was observed, a blank was run to ensure no contamination from the rotor itself, but this signal was not observed, confirming the contribution from the sample.

Discussion A complete understanding of the site preference and structural distortions of all elements which can substitute into the fluorapatite crystal structure has direct implications for the multiple uses of apatite in Earth, Materials, and Environmental Sciences. These include the use of fluorapatite as a petrogenetic and geochronologic tool, a sequestration agent for heavy metals and radionuclides and as a solid nuclear waste form. To this end, the high concentrations of Th and Y observed in the current study allow for a detailed refinement of their site preferences and the accompanying structural distortions. Our EPMA results demonstrate that fluorapatite from the Poudrette pegmatite contains the highest known mean concentrations of Th and Y yet described for natural 2- calcium phosphate apatite samples (Fig. 5). The mean Na and CO3 concentrations are also on par with the highest previously observed concentrations in natural fluorapatite, with peak values of Na in group 3 samples of 6 wt% being notably higher than any previously reported values (Chakhamouradian & Medici 2006, Chakhamouradian et al. 2017). The SCXRD data clearly demonstrate an assignment of space group P for the fluorapatites and is the first identification of a natural fluorapatite present in a space group other than P63/m, while one study has noted a synthetic type-A carbonate hydroxylapatite in this space group (Fleet & Liu 2003). ATR-FTIR 3- and MAS-NMR both clearly show the presence of the CO3F molecule in the fluorapatite structure from groups 2 and 3 based on peaks in regions where contributions have only previously been seen in fluoropolymers, i.e. C-F bonding environments.

Sodium in the fluorapatite structure The site preference of Na in fluorapatite is well documented, and the assignment of Na dominantly to the M1 sites in the current study is consistent with these previous results (Ronsbo 1989, Hughes et al. 1991, Fleet & Pan 1995). Dissymmetrization from P63/m to P-3 is the result of the high Na concentrations observed in these samples. The local bonding environment of Na is sufficiently different from Ca that the M1 site becomes split to generate a new site to accommodate most of the Na, a feature which is also observed in Belovite group minerals (Rakovan & Hughes 2000). The OccQP site occupancy refinement shows that in group 2 most of the Na is situated at the M1’ site with still a significant amount at the M1 site. While refinements from group 3 showed an approximately even distribution of Na between the M1 and M1’ sites, and a small amount of Na in the M2 site. Assignment of Na to the M2 site, while plausible, is more likely the result of imperfectly observed data and thus a minor inconsistency between the SCXRD and EPMA data. Overall, Na site assignments and bonding environments are consistent with previous studies and

the local bonding environments of the M1 sites (Rakovan & Hughes 2000, Chakhamouradian et al. 2005).

Thorium in the fluorapatite structure The site preference of Th has received less attention, save for two studies by Luo et al. (2009) & (2011). From SCXRD and micro-EXAFS data they concluded Th has a distinct site preference for the M2 site in end-member fluorapatite, while Th partitions into both M1 and M2 sites in end- member chlorapatite and strontium-fluorapatite. In chlorapatite, Luo et al. (2009) asserted the partitioning of Th between the M1 and M2 sites is likely the result of the replacement of the volatile anion component i.e. F → Cl which notably alters the stereochemical environment of the M2 site and results in a lower selectivity of this site for Th. Compared to end-member fluorapatite, the polyhedral volumes of the M1 and M2 sites expand significantly in strontium fluorapatite, which also diminishes the selectively of the M2 site for Th in the structure. Studying natural fluorapatites with significant concentrations of both Th and Sr may help constrain the crystal chemical controls the latter has on the former.

The Mineville fluorapatite studied by Luo et al. (2011) was found to contain 0.20 wt% Th but only ~150 ppm Sr which are not significant enough to allow for an investigation into the site preferences Sr may influence on Th. However, the current study observes ~2 wt% Th and ~0.13 wt% Sr in group 2, and ~0.67 wt% Th and 0.40 wt% Sr in group 3. OccQP refinements from SCXRD data show Th and Sr are both solely situated at the M2 site. This result suggests Sr concentrations need to be significantly higher to force some of the Th into the M1 site as seen by Luo et al. (2009).

The significant Th concentrations suggested these fluorapatite crystals could be at least partially metamict since these are the highest natural Th concentrations observed in any natural calcium- phosphate apatite, and the age of the samples (~120Ma) would give sufficient time for this process to occur. However, the SCXRD results show this process to be completely absent in these samples, as high-precision SCXRD refinements were able to be performed on multiple single crystals (tables 1 and 4). These results confirm the recent work by Yi et al. (2017), who experimentally demonstrated the ability of the apatite structure to heal itself through α-particle induced annealing. In the current study, the introduction of a high energy α-particle would be the result of the decay process of Th, which, as demonstrated by Yi et al. (2017), can provide significant energy to promote the recovery process from the α-recoil.

The Th concentrations in group 2 were also present in significant enough quantities to generate a new Ca2’ site, 0.48Å away from the original Ca2 site. This site has only been previously observed in calcium-phosphate apatites with significant Cl concentrations where acceptable Ca-Cl bond distances can only be achieved by the splitting of this site (Kelly et al. 2016). However, the current samples contain no detectable Cl, and so this splitting of the Ca2 site must be from the notably high Th concentrations as this is the only new unique crystal chemical aspect associated with the M2 site. Residual electron density which would correspond to a Ca2’ site in the SCXRD refinement of group 3 was observed but unsuccessfully modeled, due to the lower Th concentrations in these samples.

Yttrium in the fluorapatite structure

Unlike the rest of the REEs observed in these fluorapatites, Y appears to display a marked site preference for the M1 and M1’ sites (Fig. 9). This result is significant as it can be extrapolated to the heavy REEs (HREEs), where Y is often grouped because of its similar ionic radius and geochemical behavior. Because concentrations of Y have never been observed on this scale in natural fluorapatite, our knowledge of the site preference of this group of elements comes from synthetic studies (Hughes et al. 1991, Fleet & Pan 1995). However, some of these studies specifically warn that their conclusions may not be applicable to natural systems, which generates the need to confirm these synthetic studies by a close examination of natural apatites with elevated levels of these HREEs+Y. The current study observes a mean concentration of 5 wt% of Y in groups 2 and 3, which represents an excellent opportunity for definitive site assignments for Y in fluorapatite.

Site occupancy factor (sof) values for the M1 and M1’ sites for group 2 & group 3 hover just below or above 1, while values for the M2 site for these groups are 1.19 & 1.09 respectively (tables 5 & 8). Thus, one may assume these sof values show that any elements in the current groups of fluorapatites which are heavier than Ca would partition into the M2 site, while the Na present is the only additional element at the M1 & M1’ sites. However, the concentrations of Na, Y, and Th bring this assignment into question. If this were truly the case, M1 & M1’ site sof values should be lower, and closer to 0.90, while M2 site sof values should be even higher and closer to 1.30 for group 2 and 1.20 for group 3.

These inconsistencies can be resolved by consideration of OccQP site occupancy refinement. This refinement shows that both Na & Y are split between the M1 & M1’ sites, with a small amount of Y assigned to the M2 site in group 2, and a small amount of Na assigned to the M2 site in group 3 (table 2 & 5). These discrepancies can be explained when considering how atoms are modeled in a SCXRD refinement. In the Bruker group of SCXRD programs, Apex3, atoms are modeled using neutral atom scattering factors, so the charge of the atom does not come into play when refining the structure. For Ca, the dominant atom at the M1 & M2 sites in end member fluorapatite and the atom used as the base for the model in the current refinement, this means the M1 & M2 sites are firstly modeled off a 20-electron site. Thus, if only Ca is present, a sof of 1 is given, since the model and the observed data match perfectly. If a lighter atom replaces Ca, a sof lower than 1 is given, and vice versa for an atom heavier than Ca.

When both Na & Y replace Ca at the same site, it can look like the site is still dominantly Ca when only looking at the sof values because Na as a neutral atom is modeled with 11 electrons, while Y as a neutral atom is modeled with 39 electrons, i.e. an atom that contains half as many electrons as Ca, and an atom that contains twice as many electrons as Ca. Furthermore, Na & Y are present in the current samples at nearly equal concentrations. This ultimately means the sof values observed for the M1 & M1’ sites, which are an average, effectively hide the true substitution of these additional elements. This specific case attests to the utility of the program OccQP in solving complex crystal structures in the mineral world.

Solid solution with belovite group minerals BSE images from group 3 display significant zoning within single crystals, and EPMA analyses show a significant variation in Na and Y between the zones (Supplemental Fig. 3 and Supplemental Table 3). Not only do concentrations of these elements vary significantly between zones, but

analyses from spots near the termination of each crystal, which correspond to the first analysis on each crystal, show especially high concentrations of these elements. For spot 1 on crystal 3 Na2O values were 6.28 wt% and Y2O3 values were 10.05 wt%, which make these analyses the highest recorded Na and Y concentrations observed in a calcium-phosphate apatite, and translate to 2.3 apfu for Na and 1.01 apfu for Y. Na values of this magnitude are often observed in the belovite group of minerals, which are a subgroup of the larger apatite supergroup and are defined by their trigonal symmetry and split M1 site which contain differing cations (Pasero et al. 2010). The comparison is drawn between the current samples and belovite group minerals because of the trigonal (P) symmetry, and split M1 site in the Mont Saint-Hilaire fluorapatites. While our SCXRD results are from an average over the entire crystal and not this smaller enriched zone, we speculate that if one of these zones were isolated and a structure be solved it would reveal a structure where one M1 site is dominated by Na, the other M1 site dominated by Y, and the M2 site still dominated by Ca. A structure such as this would merit a new mineral species in the belovite group, specifically being “belovite-Y” as this mineral has not yet been described (IMA master list).

3- Carbonate in the fluorapatite structure and evidence for the CO3F molecule The carbonate content of these fluorapatites is among the highest carbonate values observed in natural fluorapatite, with values estimated at 5.5 wt% based on calculated apfu from EPMA data, and refined sof values of the P site from SCXRD data. Carbonate content of this magnitude would result in the replacement of one phosphate group with one carbonate group in 4/5 unit cells. This would require significant substitution mechanisms to allow for this much carbonate to enter the 2- structure. Several authors have proposed the CO3 molecule is locally charge balanced by F atoms in the substitution mechanism: 2- - 3- CO3 + F = PO4 Quantitative evidence for this local charge balance by F was recently put forth by Yi et al. (2013), who demonstrated that a previously observed peak in 19F MAS-NMR spectra at -88ppm is attributable to an F-C interaction with an interatomic distance of 2.5 to 2.7 Å, but specifically stated that this does not correspond to sp3 hybridization of carbon orbitals i.e. a tetrahedral carbon species. Because we also observe this signal at -88ppm in our 19F MAS-NMR spectrum, this substitution mechanism must be a major substitution mechanism for carbonate substituted fluorapatites. This local replacement of O for a F would also explain the nearly stoichiometric, indeed “excess,” F observed in the EPMA data, even though there is significant OH present along the anion column with F, putting these samples nearly halfway between F and OH end-members in terms of their anion chemistry. With one carbonate molecule per unit cell, and an associated F atom with each molecule, this would significantly increase the F concentration per unit cell, as there are only two F’s per unit cell in end-member fluorapatite. However, with the substantial substitution of F by OH, the addition of one F per unit cell would bring this concentration back to what end-member fluorapatite should look like, at least chemically, while retaining the OH component observed in the SCXRD refinement. This result is one that should be seriously considered by future studies when analyzing carbonate rich fluorapatites, as EPMA analyses alone may be insufficient to accurately assess the anion chemistry of the apatites being examined.

We also observe a set of peaks at ~1200cm-1 in the FTIR spectra (Fig.10 and 11), along with a peak at -68ppm in the NMR spectra (Fig. 12) which are consistent with C-F stretches observed in other substances such as fluoropolymers and are not consistent with any other previously observed

signals for carbonated or non-carbonated apatites (Stuart 2004, Antonakos et al. 2007). These features in the FTIR and NMR data strongly suggest a coherent molecule, composed of a carbon in tetrahedral coordination with 3 Os and 1 F, is present within the current samples. The presence of a signal at -88ppm in the NMR spectrum also support this theory, since this signal has been established by Yi et al. (2013) to be the result of a fluoride defect, wherein a F replaces one O around the tetrahedral site. These data are the first where quantitative evidence has been presented for the existence of the C-F bond in fluorapatite. This result is most significant in how the carbonate molecule is known to be accommodated in the apatite structure and suggests a new mechanism by which C could be stored in the Earth’s mantle, particularly as apatite has been observed in lithospheric mantle material (O’Reilly & Griffin 2000).

Conclusions

2- Fluorapatite from the Poudrette pegmatite contains significant quantities of Th, Y, Na, and CO3 with the Th and Y values being the highest currently observed for natural fluorapatite. The crystal structure is shown to not undergo the process of metamictization, even with ~2 wt% Th present in the structure and an age of approximately 120Ma. This result is significant in the context of utilizing fluorapatite as a solid nuclear waste form and confirms the structure can withstand high concentrations of actinides over geologic timescales without becoming amorphous. Assignment of site preference for Y was achieved for the first time in natural samples, where Y resides dominantly at the M1 and M1’ sites. Because of its similarity in ionic radius and geochemical behavior to the remaining HREEs, a site preference of these elements for the M1 site can be assumed by proxy, and these results may be significant in understanding the partitioning behavior of all REEs in apatites. We also presented, for the first time, quantitative evidence which confirms 3- the existence of the CO3F molecule in the fluorapatite structure through FTIR, NMR, and EPMA data. Lastly, the space group assigned to these fluorapatites is the P space group, instead of the typical P63/m, and is the result of the high Na concentrations which caused a splitting of the M1 site into two non-equivalent sites. This accommodation of significant quantities of Th, Y, Na, and 2- CO3 into the fluorapatite crystal structure, and subsequent dissymmetrization, is a testament to the structurally robust and chemically diverse nature of the apatite framework.

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Tables:

Table 1: SCXRD Experimental Details from group 2.

Table 2: Atomic positions, anisotropic thermal parameters, and site occupancy factors for group 2.

Table 3: Selected mean bond lengths from group 2 FAp determined by SCXRD.

Table 4: SCXRD Experimental Details from group 3.

Table 5: Atomic positions, anisotropic thermal parameters, and site occupancy factors for group 3 fluorapatites.

Table 6: Selected mean bond lengths from group 3 determined by SCXRD.

Figures:

Figure 1: Geologic map adapted from Currie 1989, generated by David Maneli. The Poudrette pegmatite is located in the southern most corner of the quarry, where it cuts across a hornfels xenolith.

Figure 2: Poudrette pegmatite where 2 of the 3 groups of samples were collected. The blue ellipse denotes the inner zone, orange ellipse the middle zone, and green ellipse the extent of the outer banded zone. Photo courtesy of László and Elsa Horváth.

Figure 3: XEDS spectrum displaying the complex chemistry. Collected with a Zeiss Supra 35 VP at 20kV. Sample was uncoated.

Figure 4: SEM image exhibiting the agglomeration like texture often observed in fluorapatite crystals which appear to be “single” crystals when examined in the light microscope.

Figure 5: Mean EPMA analyses for each element and totals from each group. The atoms per formula unit (apfu) were then calculated based on 24 oxygens per unit cell and the method from Ketcham (2015) was used.

Figure 6: CIF generated from SCXRD refinement from group 2 fluorapatite. A) is looking directly down the c-axis of the structure, while B) is looking 45o inclined to the a & b-axes with the c-axis in the vertical. Color chart corresponding each atomic species is found on the right hand side of A).

Figure 7: CIF generated from SCXRD refinement from group 3 fluorapatite. A) is looking directly down the c-axis of the structure, while B) is looking 45o inclined to the a & b-axes with the c-axis in the vertical. Color chart corresponding to each atomic species is found on the right hand side of A).

Figure 8: ATR-FTIR spectrum of polished FAp crystal from group 2. Peaks at 1468 and 1412 are contributions from the v3 carbonate stretch, while 868 is the v2 carbonate stretch. Peaks at 100 and 960 are contributions from the v3 and v1 phosphate stretches respectively. The region outlined by the box is discussed further in figure 10.

Figure 9: ATR-FTIR spectrum of polished FAp crystal from group 3. Peaks at 1460 and 1416 are contributions from the v3 carbonate stretch, while the signal at 868 results from the v2 carbonate stretch. Peaks at 1016 and 960 are contributions from the v3 and v1 phosphate stretches respectively. The region outlined in the box is discussed further in figure 11.

Figure 10: A closer look at the region outlined in the box from Fig.8. Features at 1248 and 1182 cm-1 are from the resin the crystals were mounted in, while 1212cm-1 is not attributable to the resin, or another known feature in apatites, and is firmly within the region for a feature resulting from a C-F bond to occur.

Figure 11: A closer look at the region outlined in the box from Fig.9. The doublet at 1212 and 1192cm-1 is not attributable to the resin, or another known feature in apatites, and is firmly within the region for a feature resulting from a C-F bond to occur.

Figure 12: 19F MAS NMR spectrum collected on crystals from group 3. Peak F1 at -103ppm is the contribution from F sitting in the anion column site, F3 is the contribution from the fluoride- defect site described by Yi et al 2013, and the F4 site is the previously unobserved peak which demonstrates the presence of a C-F bond within the structure and is consistent with previous NMR studies who observe this bond in fluorinated polymers.

Supplemental figure 1: BSE images of group 1 polished FAp crystals. Spots analyzed are labeled on each crystal and correspond to supplemental table 1. A) Grain 1; B) Grain 2; C) Grain 3; D) Grain 4.

Supplemental figure 2: BSE images of crystals from group 2 FAp. Spots analyzed are labeled on each crystal and correspond to values in supplemental table 1. A) Grain 1; B) Grain 2; C) Grain 3; D) Grain 4; E) Grain 5; F) Grain 6.

Supplemental figure 3: BSE images of polished crystals from group 3 FAp samples. Spots analyzed are numbered on each crystal and correspond to values on supplemental table 3. A) Grain 1; B) Grain 2; C) Grain 3.

Supplemental figure 4: OccQP refinements for groups 2 and 3. Tables on the left give site occupancy refinements assuming the total occupancy sums to 1. Tables on the right give refinements relative to site populations based on stoichiometric values for each site, which is 2 for the M1 and M1’ sites and 6 for the M2 site.

Supplemental table 1: EPMA results from group 1, total of 16 spots collected on 4 different grains.

Supplemental table 2: EPMA results from group 2, total of 10 spots collected on 6 different grains.

Supplemental table 3: EPMA results from group 3, total of 13 spots collected on 3 different grains.