John Rakovan

Nomenclature of the apatite supergroup minerals

The apatite supergroup includes minerals with a generic chemical formula IX M12 VII M23( IV TO4)3 X( Z ¼ 2); chemically they can be phosphates, arsenates, vanadates, silicates, and sulphates. The maximum space group symmetry is P63/m, but several members of the supergroup have a lower symmetry due to cation ordering and deviations from the ideal topology, which may result in an increase of the number of the independent sites. The apatite supergroup can be formally divided into five groups, based on crystal-chemical arguments: apatite group, hedyphane group, belovite group, britholite group, and ellestadite group. The abundance of distinct ions which may be hosted at the key-sites (M ¼ Ca 2þ , Pb 2þ , Ba 2þ , Sr 2þ , Mn 2þ , Na þ , Ce 3þ , La 3þ ,Y 3þ , Bi 3þ ;T ¼ P 5þ , As 5þ ,V 5þ , Si 4þ ,S 6þ ,B 3þ ;X ¼ F � , (OH) � , Cl � ) result in a large number of compositions which may have the status of distinct mineral species. Naming of apatite supergroup minerals in the past has resulted in nomenclature inconsistencies and problems. Therefore, an ad hoc IMA-CNMNC Subcommittee was established with the aim of rationalizing the nomenclature within the apatite supergroup and making some order among existing and potentially new mineral species. In addition to general recommendations for the handling of chemical (EPMA) data and for the allocation of ions within the various sites, the main recommendations of this subcommittee are the following: 1. Nomenclature changes to existing minerals. The use of adjectival prefixes for anions is to be preferred instead of modified Levinson suffixes; accordingly, six minerals should be renamed as follows: apatite-(CaF) to fluorapatite, apatite-(CaOH) to hydroxylapatite, apatite-(CaCl) to chlorapatite, ellestadite-(F) to fluorellestadite, ellestadite-(OH) to hydroxylellestadite, phospho- hedyphane-(F) to fluorphosphohedyphane. For the apatite group species these changes return the names that have been used in thousands of scientific paper, treatises and museum catalogues over the last 150 years. The new mineral IMA 2008-009, approved without a name, is here named stronadelphite. Apatite-(SrOH) is renamed fluorstrophite. Deloneite-(Ce) is renamed deloneite. The new mineral IMA 2009-005 is approved with the name fluorbritholite-(Y).

Aspects of goethite surface microtopography, structure, chemistry, and reactivity

Abstract Expanding upon our previous studies of the properties of Au complexes, we present calculations for several Hg2+ species in aqueous solution and for molecular models for cinnabar. Hydration effects are treated with a combination of “supermolecule” calculations containing several explicit water molecules and polarizable continuum calculations. We focus upon the following problems: (1) calculation of the stabilities of HgL2, L = F-, Cl-, OH-, SH-, and CN- and HgCl2-nn n = 1-4; (2) development of a molecular model for cinnabar of the form Hg3S2(SH)2; and (3) dissolution or adsorption reactions using this cinnabar model. The absolute and relative formation enthalpies of the HgL2 species can be satisfactorily reproduced at the Hartree-Fock plus Moller-Plesset second order correlation correction level using relativistic effective core potential basis sets if the hydration of neutral HgL2 is explicitly taken into account. Evaluating the energetics for the series of complexes HgCl2-nn is more difficult, because great accuracy is needed in the large hydration energies and some of the species are highly nonspherical. The Hg3S2(SH)2 species shows an equilibrium structure very much like that in cinnabar. The relative energetics for dissolution of cinnabar by H2O, H2S, SH-, and SH-+ elemental S are correctly reproduced using this model molecule. Calculations on Hg3S2ClI provide a model for understanding the adsorption of I- ions on cinnabar surfaces in the presence of Cl-.

Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES

Abstract Eu L3 X-ray absorption near edge structure (XANES) spectroscopy was conducted with a wavelength dispersive (WDS) spectrometer to determine the valence state of europium in a natural, Mn-and REE-rich apatite from Llallagua, Bolivia. Europium exists in both the divalent and trivalent states in the Llallagua apatite with a Eu2+/Eu3+ ratio between 0.12 and 0.22. With the enhanced energy resolution of WDS the EuLα1 fluorescence line can be resolved from the MnKα line, allowing for significant reduction of background in the EuL3 absorption edge region and resolution of the Eu XAS, which is difficult by conventional methods because of fluorescence peak interference. The anomalous partitioning behavior of Eu in these samples (Rakovan and Reeder 1996) can be explained by the observed presence of Eu2+ and Eu3+ and is consistent with the suggested size effect on intrasectoral zoning of REEs in apatite.

The crystal chemistry of whitlockite and merrillite and the dehydrogenation of whitlockite to merrillite

Abstract The atomic arrangements of two natural samples of whitlockite, a synthetic whitlockite specimen, a synthetic whitlockite specimen heated at 500 °C, and a synthetic merrillite specimen (formed through dehydrogenation of synthetic whitlockite by heating at 1050 °C for 24 h) have been determined in space group R3c by X-ray diffraction methods; the high-quality structure refinements yielded R < 0.019. Whitlockite, ideally Ca18Mg2(PO4)12[PO3(OH)]2 and merrillite, ideally Ca18Na2Mg2(PO4)14, are similar phases that differ by the lack of hydrogen and the concomitant addition of charge-balancing sodium (or calcium) in merrillite. The atomic arrangements of whitlockite and merrillite contain a structural unit consisting of a [(Mg,Fe)(PO4)6]216- complex anion that forms a “bracelet-and-pinwheel” arrangement. The central octahedral cation and the six coordinating phosphate tetrahedra form a pinwheel, and in whitlockite and merrillite the pinwheels are not polymerized; the structural units are linked by interstitial complexes. In unsubstituted merrillite (assuming no Na or REE substituents for Ca), the interstitial complex has a formula of [Ca19(PO4)2]32+, and in whitlockite, the terrestrial phase in which hydrogen is accommodated, the interstitial unit has the formula [Ca18(PO3[OH])2]32+, yielding the charge-balancing relationship [H(whit) ↔ Ca0.5(merr)]2. Whitlockite and merrillite are perhaps the only phases that form a solid solution with terrestrial and extra-terrestrial end-members that differ by structural adjustments that result from the accommodation of hydrogen in the terrestrial phase. The results of the study also suggest that in terrestrial samples of whitlockite, a merrillite component of the solid solution is common, but that extraterrestrial samples of merrillite are devoid of any whitlockite component.

A Concise Approach to the Synthesis of opp-Dibenzoporphyrins through the Heck Reaction

A concise approach to the synthesis of functionalized opp-dibenzoporphyrins is described. In this method, introduction of alkenyl groups to the porphyrin periphery through the vicinal 2-fold Heck reaction, 6-pi electrocyclization, and subsequent aromatization occur in one pot.

MICROSCOPY STUDIES OF THE PALYGORSKITE-TO-SMECTITE TRANSFORMATION

The transformation process between palygorskite and smectite was studied by examining the morphological and structural relationships between these two minerals in an assemblage from the Meigs Member of the Hawthorne Formation, southern Georgia. Studied samples were related to an alteration horizon with a tan clay unit above and a blue clay unit below. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) were used to study the mechanism of transformation.From AFM data, both clay units contain euhedral palygorskite fibers. Many fibers are found as parallel intergrowths joined along the [010] direction to form ‘raft-like’ bundles. Degraded fibers, which are common in the tan clay, have a distinctly segmented morphology, suggesting a dissolution texture. Many of the altered palygorskite fibers in the tan clay exhibit an oriented overgrowth of another mineral phase, presumably smectite, displaying a platy morphology. This latter mineral forms along the length of the palygorskite crystals with an interface parallel to {010} of the palygorskite. The resulting grain structures have an elongate ‘wing-like’ morphology.Imaging by TEM of tan clay material shows smectite lattice-fringe lines intergrown with 2:1 layer ribbon modules (polysomes) of the palygorskite. These features indicate an epitaxial overgrowth of smectite on palygorskite and illustrate the structural relationship between platy overgrowths on fibers observed in AFM data. The epitaxial relationship is described as {010} [001] palygorskite ‖ {010} [001] smectite.Energy dispersive spectroscopy indicates that the smectite is ferrian montmorillonite. Polysomes of palygorskite fibers involved in these textures commonly vary and polysome widths are consistent with double tetrahedral chains (10.4 Å), triple tetrahedral chains (14.8 Å), quadruple tetrahedral chains (21.7 Å) and quintuple tetrahedral chains (24.5 Å).The transformation of palygorskite to smectite and the resulting intergrowths will cause variations in bulk physical properties of palygorskite-rich clays. The observation of this transformation in natural samples suggests that this transformation mechanism may be responsible for the lower abundance of palygorskite in Mesozoic and older sediments.

Site preference of U and Th in Cl, F, and Sr apatites

Abstract Crystals of U- and Th-doped fluor-, chlor-, and strontium-apatite have been synthesized from phosphate-halide-rich melts, and their structures were refined at room temperature with single-crystal X-ray diffraction intensities to R = 0.0167-0.0255. Structure refinements of U-doped fluorapatites indicate that U substitutes almost exclusively into the Ca2 site with site occupancy ratios UCa2/UCa1 that range from 5.00 to 9.33. Similarly, structure refinements of Th-doped fluorapatites indicate that Th substitutes dominantly into the Ca2 site with ThCa2/ThCa1 values that range from 4.33 to 8.67. Structure refinements of U-doped chlorapatites show that U is essentially equally distributed between the two Ca sites with UCa2/UCa1 values that range from 0.89 to 1.17. Results for Th-doped chlorapatites show that Th substitutes into both Ca1 and Ca2 sites with ThCa2/ThCa1 values that range from 0.61 to 0.67. In the Th-doped strontium-apatites with F and Cl end-members, Th is incorporated into both the Ca1 and Ca2 sites. The range of ThCa2/ThCa1 values is 0.56 to 1.00 for the F end-member, and 0.39 to 0.94 for the Cl end-member. XANES measurements of the U-doped samples indicate that U in fluorapatite is tetravalent, whereas in chlorapatite it is heterovalent but dominantly hexavalent. According to our calculation, the volume of the Ca2 polyhedron increases by about 5.8% from fluorapatite to chlorapatite, but that of Ca1 polyhedron increases by only 0.59%. We speculate that the much greater size of the Ca2 polyhedron in chlorapatite may diminish the selectivity of this position for U and Th. The incorporation of U and Th into fluorapatite results in a decrease in the size of both Ca polyhedra, but the incorporation of U and Th into chlorapatite results in an increase in the volume of both Ca polyhedra. We suggest that the preference of U and Th for both Ca sites in chlorapatite is attributable to the large increase in size and distortion of the Ca2 polyhedron upon substitution of Cl for F.

A MICROTEXTURE STUDY OF PALYGORSKITE-RICH SEDIMENTS FROM THE HAWTHORNE FORMATION, SOUTHERN GEORGIA, BY TRANSMISSION ELECTRON MICROSCOPY AND ATOMIC FORCE MICROSCOPY

A microtexture analysis by TEM and AFM of palygorskite deposits from the Hawthorne Formation, southern Georgia is given. Palygorskite is the dominant mineral comprising an average of 65–70% of the sample volume with smaller volumes of smectite, illite and kaolinite. Morphologic observations indicate that the palygorskite formed in an unconfined environment, such as in the water column or in open-pore space. Some palygorskite textures appear to be secondary growths filling voids. An unusual texture is observed where smectite or illite-smectite (Reichweite, R = 0) form epitaxially on detrital illite and kaolinite particles. Oxides of Fe and Ti are common, and authigenic cassiterite is present but rare. Apatite is a common trace mineral in these sediments and occurs in a variety of textures. Apatite occurs as clusters which are believed to be small fecal pellets. These clusters have been partially dissolved and recrystallized and the crystals in the clusters are 50–100 µm in diameter. Other apatite crystals occur either as single crystals or in clusters that are not associated with fecal pellets.The textural data of this study suggest that there was an evolving and complex mineralogical and geochemical system during and after deposition of the palygorskite deposits in the Hawthorne. The epitaxial overgrowths of smectite on detrital illite and kaolinite particles indicate an intermittent stratified water column occurring in the system. Freshwater was introduced into the system from the northeast of the Apalachicola embayment and overrode more saline water in the southwest portion of the embayment. The results of this study are consistent with previous environmental interpretations and provide additional details.

Multiple length scale growth spirals on metamorphic graphite {001} surfaces studied by atomic force microscopy

Abstract The microtopography of {001} surfaces on single crystals of graphite from a Neoproterozoic marble of the Swakop group, near Wlotzkas Baken, western Namibia, has been studied using differential interference contrast (DIC) microscopy and atomic force microscopy (AFM). A unique aspect of the observed surface microtopography is the presence of growth spirals and hillocks on three different length scales. The largest spirals are polygonized and can be seen without magnification. Steps on this feature are roughly 4 μm high and 90 μm apart. The second-order features are hexagonal growth hillocks with an average step height of 1.5 nm and total lateral dimensions of 5-40 μm. The apex of these hillocks coincides directly with the apex of reentrants in the macrosteps of the large spiral. Morphology suggests the formation of these polygonized hillocks by some mechanism other than simple spiral growth. We speculate that these features may be due to pinning of the macrostep by impurities and subsequent formation of the second-order hillocks. The third length-scale features are spirals found on terraces forming the vicinal faces of the second-order hillocks. These spirals have steps that are 6.7 Å high (unit-cell length along [001]) and an average step spacing of 900 Å. These double-layer steps also show some regions with partial step separation into 3.3 Å high monolayer steps. The observed microtopographic features give us insight into the conditions in, and mechanisms by which these graphite crystals formed during carbonate metamorphism. Crystal growth, unrestricted by the surrounding calcite, was from a fluid phase at low graphite supersaturation and was dominated by the spiral growth mechanism. Comparison with theoretical and simulation studies suggests a critical radius for two-dimensional nucleation on the (001) surface on the order of 100 Å.

Time-resolved in situ studies of apatite formation in aqueous solutions

Abstract Formation of hydroxylapatite through the precipitation and evolution of calcium phosphate precursor phases under varying conditions of temperature (25-90 °C), pH (6.5-9.0), and calcium to phosphorus ratio (1.0, 1.33, 1.5, and 1.67) comparable to those found in many sediments and soils were studied. The products of low-temperature precipitation were analyzed by ex situ X-ray diffraction and SEM, as well as time-resolved in situ synchrotron X-ray diffraction. Rietveld refinement was used for quantitative evaluation of relative abundances during phase evolution. The results of ex situ investigations conducted at ambient temperature and near-neutral pH indicate formation of amorphous calcium phosphate, which over the course of experiments transforms to brushite and ultimately hydroxylapatite. The results of in situ X-ray diffraction experiments suggest a more complex pathway of phase development under the same conditions. Some of the initially formed amorphous calcium phosphate and/or crystalline brushite transformed to octacalcium phosphate. In the later stage of the reactions, octacalcium phosphate transforms quite rapidly to hydroxylapatite. This is accompanied or followed by the transformation of the remaining brushite to monetite. Hydroxylapatite and monetite coexist in the sample throughout the remainder of the experiments. In contrast to the near-neutral pH experiments, the results from ex situ and in situ diffraction investigations performed at higher pH yield similar results. The precipitate formed in the initial stages in both types of experiments was identified as amorphous calcium phosphate, which over the course of the reaction quite rapidly transformed to hydroxylapatite without any apparent intermediate phases. This is the first application of time-resolved in situ synchrotron X-ray diffraction to precipitation reactions in the Ca(OH)2-H3PO4-H2O system. The results indicate that precursors are likely to occur during the natural or induced (e.g., with application of Ca+PO4 amendments) formation of hydroxylapatite in many sedimentary environments.