Quantitative structural determination of active sites from in situ and operando XANES spectra: From standard ab initio simulations to chemometric and machine learning approaches

Abstract Oxygen fugacity (fo2) exerts first-order control on the geochemical evolution of planetary interiors, and the Fe3+/ΣFe ratios of silicate glasses provide a useful proxy for fO2. Fe K-edge micro-X-ray absorption near-edge structure (XANES) spectroscopy allows researchers to micro-analytically determine the Fe3+/ΣFe ratios of silicate glasses with high precision. In this study we characterize hydrous and anhydrous basalt glass standards with Mössbauer and XANES spectroscopy and show that synchrotron radiation causes progressive changes to the XANES spectra of hydrous glasses as a function of radiation dose (here defined as total photons delivered per square micrometer), water concentration, and initial Fe3+/ΣFe ratio. We report experiments from eight different radiation dose conditions and show that Fe in hydrous silicate glasses can undergo rapid oxidation upon exposure to radiation. The rate and degree of oxidation correlates with radiation dose and the product of water concentration and ferrous/ferric iron oxide ratio on a molar basis (Φ = XHO0.5·XFeO/XFeO1.5). For example, a basalt glass with 4.9 wt% dissolved H2O and Fe3+/ΣFe = 0.19 from its Mössbauer spectrum may appear to have Fe3+/ΣFe ≥ 0.35 when analyzed over several minutes at a nominal flux density of ~2 × 109 photons/s/μm2. This radiation-induced increase in Fe3+/ΣFe ratio would lead to overestimation of fO2 by about two orders of magnitude, with dramatic consequences for the interpretation of geological processes. The sample area exposed to radiation shows measureable hydrogen loss, consistent with radiation-induced breaking of O–H bonds, associated H migration and loss, and oxidation of Fe2+. This mechanism is consistent with the observation that anhydrous glasses show no damage under any beam conditions. Cryogenic cooling does not mitigate, but rather accelerates, iron oxidation. The effects of beam damage appear to persist indefinitely. We detect beam damage at the lowest photon flux densities tested (3 × 106 photons/s/ μm2); however, at flux densities ≤6 × 107 photons/s/µm2, the hydrous glass calibration curve defined by the centroid (derived from XANES spectra) and Fe3+/SFe ratios (derived from Mössbauer spectra) is indistinguishable from the anhydrous calibration curve within the accuracy achievable with Mössbauer spectroscopy. Thus, published Fe3+/ΣFe ratios from hydrous glasses measured at low photon flux densities are likely to be accurate within measurement uncertainty with respect to what would have been measured by Mössbauer spectroscopy. These new results demonstrate that to obtain accurate Fe3+/ΣFe ratios from hydrous, mafic, silicate glasses, it is first necessary to carefully monitor changes in the XANES spectra as a function of incident dose (e.g., fixed-energy scan). Defocusing and attenuating the beam may prevent significant oxidation of Fe in mafic water-bearing glasses.

A Mössbauer-based XANES calibration for hydrous basalt glasses reveals radiation-induced oxidation of Fe

Calculating biotite formula from electron microprobe analysis data using a machine learning method based on principal components regression

Amphibole is the hydrous metasomatic phase in spinel-bearing mantle xenoliths from Baker Rocks, Northern Victoria Land, Antarctica. It occurs in veins or in disseminated form in spinel lherzolites. Both types derive from reaction between metasomatic melts and the pristine paragenesis of the continental lithospheric mantle beneath Northern Victoria Land. To determine the effective role of water circulation during the metasomatic process and amphibole formation, six amphibole samples were fully characterized. Accurate determination of the site population and the state of dehydrogenation in each of these amphiboles was carried out using single-crystal X-ray diffraction, electron microprobe and secondary ion mass spectroscopy on the same single crystal. The Fe3+/ΣFe ratio was determined by X-ray absorption near edge spectroscopy on amphibole powder. The degree of dehydrogenation determined by SIMS is 0.870–0.994 O3(O2−) a.p.f.u., primary and ascribed to the Ti-oxy component of the amphibole, as indicated by atom site populations; post-crystallization H loss is negligible. Estimates of aH2O (0.014–0.054) were determined from the dehydration equilibrium among end-member components assuming that amphiboles are in equilibrium with the anhydrous peridotitic phases. A difference up to 58 % in determination of aH2O can be introduced if the chemical formula of the amphiboles is calculated based on 23 O a.p.f.u. without knowing the effective amount of dehydrogenation. The oxygen fugacity of the Baker Rocks amphibole-bearing mantle xenoliths calculated based upon the dissociation constant of water (by oxy-amphibole equilibrium) is between −2.52 and −1.32 log units below the fayalite–magnetite–quartz (FMQ) buffer. These results are systematically lower and in a narrow range of values relative to those obtained from anhydrous olivine–orthopyroxene–spinel equilibria (fO2 between −1.98 and −0.30 log units). A comparative evaluation of the two methods suggests that when amphibole is present in mantle peridotites, the application of oxy-amphibole equilibrium is preferred, because ol–opx–sp oxy-calibrations are not “sensitive” enough in recording the effects (if any) of amphibole in the peridotite matrix. Amphibole acts as the main H acceptor among the peridotite minerals and may prevent fluid circulation and buffer oxygen fugacity. The important conclusion of this study is that amphibole within the lithospheric mantle does not always means high water activity and oxidizing conditions.

Crystal-chemistry of amphiboles: implications for oxygen fugacity and water activity in lithospheric mantle beneath Victoria Land, Antarctica.

Abstract In this work, we have studied the relationships between mass concentration and unit formula of amphibole using 114 carefully selected high-quality experimental data, obtained by electron microprobe (EMP) + single-crystal X-ray structure refinement (SREF) ± secondary-ion mass spectrometry (SIMS) analyses, of natural and synthetic Li-free monoclinic species belonging to the Ca and Na-Ca subgroups, and 75 Li-free and Mn-free C2/m end-members including oxo analogs of Ca amphiboles. Theoretical considerations and crystal-chemical driven regression analysis allowed us to obtain several equations that can be used to: (1) calculate from EMP analyses amphibole unit-formulas consistent with SREF±SIMS data, (2) discard unreliable EMP analyses, and (3) estimate WO2– and Fe3+ contents in Li-free C2/m amphiboles with relatively low Cl contents (≤1 wt%). The AMFORM approach mostly relies on the fact that while the cation mass in Cl-poor amphiboles increases with the content of heavy elements, its anion mass maintains a nearly constant value, i.e., 22O + 2(OH, F, O), resulting in a very well-defined polynomial correlation between the molecular mass and the cation mass per gram (R2 = 0.998). The precision of estimating the amphibole formula [e.g., TSi ± 0.02, CAl ± 0.02, A(Ca+Na+K) ± 0.04 apfu] is 2–4 times higher than when using methods published following the last IMA recommended scheme (2012). It is worth noting that most methods using IMA1997 recommendations (e.g., PROBE-AMPH) give errors that are about twice those of IMA2012-based methods. A linear relation between WO2– and the sum of C(Ti, Fe3+) and A(Na+K) contents, useful to estimate the iron oxidation state of highly oxidized amphiboles typical of post-magmatic processes, is also proposed. A step by step procedure (Appendix Deposit item AM-18-76385, supplemental Material. Deposit items are free to all readers and found on the MSA web site, via the specific issue’s Table of Contents (go to http://www.minsocam.org/MSA/AmMin/TOC/2018/Jul2018_data/Jul2018_data.html). 1) and a user-friendly spreadsheet (AMFORM.xlsx, provided as supplementary material Deposit item AM-18-76385, supplemental Material. Deposit items are free to all readers and found on the MSA web site, via the specific issue’s Table of Contents (go to http://www.minsocam.org/MSA/AmMin/TOC/2018/Jul2018_data/Jul2018_data.html). ) allowing one to calculate amphibole unit-formulas from EMP analyses are presented. This work opens new perspectives on the unit-formula calculation of other minerals containing OH and structural vacancies (e.g., micas).

AMFORM, a new mass-based model for the calculation of the unit formula of amphiboles from electron microprobe analyses

Microanalysis of Fe 3+ /∑Fe in geological samples using synchrotron-based X-ray absorption spectroscopy has become routine since the introduction of standards and model compounds. Existing calibrations commonly use least-squares linear combinations of pre-edge data from standard reference spectra with known coordination number and valence state acquired on powdered samples to avoid preferred orientation. However, application of these methods to single mineral grains is appropriate only for isometric minerals and limits their application to analysis of in situ grains in thin sections. In this work, a calibration suite developed by acquiring X-ray absorption near-edge spectroscopy (XANES) data from amphibole single crystals with the beam polarized along the major optical directions (X, Y, and Z) is employed. Seven different methods for predicting %Fe 3+ were employed based on (1) area-normalized pre-edge peak centroid, (2) the energy of the main absorption edge at the location where the normalized edge intensity has the highest R 2 correlation with Fe 3+ /∑Fe, (3) the ratio of spectral intensities at two energies determined by highest R 2 correlation with Fe 3+ /∑Fe, (4) use of the slope (first derivative) at every channel to select the best predictor channel, (5 and 6) partial least-squares models with variable and constant numbers of components, and (7) least absolute shrinkage and selection operator models. The latter three sophisticated multivariate analysis techniques for predicting Fe 3+ /∑Fe show significant improvements in accuracy over the former four types of univariate models. Fe 3+ /∑Fe can be measured in randomly oriented amphibole single crystals with an accuracy of ±5.5–6.2% absolute. Multivariate approaches demonstrate that for amphiboles main edge and EXAFS regions contain important features for predicting valence state. This suggests that in this mineral group, local structural changes accommodating site occupancy by Fe 3+ vs. Fe 2+ have a pronounced (and diagnostic) effect on the XAS spectra that can be reliably used to precisely constrain Fe 3+ /∑Fe.

Elizabeth B. Brown

Papers

Use of multivariate analysis for synchrotron micro-XANES analysis of iron valence state in amphiboles