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Supplementary material for
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Speciation and Distribution of Copper in a Mining Soil Using Multiple
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Synchrotron-based Bulk and Microscopic Techniques
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Jianjun Yanga,b, Jin Liua, James J. Dynesc, Derek Peakd, Tom Regierc, Jian Wangc, Shenhai Zhu a, Jiyan
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Shia, 1, John S Tseb,1
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a.
Department of Environmental Engineering, Zhejiang University, Hangzhou, PR China, 310058
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b.
Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, Canada
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S7N 5E2
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c.
Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Canada S7N 0X4
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d.
Department of Soil Science, University of Saskatchewan, Saskatoon, Canada S7N 5A8
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1.
Corresponding authors.
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Jiyan Shi
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Tel: +86-571-88982019, Fax: +86-571-88982010, E-mail: shijiyan@zju.edu.cn, Post address: 866
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Yuhangtang Road, Hangzhou, Zhejiang, 310058, P. R. China
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John S Tse
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Tel: +1-306-966-6410, Fax: +1-306-966-6400, E-mail: john.tse@usask.ca, Post address: 116
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Science Building, Saskatoon, SK S7N 5E2 Canada
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1.
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Soil sample were freeze-dried and passed through the stainless steel sieve (<0.04 mm) for Cu K-edge
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bulk XANES and EXAFS measurements. Cu references of Cu(II) 3,5-diisopropylsalicylate hydrate,
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Cu(NO3)2, Cu3(PO4)2, CuSO4, Cu(OH)2, CuS, Cu2S, Cu2O, Cu and CuO were bought from Sigma
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Aldrich. Humic acid (HA) was purchased from International Humic Substances Society. Goethite was
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synthesized according to the same method described by Peak & Regier (2012). Goethite adsorbed Cu
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and humic acid adsorbed Cu were prepared following the procedures used by Strawn and Baker (2008).
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All the references and soil sample were sealed in a Teflon sample holder with Kapton tape for XANES
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and EXAFS measurements. Energy step was set to 0.3 eV at the Cu K-edge absorption near-edge
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region ranging from 8950 to 9040 eV.
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2.
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The beamline 15U in SSRF, used for μ-XRF and μ-XANES analysis, covered an electron energy
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ranging from ~5 to ~20 KeV. Soil aggregates of the mining soil (<0.04 mm) were embedded in
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Cryo-STATTM (McCormick Scientific, St.Louis MO) for cryosectioning and frozen at -20°C. Thin soil
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section was polished to ~60 µm thick using standard thin sectioning equipment and then attached on
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Kapton tape for μ-XRF measurements. The hot Spot 1, moderate Spot 2 and Sport 3 were selected to
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collect the Cu K-edge μ-XANES spectra which had an energy range from 8950 to 9060 eV with energy
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step of 0.5 eV. The dwell time for the μ-XANES measurements was set to 2 s.
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3.
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The SM beamline 10ID-1 of the CLS, used for STXM experiments, covered an electron energy ranging
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from ~130 to ~2500 eV. STXM was used analytically by acquiring XANES spectra recording images at
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a sequence of energies (i.e., stack) (Jacobsen et al., 2000; Dynes et al., 2006b). The raw transmitted
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signals were converted to optical densities (OD) using incident flux signals measured through the
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investigated regions without soil micro-aggregates. The OD (x, y, E) data cubes were converted to
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quantitative component maps by spectral fitting using singular value decomposition (SVD) procedures
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(Hunter et al., 2008). Threshold masking of the derived Cu, Fe, Al and Si component maps was then
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used to extract spectra from pixels that had similar spectral characteristics, which were subjected to
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spectral curve fitting. The distributions of Cu/Al/Si, Cu /Al /Fe (total) and Cu/Fe(III)/Fe(II) were
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presented as tricolor maps. Pixel brightness is displayed in RGB, with the brightest spots corresponding
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to the highest element signal. The microscope energy scale was regularly calibrated with secondary
Cu K-edge bulk XANES and EXAFS experiments
μ-XRF and Cu K-edge μ-XANES microanalysis
STXM nanoanalysis
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standards, typically sharp gas-phase signals. The absolute energy scales of Cu and Fe were set by
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assigning the energy of the first and second peak in the 2p3/2 signal of Cu and Fe to 931.2 eV and 709.8
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eV, respectively (Dynes et al., 2006a; Yang et al., 2011). Similarly, the corresponding second and first
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peak in the 1s signal of Al and Si were set to 1570.4 and 1846.8 eV, respectively (Wan et al., 2007).
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4.
Data processing
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The Cu K-edge bulk-XANES, μ-XANES and L-edge XANES spectra, except soil Cu Q-XANES
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spectra, were processed by the program Athena (8.050), while Cu K-edge bulk-EXAFS spectra were
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analyzed by Athena and Artemis (8.050) (Ravel and Newville, 2005). For EXAFS spectra, energy at Cu
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K-edge (E0) for each sample was first determined using the inflection point in the first derivative of the
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corresponding Cu K-edge XNAES spectra, and the spectra were normalized to unit step height using a
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linear pre-edge subtraction and quadratic polynomial as the post-edge line to conduct background
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subtraction. Then the spectra were transformed to k-space based on E0. The χ function were extracted
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from the raw data by subtracting the atomic background using a cubic-spline consisting of 7 knots set
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at equal distance fit to k3-weighted data of the mining soil and references. After that, the data were
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Fourier transformed (FT) to isolate individual frequencies in the χ (k3) spectra of mining soil with k
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range ~3.0 to 10 Å-1, without the correction for phase shift. Fitting of the EXAFS spectra of soil
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samples were processed by Artemis (8.050) integrated with FEFF6.0 code for the calculation of
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theoretical backscattering phase and amplitude functions for backscatterers using the structure mode in
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EXAFS fit for Cu(II) sorbed to Fe oxides recommended by Peacock et al.(2005)
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The Cu K-edge bulk-XANES spectra of the mining soil and references were derived from the
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corresponding EXAFS spectra with energy range from 8970 eV to 9040 eV. All the bulk-XANES
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spectra, together with Cu K-edge μ-XANES of the mining soil, were processed by Athena (8.050).
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These spectra of the mining soil and references were normalized to unit step height using a linear
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pre-edge subtraction and quadratic polynomial as the post-edge line to conduct background subtraction.
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The post-region for all XANES spectra was defined as the flat region of post-edge line between 920 to
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930 eV for soil bulk-XANES, μ-XANES and reference spectra except Cu whose normalization energy
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range was 9007.5 to 9012.5 eV. Linear combination fitting of soil bulk-XANES and μ-XANES spectra
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was conducted over the spectral region from 20 eV below E0 to 35 eV above E0 using all of the thirteen
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Cu reference spectra with E0 fixation. The goodness-of-fit was judged by the Chi-squared values and R
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values, and Cu standards yielding the best fit during LCF analysis were considered as the most possible
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Cu species in the investigated soil sample.
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For the Cu L3,2-edge XANES spectra, background corrected by a linear regression fit through the
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pre-edge region and normalized total L-edge intensity to one unit edge jump by defined the continuum
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region (1000 ~ 1010 eV) as the post-edge region (Yang et al., 2011). For the Q-XANES spectra of soil
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Cu, the I0 was first smoothed due to the relative high noise and the selected spectra of each scan were
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present as I1/I0. In order to compare the peak intensity of each scan, the selected soil Cu Q-XANES
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spectra were further subtracted by the intensity at 925.0 eV for pre-edge normalization. The absolute
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energy scales of Cu was set by assigning the energy of the first peak in the 2p3/2 signal of Cu to 931.2
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eV (Yang et al., 2011).
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5.
Other results
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Fig. S1 First derivative of the corresponding normalized Cu K-edge XANES spectra of the mining soil
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and references. Read line represents the Cu K-edge μ-XANES spectra of the mining soil; Peak α, β and
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β´ refer to the 1s to 4p electron transitions aligned with soil XANES peaks for reference, while Peak γ
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refers to the corresponding Peak 3 in the normalized Cu K-edge XANES spectra in Fig. 1a.
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a
b
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Fig. S2 The best linear combination fitting (LCF) results of Cu K-edge bulk-XANES (a) spectrum of
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the mining soil and µ-XANES spectrum (b) of the Cu hot spot 1.
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(a) Cu
(b) Si
2 µm
0.3
(c) Al
2 µm
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(d) Fe(III)
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(e) Fe(II)
2 µm
2 µm
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(f) Fe (total)
2 µm
2 µm
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0
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0
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Fig. S3 Elemental relative distribution maps within micro-aggregates of the mining soil determined by
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STXM at the nano scale.
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b
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d
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Fig. S4 Normalized Cu L3-edge (a) and Fe L3,2-edge (b), Al K-edge (c) and Si K-edge (d) XANES
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spectra of the references and the mining soil micro-aggregates analyzed by STXM.
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6.
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Dynes JJ, Lawrence JR, Korber DR et al (2006a). Quantitative mapping of chlorhexidine in natural
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