Supplemental information for “Analysis of Fe K-edge XAFS spectra of phyllosilicates of varying
crystallinity”
Leslie L. Baker and Daniel G. Strawn, Department of Soil and Land Resources, University of Idaho,
Moscow, ID 83844-2339; lbaker@uidaho.edu
Purification of Garfield nontronite sample
The nontronite was purified by size fractionation, as follows. Granules of clay were hand-picked
and hand-crushed in an agate mortar. This material was Na-saturated, washed in DI water, and
centrifuged to separate the <1-µm size fraction. The very fine clay fraction was further refined by
resuspending and centrifuging the <1-µm size fraction at 10,800 x g for 1 hour at 5°C. The supernatant
contained a very fine clay gel with pure nontronite particles approximately less than 0.05 µm in
diameter. This supernatant was decanted and freeze-dried, leaving flakes of pale green material. X-ray
diffractometry (XRD) and Fourier-transform infrared spectroscopy (FTIR) confirmed that the clay was
pure nontronite.
Detailed fitting methods
Initially, the Garfield nontronite spectrum was modeled out to 6 Å from the core Fe atom using
92 single and multiple scattering EXAFS paths that had contributions to the EXAFS spectra > 6%.
Nontronite crystal structure data for the Feff input file were taken from Manceau et al. (1998).
Amplitude reduction factor was set to 0.85 (O'Day et al. 1994), which was verified by fitting 6 O
backscatterers to the first peak in the windowed Fourier transform of the experimental Garfield
nontronite EXAFS spectrum. Multiple scattering was evaluated for up to 4 successive legs. Debye-Waller
parameters for the Fe-O1, Fe-Fe1, and Fe-Si1 (Figure 1a) were initially optimized, and found to be near
0.005 Å2, which they were fixed at for the simulation. Debye-Waller factors for all other single and
multiple scattering shells were constrained to be equal and fit; although this does not represent a
structural reality, in fitting it is reasonable to include such a constraint to minimize degrees of freedom.
This approach produced a global Debye-Waller value of 0.0089 Å2 for the single- and multiple-scattering
shells at distances greater than 3.4 Å, which is in agreement with values reported in other fitting papers
(Manceau et al. 1998; O'Day et al. 1994; Vantelon et al. 2003). The theoretical nontronite EXAFS
structure (i.e., no fitting) was in close agreement with experimental, as also observed by Manceau et al.
(1998). However, there was a slight mismatch of the Fe-Fe1 shell distance features in the EXAFS
spectrum. Thus, fitting of the Fe-O1, Fe-Fe1, and Fe-Si1 single-scattering shell bond distances was done
to refine the 92-shell optimization. Except for Fe-Fe1, the fit single-scattering path distances were in
very good agreement with the theoretical distances (additional details are provided in results). Analysis
of multiple scattering below 3.4 Å in the Fourier transform showed that contributions are small, which is
in agreement with the findings of Manceau et al. (1998) and Vantelon et al. (2003).
Unlike the nontronite, the simulated 88-shell full-scattering spectrum of Fe-substituted
montmorillonite did not agree well with the experimental EXAFS data. However, fitting of the singlescattering bond distances in the 88-shell model resulted in a model that was in good agreement with the
experimental EXAFS spectrum, and was in good general agreement with Fe positions in the
montmorillonite structure as proposed by Vantelon et al. (2003). A 6-shell model with only single
scattering contributions was used to fit the montmorillonite EXAFS spectral features out to ~3.4 Å in the
Fourier transform magnitude data. The montmorillonite 6-shell model paths were analogous to the 5shell model used for Garfield nontronite, plus an octahedral Fe-Al1 backscattering path (Table 1).
SBId-1 beidellite was fit using the 6-shell montmorillonite model. Coordination number and
Debye-Waller factor were fixed in the fitting of the clay spectra to values similar to those of the SWy-2
montmorillonite full shell fit. In a few instances Debye-Waller factors were optimized (Table 2) after the
initial coordination number fit to account for a small amount of amplitude fit residual. However,
because coordination number and Debye-Waller factor are directly correlated, simultaneously varying
both parameters makes interpretation more uncertain. Fe-Fe1 and Fe-Al1 coordination numbers were
constrained to sum to three. Path lengths were optimized for all shells. However, to stabilize the fit
optimization, in some cases the Fe-O2 and Fe-O3 path lengths were constrained after an initial fit.
Results
Simplifying the full nontronite fitting model to a 5-shell or 6-shell model
Fitting phyllosilicate EXAFS data beyond 3-4 Å in R-space is difficult without additional
information, such as polarized EXAFS, because of the closeness of Si and O scattering atoms in the
structure (Manceau et al. 1998). This range includes second shell Fe-Me1 (where Me1 is an Fe, Al, or Mg
atom) and Fe-Si1 shells. Windowing this range in exclusion of the Fe-O2 and O3 shells (Table 1), which
occur at 3.4-3.8 Å in the structure, is difficult because of the overlap of the peaks in the FT (Figure 3b).
Vantelon et al. (2003) showed that fitting of Fe EXAFS data on smectites in the range 1-3.4 Å in FT is
reliable for interpreting local molecular structure. Manceau et al. (1998) showed that MS in the
nontronite model has a small contribution. Vantelon et al. (2003) also showed that for a C2 smectite
model (cis-vacant) theoretical MS paths have minimal contributions, and thus can be ignored. Our
modeling confirmed that contributions by MS to the EXAFS are relatively small, and benefits of including
them, particularly on poorly crystalline structures such as allophane, are negated by over
parameterization of the fit. Thus, based on the minimal contributions of MS and the limitations of
fitting, using a single-scattering model to fit Fe-substituted aluminosilicate EXAFS data is a feasible
approach.
Ignoring the MS shells and analyzing only the region of the FT between 1 and 3.5 Å (the region
of the two major peaks) reduces the number of possible shells to 9 (see Table 1 and Figure 1 for
theoretical paths). However, the first three O-scattering paths (Fe-O1) are similar, as are the last three
O-scattering paths (Fe-O3) that occur between 3.74-3.82 Å in the structure. Thus the number of
theoretical paths needed for fitting the two main peaks in the FT of nontronite reduces to 5. If Al were
present in the octahedral sites, then the number of paths is 6. Figure 4 and Table 2 show the best fit
results of the Garfield nontronite EXAFS spectrum using the 5-shell model. The 5-shell model fit the data
very well, and resulting fit distances (Table 2) are the same as the 92-shell model.
Montmorillonite fitting using the full 88-shell model
Unlike the simulation of the nontronite model, the Feff multi-shell simulation of Fe-substituted
montmorillonite using all shells > 6% (88 shells) is dissimilar to the EXAFS spectrum of the SWy-2
montmorillonite sample. The discrepancy in the Feff model of montmorillonite may arise because the
unit cell structure used to generate the atomic coordinates for the Feff input model does not account
for short-range structural distortion caused by isomorphic substitution. Since Fe is a larger atom than Al
(0.785 Å vs. 0.675 Å), an Fe-centered octahedral site should be larger than an Al-centered site, and thus
have longer interatomic bond distances. To account for expansion of the structure to accommodate the
Fe, fitting of the multi-shell Feff model was done.
Allophane nanoball model
In the proposed proto-imogolite structure, the nanomineral is constructed of a rolled octahedral
sheet with unpolymerized Si coordinated to the interior of the sphere. Each Si atom is coordinated to
three Al atoms via Al-O-Si bonds, and the fourth O atom (hydroxyl) (Figure 1b) points towards the center
of the sphere. Many of the backscattering shells around the octahedral atom in this model are similar to
those in a clay mineral; i.e., the octahedral cation is surrounded by six oxygen atoms in ordinary
octahedral configuration, and three neighboring octahedral cations are present at distances comparable
to those in montmorillonite (Table 2). The most significant difference in the theoretical allophane
structure is the distance of the Si atom; three Si atoms are present at a modeled reffective distance of 3.143.16 Å, rather than the four Si atoms at 3.18 to 3.24 Å found in 2:1 phyllosilicates (Figure 1, Table 1). In
addition, because there is no Si polymerization in the proto-imogolite model, no tetrahedral O2 atoms
are present. Thus the second backscattering O shell in this structure consists of six octahedral O atoms
corresponding to the O3 atoms in the nontronite structure (also labeled O3 in Figure 1b), and three
backscattering Oi atoms at 3.98 Å from the central Fe atom (the hydroxyl on the Si-OH apices pointing
toward the interior of the nanosphere). Additional differences between the models occur at greater
distances.
Wavelet analysis
Wavelet analysis can be used to extract additional information from XAFS spectra that may be of
use in interpreting the data. In particular, it is useful for discriminating between different backscattering
atoms at similar distances (Funke et al. 2005). Here, we used wavelet analysis to help discriminate the
contributions of close Fe and Al backscattering shells in the hisingerite and allophane spectra.
Morlet wavelet analysis was carried out on spectra using the FORTRAN program HAMA (Funke
et al. 2005) using a kappa value of 6 (to examine the Fe-Fe1 backscattering peak near 3 Å) and a sigma
value of 1. To enhance the signal from more distant backscatterers, the analysis was carried out on k3weighted chi spectra. To examine the effect of varying Fe content on an otherwise unchanging
structure, several synthetic spectra were generated using the Feff 92-shell model for the Garfield
nontronite structure. Parameters for generating these model spectra were taken from Manceau et al.
(1998) (amp = 0.85; DW = 0.0047 for Fe-O1 and Fe-Me1, 0.0055 for Fe-Si1, 0.01 for all additional SS
shells, and 0.121 for MS shells). The model was weighted to contain different numbers of Fe atoms (out
of a possible total of 3) with the remainder being Al, assuming a random distribution of these atoms in
the octahedral sheet. The spectra modeled using this approach were saved and were processed using
wavelet analysis as were the spectra of the natural samples. The Garfield nontronite sample wavelet
graph (not shown) was very similar to the model with 3 Fe, as expected.
The wavelet graphs for the allophane and hisingerite samples can be compared to the
nontronite model at different Fe contents to assess the Fe coordination number fit to the spectrum. We
use the nontronite model here rather than the montmorillonite because, as discussed in the text, the
spectrum of Garfield nontronite can be reproduced almost perfectly by the model without fitting,
whereas the montmorillonite model required parameter fits. This therefore makes the nontronite
model a better choice for generation of entirely theoretical spectra. The wavelet graph for the beidellite
SBId-1 is also shown.
Shown here (Figure S-2) are the wavelet graphs for model spectra containing 1, 1.5, 2, and 3 Fe
atoms. These graphs illustrate the effect of changing Fe-Al ratio. Each graph is scaled to its maximum
value for the Fe-Me1 peak, so different graphs are scaled differently, but the shape and positions of the
Fe-Me1 peaks can be compared. These peaks are observed at R = 2.5 - 3.5 Å and k = 6 - 10 Å-1, with
maxima generally near 8.5 Å-1. It can be observed that the shape of these maxima varies with Fe-Al
ratio, extending to lower k for higher-Fe samples. The beidellite graph also illustrates this behavior, with
the maximum only at higher k for this Al-rich sample.
The wavelet graph of hisingerite also follows this trend, with a very strong shift of the maximum
to lower k values as would be expected for this almost Al-free sample. Some differences are observable
between the hisingerite graph and that of the 3-Fe nontronite model, particularly at R values >4,
supporting the argument that hisingerite is not in fact a poorly crystalline nontronite.
In the allophane wavelet graph, the maximum corresponding to the Fe-Fe1 and Fe-Al1 peaks in
the FT most closely resembles the wavelet graph of the model nontronite containing 1.5 Fe atoms, in
terms of both shape of the feature and intensity distribution. This observation is supportive of the shell
fitting model result suggesting a CN of Fe = 1.85. A 20% error applied to this CN would correspond to a
range in CN of approximately 1.5 – 2.25 Fe. Thus the lower bound is consistent with the wavelet graph,
based on the wavelet graph, the upper bound appears to be too high.
References cited
Funke H, Scheinost AC, Chukalina M (2005) Wavelet analysis of extended X-ray absorption fine structure
data. Physical Review B 71:94-110
Manceau A, Chateigner D, Gates WP (1998) Polarized EXAFS, distance-valence least-squares modeling
(DVLS), and quantitative texture analysis approaches to the structural refinement of Garfield
nontronite. Physics and Chemistry of Minerals 25 (5):347-365. doi:10.1007/s002690050125
O'Day PA, Rehr JJ, Zabinsky SI, Brown GE, Jr. (1994) Extended X-ray absorption fine structure (EXAFS)
analysis of disorder and multiple-scattering in complex crystalline solids. Journal of the American
Chemical Society 116 (7):2938-2949. doi:10.1021/ja00086a026
Vantelon D, Montarges-Pelletier E, Michot LJ, Pelletier M, Thomas F, Briois V (2003) Iron distribution in
the octahedral sheet of dioctahedral smectites. An Fe K-edge X-ray absorption spectroscopy
study. Physics and Chemistry of Minerals 30 (1):44-53
Figure S-1. Possible forms of small Fe-rich domains in allophane consistent with the Fe coordination
number of 1.85 obtained from modeling. Because Fe:Al=99:1 in the allophane, Fe-rich domains may be
separated more widely than shown here.
Figure S-2. Wavelet analysis graphs of model nontronite compositions containing 1, 1.5, 2, and 3 (out of
3 total) backscattering Fe atoms in the Fe-Me1 position, and of allophane, hisingerite, and beidellite
samples. The color scale shows 20 shades from blue = 0 to red = highest value in range for the Fe-Me1
peak for each sample.