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C: Surfaces, Interfaces, Porous Materials, and Catalysis
X-ray Absorption Near-Edge Spectroscopy Calculations on Pristine and Modified Chalcopyrite Surfaces Guilherme Ferreira de Lima, Hélio Anderson Duarte, and Lars Gunnar Moody Pettersson J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b02191 • Publication Date (Web): 14 Aug 2018 Downloaded from http://pubs.acs.org on August 15, 2018
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The Journal of Physical Chemistry
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X-ray Absorption Near-Edge Spectroscopy Calculations on
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Pristine and Modified Chalcopyrite Surfaces
3 4
Guilherme Ferreira de Limaa*, Hélio Anderson Duartea and Lars G. M. Petterssonb
5 6
a) Grupo de Pesquisa em Química Inorgânica Teórica (GPQIT), Universidade Federal
7
de Minas Gerais, Departamento de Química, Avenida Antônio Carlos, 6627, CEP:
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31270-901, Pampulha, Belo Horizonte – MG, Brazil.
9 10
b) Department of Physics, AlbaNova University Center, Stockholm University, SE-
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10691, Sweden.
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* corresponding author:
[email protected] 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 1 ACS Paragon Plus Environment
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Abstract
35 36
Understanding chemical modifications on the chalcopyrite surface is an important
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issue to improve hydrometallurgical processes to recover copper from the mineral. X-
38
ray Absorption Near-Edge Spectroscopy (XANES) can be used for this task, but the
39
interpretation of the spectrum and the correlation with chemical changes in the first
40
atomic layers are not straightforward. The present study demonstrates the potential of
41
combining spectrum measurements with theoretical X-ray spectrum simulations to
42
elucidate the chemistry behind weathering of important classes of minerals. We
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simulated the S and Fe K-edge XANES spectrum for pristine and modified
44
chalcopyrite surfaces using periodic DFT calculations and the transition-potential
45
model. The calculated S K-edge XANES spectra are in good agreement with
46
experimental data and the peaks were attributed using the Density of States. The
47
simulated Fe K-edge XANES spectra do not reproduce all features observed
48
experimentally. The effect of surface changes due to reconstruction, hydration and
49
oxidation on the spectrum was analyzed. Our results show that the S K-edge XANES
50
spectrum is more sensitive to surface modifications than the Fe K-edge XANES
51
spectrum and this sensitivity could be used to follow the evolution of the surface.
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1. Introduction
55 56
Sulfide minerals are very important both from the environmental and economical
57
points of view. Pyrite (FeS2) is the most abundant mineral in this class. It is frequently
58
associated with gold in mines and it can be oxidized by air and water releasing
59
sulfuric acid to the environment in a process known as Acid Mine Drainage (AMD)
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or Acid Rock Drainage (ARD).1 This is an important problem in mining areas
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because it decreases the pH of water and soil, changing the whole ecosystem and
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releasing heavy metals to the ground.2-3
63 64
Chalcopyrite is an important mineral within this class. With composition CuFeS2, it
65
crystalizes in the tetragonal system, space group I-42d, with four units of CuFeS2 in
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the unit cell and lattice parameters a = b = 5.289 Å and c = 10.423 Å.4 It is formed by
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alternating layers of sulfur and metal atoms along the c direction. Each sulfur atom is
68
coordinated to two iron and two copper atoms with bond length of 2.257 and 2.302 Å,
69
respectively. The electronic structure of chalcopyrite is still widely discussed.
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Although some authors claim, based on XANES measurements, that the Cu2+Fe2+(S2-
71
)2 oxidation state is possible,5-6 the configuration Cu+Fe3+(S2-)2 is more accepted
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nowadays.7-12 Chalcopyrite is an antiferromagnetic material with alternate layers of
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Fe3+ with spin up and down along c. Experiments based on neutron diffraction
74
indicate a magnetic moment of 3.85 µB,13 significantly lower than the expected value
75
of 5 µB for Fe3+ in a high-spin state.
76 77
Chalcopyrite contributes less to AMD because of its lower abundance in the planet in
78
comparison with pyrite. However, chalcopyrite is the most abundant copper mineral
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in the Earth crust and contributes more than 70% of this metal production.14-16 The 3 ACS Paragon Plus Environment
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pyrometallurgical route to extract it is effective only for high grade ores,14 which are
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not very abundant nowadays. For low-grade ores the hydrometallurgical route is
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interesting and its improvement is a necessity to obtain copper at low cost.
83 84
The hydrometallurgical process is based on leaching of chalcopyrite ore under acidic
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conditions. It can be applied to low-grade ores and allows a better control of the waste.
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Microorganisms can be used in this process with interesting results.17-18 The kinetics
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of the leaching process is slow and chemical modifications of the mineral surface with
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formation of a passivation layer have been indicated as responsible for this.15, 19-21
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However, the composition of this layer is still unclear.19,
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techniques such as X-ray diffraction,22 ToF-SIMS,23 scanning photoelectron
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microscopy,24
92
spectroscopy,30 electrochemical studies20, 31-34 together with theoretical calculations26,
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29, 35-42
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polysulfides, metal-deficient phase and jarosite have been identified and are
95
frequently pointed out as the possible origin of the hindered dissolution of
96
chalcopyrite.15,
97
suggested that sulfur-terminated surfaces reconstruct forming S22- groups on the
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surface39-40 and these results are aligned with interpretation of S 2P XPS spectra
99
obtained by Klauber on pristine chalcopyrite cleaved in inert atmosphere who
100
attributed a feature at 162 eV to the S22- group on the chalcopyrite surface.25 To the
101
best of our knowledge no consensus about the composition of the chalcopyrite surface
102
and the passivation layer has been reached up to now15-16,
103
investigation are thus necessary.
X-ray
photoelectron
spectroscopy,25-29
21
Several experimental
Raman
vibrational
have been used to better understand this complex system. Elemental sulfur,
19-21
Calculations based on Density Functional Theory (DFT)
27, 32, 43
and more
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In X-Ray Absorption Spectroscopy (XAS) X-ray photons are used to excite core-
106
electrons to empty electronic states above the Fermi level. When the electron is
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promoted to a state close to the Fermi level the technique is known as near-edge X-
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ray absorption fine structure (NEXAFS) or X-ray absorption near edge structure
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(XANES). When the electron is promoted to the far continuum the technique is
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known as extended X-ray absorption fine structure (EXAFS).44 Experiments based on
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XAS provide atom-specific information about the local chemical environment and
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oxidation state of atoms. Although the penetration depth of X-rays results in
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contributions from both surface and bulk, under grazing incidence the surface
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contribution can be significantly enhanced. This technique has been used in order to
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improve the knowledge about the chalcopyrite and other sulfur compounds.45-50
116 117
Petiau et al.,45 in 1988, compared Fe, Cu and S K-edge XANES spectra of
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chalcopyrite with the spectra of other minerals and concluded that Fe, Cu and S are in
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well-defined geometry and oxidation states. The author observed the pre-edge feature
120
at 7105 eV in the Fe K-edge XANES spectrum which is close to what is obtained for
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the Fe(II) in the chromite FeCr2O4, the reference mineral, suggesting this oxidation
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state for Fe in chalcopyrite. The Cu K-edge XANES spectrum shows a pre-edge
123
feature around 8975 eV observed also in minerals where copper is in the +2 oxidation
124
state. It is important to highlight that the authors used mainly oxides to compare with
125
chalcopyrite where the effect of covalent bonds should be more pronounced due to the
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high polarizability of the sulfur atoms. It is more accepted nowadays that Fe and Cu
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in chalcopyrite are in oxidation states +3 and +1.7-12
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Risberg et al.46 combined S K-edge XANES experiments with theoretical calculations
130
to study amino acids in aqueous solution to evaluate the nature of their unoccupied
131
molecular orbitals and the influence of the hydrogen bond and pH. Very good
132
agreement was obtained between theory and experiments. The results indicate that
133
changes in the geometry of molecules, in particular those close to the sulfur atoms in
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these amino acids affect the energy of the transitions and also the intensity in the
135
spectra.
136 137
Recently, using S and Fe K-edge XANES experiments in total electron yield (TEY)
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and partial fluorescence yield (PFY) modes with an energy step of 0.2 eV, Mikhlin et
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al.51 analyzed air-exposed and etched chalcopyrite in order to better understand the
140
oxidation of chalcopyrite. With the mineral oxidation, the Fe K-edge XANES spectra
141
in the PFY mode, with a probing depth of several hundreds of nanometers do not
142
show significant modifications. In the TEY mode, with the probing depth about 100
143
nm, a decrease in the pre-edge maximum was observed, indicating changes in the
144
oxidation state of the iron atoms and a decrease in the Fe – S bond length beneath a
145
sulfur rich layer.51 In the S K-edge XANES spectra, in the TEY mode, oxidation
146
resulted in a new small peak at 2475 eV which was attributed to an electronic
147
transition from the S 1s orbital to antibonding S 3p states in a disulfide. Based on
148
these results, and aligned with hard X-ray photoelectron spectroscopy, the authors
149
were able to elaborate a picture suggesting the formation of a thin layer of polysulfide
150
species of depth around 4 nm and in addition an around 20 nm metal-deficient layer
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with disulfide groups. Mikhlin et al.51 show that the S and Fe K-edge XANES spectra
152
of chalcopyrite are affected depending how the surfaces are polished or etched.
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Soft X-ray photons at normal incidence penetrate several atomic layers into the solid
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structure to provide mostly information about the bulk. Under special conditions,
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using grazing angle of incidence, for example, the surface contribution can be
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enhanced which allows analysis of chemical modifications on mineral surfaces.52-53
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However, the signal is still related to several atomic layers and understanding what
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happens in the very first layers is not straightforward. In this sense, theoretical
160
calculations can provide useful information. Combining some elaborate models with
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calculations using the transition-potential model54 the XANES spectrum can be
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simulated and the contribution of each atom to the overall spectrum can be
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determined.
164 165
The importance of X-ray spectroscopies for investigating chemical properties of
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interfaces and surface adsorbates is well-recognized.55-58 When combined with
167
theoretical simulations of spectra for various models, a more complete analysis and
168
assignment of the spectral features can be obtained, see e.g. refs. 59-62. However,
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most such combined experimental and theoretical works have addressed processes at
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metal surfaces under well-defined ultra-high vacuum (UHV) conditions. Nevertheless,
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XANES also has had a strong impact on geochemistry with spectrum measurements
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under realistic conditions, but commonly without theoretical spectrum simulations to
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support the interpretation.63,64 In the present paper we thus extend the theoretical
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spectrum simulations to minerals by computing the S and Fe K-edge XANES spectra
175
of chalcopyrite for various surfaces, with and without reacting adsorbates, using the
176
transition-potential method.54,65 The role of atoms in different atomic layers in
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chalcopyrite and their contribution to the overall spectrum were determined. The
178
effect of cleavage, surface reconstruction, hydration and oxidation in the spectra were
179
also investigated aiming to understand how the surface formation affects their S and 7 ACS Paragon Plus Environment
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Fe K-edge XANES spectra. We thus demonstrate the potential of theoretical spectrum
181
simulations to elucidate the origin of spectral changes also at complex mineral
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surfaces undergoing reconstruction and reactions with environmentally relevant
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adsorbates.
184 185
2. Computational Details
186 187
The effect of the mineral cleavage and reconstruction considering the sulfur-
188
terminated (001) surface were studied. This surface has already been studied
189
theoretically considering both its structure and reactivity toward different
190
molecules.37-40 It was simulated using a (2x2) slab model with 8 atomic layers and 15
191
Å of vacuum.
192 193
Spin-polarized DFT calculations were carried out with the Vienna ab initio package
194
(VASP).66-70 The core electrons were described by the projector augmented wave
195
(PAW) method proposed by Blöchl.71 The antiferromagnetism of chalcopyrite was
196
taken into account along the c axis considering alternate layers of iron with spin up
197
and down. Conejeros et al.36 have shown this is the most stable magnetic state for
198
chalcopyrite. The valence states were expanded in plane waves with a kinetic energy
199
cutoff of 400 eV and using the PBE exchange/correlation (XC) functional.72 A mesh
200
of 2x2x2 k-points, sampled by the Monkhorst-Pack method,73 was used to describe
201
the first Brillouin Zone. Calculations using the PBE+U method74-75 were carried out
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to improve the description of the strongly correlated Fe 3d-electrons. The geometry
203
optimization was performed using the conjugate-gradient method with a tolerance of
204
0.02 eV/Å.
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To set the best Hubbard parameter to describe the system, different optimizations
207
(geometry and lattice) were carried out. The values of Ueff = 1.0, 2.0, 3.0 and 4.0 eV
208
were used in our calculations. The structural results (Table 1) show that Ueff = 1.0 eV
209
gives lattice parameters in good agreement with experimental results,4 with
210
differences of just 0.01 Å or 0.6 %. The results indicate that the lattice parameters are
211
relatively insensitive to the value of Ueff (Table 1). The largest error was with Ueff =
212
4.0 eV, with differences of 1.1 and 1.3 % in a and c, respectively. For the other
213
Hubbard parameters, the errors in the lattice parameters are lower than 1%.
214 215
The Density of States (DOS) was also evaluated considering these different values of
216
Ueff as shown in Figure S1 in the Supporting Information (SI). The regions where the
217
electronic states are concentrated do not change significantly with Ueff. The band gap
218
is slightly affected, changing from 0.2 eV without the Hubbard parameters to 0.0, 0.4,
219
0.6 and 0.6 eV with Ueff = 1.0, 2.0, 3.0 and 4.0, eV, respectively. Chalcopyrite is a
220
semiconductor with a band gap estimated to be 0.3 eV,76 however, different
221
theoretical estimations of these values for the band gap in the range of 0.1 – 1.82 eV
222
have been reported in the literature using different theoretical methods.36,
223
Because Ueff = 1.0 eV gives better structural parameters in comparison with
224
experimental results (Table 1), we chose to work with it to optimize the bulk and the
225
surfaces. These optimized structures were used further to calculate the sulfur and Fe
226
K-edge XANES spectra.
40, 77
227 228
The optimized structures were used to calculate the XANES spectrum using the
229
GPAW program.78-80 These calculations were carried out with the RevPBE XC
230
functional,81 PAW71 method and a real space grid (0.2 Å). The spectra were obtained
231
with the transition-potential method.54,65 A setup with a half-occupied core-hole in the 9 ACS Paragon Plus Environment
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1s orbital was created for both S and Fe atoms and used in our calculations. A shift of
233
+7.4 eV was included to take into account the relativistic correction of the S 1s
234
ionization potential.82 For the Fe K-edge spectrum, an empirical shift of +2.2 eV was
235
applied in order to match the pre-edge feature in the calculated spectrum with the
236
experimental one.45 A broadening of 0.1 eV was used to create the spectra. To
237
compute the XANES spectrum in the bulk structure, the unit cell was replicated along
238
a and b to avoid spurious interactions between core holes in the calculations. Since, in
239
these model calculations, only excitations from the selected core-level are considered,
240
experimental complications such as background subtraction are eliminated. In
241
experimental XANES studies typically relative cross sections are measured which is
242
the case also for our computed spectra. For direct comparison with experiment
243
different normalization procedures can be applied, e.g., normalization by area or at
244
the high energy limit. In the present work we focus on the effects on the computed
245
spectra from various structural modifications and compare peak positions and relative
246
intensities with what is observed experimentally.
247 248
Table 1: Lattice parameters (Å) of Chalcopyrite and band gap (eV) calculated using
249
VASP and the PBE functional and different values of the Hubbard Ueff parameter.
250
Values in parenthesis correspond to the percentage error in relation to experiment.
a=b
c Band Gap
No
Hubbard
Hubbard
Hubbard
Hubbard
Hubbard
Ueff = 4 eV
Ueff = 3 eV
Ueff = 2 eV
Ueff = 1 eV
10.500
10.691
10.660
10.610
10.584
(-0.74)
(1.07)
(0.78)
(0.30)
(0.06)
10.370
10.560
10.510
10.475
10.431
(-0.51)
(1.31)
(0.83)
(0.50)
(0.08)
0.2
0.6
0.6
0.4
0.0
Experimental
10.5784 10.4234 0.376
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3. Results and Discussion
254
3.1 S K-edge XANES Spectrum
255
3.1.1 Bulk Chalcopyrite
256 257
To evaluate the methodology, the S K-edge XANES spectrum for bulk chalcopyrite
258
was calculated (Figure 1a). The shape of the calculated spectrum is in good agreement
259
with that recently obtained by Mikhlin et al.51 and other spectra previously reported in
260
the literature.45, 47, 49 It consists of a sharp and intense feature P1 centered at 2470.5
261
eV followed by a broader and slightly more intense feature P2 centered at 2477.8 eV
262
and a smaller one P3 at 2487.3 eV. Good agreement is observed with the
263
experimental values reported by Mikhlin et al.51 and by Li et al.49
264
265 266
Figure 1: (a) Experimental (from Ref. 51) and calculated Sulfur K-edge XANES
267
spectrum, and (b) density of unoccupied states of bulk chalcopyrite calculated at the
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The transitions in XANES are governed by the following selection rules: ∆L = ±1, ∆S
271
= 0 and ∆J = ±1.44 Thus, S K-edge XANES provides information mainly about the
272
sulfur empty p states in the conduction band of chalcopyrite. To make the assignment
273
of the peaks in the S K-edge XANES spectrum, we calculated the DOS and its
274
projection onto sulfur p states (Figure 1b).
275 276
The DOS calculated with the RevPBE XC functional in GPAW indicated no band gap,
277
suggesting a metallic behavior for the material, and similar to that obtained with
278
VASP with Ueff = 1 eV (Figure S2). Chalcopyrite is a semiconductor with band gap
279
around 0.3 eV.76 It is well known that DFT using GGA XC functionals
280
underestimates the band gap. Edelbro et al.,77 for example, obtained a band gap of 0.1
281
eV with a local VWN functional. Similar results were obtained by de Oliveira and
282
Duarte using the PW91 functional and plane waves.40 More recently, Conejeros et
283
al.36 investigated the dependence of the band gap of chalcopyrite on the XC functional
284
and magnetic state. They obtained a band gap of 0.94 eV for the more stable
285
antiferromagnetic state using PBE+U (Ueff = 4.3 eV) and 1.82 eV with the B3LYP
286
functional in the same magnetic state.
287 288
The beginning of the conduction band was set at 2470 eV to make a direct
289
correspondence with the absorption energies in the S K-edge XANES spectrum. P1
290
corresponds to transitions to the conduction band edge, which is formed mainly by Fe
291
3d states, but with a significant contribution also of S 3p. This attribution is in good
292
agreement with earlier assignments.45, 47, 49 This first intense feature P1 is important
293
since it is sensitive to chemical modifications involving the sulfur atoms. For example,
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in ionic materials, such as ZnS, the formal oxidation state of S is -2 and the 3p orbitals
295
are fully occupied and the first intense peak is absent, since no transition from S 1s
296
orbital to S 3p is allowed.45 In covalent materials like elemental sulfur, pyrite and
297
other sulfide minerals P1 is a characteristic feature,
298
transferred from sulfur to other atoms, making some of the 3p states available to
299
receive the electron from the 1s orbital. This is observed in chalcopyrite, in which
300
sulfur atoms are in tetrahedral environment (sp3 hybridization) and oxidation state -2.
301
Due to the covalent bond with metal atoms, some charge is transferred to them,
302
resulting in some empty p states. P2 is around 7 eV higher in energy in comparison
303
with P1. The DOS suggests that it is an electronic state formed mainly by Cu 3p states,
304
but with significant contributions also of Fe 3p and some S 3p states where the latter
305
give the intensity. A small shoulder (S*) at 2482 eV is observed in the calculated
306
spectrum. According to the DOS, it corresponds to S 3p states mixed with p states
307
from Cu and Fe. It is important to note that the computational approach describes
308
single-electron excitations rather accurately, including secondary scattering
309
contributing to the low-energy EXAFS wiggles.65
45-46, 48-49
because some charge is
310 311
The surface reactivity of chalcopyrite is responsible for the leaching of this mineral
312
and also its oxidation mechanism, hence it has to be better understood. However,
313
experimental analysis of the surface phenomena such as leaching and oxidation is not
314
straightforward. The S K-edge XANES spectrum of the sulfur-terminated (001)
315
surface was simulated and some possible modifications of the surface due to its
316
oxidation by species like oxygen and water were investigated.
317 318
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Table 2: Main feature positions (eV) in computed Sulfur K-edge X-ray absorption
320
spectra of different chalcopyrite surfaces. Values in parenthesis refer to the shoulder.
Bulk
Calculated Miklin et al.
51
Li et al.49
P1
P2
P3
2470.5
2477.8
2487.3
2471
2479
2488
2469
2475.8
2486.5
P1 (S1)
P2
P3
2472.0
2479.2
2488.0
2472.1 (2471.0)
2478.1
2488.0
2477.2
2488.1
Surfaces Structure Non-Reconstructed (001) Surface Reconstructed (001) Surface 2471.7 (2471.0) Diss1 Surface (2472.7*)
321
Diss2 Surface
2472.9 (2471.8)
2478.4
2488.6
Diss3 Surface
2472.1 (2471.3)
2478.0
2488.1
S – O Surface
2472.9 (2470.8)
2478.1
2487.9
* Shoulder S2.
322 323
3.1.2 Non-reconstructed sulfur-terminated (001) chalcopyrite surface
324 325
The effect of cleaving the chalcopyrite surface on the (001) cleavage plane exposing
326
the sulfur atoms was analyzed. Chalcopyrite is brittle, without a preferential cleavage
327
plane.4 Some theoretical works have investigated different surfaces.35,
328
present work all analyses were performed considering the sulfur-terminated (001)
329
surface, since structure39-40 and reactivity37-38 of this surface have been studied
330
extensively in previous theoretical work. Aiming to make the calculated spectrum
331
more comparable to what is obtained experimentally, the spectrum was calculated
39-40
In the
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332
setting the core-hole in sulfur atoms at three different layers, 1st, 3rd and 5th, in the slab
333
model. The sulfur atoms in the first, third and fifth atomic layer are denoted surface,
334
mix and bulk, respectively (Figure 2a). This nomenclature will be used throughout
335
this paper. The spectra were calculated averaging over all these three different
336
possibilities. When sulfur atoms in the first layer are chemically different, the
337
contribution of each species is calculated and weighted properly. The contribution
338
from atoms in different layers will depend on the geometry in the experimental
339
measurement which is why we report the individual contributions here and an
340
unweighted sum.
341 342
The calculated spectrum for the non-reconstructed surface and the contribution of the
343
distinct sulfur atoms are presented in Figure 2b. Similar features in comparison to the
344
bulk structure are observed. P1 is sharper, and more intense than that calculated for
345
the bulk structure and centered at 2472.6 eV (Table 2), with a very small shoulder
346
(S1) at 2471 eV. The surface sulfur atoms are responsible for this higher intensity and
347
also for the shoulder, as shown in Figure 2b. The P2 feature is broader and centered at
348
2479.2 eV. Its decomposition suggests that it is a combination of two bands of
349
different origins. The first one centered at 2478.5 eV (P2B) is mainly due to a bulk
350
sulfur atom while mix sulfur atoms contribute more to a peak at 2479.9 eV (P2M). P3
351
corresponds to the first EXAFS oscillation and is centered at 2488.0 eV, slightly
352
higher in energy than that calculated for the bulk structure (2487.3 eV) due to
353
contributions from the somewhat shorter distances as the surface layer contracts. The
354
decomposition suggests that the surface atoms contribute less to the intensity of this
355
feature. With the cleavage on the (001) plane, an overall shift by around 1.0 eV to
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Page 16 of 42
356
higher energy is observed in the spectrum of the non-reconstructed surface in
357
comparison with that of the bulk structure (Figure 3).
358
359 360
Figure 2: (a) Non-reconstructed sulfur-terminated (001) chalcopyrite surface and its
361
(b) sulfur K-edge XANES spectrum (black filled line) calculated as an average of
362
three spectra evaluated with the core-hole at different depths in our slab model
363
(colored dashed lines). S (Yellow), Cu (blue) and Fe (pink).
364 365
The assignments are similar to those of the bulk structure. P1 is related to a transition
366
from the 1s orbital in a sulfur atom to the Fermi level, which contains not only 3p
367
states of sulfur but also 3d states mainly of iron (Figure S3). The feature P2
368
corresponds to a transition from the 1s orbital to states that are around 8 eV above the
369
Fermi level, which are mainly formed by 3p states from sulfur but also 3d states from
370
both metal atoms (Figure S3).
371
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372
373 374
Figure 3: Sulfur K-edge XANES spectrum of chalcopyrite bulk and surfaces.
375
Experimental spectrum extracted from ref. 51.
376 377
3.1.3 Reconstructed sulfur-terminated (001) surface
378 379
The (001) surface was reconstructed in VASP and the formation of sulfur – sulfur
380
bonds was observed at the chalcopyrite surface (Figure 4a) with bond length close to
381
2.12 Å (Figure 4b). De Oliveira et al.39-40 have shown that the sulfur-terminated (001)
382
surface reconstructs forming disulfide groups on the chalcopyrite surface by a redox
383
process with transfer of two electrons to the iron atoms in the second atomic layer.
384
The S-S bond length was calculated to be 2.15 Å, indicating that our structure is quite
385
similar to that obtained by de Oliveira et al.39 The presence of disulfide on the
386
chalcopyrite surface has already been reported experimentally. Klauber attributed a
387
feature at 162 eV in the S 2p XPS of pristine chalcopyrite, cleaved in inert
388
atmosphere of N2, to S22- groups at the chalcopyrite surface25 and also more recently
389
Mikhlin et al.51 attributed a feature at 2475 eV to disulfide groups based on S K-edge
390
XANES experiments.
391
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392 393
Figure 4: (a) Side and (b) top view of the reconstructed sulfur-terminated (001)
394
chalcopyrite surface and its (c) sulfur K-edge XANES spectrum (black filled line)
395
calculated as an average of three spectra evaluated with the core-hole at different
396
depths in our slab model (colored dashed lines). S (Yellow), Cu (blue) and Fe (pink).
397 398
The spectrum of this reconstructed surface was calculated making an average of three
399
spectra with the core-hole in sulfur atoms at different depths in the slab model (Figure
400
4a). Although there are small differences in the S – S bond lengths in the first atomic
401
layer, all sulfur atoms in this layer were considered to be equivalent. The P1 feature of
402
the spectrum is shifted by around 1.0 eV to higher energy in comparison with P1 in
403
the bulk structure and it is centered at 2472.1 eV. The surface sulfur atoms contribute
404
significantly to the increase in the intensity of this peak (Figure 4c). A shoulder S1
405
localized at 2471.0 eV is more pronounced than for the non-reconstructed surface and
406
can be related to the formation of the S – S bonds with the reconstruction. The other
407
peaks in the reconstructed surface are broader and less structured in comparison with
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The Journal of Physical Chemistry
408
the bulk structure and non-reconstructed surface (Figure 3). The P2 and P3 features
409
are centered at 2478.1 and 2488.0 eV, respectively.
410 411
3.1.4 Hydrated (001) chalcopyrite surface
412 413
Several chemical modifications of the reconstructed sulfur-terminated (001) surface
414
of chalcopyrite were investigated and the S K-edge XANES spectra were calculated.
415
Within a wide variety of molecules that could interact with the chalcopyrite surface,
416
water is one very important because it is the most abundant under leaching conditions.
417
Herein the possibility of a water molecule interacting with the chalcopyrite surface in
418
both molecular and dissociative pathways was investigated.
419 420
The water molecule was considered binding to the Fe site on the chalcopyrite (001)
421
surface (Figure S5). This is the most acidic site on this surface37 and the Fe – O bond
422
length was calculated to be 2.46 Å. This is slightly larger than the value of 2.38 Å
423
obtained by de Lima et al.37 based on PBE/Numerical basis set/Ultrasoft
424
pseudopotential calculations. The water adsorption bonded to the iron atoms in the
425
surface affects just slightly the bond length of the disulfide groups at the mineral’s
426
surface and does not affect the S K-edge XANES spectrum, as shown in Figure S6, in
427
the SI.
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428 429
Figure 5: Top-view of dissociative water adsorption at different sites in the
430
reconstructed sulfur-terminated (001) chalcopyrite surface (a) Diss1, (b) Diss2, (c) 20 ACS Paragon Plus Environment
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431
Diss3 and the oxidized (d) S-O surface and (e) the respective S K-edge XANES
432
spectra for the surface modified by ¼, indicated by full lines, and the fully modified
433
surface, indicated by dashed lines. S (Yellow), Cu (blue), Fe (pink), O (red) and H
434
(white). Bond lengths are in Ångström.
435 436
The water molecule is not expected to interact directly with the sulfur atoms in
437
chalcopyrite.37 However, the water molecule can dissociate on the chalcopyrite
438
surface with fragments interacting with disulfide groups. Herein, three different
439
possibilities for dissociative adsorption of a water molecule were considered. In the
440
first, named Diss1, the OH- group is considered to bind to an iron atom, while the H+
441
is binding to a disulfide group. In the structure named Diss2 each fragment of water is
442
binding to different disulfide groups and in Diss3 both OH- and H+ are binding to
443
different sulfur atoms in the same disulfide group. Figures 5a, 5b and 5c show the
444
optimized structures obtained for Diss1, Diss2 and Diss3, respectively.
445 446
3.1.4.1 Diss1 Structure
447 448
In an initial approach, just one water molecule dissociating and interacting with the
449
surface was considered. For Diss1, the OH- binds to iron with a Fe – O bond length of
450
1.86 Å. The protonation of one disulfide group breaks the S – S bond, increasing the S
451
– S bond distance to 3.78 Å (Figure 5a) with the three other disulfide groups just
452
adjusting slightly their bond lengths. A similar effect was observed previously by de
453
Lima et al.37 The computed S K-edge XANES spectrum shows three features, similar
454
to what is observed for the reconstructed surface (Figure 5e). P1 is centered at 2471.7
455
eV with a shoulder, S1, at 2471.0 eV and another shoulder S2, after P1 at 2472.7 eV.
456
S2 is slightly different from that observed for the reconstructed surface (S1), where it
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Page 22 of 42
457
is located before the P1 feature. The main contribution is from the surface sulfur
458
atoms that form the disulfide groups in the first layer. The decomposed spectrum
459
shows a very intense P1 peak for these surface atoms at somewhat higher energy
460
compared to the sulfur atoms in deeper layers (Figure S7). The sulfur atom that binds
461
to hydrogen (Figure 5a) has some contribution around 2475 eV, while the surface
462
sulfur atom that is just bonded to the metallic atoms in the second atomic layer
463
absorbs at 2470 eV. The impact of replacing all the S – S bonds by S – H and S in the
464
spectrum was simulated. This was done by just changing the weight of this sulfur
465
species in the first atomic layer and removing the contribution of S – S. The result
466
indicated in Figure 5e (dashed lines) suggests a decrease in the intensity of the P1
467
feature. This is expected, since the high intensity of the first peak in the reconstructed
468
surface is mainly due to sulfur atoms in the S – S disulfide groups. We also observe a
469
small shoulder that appears at 2475 eV which is due to the increase of the contribution
470
of the sulfur atom bonded to hydrogen (Figure S7).
471 472
3.1.4.2 Diss2 Structure
473 474
For Diss2 the XANES spectrum features P1, P2 and P3 are at 2472.9, 2478.4 and
475
2488.6 eV, respectively, around 1 eV higher than those calculated for the
476
reconstructed surface (Figure 5e). The water molecule dissociated as proposed in
477
model Diss2 changes the structure of the surface significantly, as shown in Figure 5b.
478
The high intensity of P1 is mainly due to S-S bonds (Figure S8). The S-OH and S-H
479
groups are responsible for some contribution at 2474 eV (Figure S8). The spectrum
480
contributions from all eight atoms in the surface layer were computed (Figure S9).
481
Results indicate that all atoms involved in an S – S bond are very similar, including
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The Journal of Physical Chemistry
482
the one that is bonded to the sulfur atom bonded to the hydrogen atom. The sulfur
483
atom that is just bonded to metal atoms, that results from the breaking of the S – S
484
bond due to the OH bonding, behaves in a similar way to the sulfur atom in model
485
Diss1, with absorption at 2470 eV. The bonding of H and OH shifts the spectrum to
486
higher energy. The simulation of a full coverage surface also suggests a decrease of
487
intensity of P1 (Figure 5e, dashed lines).
488 489
3.1.4.3 Diss3 Structure
490 491
In Diss3, one S – S group is replaced by HO–S and S–H. The S – S distance increases
492
to 3.81 Å, suggesting no chemical bond between these sulfur atoms (Figure 5c). The
493
features in the spectrum are very similar in position to what is observed for the
494
reconstructed surface, i.e., 2472.1, 2478 and 2488.1 eV, for P1, P2 and P3,
495
respectively (Table 2). The intensity of the P1 peak is decreased and it is similar to P3
496
(Figure 5e), which differs from the reconstructed surface. The spectrum
497
decomposition (Figure S10) indicates that a sulfur atom bonded to OH absorbs around
498
2474 eV, while the sulfur atom bonded to H absorbs at 2475 eV with small intensity.
499
Considering that all S – S disulfide groups in the surface are replaced by HO–S and
500
S–H groups the spectrum should look like Figure 5e dashed lines), with a shoulder at
501
2474 eV due to an increased S – OH contribution. The P1 feature also decreases in
502
intensity, as observed in Diss1 and Diss2.
503 504
3.1.5 Oxidized (001) chalcopyrite surface
505 506
The effect of replacing one sulfur atom by an oxygen atom in the S – S group in the
507
first atomic layer was also investigated. Santos-Carballal et al.83 studied in detail 23 ACS Paragon Plus Environment
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Page 24 of 42
508
different pathways in the reaction between water and the Greigite Fe3S4 (001) surface.
509
Three different mechanisms in which oxygen atoms from water molecules replace
510
sulfur atoms in the sulfide surface were proposed. Here we investigate the possible
511
effects of such replacements on the S K-edge XANES spectrum of chalcopyrite. The
512
results show a S – O bond length of 1.61 Å and very little effect on the other S – S
513
bonds (Figure 5d). The spectrum has the P1 feature at 2472.9 eV with a shoulder (S1)
514
at 2470.8 eV (Figure 5e). The decomposition of the spectrum (Figure S11) indicates
515
that the higher intensity of P1 is due to the surface sulfur atoms in the S – S bonds.
516
These surface atoms also absorb at higher energy than mix and bulk atoms. The S1
517
feature has some contribution from deeper sulfur atoms. The surface sulfur atom
518
bonded to oxygen absorbs at 2474 eV. There is a broad P2 feature centered at 2478
519
eV and P3 at 2487.9 eV, which is mainly due to mix and bulk atoms
520 521
The spectrum of chalcopyrite with all S – S bonds replaced by S – O was furthermore
522
simulated (Figure 5e, dashed lines). P1 splits in two peaks with similar intensity. In
523
comparison with the reconstructed surface, there is a significant loss of intensity in P1,
524
which is explained by the absence of S – S groups. A broadening of this feature is
525
also observed. P2 is also affected, in comparison to the reconstructed surface.
526 527
3.2 Fe K-edge XANES Spectrum
528 529
The Fe K-edge XANES spectrum for chalcopyrite was also calculated (Figure 6). An
530
overall shift of +2.2 eV was applied to all calculated spectra to put the calculated pre-
531
edge feature at the same energy as that obtained experimentally by Petiau et al.45
532
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The Journal of Physical Chemistry
533 534
Figure 6: Calculated Fe K-edge XANES spectra for Chalcopyrite bulk and modified
535
surfaces.
536 537
For the bulk structure, the pre-edge feature P1 centered at 7105 eV is attributed to a
538
dipole forbidden 1s → 3d transition, which becomes allowed due to hybridization
539
with 3p states and with the absence of an inversion center at the iron atom due to its
540
tetrahedral coordination to the sulfur atoms.45 Recent experiments indicate that iron in
541
chalcopyrite is in the oxidation state (III),7-12 in Td symmetry, suggesting that the pre-
542
edge transition corresponds to 1 → 3. The DOS (Figure 1b) indicates the
543
presence of Fe 3d and, to a lesser extent, Fe 3p states at the Fermi level. The S1
544
feature is centered at 7109.9 eV and the DOS calculation indicates that is a mixture of
545
3p states from iron, copper and sulfur atoms (Figure 1b). P2 at 7112.5 eV in the
546
calculated spectrum corresponds to a transition to electronic states also formed by 3p
547
states from all three atoms that are located around 7 eV above the edge. The feature
548
P3 is calculated to be at 7116.8 eV and corresponds to a transition to electronic states
549
formed mainly by Cu 3p states, but with significant contribution of S and Fe 3p states
550
too. Several other small features appear above 7120 eV and can be justified by the
551
presence of Fe 3p states in a large energy region above the edge (Figure 1b). 25 ACS Paragon Plus Environment
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Page 26 of 42
552 553
No good agreement is obtained between the calculated spectrum and experimental
554
measurements published previously.45,51 Petiau et al.45 obtained the Fe K-edge
555
spectrum of chalcopyrite in a transmission mode using a Si(400) monochromator with
556
points collected at 0.1 eV steps. The experimental spectrum has three main features
557
named here as P1E, P2E and P3E. The pre-edge feature P1 calculated here is in good
558
agreement with experimental P1E showing a similar shape and width. However, there
559
is no experimental correspondence for the feature S1 obtained in the calculations. The
560
P2 feature that was calculated to be 7.5 eV above P1 has some correspondence with
561
P2E, which is 10 eV above P1E. However, the experimental spectrum indicates a
562
broader and more intense P3E feature around 3 eV higher in energy than P2E, while
563
the calculated P3 is less intense and 4.3 eV above P2. After P3E the experimental
564
spectrum does not show the features obtained in the calculations, but it could be
565
justified by disorder in the sample.
566 567
The Fe K-edge spectrum for the reconstructed surface and hydrated surfaces with
568
non-dissociated and dissociated water molecule were also evaluated (Figure 6). The
569
same protocol used to calculate the S K-edge XANES spectrum and averaged over
570
iron atoms at three different depths in our slab model was used. Very small
571
differences in these spectra are observed in comparison with that calculated for the
572
bulk, with just a shift about 1 eV of P2 to lower energy.
573 574
Our calculations suggest different oxidation states of the iron in the 2nd atomic layer
575
in comparison with deeper iron atoms in the model. An overall shift around 2 eV is
576
observed for the iron atoms in the reconstructed and hydrated surfaces (Figures S12
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The Journal of Physical Chemistry
577
and S13) suggesting the reduction of iron on the surface. de Oliveira et al.39 reported
578
that the reconstruction of the chalcopyrite surface by forming disulfide groups occurs
579
with the reduction of iron(III) to iron(II). This suggests that the results obtained herein
580
are in good agreement with previous calculations reported.39
581 582
4. Conclusion
583 584
Using periodic DFT calculations and the transition-potential method to compute
585
spectra the S K-edge and the Fe K-edge XANES spectrum were simulated to compare
586
with data available in the literature49, 51 and to determine how different modifications,
587
structural and chemical, affect the peak positions and intensities in the spectra. The
588
present study shows the potential of analyzing experimental XANES data in terms of
589
structural models.
590 591
For the bulk structure, the calculated S K-edge spectrum is in good agreement with
592
experimental measurements showing three features in the region of 2470, 2478
593
(broad) and 2487 eV (broad), similar to what is observed experimentally. The
594
cleavage of the mineral in the (001) plane with the formation of S – S bonds due to
595
surface reconstruction is responsible for the increase of the intensity of the first
596
feature (P1) and also the formation of a small shoulder (S1).
597 598
Water molecules can interact with the chalcopyrite surface in different ways. In a
599
molecular fashion, the water molecule interacts with iron atoms and does not affect
600
the S K-edge spectrum in a significant way. In a dissociative pathway, the OH and H
601
groups can interact with the S – S dimers which changes the spectrum slightly. The
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Page 28 of 42
602
presence of sulfur atoms in the surface that are not bonded to another sulfur atom or
603
to OH or H is responsible for a feature around 2470 eV in the S K-edge XA spectra,
604
while sulfur atoms bonded to H or OH produce a signal close to 2475 eV. All the
605
modifications on the chalcopyrite surface suggest that the P1 feature around 2470 eV
606
in the S K-edge XANES spectra is very sensitive to the sulfur chemical species on the
607
chalcopyrite surface and can be used as probe of the chemical state of the surface
608
species.
609 610
The Fe K-edge spectrum is less sensitive to chemical modification of the chalcopyrite
611
surface. Our results show that no significant differences are observed in the Fe K-edge
612
spectrum between the bulk, reconstructed and hydrated surfaces. The spectrum
613
decomposition indicates that the iron atoms in the second atomic layer are in a
614
different oxidation state than deeper iron atoms, which supports the suggestion that
615
the reconstruction of the chalcopyrite surface with the formation of disulfide groups
616
on the surface reduces iron(III) to iron(II).39 However, since this just occurs within
617
one atomic layer, the impact on the total spectrum is small.
618 619
S K-edge XANES experiments on chalcopyrite changing the angle of incidence of the
620
beam in order to vary the probing depth and enhance the surface sensitivity could be
621
able to detect this small difference and would be able to follow the chemical
622
modification of the mineral surface. In the present work the contributions from atoms
623
at different depths from the surface, which can be used to generate incidence-angle-
624
dependent theoretical spectra to compare with specific experimental situations were
625
computed. This demonstrates the potential of combining experimental measurements
626
with theoretical simulations of spectra to decipher complicated structural and
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The Journal of Physical Chemistry
627
chemical changes to the weathering surface in mineral chemistry was demonstrated.
628
The present study is thus expected to stimulate further experimental applications of
629
X-ray spectroscopies to mineral chemistry where theoretical modeling of the spectra
630
is an integral part.
631 632
5. Supporting Information Description
633 634
Details on the Density of States of Chalcopyrite; details of the contribution of
635
different atomic layers on the S K-edge spectrum; details of the contribution of
636
different atomic layers on the Fe K-edge spectrum and optimized coordinates for all
637
structures used in this work.
638 639
6. Acknowledgment
640 641
This work was funded by CNPq, FAPEMIG, CAPES, INCT-Acqua (www.acqua-
642
inct.org), RENOVAMIN and the Swedish Research Council through the Swedish
643
Research Links program (Grant No. 348-2013-6723). The calculations were
644
performed using resources provided by the Swedish National Infrastructure for
645
Computing (SNIC) at the HP2CN center.
646 647
7. References
648 649 650 651 652 653 654
1. Chandra, A. P.; Gerson, A. R., The Mechanisms of Pyrite Oxidation and Leaching: A Fundamental Perspective. Surf. Sci. Rep. 2010, 65, 293-315. 2. Valente, T. M.; Gomes, C. L., Occurrence, Properties and Pollution Potential of Environmental Minerals in Acid Mine Drainage. Sci. Total Environ. 2009, 407, 1135-1152. 3. Azzali, E.; Marescotti, P.; Frau, F.; Dinelli, E.; Carbone, C.; Capitani, G.; Lucchetti, G., Mineralogical and Chemical Variations of Ochreous Precipitates from
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