X-ray Absorption Near-Edge Spectroscopy Calculations on Pristine

Pristine and Modified Chalcopyrite Surfaces. 2. 3. Guilherme Ferreira de Limaa*, Hélio Anderson Duartea and Lars G. M. Petterssonb. 4. 5 a) Grupo de ...
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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

1

X-ray Absorption Near-Edge Spectroscopy Calculations on

2

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]

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Page 2 of 42

Abstract

35 36

Understanding chemical modifications on the chalcopyrite surface is an important

37

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

43

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.

52 53

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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)

60

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

62

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

66

the unit cell and lattice parameters a = b = 5.289 Å and c = 10.423 Å.4 It is formed by

67

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.

70

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

72

nowadays.7-12 Chalcopyrite is an antiferromagnetic material with alternate layers of

73

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

79

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

82

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

87

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,

93

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

107

promoted to a state close to the Fermi level the technique is known as near-edge X-

108

ray absorption fine structure (NEXAFS) or X-ray absorption near edge structure

109

(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

111

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

122

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

126

high polarizability of the sulfur atoms. It is more accepted nowadays that Fe and Cu

127

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)

138

and partial fluorescence yield (PFY) modes with an energy step of 0.2 eV, Mikhlin et

139

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

155

structure to provide mostly information about the bulk. Under special conditions,

156

using grazing angle of incidence, for example, the surface contribution can be

157

enhanced which allows analysis of chemical modifications on mineral surfaces.52-53

158

However, the signal is still related to several atomic layers and understanding what

159

happens in the very first layers is not straightforward. In this sense, theoretical

160

calculations can provide useful information. Combining some elaborate models with

161

calculations using the transition-potential model54 the XANES spectrum can be

162

simulated and the contribution of each atom to the overall spectrum can be

163

determined.

164 165

The importance of X-ray spectroscopies for investigating chemical properties of

166

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,

169

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,

171

XANES also has had a strong impact on geochemistry with spectrum measurements

172

under realistic conditions, but commonly without theoretical spectrum simulations to

173

support the interpretation.63,64 In the present paper we thus extend the theoretical

174

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

182

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

202

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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The Journal of Physical Chemistry

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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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Page 10 of 42

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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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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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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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