# Opportunities from energy-loss near-edge fine structure analysis to track chemical and structural damage in zircon

Matthieu Bugnet, Pierre-Marie Zanetta, Sergio Sao Joao, Anne-Magali

Seydoux-Guillaume, E. Balan, G.A. Botton, Delphine Cabaret, Guillaume

Radtke

► To cite this version:

Matthieu Bugnet, Pierre-Marie Zanetta, Sergio Sao Joao, Anne-Magali Seydoux-Guillaume, E. Balan, et al.. Opportunities from energy-loss near-edge fine structure analysis to track chemical and structural damage in zircon. Micron, 2026, 200, pp.103928. 10.1016/j.micron.2025.103928. emse-05326796

HAL Id: emse-05326796

https://hal-emse.ccsd.cnrs.fr/emse-05326796v1

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# Opportunities from energy-loss near-edge fine structure analysis to track chemical and structural damage in zircon☆

M. Bugnet<sup>a, D, *,</sup> , P.-M. Zanetta<sup>b, D</sup> , S. Sao Joao<sup>c, D</sup> , A.-M. Seydoux-Guillaume<sup>b, D</sup> , E. Balan<sup>d, D</sup> , G.A. Botton<sup>e,f, D</sup> , D. Cabaret<sup>d, D</sup> , G. Radtke<sup>d, D</sup>

## ARTICLE INFO

### Keywords:

EELS

Core-level excitation

Near-edge structures

Zircon

Mineral

DFT

## ABSTRACT

Zircon (ZrSiO$_4$) is the oldest-known mineral of Earth and an ubiquitous silicate in geochronology. More specifically, the accumulation of alpha decay damage in zircon over time significantly affects its physical and chemical properties, and can lead to a disturbance of the ages measured in this mineral. Therefore, analytical tools that enable comprehensive structural and chemical information at the nanoscale in this compound are highly sought after. In this context, we explore the electron energy-loss fine structures resulting from the excitation of O 1s and Si 2p core electrons in zircon, which are interpreted from *ab initio* calculations in a single-particle framework. An excellent agreement is obtained between the experimental and calculated fine structures, emphasizing the large distortion of the final electronic states induced by the core-hole potential. The O-K edge is particularly rich in information, with intense peaks dominated by O 2p - Zr 4d and O 2p - Si 3sp hybrids. This work suggests that the near-edge structures from the O 1s and Si 2p excitations accessible from electron energy-loss spectroscopy or X-ray absorption spectroscopy could be used as tools to follow, interpret and understand structural and chemical modifications in zircon subject to natural radiation damage. We illustrate the potential of this approach through the evolution of near-edge fine structures in a zircon sample that exhibits a locally amorphized zone formed by ultrafast laser excitation.

## 1. Introduction

Zircon (ZrSiO$_4$), notably due to its atomic structure, which remains stable over long periods of time, is the oldest-known natural mineral found on Earth. As a result of this singular status, it is also the most widely used mineral in U-Pb geochronology and thermochronometry to assess the effect of high-temperature and high-pressure events resulting from, e.g., impact events, crust formation, orogenesis, sediment deposition, extinction events, etc. Harley and Kelly (2007). A mineral of such importance has been and remains central to a wide range of investigations, in particular to understand the dissolution and recrystallization processes of zircon from the accumulation of radiation damage over time from, e.g., U/Th decay, which critically affects its physical and chemical properties (Seydoux-Guillaume et al., 2018). Distinguishing pristine zircon from complex and tiny damaged areas

requires experimental tools that can provide structural and chemical information with nanometer spatial resolution, like analytical scanning and transmission electron microscopy (Sanborn et al., 2000; Seydoux-Guillaume et al., 2015) and atom probe tomography (Valley et al., 2014).

Electron energy-loss spectroscopy (EELS) combined with (scanning) transmission electron microscopy (S)TEM is a powerful tool to probe structural and chemical information in a wide range of materials, down to the sub-nanometer scale. EELS provides access to a wide range of excitations like phonons, excitons, interband transitions, plasmons, etc., from the far-infrared range up to high-energy core-level excitations (Egerton, 2011). For K edges of light elements (C, N, O, Al, etc.) and L$_{2,3}$ edges of A-group elements like Si, the latter provides a probe of element-specific electronic unoccupied density of states (DOS) in the material of interest. A large part of the success of (S)TEM-EELS has been

<footnote><sup>a</sup> CNRS, INSA Lyon, Université Claude Bernard Lyon 1, MATEIS, UMR 5510, 69621 Villeurbanne, France</footnote>

<footnote><sup>b</sup> CNRS, UJM Saint-Etienne, LGL-TPE, UMR5276, 42023 Saint Etienne, France</footnote>

<footnote><sup>c</sup> Mines Saint-Etienne, CNRS, UMR 5307 LGF, Centre SMS, 42023 Saint Etienne, France</footnote>

<footnote><sup>d</sup> Sorbonne Université, CNRS UMR 7590, MNHN, IMPMC, F-75005 Paris, France</footnote>

<footnote><sup>e</sup> Department of Materials Science and Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada</footnote>

<footnote><sup>f</sup> Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom</footnote>

<footnote>☆ This article is part of a Special issue entitled: 'EDGE 2024 Proceedings' published in Micron.</footnote>

<footnote>* Corresponding author.
E-mail address: matthieu.bugnet@cnrs.fr (M. Bugnet).</footnote>
the detection of these spectral signatures at the (sub-)nanometer scale, making this technique ubiquitous in research on defects and interfaces in solids.

Minerals, in particular oxides, display a wide range of crystal structures and chemical compositions inherited from primary crystallization as well as defects recording pressure, temperature, and chemical potential variation resulting from secondary transformation in their natural environment. The sensitivity of spectral fine structures resulting from core-level excitations (energy-loss near edge structures - ELNES) at K edges of light elements and at L<sub>2,3</sub> edges of transition metals and A-group elements, to the local atomic environment and the chemical bonding in these compounds makes core-level EELS well suited for probing their electronic structure (McComb et al., 1991; Garvie et al., 1994, 1995a,b; Van Aken et al., 1998a; Golla-Schindler et al., 2003; Van Aken et al., 2004; Golla-Schindler et al., 2006). The degree of covalence or ionicity of the bonding, the geometry of the local atomic environment, and the valence of metals are parameters that can be assessed from ELNES, e. g., the peak intensity ratios at Fe-L<sub>2,3</sub> edges have been used to quantify the iron oxidation state in various minerals (Van Aken et al., 1998b; Garvie and Buseck, 1998; Golla-Schindler et al., 2003; Brown et al., 2017). In the case of zircon, the Si-L<sub>2,3</sub> (~100 eV) and O-K (~530 eV) edges are easily accessible with a high signal/noise ratio in normal acquisition conditions (Garvie and Buseck, 1999; McComb et al., 1992). Edges at higher energy, like Si-K and Zr-L<sub>2,3</sub>, are also accessible but at the cost of longer dwell time and are prone to larger broadening due to the core-hole lifetime (Fuggle and Inglesfield, 1992). Furthermore, the Si-K edge is less structured thus potentially less prominent to inform on the chemistry and structure whereas the Zr-L<sub>2,3</sub> edges typically require a multi-electronic formalism like ligand-field multiplet calculations and is not directly interpretable in terms of unoccupied DOS (Galoisy et al., 1999).

The interpretation of ELNES, or its counterpart from X-ray absorp-
tion spectroscopy (XANES), is key to unlock in-depth understanding of
subtle effects on the local atomic structure and chemistry in minerals.
Spectral fingerprinting is a widely used approach in mineral science
to interpret near-edge fine structures. It is, however, hardly predic-
tive as it relies on the comparison with spectra acquired on different
reference crystals with known structures, to propose plausible origins
to the different spectral features. First-principles calculations are thus
often mandatory to link specific spectral features to fine details of the
electronic structure sensitive to chemical bonding or local symmetry,
and thus to interpret complex chemical phenomena susceptible to
affect the crystal chemistry in minerals. Several studies highlight the
strength of this approach, which demonstrated the high sensitivity
of XANES to, e.g., the local structural relaxation induced around 3d
impurities in gemstones (Gaudry et al., 2005, 2007; Juhin et al.,
2008), the Ge coordination and site geometry in germanates probed
through the O-K edge (Cabaret et al., 2007), the degree of disorder
induced by cationic site exchange in the MgAl<sub>2</sub>O<sub>4</sub> spinel (Yoshioka
et al., 2018), and of ELNES to, e.g., the nature of chemical bonding in
aluminides (Botton et al., 1996; Muller et al., 1998; Lie et al., 1998),
the local arrangement of atoms in polymorphs of wide band-gap binary
compounds (Mizoguchi et al., 2004), the small tetragonal distortion of
ferroelectric BaTiO<sub>3</sub> (Bugnet et al., 2013b), or subtle anisotropic effects
in crystals (Hébert-Souche et al., 2000).

The interpretation of ELNES and XANES from simulations has heav-
ily relied on the advent of first-principles calculations, typically based
on the single-particle approximation in the framework of density func-
tional theory (DFT) (Taillefumier et al., 2002; Hébert, 2007) or multiple
scattering (MS) (Rehr et al., 2010) for K edges and certain L<sub>2,3</sub> edges
of light elements, and on semi-empirical ligand-field multiplet theory
for edges involving partly *d* or *f* shells such as transition metals or
rare-earth ions (De Groot et al., 1990; De Groot, 2005; Haverkort
et al., 2012). In the specific case of zircon, MS approaches have
been employed to model the O-K edge (McComb et al., 1992; Wu
and Seifert, 1996; Jiang and Spence, 2009). While the main peaks

have been identified, the MS approach could not reproduce subtle
fine structures variations, nor the experimental spectrum with high
precision. Furthermore, with the higher energy resolution provided by
monochromators currently fitted on high-brightness electron guns of
transmission electron microscopes, a better definition of experimental
fine structures is accessible.

In this study, we report the experimental Si-L<sub>2,3</sub> (~100 eV) and O-K (~530 eV) edges recorded in a pristine zircon using monochromated EELS to resolve all near-edge fine structures. Overall, the ELNES are well reproduced by DFT calculations, which allows their interpretation in terms of projected density of states and for discussion about the core-hole screening by the valence electrons. The potential of using the ELNES at the nanoscale to analyze structural modifications in zircon is exemplified in a sample locally exposed to damage induced by ultrafast laser excitation, which reveals a clear evolution of the near-edge fine structures between the pristine and amorphized regions. This work suggests that high-resolution near-edge structures resulting from core-level excitation, the O 1s in particular, could be used to track and understand structural damage in zircon minerals.

## 2. Materials and methods

2.1. *Experiments*

In this work, two zircon samples were used. A natural zircon grain
collected from industrial Florida zircon sand was crushed in ethanol
and dispersed onto a lacey-carbon grid prior to observation. A second
sample was a piece of a well-characterized standard Mudtank zircon
crystal (Horstwood et al., 2016) subjected to ultrafast laser excitation.
A thin lamella for TEM observation, specifically sampling the interface
between the damaged and pristine regions was extracted from this
specimen using focused ion beam milling and the lift-out technique in
a ThermoFisher Scientific (FEI) 125 Helios Nanolab 600i focused-ion
beam scanning electron microscope (FIB/SEM).

Monochromated STEM-EELS acquisitions were performed on the
powder zircon sample in a double-corrected monochromated FEI Titan
Cubed 80–300, operated at 300 kV. The monochromator was used to
reach a zero-loss peak full-width at half-maximum of ~0.15 eV, the
spectra were acquired at a dispersion of 0.05 eV/ch. Additional STEM-
EELS experiments were performed on the FIB lamella using a Jeol
ARM-200F NeoARM equipped with a cold field emission gun (C-FEG), a
CEOS ASCOR probe corrector, and a Gatan GIF Quantum spectrometer
fitted with a Quantum Detector MerlinEELS direct electron detector.
The energy resolution was ~0.4 eV, and the EELS acquisitions were
performed with a dispersion of 0.13 eV/ch. The spectra were back-
ground subtracted with a power-law function; a Savitzky-Golay filter
was applied to all spectra. TEM mode was used for selected area
electron diffraction (SAED).

## 2.2. Calculations

EELS spectra were calculated using XSPECTRA (Taillefumier et al., 2002; Gougoussis et al., 2009; Bunäu and Calandra, 2013), a module of the Quantum ESPRESSO suite of codes (Giannozzi et al., 2009), which is based on DFT, and uses a plane-wave basis set, pseudopotentials, and periodic boundary conditions. Ultrasoft pseudopotentials from the PSLIBRARY (Dal Corso, 2014) were generated in the Rappe, Rabe, Kaxiras and Joannopoulos formalism (Rappe et al., 1990) within the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE) (Perdew et al., 1996). The pseudopotentials for the excited atoms were obtained by removing a 1s (K edge) and a 2p (L<sub>2,3</sub> edges) electron from the oxygen and silicon electronic configurations, respectively, and by reducing ionic radii to slightly smaller values to account for the overall contraction of the electronic shells in the presence of a core-hole.
<figure><img src="image_2.png" /><figcaption>**Fig. 1.** Crystal structure and simulation of near-edge fine structures compared to experimental data. (a) ZrSiO₄ crystal structure and local environment around the O atom in the zircon lattice. (b, c) Ab initio calculations (bottom, orange and blue lines) compared to monochromated experimental spectra (top, circles and black lines) of the O-K (b) and Si-L₂,₃ (c) ELNES. The bottom panels are a closer view of the fine structures up to 17 eV above the edge onset. Raw experimental data were recorded using a monochromated electron beam at 300 keV (see methods for details) and are shown as circles, while Savitzky-Golay filtered data are shown as full lines.</figcaption></figure>

Calculations were performed in a 192-atom 2 × 2 × 2 supercell comprising a single excited atom based on the experimental structural parameters given in Robinson et al. (1971). This ensured a spatial separation of ~12 Å between the excited atom and its periodically repeated images, a distance large enough to minimize their spurious interaction. Charge neutrality in the presence of a core-hole was preserved by modeling the excited electron as a uniform background negative charge in the supercell. Self-consistent calculations of the electron density were carried out using an energy cutoff of 80 and 800 Ry for the electronic wave-function and the charge density, respectively, and a single-point sampling of the Brillouin zone.

Powder EELS spectra were then calculated in the dipole approximation on a 3 × 3 × 3 k-point grid. An energy-dependent arctangent-like broadening parameter described in De Clermont Gallerande et al. (2018) with parameters Γ<sub>H</sub> = 0.2 eV (Si-L<sub>2,3</sub> edge) or Γ<sub>H</sub> = 0.4 eV (O-K edge), Γ<sub>M</sub> = 8 eV, A<sub>c</sub> = 40 eV and A<sub>w</sub> = 25 eV was used in the continued fraction to obtain the EELS spectra displayed in the following. A subsequent Gaussian broadening of full-width at half-maximum 0.2 eV has been added to account for the experimental resolution. In the case of the Si-L<sub>2,3</sub> edge, the L<sub>3</sub> contribution only has been computed. Within a single-particle framework, the L<sub>2</sub> edge was simply obtained by duplicating the L<sub>3</sub> edge. A statistical branching ratio (L<sub>3</sub>/L<sub>2</sub>) of 2 has been applied on their intensities to account for the respective degeneracies of the 2p<sub>3/2</sub> and 2p<sub>1/2</sub> initial states and an energy separation of 0.5 eV, close to the reported experimental value (Thompson et al., 2001; Bunău and Calandra, 2013), was employed to reproduce the spectrum.

Electronic DOS calculated in the presence of the core-hole were converged on a 5 × 5 × 5 k-point grid and convoluted by a constant Gaussian broadening function of 0.3 eV full-width at half-maximum.

The crystal structures and valence electron screening maps, obtained as the difference between the ground-state electron densities calculated, respectively, with and without the presence of an excited atom, are displayed using the VESTA software (Momma and Izumi, 2008). Note that in this latter case, the excited electron has been explicitly added to the conduction states and not as a uniform background charge.

## 3. Results and discussion

### 3.1. Ab initio calculations of the O-K and Si-L<sub>2,3</sub> ELNES

In its bulk form, ZrSiO₄ crystallizes in a tetragonal structure with edge-sharing ZrO₈ polyhedra and SiO₄ tetrahedra, as shown in Fig. 1a. The O atom occupies a single Wyckoff position and is chemically bonded to one Si atom and two Zr atoms, the four atoms being located in the same plane. The Si-O bonds are significantly shorter than the Zr-O ones. The experimental and theoretical spectra at the O-K edge and Si-L<sub>2,3</sub> edges are compared in Fig. 1b and 1c, respectively. Both experimental edges show very clear and strong peaks in the fine structures, and are in good agreement with previously published work (Garvie and Buseck, 1999; McComb et al., 1992; Jiang and Spence, 2009). The general shapes of both edges are well reproduced by calculations up to ~30 eV above the edge including the first extended fine structures. All simulated O-K near-edge fine structures identified as A-H agree well with the experiments, with appropriate energy positions and relative intensities. This is also the case for the Si-L<sub>2,3</sub> ELNES, which are accurately reproduced in the calculations both in terms of energy positions and relative intensities except for peak D', for which the calculated intensity is underestimated. The monochromated data
<figure><img src="image_3.png" /><figcaption>Fig. 2. O 1s core-hole valence electron screening maps and projected density of states for the O-K ELNES. (a) Valence electron screening map for the O 1s core hole in ZrSiO₄. Electron depletion (blue) and enrichment (yellow) are shown with isosurfaces ±0.012 e·bohr³. (b) Calculated O-K ELNES (top), and projected density of states calculated with a core hole unless specified otherwise.</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>Fig. 3. Si 2p core-hole screening and projected density of states for the Si – L$_{2,3}$ ELNES. (a) Valence electron screening maps for the Si 2p core hole in ZrSiO$_4$. Electron depletion (blue) and enrichment (yellow) are shown with isosurfaces ±0.012 e·bohr$^3$. (b) Calculated Si-L$_{2,3}$ ELNES (top), and projected density of states calculated with a core hole unless specified otherwise.</figcaption></figure>
<figure><img src="image_5.png" /><figcaption>Fig. 4. STEM-EELS of pristine and laser-amorphized zircon. (a) HAADF STEM of a laser-amorphized zircon crystal observed along [110] zone axis. Insets: (i) high resolution HAADF of the pristine zircon area, and (ii) SAED pattern from the zircon area exposed to the laser. Scale bars: 200 nm, 1 nm (inset i), 5 nm⁻¹ (inset ii). (b) Si-L₂,₃ edges, (c) O-K edge: amorphized zircon (green) and pristine zircon (black). Background-subtracted raw experimental data were recorded at 200 keV (see methods for details) and are shown as circles, while Savitzky-Golay filtered data are shown as full lines.</figcaption></figure>

also enables resolving the split of peak B', which seems to correlate with the Si 2p spin-orbit coupling of ~0.5 eV visible in the calculated spectrum.

### 3.2. O 1s and Si 2p core-hole screening and projected density of states

In the dipole approximation, the O-K ELNES can be interpreted as transitions from the O 1s to empty p states. The core hole introduced in the DFT calculations is intended to account for final-state effects resulting from the excitation of the core electron. Indeed, the screening of the hole left on the core-level of the excited atom by the valence electrons is only partial, resulting in a substantial modification of local electronic states. The screening of the core hole by the valence electrons, shown in Fig. 2a, produces similar effects along the O-Zr₁ and O-Zr₂ directions. However, the more covalent and shorter O-Si bond leads to a stronger modification of the valence electron density.

The site- and symmetry-projected density of states (PDOS) provide insight into the origin of the O-K near edge structures. The dominant effect of the core-hole is to shift the spectral weight of the empty O p states towards the bottom of the conduction band (Fig. 2b, gray vs red lines), an effect that has already been observed in a number of oxides (Bugnet et al., 2013b; Mizoguchi et al., 2000; Mo and Ching, 2000; Nufer et al., 2001; Van Benthem et al., 2003; Duscher et al., 2001; Mauchamp et al., 2009). The origin of the spectral features can easily be interpreted by inspecting the different electronic PDOS shown in Fig. 2b. The lowest energy fine structures A, B, C are dominated by the hybridization of O p with Zr 4d states (for clarity, the PDOS of both Zr₁ and Zr₂ atoms are represented as a summed contribution), while structures D, E and F mostly arise from Si 3s and 3p states. At higher energy, structures G and H are related to high-lying Zr 5s and 5p states. Overall, the energy separation of peaks in the O-K near-edge structures is clear and their origin easily interpreted in terms of hybridized electronic states.

The Si-L₂,₃ ELNES corresponds to transitions from the Si 2p to empty s and d states in the dipole approximation. Whereas a clear energy separation between these two transition channels could have been expected, with anti-bonding Si sp³ states close to the edge onset and unbound Si d states dominating higher-lying structures, inspection of the PDOS displayed in Fig. 3b reveals a different situation. Si s and d states indeed already occur at similar energies in the ground-state, as visible at the bottom of Fig. 3b, although the latter extend to much higher energies. The 2p core-hole potential has a major effect on these electronic states, pulling them down in energy by a few electron-volts, at the bottom of the conduction band originally dominated by the Zr 4d states. This

effect is particularly visible on the Si s states which experience a large splitting, resulting in two peaks separated by about 5 eV. The higher symmetry of the tetrahedral Si atomic site, although not regular, leads to a more symmetric relaxation of the valence density, shown in Fig. 3a, where a close-to-spherical electron accumulation is visible around the cation accompanied by small depletion zones close to the oxygen ions. The local electronic structure, strongly perturbed by the presence of the hole, therefore shows intermingled Si s states, responsible for peaks B' and D', and Si d dominating the shoulder A' at the edge onset, structure C' and higher-lying features E' to G'. It is interesting to note that the main discrepancy between experimental and theoretical Si-L₂,₃ fine structures lies in the underestimated intensity of peak D' and to a lesser extend, of peak B'. These two spectral features are predominantly associated with the Si *p* → *s* transition channel. Comparing the PDOS of the excited Si atom with those of a distant enough reference Si atom from the same supercell, it appears that the effect of the core-hole potential on the lower-lying Si sp³ hybrids responsible for the Si-O chemical bond is much larger than on the diffuse, higher-lying Si d states. The above-mentioned discrepancy might therefore arise from the very different nature of unoccupied electronic states simultaneously probed through *p* → *s* and *p* → *d* channels, respectively, and from our approximate treatment of the excitation process on these states.

### 3.3. Laser-irradiated zircon

STEM-EELS acquisitions were performed on the zircon sample subjected to laser exposure. An example of laser-irradiated zircon is shown in Fig. 4a, where the area exposed to the laser beam is visible. The changes in HAADF contrast at the interfaces between the pristine and laser-irradiated areas illustrate the effect of the laser-induced microstructural modifications of zircon, for which the pristine lattice is confirmed at high resolution along the [110] zone axis (inset i of Fig. 4a). Conversely, a representative SAED pattern recorded in the area exposed to the laser suggests an amorphized structure (inset ii of Fig. 4a).

The core-loss Si-L₂,₃ and O-K edges in pristine zircon are reported in Fig. 4b and 4c (symbols and black lines), respectively. In pristine zircon, most O-K near-edge fine structures are visible in the C-FEG spectrum (Fig. 4b), even though some peaks like A, B, C, F and G were better resolved using the monochromator (Fig. 1b). In the case of the Si-L₂,₃ ELNES shown in Fig. 4c, the monochromated data also revealed more details about the fine structures than the C-FEG spectrum. The fine structures of both edges are strongly modified in the amorphized zircon (symbols and green lines). The Si-L₂,₃ ELNES shows a low-energy
peak at half the intensity of a sharp and most intense peak at ~109 eV followed by a broad peak centered at ~116 eV. This contrasts with the five peaks of pristine zircon in the same energy range. The extended fine structures above 123 eV also change with a broader structure in the amorphized zircon up to ~140 eV. The O-K ELNES also show clear differences between pristine and amorphized zircon. The multiple peaks of the near-edge structures up to ~547 eV in pristine zircon disappear, as the O-K edge for the amorphized zircon is dominated by a broad shoulder at low energy and an intense peak centered at ~535 eV. Above 550 eV, the extended fine structure is comparable in energy and shape for the bulk and amorphized zircon.

Complementary information to core-level excitations could be ex-
tracted from the low-energy loss part of the EELS spectrum. Never-
theless, the origin of spectral features in this part of the spectrum
was shown to be complex, comprising interband transitions, surface
and bulk plasmons (Jiang and Spence, 2013). Structural information
at the scale of the lattice is instead embedded in the ELNES resulting
from core-level excitations. For instance, the latter have been shown
to be useful to track irradiation-induced structural modifications in a
wide range of materials, including minerals (Rafiuddin and Grosvenor,
2015), ceramics (Bugnet et al., 2013a), superconductors (Nicholls et al.,
2022), and 2D materials (Benmoumen et al., 2024; Pazniak et al.,
2021).

Our detailed investigation of near-edge fine structures provides relevant information to interpret structural changes in zircon. The O-K and Si-L₂,₃ ELNES of amorphized zircon, presented in Fig. 4b,c, indeed show drastic changes compared to those of the pristine sample, indicative of the extreme modifications of the crystal structure induced by the laser. The Si-L₂,₃ ELNES spectrum of the amorphized zircon (Fig. 4b) bears strong similarities to amorphous SiO₂ or amorphized quartz (Garvie and Buseck, 1999), with a weak shoulder at ~106 eV and a dominant peak near ~109 eV, which confirmed the amorphized or highly disordered structure inferred from the SAED pattern in the inset (ii) of Fig. 4a. The experimental O-K ELNES of amorphized zircon (Fig. 4c) also shows much broader features than in bulk zircon. This edge, dominated by a leading peak at ~535 eV at a position close to the O 2p-Si 3sp hybrids in pristine zircon, is characteristic of amorphous SiO₂ (Jiang and Spence, 2006; Muller et al., 1999; Botton et al., 2002). However, in the present case, a broad shoulder is present at the edge onset near 530–532 eV which, by analogy to pristine zircon, can be attributed to the hybridization between O 2p and Zr 4d states. Interestingly, this pre-edge peak is absent in amorphous SiO₂ (Jiang and Spence, 2006; Muller et al., 1999; Botton et al., 2002), further suggesting that it is probably related to the Zr atoms in amorphized zircon. The picture of amorphized zircon obtained from the near-edge fine structures is therefore that of a SiO₂-ZrO₂ glassy material. Studying higher energy edges such as Si-K and Zr-L₂,₃ could provide complementary insight into the structure of the amorphized phase. Further studies of the structure of amorphized zircon, such as the one introduced here, are ongoing and will be the focus of a future report. Additionally, the near-edge fine structure analysis presented in this work would probably bring complementary insights into nanoscale phase mapping of zircon in minerals containing multiple phases and often complex microstructures (Gilbert et al., 2003; Roddatis et al., 2025).

4. Conclusion

All experimental fine structures of the O-K and the Si-L₂,₃ ELNES
in zircon are reproduced in the calculated spectrum, enabling the
interpretation of peaks in terms of orbital hybrids through ab initio
calculations. The DFT-based approach chosen here appears to provide
a clear agreement with the experimental O-K and Si-L₂,₃ spectra. This
analysis reveals that the O-K ELNES offers clear and identifiable sig-
natures of orbital hybrids O 2p-Si 3sp and O 2p-Zr 4d, which could
be used as signatures of zircon structural and chemical degradation

in its natural environment. For the Si-L₂,₃ ELNES, the local electronic
structure is strongly perturbed by the presence of the core-hole and
shows strong signatures of intermixed Si *s* and Si *d* states. The main
discrepancy between experimental and theoretical Si-L₂,₃ fine structures
lies in the underestimated intensity of two spectral features that are
predominantly associated with the Si *p* → *s* transition channel. The
application of this ELNES analysis to an amorphized zircon illustrates
the potential of this approach and shows the evolution of characteristic
fine structures linked to the Zr-O and Si-O bonds in the amorphized
area.

CRediT authorship contribution statement

**M. Bugnet:** Writing – review & editing, Writing – original draft, Methodology, Investigation, Funding acquisition, Data curation, Conceptualization. **P.-M. Zanetta:** Writing – review & editing, Investigation, Funding acquisition, Data curation. **S. Sao Joao:** Investigation, Funding acquisition. **A.-M. Seydoux-Guillaume:** Writing – review & editing, Investigation, Funding acquisition. **E. Balan:** Writing – review & editing, Investigation, Funding acquisition. **G.A. Botton:** Writing – review & editing, Investigation, Funding acquisition. **D. Cabaret:** Writing – review & editing, Investigation, Funding acquisition. **G. Radtke:** Writing – review & editing, Methodology, Investigation, Funding acquisition, Data curation, Conceptualization.

Funding sources

MB acknowledges funding from the French National Research Agency through grant number ANR-22-CE29-0019. PMZ, SSJ, and AMSG acknowledge funding from the French National Research Agency through grant numbers ANR-21-CE49-0014-03 and ANR-21-CE08-0005. GR acknowledges CNRS for funding through grant PICS. The Canadian Centre for Electron Microscopy is a national facility supported by CFI under the MSI program, NSERC and McMaster University. GAB acknowledges funding from a NSERC Discovery Grant for this work. Acquisition of the Jeol ARM-200F NeoARM instrument was supported by St-Etienne Métropole under the CPER program.

Declaration of competing interest

Matthieu Bugnet reports financial support was provided by French National Research Agency. Anne-Magali Seydoux-Guillaume reports financial support was provided by French National Research Agency. Pierre-Marie Zanetta reports financial support was provided by French National Research Agency. Sergio Sao Joao reports financial support was provided by French National Research Agency. Gianluigi Botton reports financial support was provided by Natural Sciences and Engineering Research Council of Canada, Canada Foundation for Innovation, and McMaster University. Guillaume Radtke reports financial support was provided by Centre National de la Recherche Scientifique. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

The EELS work has been performed at the Canadian Centre for
Electron Microscopy (McMaster University, Ontario, Canada), and at
the Microscopy Consortium of Lyon-St-Etienne (St-Etienne, France).
The FIB work was performed at the MANUTECH USD platform in
Saint-Etienne (France). The authors acknowledge Rajeev Dwivedi and
Thomas Bilyk for their assistance in obtaining the laser-irradiated
zircon. The technical staff members at all facilities are acknowledged
for instrument maintenance. This work was granted access to the HPC
resources of the SACADO MeSU platform at Sorbonne Université.
# Data availability

Data will be made available on request.

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