ORIGINAL RESEARCH article

Front. Electron. Mater, 25 June 2025

Sec. Superconducting Materials

Volume 5 - 2025 | https://doi.org/10.3389/femat.2025.1572940

This article is part of the Research TopicUnveiling Strongly Correlated Materials with Resonant Inelastic X-ray ScatteringView all 4 articles

Characterizing sample degradation from synchrotron based X-ray measurements of ultra-thin exfoliated flakes

M. F. DiScalaM. F. DiScala1V. HsiehV. Hsieh2B. S. JessenB. S. Jessen2Y. GuY. Gu3D. J. RizzoD. J. Rizzo2J. M. AmontreeJ. M. Amontree4X. YanX. Yan4Q. WangQ. Wang1M. KapferM. Kapfer2T. KimT. Kim3M. GeiwitzM. Geiwitz5G. NataleG. Natale5J. PelliciariJ. Pelliciari3J. C. HoneJ. C. Hone4K. S. BurchK. S. Burch5D. N. BasovD. N. Basov2C. R. Dean
C. R. Dean2*V. Bisogni
V. Bisogni3*K. W. Plumb
K. W. Plumb1*
  • 1Department of Physics, Brown University, Providence, RI, United States
  • 2Department of Physics, Columbia University, New York, NY, United States
  • 3National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
  • 4Department of Mechanical Engineering, Columbia University, New York, NY, United States
  • 5Department of Physics, Boston College, Chestnut Hill, MA, United States

It is undeniable that novel 2D devices and heterostructures will have a lasting impact on the advancement of future technologies. However, the inherent instability of many exfoliated van der Waals (vdW) materials is a well-known hurdle yet to be overcome. Thus, the sustained interest in exfoliated vdW materials underscores the importance of understanding the mechanisms of sample degradation to establish proactive protective measures. Here, the impact of prolonged synchrotron-based X-ray beam exposure on exfoliated flakes of two contemporary vdW materials, NiPS3 and α-RuCl3, is explored using resonant inelastic X-ray scattering (RIXS) and total fluorescence yield X-ray absorption spectroscopy (XAS). In NiPS3, the resulting RIXS and XAS spectra show a suppression, then vanishing, of NiS6 multiplet excitations coupled with an upward shift of the peak energy of the XAS as a function of X-ray dose. In α-RuCl3, the signs of beam damage from the RIXS spectra are less evident. However, the post-experiment characterization of both materials using Raman spectroscopy exhibits signals of an amorphous and disordered system compared to pristine flakes; in addition, energy-dispersive X-ray spectroscopy of NiPS3 shows evidence of ligand vacancies. As synchrotron radiation is fast becoming a required probe to study 2D vdW materials, these findings lay the groundwork for the development of future protective measures for synchrotron-based prolonged X-ray beam exposure, as well as for X-ray free electron laser.

1 Introduction

Advancements in the fabrication of 2D magnetic van der Waals (vdW) materials have largely been driven by the potential to reveal unique magnetic states not achievable in three dimensions, and the possibility of engineering new magnetic phases through extrinsic perturbations, such as stacking (Park, 2016; Sivadas et al., 2018; Gong et al., 2017; Tang et al., 2023). Such progress is crucial for the production of future magnetic based spintronic devices (Hellman et al., 2017; Burch et al., 2018). The first steps towards this goal however, requires a comprehensive picture of a materials magnetic properties, which necessitates understanding the propagation of spin-waves.

The momentum and energy-resolved magnetic excitation spectra in bulk materials are readily measured by inelastic neutron scattering (INS) or resonant inelastic X-ray scattering (RIXS). However, the extremely small sample volumes of 2D magnetic materials make INS not feasible. Optical measurements can be used to obtain some information about the magnetic excitations in 2D materials, but are limited to negligible momentum transfers so can only provide limited information of magnetic excitations in antiferromagnets. Hence, X-ray scattering techniques are essential for advancing our understanding of 2D magnetism (Ahn et al., 2024).

Sample degradation has been a persistent problem in the fabrication of clean, few-layer vdW materials. A primary source of degradation is the physical adsorption of oxygen on the surface, or the chemisorption of oxygen into ligand vacancies (Grünleitner et al., 2022; Wu et al., 2021). Extensive research has been conducted on methods to protect exfoliated flakes from degredation in ambient atmosphere. These predominantly involve the placement of a capping layer of hBN or thin-films such as Al2O3 (Li Q. et al., 2019) on top of the 2D material. However, during an X-ray or light scattering experiment, large quantities of energy are potentially deposited into the 2D material, and in this case, it is also possible that the measurements damage or degrade the sample quality. For instance, light induced sample damage has been reported when conducting Raman measurements on exfoliated flakes, even when using low powers (Sandilands et al., 2010; Kuo et al., 2016; Kim et al., 2019). So far, little is known about how such damage occurs or about the robustness of any protections against such effects.

In this work, we demonstrate the X-ray induced generation of ligand vacancies using a combination of resonant inelastic X-ray scattering (RIXS) and X-ray absorption spectroscopy (XAS) in two contemporary magnetic vdW materials, NiPS3 and α-RuCl3, including both bare and graphene capped α-RuCl3, each studied for their potentially unique 2D magnetism. NiPS3 has emerged as a highly promising material for studying the XY model in a real 2D system, while α-RuCl3 is recognized as a prime candidate to host the long-sought Kitaev quantum spin-liquid state in 2D (Kim et al., 2019; Sarikurt et al., 2018; Kim et al., 2022). Prolonged exposure to intense X-ray beams that is necessary to carry out RIXS measurements was found to result in significant degradation of both samples.

The RIXS spectra of NiPS3 show transient multiplet excitations and a transition towards predominantly fluorescence-like excitations as a function of X-ray dosage, which is reflected in the disappearance of majority multiplet excitation peaks in the XAS spectra. On the other hand, degradation of α-RuCl3 was only observed and characterized post RIXS measurements.

Post-irradiation EDS analysis of NiPS3 revealed a reduction in sulfur and phosphorus when compared to a pristine sample, and increased levels of chemisorbed oxygen. Additionally, Raman spectra of both materials were indistinguishable from the Si substrate apart from a tapering background. These results are consistent with X-ray induced ligand expulsion and a significant crystallographic reorganization. These results emphasize the requirement for developing more robust and specialzed sample protection techniques in light of the necessity for synchrotron based X-ray scattering to explore dispersive magnetic excitations in the 2D limit of exfoliated flakes, and especially for novel heterostructure devices.

2 Materials and methods

Single crystal samples of NiPS3 were grown by vapor transport, following previously published methods (Wildes et al., 2015; Lançon et al., 2018; DiScala et al., 2024; See supplementary material for details) (See Table. SI for more details). NiPS3 crystallizes in the monoclinic C2/m space group with Ni (S = 1) atoms on honeycomb lattices in the ab-planes. Each Ni atom is octahedrally coordinated by 6 S atoms, with P atoms situated between the 2D sheets of NiS6 that form the vdW gap along the c-axis with an interlayer spacing of 0.636 nm (Kuo et al., 2016; Wildes et al., 2015). NiPS3 magnetically orders at a transition temperature of TN = 155 K, forming ferromagnetic zig-zag chains with moments parallel to the a-axis and antiferromagnetically coupled along the b-axis, along with a small out of plane component (Wildes et al., 2015; Wildes et al., 2022).

To prepare NiPS3 samples for RIXS measurements, bulk crystals were exfoliated using conventional scotch-tape methods (Kuo et al., 2016), deposited onto Polydimethylsiloxane (PDMS), and then transferred to Si substrates pre-patterned with Au fiducial markers, as seen in Supplementary Figure S1a. The Au fiducial markers provide a fluorescence contrast to the Si substrate that allows for unambiguous location of few layer samples whose signals were weak under an X-ray beam (DiScala et al., 2024; See supplementary material for details; Lupascu et al., 2012). Lastly, to protect from ambient air exposure, samples were coated with 3 nm thick Al2O3 using electron beam sputtering deposition. At this thickness, the Al2O3 capping layer is transparent to X-rays at the Ni L3 edge. Exfoliation and PDMS transfer were preformed in ambient air; within 1 hour of exfoliation, ideal samples were identified and transferred onto Si-substrates, then stored under vacuum and in an argon-filled glovebox until the Al2O3 capping layer was deposited. Post deposition, samples were returned to vacuum storage in an argon-filled glovebox. Optical contrast between sample and PDMS was used to determine sample layer count. The optical contrast on PDMS was determined using a combination of previously determined atomic-force microscope thickness measurements and optical contrast with SiO2 substrate (DiScala et al., 2024). The thickness of the irradiated sample was determined to be 20 layers (L), or 12.72 nm.

To avoid stoichiometric variation between samples, pristine exfoliated samples used as a baseline for the various characterization techniques explored were exfoliated from the same bulk NiPS3 as the X-ray irradiated sample. These samples were prepared following the aforementioned exfoliation process, but then transferred onto Si/SiO2 substrates for further confirmation of sample thickness. Of these samples, one was left in air to test the effect of oxygen and water adsorption on exfoliated samples, while the other was kept under vacuum and stored in an argon-filled glovebox along with the X-ray irradiated sample; this latter sample was only removed from vacuum when measurements were taken, and immediately placed back under vacuum and in the glovebox afterwards.

α-RuCl3 crystals were grown by the sublimation of RuCl3 powder sealed in a quartz tube under vacuum. About 1 g of powder was loaded in a quartz tube of 19 mm in outer diameter, 1.5 mm thick, and 10 cm long. The growth was performed in a box furnace. After dwelling at 1,060°C for 6 h, the furnace was cooled to 800°C at a rate of 4°C/h.

To prepare α-RuCl3 samples for RIXS measurements, bulk crystals were exfoliated onto a Si/SiO2 substrate with pre-patterned Cr/Au alignment markers for easier optical identification of sample location. α-RuCl3 flakes of varying thickness were characterized using optical contrast with the SiO2 substrate as well as using atomic force microscopy.

To prepare graphene/α-RuCl3 heterostructure (G/RuCl3) samples, graphene films were transferred onto a Si/SiO2 substrate containing varying thicknesses of exfoliated and pre-characterized α-RuCl3 crystals. The graphene films grown on Cu foils (Graphene Supermarket) were transferred using the conventional wet transfer method (Suk et al., 2011). The graphene was spin-coated with a thin layer of polymethyl methacrylate (495 PMMA A4 from Kayaku, 4,000 rpm, 1 min, bake at 180°C, 5 min) to provide mechanical support for the transfer. The backside graphene was removed by O2 plasma for a duration of 1 minute at 100 W. The PMMA/graphene was detached from the copper by placing the sample in copper etchant (Ammonium persulfate (NH4)2S2O8) for 2 h. After washing with DI water 3x, the floating PMMA/graphene layer was transferred to the Si/SiO2 substrate and dried in vacuum (1 Torr) overnight. Next, the sample was heated on a hot plate at 80°C for 20 min and 180°C for 20 min in an ambient environment. Finally, the sample was soaked in acetone for 30 min, rinsed with IPA, and dried with N2. All RuCl3 samples were prepared and characterized in air, with no additional precautions taken during the preparation of the G/RuCl3 heterostructures with the wet transfer process due to the literature-reported stability of RuCl3 in air (Zhou et al., 2019). Raman after the wet-transfer process confirms that ambient oxygen and humidity did not affect the quality of either the bare RuCl3 or the G/RuCl3 heterostructures, consistent with the findings in Refs. (Zhou et al., 2019; Breitner et al., 2023). While Breitner et al. perform heat treatment on RuCl3 in an inert environment, they demonstrate that clear signatures of sample degradation only appear for annealing temperatures beyond 300°C, temperatures which we do not approach in our sample preparation process.

All G/RuCl3 heterostructure samples, and some of the α-RuCl3 flakes, were coated with 10 nm thick Al2O3, using atomic layer deposition in a Cambridge Nano Tech S200. Using electron beam lithography and evaporation, these samples were then patterned with Au markers, as shown in Figures 1e–h, for easier identification of sample location optically and with X-ray fluorescence, in addition to helping heat dissipate from the beam. To do so, samples were spun with a bilayer resist of 950k and 495k PMMA, at 50 nm and 200 nm, respectively. Electron beam exposure was done at 80 kV with a current of 10 nA, and the sample was subsequently developed in a 5°C solution of IPA: H2O (3:1). Cr/Au (3/50 nm) was then deposited, and the samples were subsequently immersed in acetone for metal lift-off. Samples were then stored at ambient pressure in a nitrogen-filled dry box.

Figure 1
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Figure 1. (a, d) Crystal structure of NiPS3 (a) and α-RuCl3 (d) and orientations on substrate, as shown in the microscope images. (b,c) Microscope images of NiPS3 pre- (b) and post-irradiation (c). Microscope images of 22 nm α-RuCl3 before (e) and after (f) X-ray beam exposure. Dashed black circles in (b) mark regions of X-ray induced SiO2 substrate damage. Red and green circles in (f) mark the on and off X-ray beam spots for the Raman spectra shown in Figure 8. Microscope images of the G/RuCl3 heterostructure before (g) and after (h) X-ray beam exposure; green brackets in (h) demarcate the beam spot region. The red dashed square marks the Raman map region shown in Figure 9.

RIXS and XAS measurements were carried out on the SIX 2-ID beamline of the National Synchrotron Light Source II (Dvorak et al., 2016). For NiPS3, horizontal scattering geometry was set to 2θ=90° and sample angle θin=77.5°. RIXS spectra at Ni L3 edge were collected in 20 min segments using linear vertical polarization with an 28.8 meV energy resolution (full width at half max, FWHM), after which XAS spectra were collected. Incident X-ray energies varied between 852.6–853.2 eV; with 1012 photons/s and a beam spot size of 15 μm (H) x 1.7 μm (V) (focused by an ellipsoidal mirror placed after the monochromator exit slit), resulting X-ray dosage at the Ni L3-edge is 8.3 μJ/μm2s. Bulk NiPS3 spectra were collected with an identical scattering angle, but in specular geometry, and with an 55.1 meV overall energy resolution FWHM. Sample orientation and structure are shown in Figure 1a, with the c-axis along the direction of the incident beam. Microscope images of NiPS3 pre- and post-irradiation are shown in Figures 1b,c.

For α-RuCl3, horizontal scattering geometry was set to 2θ=90°. RIXS spectra were collected for one and a half hours each at three incident energies across the Ru M3 edge, using linear horizontal polarization, with 67 meV of energy resolution (full width at half max, FWHM). Incident X-ray energies varied between 460.7 and 465 eV; with 81012 photons/s and a projected beam spot size of 58 μm (H) x 8.3 μm (V) (θin=15°) and 20.2 μm (H) x 8.3 μm (V) (θin=48°), resulting X-ray dosages at the Ru M3-edge are 1.58 μJ/μm2s and 4.5 μJ/μm2s, respectively. In the following, we will present the RIXS data taken at one excitation energy, coinciding with the maximum of the Ru M3 edge. Sample orientation and structure are shown in Figure 1a, with the c-axis along the direction of the incident beam. Microscope images of α-RuCl3 and G/RuCl3, pre- and post-irradiation, are shown in Figures 1e–h.

For NiPS3, Raman measurements were conducted on a pseudo-confocal Raman microscopy spectrometer (TriVista CRS3) at room temperature in an Argon atmosphere, with an excitation wavelength of 633 nm, excitation power 1 mW, and spectrometer grating of 1,500 lines/mm. EDS measurements were conducted using a Thermo Scientific Quattro S using a 20 kV accelerating voltage. For α-RuCl3, Raman measurements were conducted using a Renishaw inVia micro-Raman spectrometer at room temperature in ambient air, with an excitation wavelength of 532 nm, excitation power 2 mW, and spectrometer grating of 1800 lines/mm.

3 Results

3.1 NiPS3

Figure 2A shows the evolution of the first two NiS6 multiplet excitations, centered at Eloss = 1.05 eV and 1.68 eV respectively, as a function of X-ray beam dosage and exposure time. Figure 2b shows the characteristic NiPS3 RIXS spectrum at t = 0 min (t0), along with its respective XAS spectrum shown in the inset. These two multiplet excitations are clearly resolved up to t = 60 min (t3). At t = 80 min (Figure 2c) signatures of these two peaks can still be seen, however, superimposed by a large background. Additionally at this time, the XAS spectrum shows the first qualitative change, transitioning from a clear two-peak structure to a single peak, and shifting upwards in incident energy by 200 meV. As X-ray beam dosage increases, the two multiplet excitations vanish into the electron-hole continuum. Concurrently, the XAS peak continues to shift upward in incident energy, plateauing at Einc 853.2 eV (Figure 2d). The full time evolution of RIXS and XAS are shown in the Supplementary Materials (Supplementary Figures S2–4) (See Supplementary Material for details).

Figure 2
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Figure 2. (a) Evolution of NiS6 multiplet excitations irradiation dose (left) and time (right). Changes in spectra are immediately apparent after 20 min of irradiation (171 μJ/μm2), however, multiplet excitations only vanish after more than 80 min of irradiation (683 μJ/μm2). Horizontal dashed red lines indicate the selected RIXS scans of (b–d) along with respective XAS spectra shown in insets. Vertical green lines indicate the centroid positions of the first two multiplet excitations.

In order to elucidate the affect of prolonged X-ray beam exposure, we begin our analysis with the time/dosage dependent XAS signal. At t0 we find that four Voigt profiles are required to fit the data, as shown in Figure 3a. The peaks labeled A and B correspond to the white-line, while SP1 and SP2 represent the satellite peaks (Kim et al., 2018; He et al., 2024). As X-ray beam exposure continues, both peaks A, SP1, and SP2 decrease intensity, and after t3, SP1 and SP2 vanish into the background. Simultaneously, peak A nearly reached its minimum intensity and was significantly overlapped by the fit of peak B, causing the XAS to assume a seemingly one-peak structure (inset of Figures 2b,c and Figure 3b). However, from t t3, the best fits minimizing the residuals were still achieved with two peaks (Supplementary Figure S3). As seen in Figure 3c, from t = 0 260 min, peak A shifts upwards in incident energy by 470 ± 40 meV. During the same time frame, peak B only shifts upwards in incident energy by 331 ± 83 meV, with an average ΔEInc̄ = 25 ± 18 meV. Notably, the FWHM of peak B stayed fairly constant, averaging 1.85 ± 0.01 eV across the full time range measured (Figure 3d). The change in FWHM of peak A, however, is not so readily gleaned after t3 as discussed in the full fitting procedure found in the Supplementary Material (See supplementary material for details).

Figure 3
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Figure 3. t = 0 min (a) and t = 260 min (b) NiPS3 XAS sepctra at Ni L3-edge. Black points are experimental data and red lines show total fit to the data using four Voigts (a) and two Voigts (b) along with an error step function. (c) Centroid positions of A and B with irradiation dosage (bottom) and time (top). Vertical dashed red line demarcates the last time both satellite peaks were reliably fit before vanishing into background, corresponding to 512 μJ/μm2. (d) Evolution of the FWHM of peaks A and B, and of the step error function, with irradiation dosage and time. Vertical dashed red lines again demarcate the vanishing of the satellite peaks.

Using the bulk NiPS3 RIXS map, shown in Figure 4, we are able to disentangle the origin of each feature in the XAS. Figure 4a shows RIXS map function of incident energy (Einc) vs energy loss (Eloss). Features of constant Eloss are Raman-like excitations and have been previously characterized as multiplet excitations (DiScala et al., 2024; He et al., 2024), while the slopped features are fluorescence excitations (Ament et al., 2011). We then find great agreement between the exfoliated XAS at t0 compared to the partial fluorescence yield (PFY), defined as the sum of Eloss values for each Einc in the RIXS map. Figure 4b then shows the RIXS map as a function of Einc vs outgoing energy (Eout) in order to highlight the constant outgoing energy of the fluorescence exciations. By subtracting the elastic line and first two NiS6 multiplet excitations from the RIXS map in Figure 4b, we again compare the XAS and PFY and find that the majority of the intensity within the region of peak B is associated with fluorescence excitations.

Figure 4
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Figure 4. Bulk NiPS3 RIXS map shown as functions of incident energy (Einc) vs energy loss (Eloss) (a) and Einc vs outgoing energy (Eout) (b). Both maps are also shown with their respective PFY spectra and the exfoliated NiPS3 XAS. The XAS white-line has been shifted to coincide with the PFY white-line. The RIXS map in (b) has had the elastic line and first two multiplet excitations removed, which is reflected in the intensity dip in the PFY. The PFY after excitation subtraction was normalized to the maximum of the PFY prior to subtraction.

To better understand the effects of X-ray induced sample degradation, we performed a suite of sample characterization experiments and compared results with pristine flakes of comparable thickness. Figure 5 shows the elemental EDS mapping of the irradiated NiPS3 (Figure 5a) compared to a pristine sample (Figure 5c). The irradiated NiPS3 shows significantly less sulfur when compared to the pristine sample and, additionally, increased levels of carbon and oxygen. The oxygen is not associated with the substrate or Al2O3 capping layer, as evidenced by the EDS spectrum of the neighboring Si substrate, which showed lower oxygen levels than the sample and substrate combined (see Supplementary Figure S5 in (See Supplementary Material for details)). We note again that the pristine NiPS3 sample was exfoliated on an SiO2 substrate, and thus, the oxygen in Figure 5c arises from the substrate alone. The presence of carbon on the sample can be explained by the outgassing of carbon from stainless steel in ultra-high vacuum (Calder and Lewin, 1967; Nevshupa and de Segovia, 2002; Ashraf et al., 2019). Physical adsorption of oxygen is a known source of contamination/degradation for a variety of exfoliated flakes (Li Q. et al., 2019). However, it has also been suggested that chemisorption of oxygen on exfoliated flakes is possible, especially in the presence of sulfur vacancies, albeit slow in ambient air (Grünleitner et al., 2022; Wu et al., 2021; Liu et al., 2016).

Figure 5
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Figure 5. EDS spectrum on (a) irradiated NiPS3, (b) irradiated NiPS3 post high-vacuum annealing, and (c) pristine exfoliated NiPS3. Shaded regions highlight the edge energy region for the respective elements present in each spectrum.

Although removal of adsorbed oxygen on the surface of exfoliated flakes is not widely reported, there is evidence suggesting high-vacuum annealing can expel this adsorbed oxygen (Grünleitner et al., 2022). Thus, we assessed the degree of oxygen passivization of sulfur vacancies through chemisorption on the irradiated sample via high-vacuum annealing at 120°C for 150 min. However, the elemental EDS mapping post-vacuum annealing did not show a reduced oxygen content (Figure 5b), suggestive of chemisorption of oxygen, rather than physical adsorption. By subtracting the EDS spectrum of the substrate alone, it is evident that the excess oxygen in the sample is not associated with Al2O3 capping layer. It is then likely that this oxygen originated from the short time frame of moving the sample from the ultra-high vacuum RIXS chamber to the vacuum desiccator; a normally slow process in ambient air sped up by the generation of sulfur vacancies.

It is clear from the EDS analysis that the prolonged, high-flux X-ray beam exposure produced sulfur vacancies in exfoliated flakes of NiPS3. Despite these vacancies, it is possible that the structure of NiPS3 stays somewhat intact (Grünleitner et al., 2022). We thus probe the structure of the irradiated sample using Raman spectroscopy with an excitation wavelength of 633 nm, again comparing to a pristine sample of comparable thickness. Figure 6a shows the Raman spectra of the irradiated sample, taken before high-vacuum annealing, which shows none of the Raman modes indicative of NiPS3 and appears indistinguishable from the Si substrate apart from a background shift that tapers off beyond the 520 cm1 Si peak. In contrast, Figure 6b shows the Raman spectrum for the pristine NiPS3 sample, where we clearly identify the previously reported 8 Raman-active phonon modes in NiPS3 (3A1g + 5Eg), including the new peak at 204 cm1 that appears in thin exfoliated flakes (Kuo et al., 2016; Kim et al., 2019; Bernasconi et al., 1988). In addition, we find signals of amorphous carbon in the irradiated NiPS3 Raman spectra that is absent in the non-irradiated samples (Supplementary Figure S6a). Lastly, we tested the affect of physically adsorbed oxygen on the modulation of Raman modes in exfoliated NiPS3. Figure 6c shows the Raman spectra of a five layer flake of NiPS3 left in ambient air for 3 weeks, where all previously reported Raman modes are identifiable. This result indicates that adsorbed oxygen is not responsible for the Raman mode suppression seen in the irradiated sample (Kuo et al., 2016).

Figure 6
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Figure 6. Raman spectra on (a) irradiated sample and Si substrate, (b) pristine NiPS3 of comparable thickness, and (c) five layer NiPS3 after 3 weeks in ambient air. All spectra were acquired with an excitation wavelength of 633 nm. Spectra in (b, c) are normalized to the Si mode at 520 cm1, which has been omitted from each figure. We identify 8 Raman modes within the range measured, adopting the notation of C.-T. Kuo et al. (2016). Data at 318 cm1 has been excluded due to an artifact arising from dust on the detector.

3.2 α-RuCl3

The goal of the α-RuCl3 measurements was to investigate the electronic evolution in α-RuCl3 at the interface with graphene (Rizzo et al., 2020; Wang et al., 2020). A thin layer of α-RuCl3 was preferred to enhance the contrast of the interface effect. Therefore, we first investigated several samples of α-RuCl3 with variable thicknesses from, 100 nm (bulk) down to 7 nm, to explore possible changes in the electronic structure occurring due to the reduced number of layers (DiScala et al., 2024). For this step, we considered bare flakes of α-RuCl3, and flakes capped with Al2O3 and framed by gold markers. Next, we investigated heterostructures (G/RuCl3) made by stacking α-RuCl3, graphene, and Al2O3, ultimately framed by gold markers.

In Figure 7, we present the bulk Ru M3 RIXS data compared to spectra obtained from α-RuCl3 flakes of an intermediate thickness range (22–25 nm), chosen as a representative case. All spectra were measured with the same scattering geometry (θin=15° and 2θ=90°) and at the same excitation energy, main peak of the Ru M3 XAS (see inset in Figure 7). The bulk RIXS spectrum is in good agreement with previous studies (Lebert et al., 2020). The RIXS spectrum measured on a 22 nm bare flake of α-RuCl3 presents the overall same features observed in the bulk, but with reduced intensity and a strongly enhanced elastic line. The green and the red RIXS spectra in Figure 7 refer to the Al2O3 capped α-RuCl3 flake (24 nm) and to the heterostructure α-RuCl3 (25 nm)/graphene/Al2O3, respectively. These spectra present similar intensity: they are weaker than the bulk signal, but stronger than the signal from the 22 nm flake. Their elastic lines are also comparable with the one from the bulk. The intensity variation obtained between these RIXS spectra opens the question whether the effect is intrinsic to the physics of the samples or caused by beam damage. For this reason, a post-characterization investigation was performed on all samples, including optical microscope images and Raman spectroscopy.

Figure 7
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Figure 7. RIXS spectra of α-RuCl3 at Ru M3 edge, T = 300 K. The black spectrum refers to a bulk sample, the blue spectrum to a 22 nm thick flake, the green spectrum to a 24 nm thick flake capped with Al2O3 (10 nm), and the red spectrum to a 25 nm thick flake capped with graphene and Al2O3 (10 nm). The inset displays the Ru M3 edge X-ray Absorption of α-RuCl3, and the red dashed line highlights the excitation energy used for the RIXS measurements with σ polarization.

Post-irradiation characterization of bare α-RuCl3 suggests that sample degradation due to X-ray beam exposure is remarkably similar to that of NiPS3. The Raman spectra of irradiated α-RuCl3 lacks any visible phonon modes indicative of α-RuCl3 (Figure 8c). In contrast, the Raman spectra on the non-irradiated region of the sample retains the six characterizing phonon modes of α-RuCl3 (Figure 8c) (Li G. et al., 2019). As was the case for irradiated NiPS3 sample, these results are indicative of a drastic structural reorganization of α-RuCl3 due to irradiation. In addition, we find traces of amorphous carbon in the Raman spectra of bare α-RuCl3, on and off the beam-spot (Supplementary Figure S7b). The presence of amorphous carbon off the beam-spot originates from the X-ray beam rastering process used for sample localization.

Figure 8
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Figure 8. Raman spectra on and off the X-ray beam spot, as marked by red and green circles in Figure 1f. All spectra were acquired with an excitation wavelength of 532 nm. Off the beam spot, we identify the 5 Raman modes representative of α-RuCl3, written in the D3d point group (Li G. et al., 2019). On the beam spot, the only visible Raman mode belongs to Si peak at 295 cm1.

Interestingly, signs of substrate damage can be seen when comparing the optical microscope images of bare α-RuCl3 before (Figure 1e) and after irradiation (Figure 1f, black dashed circles). Optical contrast is a powerful tool to quickly and reliably determine the thickness of ultra-thin exfoliated flakes (Ivanova et al., 2024); a prerequisite of reliable optical contrast measurements is a nominally uniform SiO2 layer beneath the sample. However, if irradiation alters the uniformity of the SiO2 layer, then optical contrast would no longer be a reliable determinant of sample thickness.

Similar optical indications of sample damage were seen on the G/RuCl3 heterostructure, as displayed in Figure 1g (before) and Figure 1h (after, demarcated by green brackets). Herein, we explore the sample degradation of the graphene capping layer due to the prolonged irradiation. Figure 9c shows a spatial map of the carbon D-peak (1,350 cm1) fitted intensity extracted from Raman measurements. The mapped area is demarcated by a dashed red box in Figure 9b, and it spans across a beam irradiated area and a non-irradiated area. Figures 9d,e show characteristic Raman spectra measured on and off the irradiated region, respectively. Both spectra display characteristic graphene peaks, the G-peak (1,580 cm1) and the 2D-peak (2,690 cm1); whereas the D-peak is only visible in the spectra collected within the irradiated area (Figure 9d) and is a fingerprint of amorphous carbon (Saito et al., 2011). Additionally, fitting the intensity of the G-peak and 2D-peak across the scanned area resulted in an intensity ratio of (I2D/IG) two in the non-irradiated region and a ratio of 0.5 in the irradiated region: this ratio is representative of low and high levels of disorder in graphene, respectively (Saito et al., 2011; Kim et al., 2009).

Figure 9
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Figure 9. (a) Fitted Raman intensity map of amorphous carbon D-peak on and off the X-ray beam spot. The corresponding map region is marked by dashed red square in Figure 1h. Representative Raman spectra of graphene on (b) and off (c) the X-ray beam spot: the amorphous carbon D-peak is only resolvable on X-ray beam spot. All spectra were acquired with an excitation wavelength of 532 nm. Spectra were rebinned using a window of 5Δ(cm1).

4 Discussion

The EDS analysis on NiPS3 clearly indicates the expulsion of sulfur and phosphorus due to X-ray beam exposure. Yet, simply creating ligand vacancies does not tell the complete story of the extent of sample degradation. Ligand vacancies are naturally present in exfoliated samples, however the transience of multiplet excitations in the RIXS spectra, and the majority multiplet peaks in the XAS spectra (A, SP1,SP2) are indicative of a more severe structural reorganization. Density functional theory (DFT) calculations on NiPS3 with 5% sulfur vacancies found drastic crystallographic and electronic structure changes (Wu et al., 2021). In fact, the calculated DOS of monolayer NiPS3x shows two new states; one of mostly S-3p character just below EF, and one of Ni-3d character in the energy gap above EF. These results are consistent with our RIXS spectra which showed progressively favorable fluorescence excitations with increasing sulfur vacancy generation.

The Raman spectra on the irradiated NiPS3 sample further substantiate the claim of drastic crystallographic structure changes due to ligand vacancies. The lack of visible phonon modes associated with NiPS3, and the large tapering background that the Si modes sit atop, are suggestive of a disordered system with decoherent modes. In pristine NiPS3, the modes below 220 cm1 are dominated by Ni-S, Ni-P, S-S, S-P, and P-P bond bending, while modes above 300 cm1 are mostly associated with intra-molecular vibrations from the (P4S6)4- bipyramid (Kim et al., 2019; Bernasconi et al., 1988). While small amounts of sulfur vacancies may lead to modulations in the (P4S6)4- bipyramidal dominant modes, the absence of the lower cm1 bond bending dominant modes is again indicative of a more severe structural reorganization.

The connection between the adsorbed oxygen and the absence of visible Raman modes, however, is still not fully understood. C.-T. Kuo et al. have shown that, for a three layer flake of NiPS3 left in air for 11 days, only remnants of the A1g(2) and A1g(3) modes are visible (Kuo et al., 2016), implying that adsorbed oxygen has a destructive affect on the modulation of sulfur planes and of the nickel atoms. However, when measuring the Raman spectra of a five layer flake of NiPS3 left in air for 3 weeks, we are still able to clearly resolve all reported Raman modes.

For the case of α-RuCl3, the Raman spectra of the irradiated bare flake show no visible phonon modes associated with crystalline α-RuCl3, suggesting similar sample damage as was characterized in NiPS3. Additionally, the spatial D-peak Raman intensity map of G/RuCl3 clearly depicts a departure from ordered graphene outside of the irradiated region, to disordered graphene, or amorphous carbon, within. The change in I2D/IG across the boundary of the irradiation region is further indicative of this departure. As previously mentioned, the outgassing of carbon from stainless steel in ultra-high vacuum is a commonly known phenomenon. Thus, a portion of the amorphous carbon within the irradiated area originated from the outgassing process, while the remainder was generated from the irradiation of the original ordered graphene. However, as no signatures of amorphous carbon were observed in the Raman spectra outside the irradiated region, it is reasonable to assume that most of the amorphous carbon observed within the irradiated region originates from the structural disorder of the graphene caused by the X-ray beam exposure. Based on this evidence, the RIXS spectra measured on the thin α-RuCl3 samples were considered non-representative of the pristine systems. Although there was no post-characterization performed on the Al2O3 capped α-RuCl3 flake, the fact that its RIXS spectrum overlapped well with that of the clearly damaged G/RuCl3 heterostructure brings into question the α-RuCl3 RIXS measurement quality as well.

The stability of exfoliated flakes is in general quantified by the materials defect generation energy (DGE), often calculated using DFT. (Wu et al., 2021; Hu et al.; Yang et al., 2023). Al2O3 capping layers have proven an effective passivization method to prevent oxidation in ambient conditions for a variety of vdW materials (Li Q. et al., 2019; Geiwitz et al., 2024). However, up to 10 nm of Al2O3 was unable to prevent sample damage during X-ray beam exposure. Thus, calculations detailing the changes in the DGE of various multilayer/capping layer systems are desirable as they can provide a means of testing various capping layers prior to experimentation.

In summary, we characterized the means of sample degradation due to high-flux synchrotron based X-ray scattering on two contemporary vdW materials, NiPS3 and α-RuCl3. RIXS and XAS measurements of NiPS3 showed transient multiplet excitations as a function of X-ray dosage, while EDS and Raman confirmed the expulsion of sulfur and structural reorganization. Although EDS measurements of post-irradiation α-RuCl3 is needed to conclusively determine ligand expulsion as the exact means of sample damage, the remarkably similar Raman spectra of α-RuCl3 and NiPS3 post-irradiation suggests a consistent degradation route. These results emphasize the necessity for more robust protection techniques for 2D exfoliated flakes beyond ambient conditions, else the novel magnetic prospects these, and other magnetic vdW materials offer will remain unrealized. In addition, we showed evidence of local graphene amorphousization in the irradiated region of G/RuCl3. This finding is significant for future synchrotron experiments on graphene-based heterostructures, as the structural integrity of graphene is crucial for preserving the emergent phenomenon of these systems. More broadly, our work should stimulate systematic pre- and post-characterization methods of samples, especially when the thickness is reduced and when high-brilliance X-ray sources are used, including X-ray free electron lasers.

Data availability statement

The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

Author contributions

MD: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Supervision, Visualization, Writing – original draft, Writing – review and editing. VH: Data curation, Formal Analysis, Methodology, Writing – review and editing. BJ: Data curation, Formal Analysis, Methodology, Writing – review and editing. YG: Data curation, Formal Analysis, Writing – review and editing. DR: Data curation, Writing – review and editing. JA: Data curation, Writing – review and editing. XY: Data curation, Writing – review and editing. QW: Data curation, Writing – review and editing. MK: Data curation, Writing – review and editing. TK: Data curation, Formal Analysis, Writing – review and editing. MG: Methodology, Supervision, Validation, Writing – review and editing. GN: Methodology, Supervision, Writing – review and editing. JP: Investigation, Methodology, Supervision, Writing – review and editing. JH: Funding acquisition, Project administration, Resources, Supervision, Writing – review and editing. KB: Funding acquisition, Project administration, Resources, Supervision, Writing – review and editing. DB: Funding acquisition, Project administration, Resources, Supervision, Writing – review and editing. CD: Funding acquisition, Project administration, Resources, Supervision, Writing – review and editing. VBi: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Writing – review and editing. KP: Conceptualization, Funding acquisition, Investigation, Project administration, Resources, Supervision, Writing – review and editing.

Funding

The author(s) declare that financial support was received for the research and/or publication of this article. Work at Brown University was supported by the National Science Foundation under Grant No. 2429695. The work on α-RuCl3 was supported as part of Programmable Quantum Materials, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES), under award DE-SC0019443. This research uses the beamline 2-ID of the National Synchrotron Light Source II, a DOE Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under Contract No. DE-SC0012704. The work of GN was supported by the National Science Foundation (NSF) EPMD program via Grant No. EPMD-2211334. MGe acknowledges the primary support of the U.S. department of energy (DOE), Office of Science, Office of Basic energy Sciences under award number DE-SC0018675. K.S.B acknowledges support by the Air Force Office of Scientific Research under award number FA2386-24-1-4071.

Acknowledgments

We thank Matthias Kuehne for providing access to their Raman spectroscopy equipment and for their assistance during data collection.

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Generative AI statement

The author(s) declare that no Generative AI was used in the creation of this manuscript.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/femat.2025.1572940/full#supplementary-material

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Keywords: resonant inelastic soft X-ray scattering (RIXS), 2D magnetism, magnetism, prospects, van der Waals (vdW), NiPS3, RuCl3, graphene

Citation: DiScala MF, Hsieh V, Jessen BS, Gu Y, Rizzo DJ, Amontree JM, Yan X, Wang Q, Kapfer M, Kim T, Geiwitz M, Natale G, Pelliciari J, Hone JC, Burch KS, Basov DN, Dean CR, Bisogni V and Plumb KW (2025) Characterizing sample degradation from synchrotron based X-ray measurements of ultra-thin exfoliated flakes. Front. Electron. Mater. 5:1572940. doi: 10.3389/femat.2025.1572940

Received: 07 February 2025; Accepted: 14 May 2025;
Published: 25 June 2025.

Edited by:

Naurang Saini, Sapienza University of Rome, Italy

Reviewed by:

Aditya Sharma, University of Petroleum and Energy Studies, India
Raphaela De Oliveira, Brazilian Synchrotron Light Laboratory, Brazil

Copyright © 2025 DiScala, Hsieh, Jessen, Gu, Rizzo, Amontree, Yan, Wang, Kapfer, Kim, Geiwitz, Natale, Pelliciari, Hone, Burch, Basov, Dean, Bisogni and Plumb. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: C. R. Dean, Y2QyNDc4QGNvbHVtYmlhLmVkdQ==; V. Bisogni, Ymlzb2duaUBibmwuZ292; K. W. Plumb, a2VtcF9wbHVtYkBicm93bi5lZHU=

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.