The spatial distribution of
transition metal valence states is of broad interest in the microanalysis of
geological and environmental samples. An example is rock varnish, a natural
manganese (Mn)-rich rock coating, whose genesis mechanism remains a subject
of scientific debate. We conducted scanning transmission X-ray microscopy
with near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS)
measurements of the abundance and spatial distribution of different Mn
oxidation states within the nano- to micrometer thick varnish crusts. Such
microanalytical measurements of thin and hard rock crusts require sample
preparation with minimal contamination risk. Focused ion beam (FIB) slicing
was used to obtain ∼100–1000 nm thin wedge-shaped slices of the
samples for STXM, using standard parameters. However, while this preparation
is suitable for investigating element distributions and structures in rock
samples, we observed artifactual modifications of the Mn oxidation states at
the surfaces of the FIB slices. Our results suggest that the preparation
causes a reduction of Mn4+ to Mn2+. We draw attention to
this issue, since FIB slicing, scanning electron microscopy (SEM) imaging,
and other preparation and visualization techniques operating in the
kilo-electron-volt range are well-established in geosciences, but researchers
are often unaware of the potential for the reduction of Mn and possibly other
elements in the samples.
Introduction
Rock varnish, a thin natural crust on rock surfaces with thicknesses of up
to ∼250µm, typically consists of 5 wt %–20 wt % Mn
oxyhydroxide minerals, which cement mineral dust grains forming a hard,
black coating. The relevant Mn oxidation states in varnish and other natural
Mn minerals are Mn2+, Mn3+, and Mn4+. Even though a large
number of publications on rock varnish is available, the process of Mn
oxidation and precipitation of the matrix is still under controversial
debate (e.g., Liu and Dorn, 1996; DiGregorio, 2002; Perry and Kolb, 2004;
Thiagarajan and Lee, 2004; Dorn and Krinsley, 2011; Goldsmith et al., 2014).
Varnish often consists of layers with different manganese-to-iron (Mn/Fe)
ratios, which are a few tens up to a few hundreds of nanometers thick and
resemble sedimentary features (e.g., Garvie et al., 2008; Krinsley et al.,
1995; Macholdt et al., 2017a). It has been assumed that this layering
results from variations in the mass fraction of Mn, which initially
precipitates homogeneously in a single oxidation state. The oxidation state
of Mn could have changed subsequent to its deposition, e.g., due to the
presence of oxidizable iron species (i.e., Fe2+) or organic matter,
since Mn oxyhydroxides are known to be amongst the strongest occurring
natural oxidizers and element scavengers (Tebo et al., 2005). Another
process potentially reducing Mn4+ is photoreduction, supported by
available organic matter as electron supply. Photoreduction occurs due to
narrow band gaps in all Mn oxyhydroxides (Sherman, 2005). This process
effectuates the dissolution of the solid Mn oxyhydroxide minerals by
the reduction of immobile Mn4+ to Mn3+ and further to mobile
Mn2+. In most cases the released Mn2+ is re-adsorbed to the Mn
oxyhydroxide surface instead of being released into the surroundings. Since
the genesis of varnish and the precipitation process of the Mn oxyhydroxides
are still under debate, the aforementioned statements remain assumptions
until they can be verified experimentally.
In view of the controversy regarding the varnish genesis and the scarcity of
information on the varnish microchemistry, we conducted scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy
(STXM-NEXAFS) measurements to investigate element distributions within the varnish
coatings, along with spectroscopic information on the elements' binding
environments and oxidation states. Experimental details on STXM-NEXAFS can
be found in Kilcoyne et al. (2003) and Moffet et al. (2011). Thirteen
different rock varnish samples from different environments and locations
worldwide, containing diverse structures and compositions, were investigated
(for details, see Macholdt et al., 2015, 2017a, b). The soft X-rays in
the STXM-NEXAFS analysis generate comparatively low radiation damage,
provide a high penetration depth (Guttmann and Bittencourt, 2015), and allow
investigating comparatively rich spectroscopic features for a variety of
elements (Hitchcock, 2015). Among the accessible elements are C, N, and O –
and, thus, the composition of organic matter inside the varnish – as well
as the L-shell absorption edges of high-Z elements, such as the
varnish-relevant elements Mn and Fe (Cosmidis and Benzerara, 2014). The Mn
L3 and L2 absorption edges (short the Mn L3,2 edge) are
located in the energy range from ∼635 to ∼660 eV (i.e., electron binding energies in elemental Mn: 638.7 eV at L3
and 649.9 eV at L2 according to Fuggle and Mårtensson, 1980). The
L3 and L2 edges consist of multiplets of peaks, which reflect the
density of unoccupied 3d states (Gilbert et al., 2003). It is well
documented in the literature that the NEXAFS spectra show different spectral
patterns for the oxidation states Mn2+, Mn3+, and Mn4+
(Cramer et al., 1991; Pecher et al., 2003; Gilbert et al., 2003; Nesbitt and
Banerjee, 1998) and that the ratio of the L3 and L2 edge
intensities can be taken as a measure of the 3d occupancy and thus of the
valence state (Cramer et al., 1991; Kurata and Colliex, 1993). The energies
of the most intense peaks within the L3 multiplets for the individual
oxidation states are the following: Mn2+∼640.2 eV; Mn3+∼642.2 eV; Mn4+∼643.2 eV
(Gilbert et al., 2003).
For X-ray microspectroscopic analysis, the samples must be thin enough to
ensure sufficient X-ray photon transmission (Cosmidis and Benzerara, 2014).
Such ultrathin samples can be prepared by focused ion beam (FIB) milling,
for example by gallium ion (Ga+) sputtering (Wirth, 2004; Volkert and Minor, 2007)
Sputtering is the
physical process behind ion beam milling and means an erosion of a target
material due to the transfer of kinetic energy and momentum from accelerated
particles to the target material, which leads to a subsequent ejection of
surface atoms in the course of a collision cascade (Wirth, 2004; Volkert
and Minor, 2007).
. The FIB
preparation provides several experimental advantages, such as efficient and
flexible thinning of the slices as well as no risk of carbon contamination.
However, several drawbacks have also been described, of which the ion-beam-related damaging of samples is the most significant.
When an accelerated ion interacts with a material, it loses its kinetic
energy either via electronic (inelastic scattering of electrons) or nuclear
processes (elastic collisions). Both pathways are relevant in ion milling,
but nuclear processes play the predominant role (Ishitani and Kaga, 1995;
Prenitzer et al., 2003). Besides the sputtering of material, it is well-known
that FIB milling also implants Ga+ ions in a surface-near layer
(Balcells et al., 2008; Cairney et al., 2000; Prenitzer et al., 1998; Rubanov
and Munroe, 2001) and thus creates Ga-rich phases with Ga fractions of up to
20 wt % in the damage layer (Susnitzky and Johnson, 1998) and up to 30 wt % in the redeposition layer (Rajsiri et al., 2002), which can melt at
low temperatures (Li and Liu, 2017). The sputtered material might redeposit
on the surface in some cases (Rajsiri et al., 2002). Along with the Ga+
ion implantation, an amorphous damage layer is created at the surface, due
to the high energy of the ion collisions (Bassim et al., 2012; Mardinly and
Susnitzky, 1998; Siemons et al., 2014). In silicon, this amorphous film is
typically 20–30 nm thick when using 30 keV Ga+ ions (Giannuzzi et al.,
2005; Rubanov and Munroe, 2004); however, even a layer as thick as 80 nm at
25 keV has been observed by Prenitzer et al. (2003). By reducing the FIB
beam acceleration voltage from 30 to 6–10 kV the thickness of the
amorphous layer can be reduced by a factor of 2 (Jamison et al., 2000;
Rubanov and Munroe, 2004). At low FIB energies, the Ga-enriched region can
have a spatial extent beyond the amorphous layer depth (Moberlychan et al.,
2007).
In addition, microstructural modifications from FIB milling of metals and
ceramics have been reported, e.g., for copper (Cu) (Michael, 2006) and in manganite
thin films (Balcells et al., 2008; Pallecchi et al., 2008). FIB preparations
can result in reduced crystallinity of the material by generating point
defects such as vacancies, interstitials, and antisite defects, due to
charging effects (Li and Liu, 2017; Siemons et al., 2014), and these defects
can even exceed the Ga+ ion implantation depths, e.g., in BiFeO3
(Siemons et al., 2014).
The amorphization coincides with the heating of the outer sample surface in the
course of the collision cascade (Volkert and Minor, 2007; Fischione et al.,
2017) along with the occurrence of so-called “thermal spikes”, which can
easily reach a few thousand kelvin (Ovchinnikov et al., 2015). Because of
the immediate vaporization of the affected volume within 10-12 s
(Ovchinnikov et al., 2015), the thermal effect on the bulk material is
rather low. For samples with both good thermal conductivity and good
thermal connection, ion beam heating plays a negligible role in the bulk
(Volkert and Minor, 2007), but for materials with inefficient heat
dissipation (e.g., due to low thermal conductivity, such as in SiO2)
a temperature increase up to 500 ∘C was calculated (Ishitani and
Kaga, 1995). If samples are very thin, even in metals, temperatures up to
370 ∘C (Kim and Carpenter, 1987) or even >400∘C (Cen and Van Benthem, 2018) can be reached. This is
especially destructive for organic samples, such as polymers, which tend to
melt and decompose under common FIB conditions (Volkert and Minor; 2007,
Schmied et al., 2014). For instance, a temperature rise of 171 ∘C has been observed by Bassim et al. (2012) for polyacrylamide. During
thinning with rather low beam currents of 0.23 nA, a temperature rise to
above the melting temperature of Crystalbond™ 509
(121 ∘C) has been observed by Li and Liu (2017). This heating can
be reduced to a large extent with optimized scanning patterns (Schmied,
2014) or simply by cooling the sample (Fischione et al., 2017). The
susceptibility for beam damage and the thickness of the amorphous layer
strongly depends on the type of ion and the sputtered material. The damaged
layer thickness typically ranges from a few to a few tens of nanometers
(Mayer et al., 2007; Mikmekova et al., 2011). Sample heating also
facilitates the occurrence of uncommon types of beam damage, such as
preferential sputtering (Volkert and Minor, 2007), which occurs in materials
with more than one atom species, especially if the compound can decompose
chemically. In-depth information on sample heating (Kim and Carpenter, 1987;
Cen and Van Benthem, 2018; Volkert and Minor, 2007; Ovchinnikov et al.,
2015; Ishitani and Kaga, 1995), beam damage (Gutierrez-Urrutia, 2017; Mayer
et al., 2007; Betz and Wehner, 1983; Prenitzer et al., 2003), and
experimental reduction strategies of these effects (Bassim et al., 2012;
Barber, 1993) can be found in the cited literature.
Beam damage in the samples might also result from interactions with the
electron beam during scanning electron microscopy (SEM) observation, which is
an integral part of the FIB preparation procedure. Inelastic scattering of
electrons results in radiolytic processes, whereas elastically scattered
electrons cause knock-on displacement of atoms in the substrate or from the
surface, which is also known as electron beam sputtering in analogy to the
above-mentioned ion beam sputtering (Saifullah, 2009; Egerton et al., 2004;
Egerton, 2012; Jiang, 2016). Unsurprisingly, preferential sputtering of
oxides by ions has been observed as well for electrons (Jiang, 2016). Organic
molecules are more prone to radiolysis, for the main part induced by
secondary electrons (Egerton, 2012). In the course of this process, molecules
do not return into their original electronic states, but chemical bonds
break, changing the molecule's structure, shifting their position, and
causing a loss of crystallinity (Egerton et al., 2004; Henderson and Glaeser,
1985). Mass loss or mass gain of organics due to polymerization by incoming
or outgoing electrons might occur as well (Egerton et al., 2004). Inorganic
samples are sensitive to both radiolysis and knock-on displacement.
Radiolysis generally predominates in electrically insulating materials. In
conducting specimens, “radiolysis is suppressed because of the high electron
density” (Egerton, 2012) and “knock-on displacement is the sole damage
process” (Egerton, 2012). For instance, alumina and transition metal oxides
with Pauling electronegativity differences >1.7 are well known
to decompose under oxygen loss through a radiolytic process named
Knotek–Feibelman mechanism (Knotek and Feibelman, 1978; Egerton et al.,
2004; Saifullah, 2009; Betz and Wehner, 1983; Pantano and Madey, 1981;
Hoffman and Paterson, 1996). Radiolysis happens as well with high efficiency
in almost all alkali and alkaline earth halides. As radiolysis shows a
temperature dependence, its damaging potential can be minimized when the
irradiated specimens are cooled (Pantano and Madey, 1981; Egerton et al.,
2004; Egerton, 2012). This should not lead to the false conclusion that
sample heating due to the electron beam is as significant as with ions. The
temperature rise through electron exposure is not expected to exceed a few
kelvin (Tokunaga et al., 2012; Holmes et al., 2000; Hoffman and Paterson,
1996). It should be noted that radiolytic processes come mainly into effect
at the immediate surface of the sample because atom desorption is much more
likely to happen here. Electron-stimulated desorption (ESD) is therefore a
well-established synonym for this effect (Pantano and Madey, 1981; Egerton et
al., 2004).
In this study, we summarize our observations on FIB-related damage observed during the X-ray microspectroscopic investigation of the Mn
oxidation states in several rock varnish samples. The observed beam damage
patterns were largely independent of the type or origin of varnish examined.
We illustrate our observations by means of four different varnish samples
and link them subsequently to the varnish classification scheme of Macholdt
et al. (2017a).
Materials and methodsFocused ion beam preparation
The preparation of ultrathin slices from the rock varnish samples was
performed using the lift-out FIB technique. This slicing technique was
chosen since it is relatively contamination-free (except for Ga+ ion
implantation) and relatively fast and allows a precise selection of the
preparation target area independent of the nature of the sample material or
combination of materials (Mayer et al., 2007; Siemons et al., 2014). The
preparation was performed at the Max Planck Institute for Polymer Research,
Mainz, Germany, using an FEI Nova600Nanolab FIB dual-beam instrument
(ThermoFisher Inc.). Milling was done by Ga+ ion sputtering with a
resolution of ∼10 nm. The FIB preparation procedure includes
the following steps.
Before introduction of the rock varnish samples into the FIB instrument, the
entire stone surface was sputter coated with 50 nm of platinum (Pt) using a
Baltec MED020 sputtering equipment. The thin Pt coating makes the sample
electrically conductive and thus reduces charging effects and sample shift
effects.
In addition, the preparation site was coated within the FIB instrument with
an additional, 2–3 µm thick protective Pt stripe (50×3µm2) using beam-induced Pt deposition from a metallo-organic
precursor gas (1 nA at 30 kV for 15 min). The Pt stripe acts as a mask to
reduce damage from perpendicular ion collisions on the sample surface
throughout the subsequent milling steps.
In a first rough cutting step (20 nA, 30 kV), two step-like trenches with a
volume of about 45×45×30µm3 on both sides of the Pt
stripe were milled. This took more than 3 h on each side, depending on
the individual sample characteristics.
The milling was followed by cleaning cross-section steps at lower beam
currents (7 and 5 nA at 30 kV) to smooth the surfaces of the pre-thinned
lamella (∼1µm thick), which were strongly affected by
“curtaining”. This step lasted for approximately 3 h in total on each
side.
The samples were milled out, lifted out, transferred to an FIB lift-out grid, and
soldered with Pt to a Cu post for the STXM-NEXAFS measurements.
A final stepwise thinning and polishing (1 and 0.5 nA at 30 kV) with a
sample slightly tilted (∼1∘) was conducted to
produce wedge-shaped FIB slices with minimal thicknesses of about 100 nm at
the top. This final thinning was performed from the top of the sample
downwards, four to five times from each side, with decreasing currents. This
step lasted for about 3.5 h for each side. To avoid breaking the FIB slices,
several samples were not thinned completely but divided into two halves, one of which was thinned out more strongly than the other, as illustrated by means
of one example in Fig. 1b.
SEM observation of the samples (with an acceleration voltage of 5 kV) took
place during the entire FIB process and fulfilled three main purposes: (i)
it allowed us to precisely define the site of milling on the varnish coated
rock surfaces (step 2); (ii) it allowed monitoring the sample throughout the
entire preparation procedure (steps 2–6); (iii) the electron beam
neutralizes ions, which reduces charging and, therefore, minimizes drift
effects.
STXM-NEXAFS measurements and data analysis
Subsequent to the preparation by FIB, the samples were studied using two
X-ray microscopes. (i) The first STXM is located at beamline 5.3.2.2 of the
synchrotron Advanced Light Source (ALS), Lawrence Berkeley National
Laboratory, Berkeley, California (for details, see Kilcoyne et al., 2003).
The associated bending magnet beamline allows measurements over an energy
range from 250 to 800 eV. (ii) The second STXM, called MAXYMUS, is located
at beamline UE46-PGM-2 of the synchrotron BESSY II, Helmholtz-Zentrum
Berlin, Germany (for details, see Weigand, 2015). The associated undulator
beamline allows measurements over an energy range from 250 to 1900 eV
(Follath et al., 2010). Both instruments are equipped with high-energy-resolving gratings (resolving power at the carbon K edge: ALS
E/ΔE≤5000; BESSY II: E/ΔE≤8000), a Fresnel zone
plate providing a spatial resolution of about 40 nm, and phosphor-coated
Lucite photomultiplier tubes for the detection of transmitted photons. At
the ALS, the measurement chamber is filled with helium prior to measuring,
whereas at BESSY II the measurements are conducted in a vacuum.
Measurements at both instruments are based on soft X-ray analytics, imposing
less beam damage on the samples than comparable techniques, such as
transmission electron microscopy with electron energy loss spectroscopy
(TEM-EELS). For energy calibration, the characteristic π resonance peak
at 285.2 eV was measured on polystyrene latex (PSL) spheres prior to each
measurement session. As Mn reference materials, Mn(acac)2,
Mn(acac)3 (acac: acetylacetonate), and MnO2 were used. The Mn
salts were purchased from Sigma Aldrich (St Louis, USA). For the purpose of
this study, STXM image “stacks” were analyzed in detail. As a routine
measurement protocol, we recorded image stacks either on the entire varnish
FIB slice or (with higher resolution) on specific regions of interest. The
stacks typically covered the energy range from ∼270 to
∼750 eV (sometimes even further) and, thus, included the
absorption edges of the elements carbon, potassium, calcium, nitrogen,
titanium, oxygen, manganese, and iron. The Mn L3,2 absorption edge is
of primary relevance for this study.
The STXM-NEXAFS data analysis was conducted using the Interactive Data
Language (IDL) widget “Analysis of X-ray microscopy Images and Spectra”
(aXis2000) (Hitchcock et al., 2018), the Multivariate ANalysis Tool for
Spectromicroscopy software (MANTiS-2.1.02) (Lerotic et al., 2004, 2005,
2014), as well as several custom-made software tools, programmed in Python
3.6.5. To analyze the spatial distribution of different Mn oxidation states
in the FIB slices, the STXM image stacks were analyzed by a k-means cluster
analysis with Euclidian distances. The analysis sequence included the
following specific steps.
A careful alignment of the images in the stack was conducted with the help
of a custom-made alignment tool.
For the subsequent analysis steps, the energy range was limited in MANTiS
from 630 to 665 eV, which covers the Mn L3,2 absorption edge. Note that
in the plots of this study the energy range from 631 to 664 eV is shown.
According to Beer–Lambert's law,OD(E)=-lnIEI0E=μ(E)ρd,with E being the X-ray photon energy, OD(E) the optical density of varnish sample at
given E, I(E) the photon flux at given E through the sample,
I0(E) the incident photon flux at given E through a sample-free region,
μ(E) the energy-dependent mass absorption coefficient (see Henke et al., 1993),
ρ the density of absorbing atoms in the sample, and d the sample
thickness. The background I0(E) spectrum was determined to convert all the stack data into OD(E). A modified version of the histogram-based
background selection routine in MANTiS was used here.
An OD filter was applied to exclude pixels with OD > 2.5 from
the analysis, which are well outside the linear regime of Beer–Lambert's
law.
For every pixel, the Mn pre-edge value ODpre (averaged between 630 and
636 eV) was subtracted from the pixel-specific spectrum. Depending on the
energy resolution of the stacks, data from 3 to 20 images were averaged here.
For every pixel, the step-function-like absorption edge was subtracted from
the spectral signature. The generalized logistic function, also known as
Richards' curve (Richards, 1959), was used:OD(E)no-edge=OD(E)-ODpostαwithα=[1+exp(-OD(E)+0.5⋅ODpost)]25/ODpostand OD(E)no-edge being the optical density of varnish sample at given E after
subtraction of the absorption edge OD from OD(E), here represented by a
logistic function, and ODpost the optical density at Mn post edge,
averaged between 660 and 665 eV. The pre-factor 0.5 ensures that the
inflection point of the curve is located at half the edge height. The
pre-factor 25 determines the steepness and symmetry of the curve. This value
was found empirically and worked well for the current application. Note that
without prior subtraction of ODpre (step 5), Eq. (4) would be relevant:OD(E)new=ODE-ODpre-ODpost-ODpreα.
After the preprocessing steps 1 to 4, as well as normalization steps 5 and
6, the pixels were pre-classified by means of principle component analysis
(PCA) as implemented in MANTiS.
With the PCA results as start values, the MANTiS k-means cluster analysis was
applied. For the current analysis k=4 was chosen since it represents the
smallest k that still covers the observed spectral variability in the
samples. Within MANTiS the “reduce thickness effect” box was checked to
exclude the first PCA component in the subsequent cluster analysis (Lerotic
et al., 2004), which is roughly equal to the total Mn absorption per pixel
in the observed energy range. The normalization steps 5 and 6 in combination
with exclusion of PCA component s=1 ensure that the cluster analysis
partitions the pixel spectra neither by physical thickness of the FIB slice
nor by the heterogeneities in Mn distribution and ρMn but only
by the spectral patterns at the Mn L3,2 edge, which can be related to
Mn oxidation states (Gilbert et al., 2003).
For the further analysis steps beyond the cluster analysis, the nonnegative
matrix approximation (NNMA) routine, as implemented in MANTiS, was used to
extract spectral features while constraining the weightings to be
nonnegative (for details, see Mak et al., 2014). In this work, the NNMA
allowed obtaining relative fractions of Mn2+ and Mn4+ in every
pixel of the stack. Within the MANTiS NNMA routine, we used the following
settings: cluster analysis output (k=4) as input for NNMA; spectra
similarity: 15; smoothness: 0; sparseness: 0.05;
iterations: 500.
Results and discussion
The SEM overview images and STXM Mn maps in Fig. 1, which illustrate the
coating thickness, morphology, and heterogeneity of the selected varnish
samples, provide the context for the regions of interest that were analyzed
spectroscopically (Fig. 2). The FIB slices were prepared with a wedge-like
shape as illustrated in Fig. 1a2 and 1b2. Dedicated SEM
measurements with a perpendicular view on the tip of the wedge showed that
the thinnest part is ∼100 nm thick, whereas the thickest part
measures ∼1µm. For certain samples, part of the wedge
was thinned out even further, allowing a comparative analysis of thicker vs.
thinner wedges within the same slice (see Fig. 1b1–3).
SEM images (a1–d1), Mn pre-edge STXM images
(a2–d2), and Mn STXM maps (a3–d3) of FIB slices of the
rock varnish samples AR14 J1 (a1–3), SA14 DV09a (b1–3), SA10 #9
(c1–3), and AR14 Y1 (d1–3). All samples are oriented such that the
sample support with the Pt solder is on the left side and the rock surface
at the top. The varnish layer is visible in the upper part of the images and
the bedrock in the lower part in (c1–3) and (d1–3). In panels (c) and (b), the
Mn-rich varnish layer spans across the whole FIB slice. The luminance values
represent transmittance and are to some degree proportional to the sample
thickness. Although this is only true of a homogeneous sample, differences
in thickness due to the sample preparation and the curtaining effect are
obvious and, in some cases, indicated by arrows pointing towards thicker areas in (a2) and (b2) and in addition by brackets in (b2). The Mn spectra shown in Fig. 2 were
collected within the dashed regions highlighted as “stack region” in the middle and right-hand columns. The Mn pre-edge images were obtained at 635 eV photon energy.
The Mn maps were calculated from single images at 635 eV (pre-edge) and
643 eV (on-edge) photon energy.
Results from k-means cluster analysis applied to STXM image
stacks of four different varnish samples, showing the influence of beam damage
(i.e., reduction of Mn oxyhydroxides) as a function of FIB slice thickness.
For background information on the selected varnish samples AR14 J1, SA14
DV09a, SA10 #9, and AR14 Y1, refer to Macholdt et al. (2017a). Panels
(a1) to (d1) show relative optical
thickness maps obtained by averaging Mn pre-edge images between 630 and 636 eV. Relative optical thickness maps were normalized to a numeric range from
0 to 1 (0: lowest transmission in observed area; 1: full
transmission). White contour lines have been calculated based on relative
optical thickness maps. Panels (a2) to
(d2) show spatial distribution of pixels across FIB
slices partitioned into four clusters based on pixel-specific spectral
patterns at the Mn L3,2 absorption edge. White contour lines project
relative optical thicknesses at the Mn pre-edge onto cluster maps. Black
regions represent filtered pixels with OD > 2.5, bedrock, and Pt.
Grey regions represent background pixels. Panels (a3)
to (d3) show corresponding spectra from clustering
(same cluster colors in (a2) to
(d2) in (a3) to
(d3)). Reference spectra for Mn2+, Mn3+, and
Mn4+ obtained from Gilbert et al. (2003) are shown in
(d3). The spectral pattern of cluster 1 (red)
corresponds to the most reduced Mn species – similar to Mn2+ – and is
located mostly in thinnest parts of FIB slices. The spectral pattern of
cluster 4 (purple) corresponds to the most oxidized Mn species – similar to
Mn4+ – and is located mostly in the thickest parts of the FIB slices.
Clusters 2 (yellow) and 3 (cyan) represent intermediate states.
In the course of our STXM-NEXAFS analysis of various varnish samples from
different locations worldwide (see Macholdt et al., 2017a), we observed
clear indications of beam-related changes in the sample composition.
Specifically, differences in the spectral patterns at the Mn L3,2 edge
indicate that a beam-related reduction of the Mn oxyhydroxides has occurred.
For the cluster analysis used to discriminate between these spectral patterns at the
Mn L3,2 edge – which are a proxy for Mn oxidation states – it is
important to eliminate any influence of the overall sample thickness as well
as heterogeneous Mn distributions (e.g., layering) as outlined in Sect. 2.2.
As a general trend, low-valence-state Mn species – similar to the Mn2+
reference spectra – were observed in thinner regions of the FIB wedge,
whereas more oxidized Mn species – similar to the Mn4+ reference spectra – dominate in the thicker regions. Figure 2 emphasizes those
samples where the relationship between the optical thickness of the sample
and the Mn oxidation state is resolved clearly. The gradient is most obvious
in the example shown in Fig. 2d1–3. For certain samples, reduced Mn has
also been observed around holes within the specimen (e.g., see cracks in
Figs. 1d and 2d), which was first interpreted as a sign of the reduction of Mn
by organics that had previously filled those cavities, especially since some
cavities are lined with C-rich material (Macholdt et al., 2015). However,
further observations suggest that the reduced Mn in the periphery of the
holes can also be explained by a stronger beam exposure in the FIB preparation. For the sample AR14 Y1 in Fig. 2d1–3, we further conducted
an NNMA analysis (see Sect. 2.2), which provides a proxy for the relative
fractions of Mn2+ and Mn4+ in every pixel. This particular sample
was chosen because it has the most pixels, thus providing good statistics,
and the most homogeneous varnish layer (i.e., no visible clay minerals, low
porosity). In Fig. 3, the scatterplots of the obtained Mn2+ and
Mn4+ fractions against the relative (optical) thickness of the wedge
further emphasize the gradients observed in Fig. 2, with the highest Mn2+
fractions in the thinnest and highest Mn4+ fractions in the thickest
part.
Nonnegative matrix approximation (NNMA) of sample AR14 Y1. Panel (a)
shows the spatial distribution of the Mn2+-associated (most reduced)
cluster (red) and the Mn4+-associated (most oxidized) cluster (violet).
Panels (b) and (c) show the pixel weights from the NNMA analysis of each cluster
against the “relative thickness” represented by the Mn pre-edge luminance
values, scaled from 1 to 0, where 0 represents full transmission and 1
stands for the darkest pixel in the observed area. Thick areas with a relative
thickness > 0.6 were masked, as were non-varnish regions
(background, Pt, or rock). Compare with Figs. 1d1–3 and 2d1–3. There is a
positive correlation with thickness for the more oxidized cluster and an
anticorrelation for the more reduced cluster. Linear fits along with their
slopes and R2 values are shown to emphasize the observed
trend. The increased weight of Mn2+-like pixels in
thin regions at the top, along the crack (compare with Fig. 1d2), and
along the outer cutting line (right side), is very striking.
The beam-damage-related gradient dominates the oxidation state distribution
and, thus, is superimposed on the natural heterogeneity in Mn valence states in
the varnish. Accordingly, the beam damage fundamentally hampers our original
aim to use spatially resolved measurements of the Mn oxidation states for
further insights into possible varnish genesis mechanisms. Some indications
of layered structures, which may represent residues of the original
distribution of Mn valence states, can be seen in Fig. 2a2 to b2,
however, an interpretation of these structures is highly uncertain. The
beam-related Mn reduction has been observed in many samples for which
appropriate image stacks were recorded. Table 1 specifies whether a
beam-damage effect was found in the analyzed samples and relates the samples
to the varnish classification scheme, discriminating five varnish types,
proposed by Macholdt et al. (2017a). According to this scheme, three of the
samples in Fig. 2 (i.e., AR14 J1, AR14 Y1, and SA14 DV09a) belong to the
arid desert varnish type I, whereas one sample (i.e., SA10 #9) belongs to
the semiarid desert varnish type III. Multiple type I and type III samples
confirm the observed trend. For statements on the varnish types II, IV, and
V, however, our experimental basis is sparse: no STXM-NEXAFS data are available for type II varnish samples. For type IV and V, STXM stacks have
been recorded; however, the varnish coatings of the analyzed samples were
too thin to identify clear gradients.
Overview of all varnish samples analyzed by STXM-NEXAFS
stacks, specifying whether beam-related Mn reduction was observed. Samples
are grouped according to the classification scheme of Macholdt et al. (2017a): type I – arid desert varnish; type II – semiarid desert
varnish; type III– semiarid desert varnish; type IV – urban area
varnish; type V – river splash zone varnish.
Sample name*Varnish typeBeam-damage-related Mn reduction observedCommentAR14 J1 (AR-J)IYes, clearlyRefer to Figs. 1 and 2AR14 Y1 (AR-Y)IYes, clearlyRefer to Figs. 1, 2, and 3CA14 DV11 (CA-DV)IUnknownSpectral gradient overlaps with porous regions, dominant varnish–rock boundary zoneCA14 JC8 (CA-JC)IYes, clearly–IS13 V1 (IS)IUnknownLow spectral quality and varnish coating too narrowIS13 V3 (IS)IUnknownIf yes, superimposed by sample layering–II–No STXM-NEXAFS data for type II availableSA10 #9 (SA-1)IIIYes, clearlyRefer to Figs. 1 and 2SA13 mM-f (SA-1)IIIUnknownSample too thick in most parts, remaining pixels indicate rather a random species distributionSA14 DV09a (SA-2)IIIYes, clearlyRefer to Figs. 1 and 2SA14 DV09b (SA-2)IIIYes, but uncertainSample too thick in most parts and low statisticsSCIVUnknownVarnish coating too narrow to resolve gradientsFMIVUnknownVarnish coating too narrow to resolve gradientsE CanalVUnknownVarnish coating too narrow to resolve gradients
* Sample names kept consistent with Table 1 in Macholdt et al. (2017a).
The following sections discuss which part of the preparation and analysis
procedure has most likely caused the observed beam damage and further
explore mechanistic pathways for the Mn reduction. Generally, the varnish
samples experienced an intense ion and electron bombardment as well as high
X-ray exposure in the course of the preparation and analysis. Accordingly,
all applied techniques – FIB, SEM, and STXM – are in principle potential
sources for the beam damage (Süzer, 2000; Bassim et al., 2012). The soft
X-rays in STXM (∼0.3 to 0.7 keV), accelerated electrons in
SEM (∼2 to 5 keV), and accelerated Ga+ ions in FIB
(∼30 keV) are characterized by widely different energies.
Moreover, their energies – and thus the potential damage – are deposited
in the samples via different mechanistic pathways: soft X-rays mostly act
via core electron excitation up to an ionization of the atom, followed by a
relaxation and filling of the core hole vacancy with associated photon and
Auger electron emissions. As stated in the introduction, accelerated
electrons mostly interact with varnish-like specimens via inelastic
scattering, possibly causing radiolytic processes in the course of
electronic excitations. Accelerated ions mostly act via nuclear, i.e.,
elastic collisions, resulting in sputtering, but electronic excitations
should not be neglected. Our experiments showed, however, that the damaging
effect of STXM is negligible: in dedicated tests, sequences of successive
stack scans were recorded on the same area and no difference in the spectral
patterns (i.e., at the absorption edges of Mn and other elements) could be
observed. Moreover, previous X-ray microspectroscopy measurements have been
successfully performed on materials with different Mn oxidation states
(e.g., Bargar et al., 2001; Glasauer et al., 2006; Pecher et al., 2000,
2003; Tebo et al., 2004; Toner et al., 2005).
The electrons in SEM analysis have a comparatively large penetration depth
in materials due to their high velocity and small size compared with
accelerated ions, such as Ga+ (Mikmekova et al., 2011; Ohya and
Ishitani, 2002; Prenitzer et al., 2003; Bassim et al., 2012; Pantano and
Madey, 1981). Beam damage from SEM observation is particularly strong in
organic matter (Bassim et al., 2012; Egerton et al., 2004). However, it
seems unlikely that the 5 keV electron beam from the SEM alone caused the
damage visible in our STXM-NEXAFS analyses for the following reasons. (i)
The critical dose for radiolytic processes in most inorganic materials
(e.g., the Knotek–Feibelman mechanism in oxides), defined as the dose of
10 % compositional change of a species, is of the order of 10-3 to
10-2 C cm-2 (Pantano and Madey, 1981) and thus well within reach
of our SEM-assisted FIB preparation procedure. However, the escape of Auger
electrons, which is an essential part of the Knotek–Feibelman process along
with the desorption of O+ ions from the bulk, is confined within a
shallow depth. For various oxides, the most probable secondary electron
escape depths have been calculated by Kanaya et al. (1978), reaching a
maximum at ∼8 nm for ZnO and BaO. In a worst case scenario,
where 100 % Mn4+ is converted to Mn2+, this would mean a
maximum of 16 % damaged volume at the top and 1.6 % at the bottom of
our FIB slices because of the double-sided polishing. By looking at the
sample NEXAFS spectra and the reference spectra in Fig. 2, it is obvious
that the damaged layer we observe here is considerably thicker than that.
Furthermore, part of the expected damaged layer is abraded during the final
polishing phase. Moreover, Pantano and Madey (1981) showed for
soda–lime–silicate glass that intermittent electron exposure, like during
the SEM's scanning movement, is potentially less harmful compared to
continuous exposure. In view of these aspects, the SEM's overall
contribution to radiolytic damage is probably minor. (ii) The accelerating
voltages necessary for knock-on displacement (electron beam sputtering) are
much higher than 5 keV (Egerton et al., 2004). Therefore, a preferential
sputtering of manganese oxides or in our case oxyhydroxides by the electron
beam can likely be excluded. (iii) A solely SEM-induced thermal
decomposition or desorption seems unlikely because electrons contribute
only little to sample heating as stated before. Moreover, rock varnish is
well known to have been already exposed to high temperatures in desert
environments, such as up to 57 ∘C in Death Valley (Roof and
Callagan, 2003), which is significantly beyond the temperature rise expected from
electron beam exposure.
We cannot fully exclude a contribution of the electron beam to radiolytic
damaging processes, however. In case of significant sample heating, which is
likely to occur during the FIB treatment, as stated in the introduction,
electron-induced radiolytic processes will speed up as well and might become
relevant.
Considering the exceptional porosity and fragility of the analyzed samples,
which can be seen from Fig. 1, thermal stress due to low thermal
conductivity is in our opinion one key aspect when discussing damaging
effects. The more a sample region is being thinned, the worse the heat can be
dissipated, in particular at edges and around holes. We therefore assume
that ion bombardment during FIB preparation is at least an essential
ingredient for, if not the main contributor to, the observed changes in Mn
valence states for two reasons: (i) the high kinetic energy (Sezen et al.,
2011) of the Ga+ ions (∼5700 times higher than 5 keV
electrons), which is almost fully converted to heat within the sample, and
(ii) the rather long ion beam exposure during milling. Very little
information on ion-induced alterations of the composition of complex (e.g.,
geological) samples is available in the literature. However, analogies and
extended literature on related effects can be found in the research fields
of planetary science and materials science, which are helpful for the
interpretation of our observations. Accordingly, the following sections
provide a literature synthesis as a basis for further discussion of our
results.
Chemical reduction by means of an electronic process should in principle
play a minor role in ion beam milling, as stated in the introduction. But
evidence for effective “bombardment-induced decomposition” (Kelly, 1989)
and reduction can even be found in outer space. The low albedo of silicate
rocks from the moon's surface was attributed to solar wind bombardment
(Hapke, 1973), which causes an enrichment of nanoscale metallic iron
particles in the near-surface layer of lunar regolith via a preferential
sputtering mechanism, where oxygen is preferentially sputtered off, leaving
the reduced bare metal behind (Betz and Wehner, 1983). Whether
micrometeoroid impacts have a major contribution to this so-called lunar
“space weathering” by (re)melting the surface layer of lunar soil grains or whether solar wind contributes more due to ion (H and He) implantation is still under discussion, however (Kuhlman et al., 2015; Pieters and Noble,
2016). Note that Christoffersen et al. (2012) tried to simulate space
weathering by Ga+ ion FIB milling but without success. In their study,
the irradiation only lasted 25 min, however, compared with many
hours of FIB milling from both sides in our sample preparation procedure.
Besides that, we do not want to make oversimplifications by directly
comparing lunar pyroxene reduction to elemental iron with desert varnish Mn
species reduction to Mn2+.
In materials science, the sputter reduction by ions during milling is well
known, especially in metal oxides (Hofmann and Sanz, 1983; Betz and Wehner,
1983; Mitchell et al., 1990; Parker and Kelly, 1973; McIntyre and Zetaruk,
1977; Fondell et al., 2018). Hydroxides are reduced upon ion bombardment as
well, as was shown for Ni(OH)2, Co(OH)2, and FeOOH by Chuang et al. (1978). The associated oxygen loss was often attributed to preferential
sputtering (Malherbe et al., 1986; Mitchell et al., 1990; Parker and Kelly,
1973; Betz and Wehner, 1983) “triggered by differences of mass, chemical
binding or volatility” (Kelly, 1989). The decomposition caused by
volatility differences, known as thermal sputtering was “found to explain
many examples of oxygen loss from oxides” (Kelly, 1989). However, in many
cases there is no single mechanism responsible for the observed
decomposition, but rather there is interplay between several chemical and physical
effects (Kelly, 1989; Mitchell et al., 1990; Barber, 1993). In the
aforementioned studies, the oxides or hydroxides were either grown as films
on a substrate or on macroscopically thick bulk materials and thus thermally
rather well connected. The observed thicknesses of the damage layer
typically range from a few nanometers (Mitchell et al., 1990; Hofmann and Sanz,
1983) to a few tens of nanometers (Betz and Wehner, 1983), although for MoO3 an
altered layer of approximately 115 nm thickness has been observed (Naguib
and Kelly, 1972). The oxygen-depleted layer thicknesses are therefore in the
same size range as the surface amorphization. Our samples are only 100 nm
thick at the top and were ion-milled from both sides, although final
thinning and polishing only happened under grazing irradiation conditions.
The implication of different impact angles is mentioned by Prenitzer et al. (2003) and Mikmekova et al. (2011). While it is true that the penetration
depths and therefore the damaged volumes become generally smaller under
grazing incidence, the complex sample morphology and composition in our case
adds a large uncertainty to the real ion impact angles and the depth of
penetration.
During our in-depth literature search for samples comparable to rock varnish, we came across the recent study on ion bombardment of iron oxide thin films
by Fondell et al. (2018). They report sputter reduction to FeO under
remarkably soft conditions (200 V, Ar+ ions) after just 8 min of
sputtering. Only very few data on Mn oxides were published by Mitchell et al. (1990) along with various other oxides. Kelly (1989) states in his
comprehensive overview that Mn oxides are not reduced further than to MnO,
which is thermodynamically stable at least to temperatures up to 900 K. This
agrees well with our observations. The spectral signatures in Fig. 2a3–d3 approach the Mn2+ spectral pattern in the highly
thinned regions. In consideration of the findings by Fondell et al. (2018),
a similar behavior of oxidic Mn compounds can be reasonably assumed and due
to the comparably harsh milling parameters we used, a more extensive
reduction at greater depths seems plausible.
Conclusions
In this study, we found that the Mn oxidation states investigated using
STXM-NEXAFS were modified during the sample preparation procedure by
reducing Mn4+ to Mn2+. Overall, we found that artifacts are
produced during the preparation of the samples by FIB and monitoring by SEM,
which creates a high degree of uncertainty for oxidation state analyses.
This study supplies a clearer picture on the type of artifacts created,
providing the possibility to address these issues carefully in follow-up
studies. Although we were not able to confirm oxidation state alteration in
all the samples given in Table 1, we see no reasons why varnish types II,
IV, and V, from which no suitable samples were available, should behave
differently.
From an overview of the existing literature we further conclude the following points. (i) Ion-bombardment-induced reduction in multicomponent specimens is a common
phenomenon. The effect has been extensively discussed by Kelly (1989). (ii)
Ion beam heating of thermally low-conducting specimens plays a significant
role therein because it facilitates preferential sputtering (i.e., thermal
sputtering) as well as chemical decomposition reactions (i.e., radiolysis).
For instance, Fondell et al. (2018) report that sputter reduction of
maghemite is similar to heat treatment of the sample in vacuum. The
dissociation of carbonates (Christie et al., 1981) and sulfates (Contarini
and Rabalais, 1985) has been observed and attributed to a combination of
thermal sputtering connected to thermal spikes and electron sputtering.
Momentum transfer alone (preferential sputtering due to mass differences)
could not explain the observed reactions. A follow-up study on previously
heated samples could therefore help to better understand the potential
thermal decomposition of rock varnish. (iii) The expected damaged layer
depths in FIB milling might have been underestimated in multicomponent
samples, especially when they consist of oxidic compounds. (iv) The possible
contribution of the electron beam from SEM is as yet unknown. In combination
with ion beam heating, electron-induced radiolytic processes might come into
effect. Further damaging contribution from electrons might arise from
interaction with the ions' shell electrons and from secondary electrons
liberated in the course of the collision cascade.
As FIB is a widely used technique to produce ultrathin slices of rock
samples, one needs to be aware of these problems and choose preparation
parameters that help to keep damage to a minimum. To reduce or minimize the
damaged volume, the preparation procedure could be conducted using not only
low currents but lower voltages during FIB preparation. In contrast,
lowering the accelerating voltage in SEM might have an opposing, more
damaging effect (Joy and Joy, 1996). If available, a cryo-FIB approach
(Bassim et al., 2012) could be applied. Sezen et al. (2011) showed, however,
that cryogenic conditions could not prevent or even slow down the
degradation of conjugated polymers during FIB milling. Alternatively, argon
ion slicing (Stojic and Brenker, 2010) may be a more gentle and, therefore,
suitable approach to reduce beam damage (e.g., Mn reduction) in the
preparation of ultrathin varnish slices. Iodine ion milling as mentioned in Barber (1993) might be even less damaging. Fischione et al. (2017)
established a method in which the damaged surface layers can be removed
after FIB milling by a small-spot argon ion milling process. However, it is
left to further studies to investigate whether oxidation states can indeed
be kept unchanged using such more gentle preparation approaches.
Data availability
The STXM-NEXAFS stacks used for Figs. 2 and 3, the cluster
analysis results, and the corresponding spectra have been deposited in
Edmond, the Max Planck society's open-access data repository under
10.17617/3.22 (Förster and Pöhlker, 2019). For specific data requests beyond the deposited data, please contact the
corresponding authors.
Author contributions
JDF, CP, and DSM are responsible for the data analysis, the
conceptual design of the paper, the literature search, and the paper writing.
CP and MOA supervised this study and the paper writing. DSM, CP, JDF, MOA,
and BW performed the STXM measurements, which were conducted with the
technical assistance of ALDK and MW. The FIB preparation was done by MM and
MK. All authors contributed to data discussion and paper
finalization.
Competing interests
The authors declare that they have no conflict of
interest.
Acknowledgements
This work was supported by the Max Planck Society, the Max Planck Graduate
Center with the Johannes Gutenberg University Mainz (MPGC), and the King Saud University.
This research used resources of the Advanced Light Source, which is a DOE Office of Science
User Facility under contract no. DE-AC02-05CH11231. We thank the Helmholtz-Zentrum Berlin for the allocation
of the synchrotron radiation beam time at BESSY II. We thank Ulrich Pöschl and Gerald Haug for support and stimulating discussions. We also
thank Adam Hitchcock for his support providing information, literature, and
constructive criticism during the review process. We further thank referee 2
for helpful comments.The article processing charges for this open-access publication were covered by the Max Planck Society.
Edited by: Maria Genzer
Reviewed by: Adam Hitchcock and one anonymous referee
ReferencesBalcells, L., Abad, L., Rojas, H., and Martínez, B.: Material damage
induced by nanofabrication processes in manganite thin films,
Nanotechnology, 19, 135307, 10.1088/0957-4484/19/13/135307, 2008.Barber, D. J.: Radiation damage in ion-milled specimens: characteristics,
effects and methods of damage limitation, Ultramicroscopy, 52, 101–125,
10.1016/0304-3991(93)90025-S, 1993.
Bargar, J., Tebo, B., K., P., McCubbery, D., Chiu, V., and B., T.: Manganese
Oxide Biomineralization by Spores of the Marine Bacillus sp. Strain SG-1,
AGU Fall Meeting Abstracts, 2001.Bassim, N. D., De Gregorio, B. T., Kilcoyne, A. L. D., Scott, K., Chou, T.,
Wirick, S., Cody, G., and Stroud, R. M.: Minimizing damage during FIB sample
preparation of soft materials, J. Microsc., 245, 288–301,
10.1111/j.1365-2818.2011.03570.x, 2012.
Betz, G. and Wehner, G. K.: Sputtering of multicomponent materials, in:
Sputtering by Particle Bombardment II, Topics in Applied Physics, vol 52.,
edited by: Behrish, R., 11–90, Springer Berlin, Heidelberg, 1983.Cairney, J. M., Smith, R. D., and Munroe, P. R.: Transmission Electron
Microscope Specimen Preparation of Metal Matrix Composites Using the Focused
Ion Beam Miller, Microsc. Microanal., 6, 452–462,
10.1007/s100050010048, 2000.Cen, X. and van Benthem, K.: Ion beam heating of kinetically constrained
nanomaterials, Ultramicroscopy, 186, 30–34,
10.1016/j.ultramic.2017.12.005, 2018.Christie, A., Sutherland, I., and Walls, J.: An XPS study of ion-induced
dissociation on metal carbonate surfaces, Vacuum, 31, 513–517,
10.1016/0042-207X(81)90051-8, 1981.
Christoffersen, R., Rahman, Z., and Keller, L. P.: Solar Ion Sputter
Deposition in the Lunar Regolith: Experimental Simulation Using Focused-Ion
Beam Techniques, in: 43rd Lunar and Planetary Science Confernece, 19–24
March
2012, The Woodlands, TX, United States, 2012.Chuang, T. J., Brundle, C. R., and Wandelt, K.: An X-ray photoelectron
spectroscopy study of the chemical changes in oxide and hydroxide surfaces
induced by Ar+ ion bombardment, Thin Solid Films, 53, 19–27,
10.1016/0040-6090(78)90365-6, 1978.Contarini, S. and Rabalais, J. W.: Ion bombardment-induced decomposition of
Li and Ba sulfates and carbonates studied by X-ray photoelectron
spectroscopy, J. Electron Spectros. Relat. Phenomena, 35, 191–201,
10.1016/0368-2048(85)80056-6, 1985.
Cosmidis, J. and Benzerara, K.: Soft X-ray scanning transmission
spectromicroscopy, in: Biomineralization Sourcebook: characterization of
biominerals and biomimetic materials, edited by: DiMasi, E. and Gower, L.,
CRC Press, Boca Raton, 2014.Cramer, S. P., DeGroot, F. M. F., Ma, Y., Chen, C. T., Sette, F., Kipke, C.
A., Eichhorn, D. M., Chan, M. K., and Armstrong, W. H.: Ligand field
strengths and oxidation states from manganese L-edge spectroscopy, J. Am.
Chem. Soc., 113, 7937–7940, 10.1021/ja00021a018, 1991.
DiGregorio, B. E.: Rock varnish as a habitat for extant life on Mars, edited
by: Hoover, R. B., Levin, G. V., Paepe, R. R., and Rozanov, A. Y., 120–130,
2002.Dorn, R. I. and Krinsley, D.: Spatial, temporal and geographic
considerations of the problem of rock varnish diagenesis, Geomorphology,
130, 91–99, 10.1016/j.geomorph.2011.02.002, 2011.Egerton, R. F.: Mechanisms of radiation damage in beam-sensitive specimens,
for TEM accelerating voltages between 10 and 300 kV, Microsc. Res. Tech.,
75, 1550–1556, 10.1002/jemt.22099, 2012.Egerton, R. F., Li, P., and Malac, M.: Radiation damage in the TEM and SEM,
Micron, 35, 399–409, 10.1016/j.micron.2004.02.003, 2004.Fischione, P. E., Williams, R. E. A., Genç, A., Fraser, H. L.,
Dunin-Borkowski, R. E., Luysberg, M., Bonifacio, C. S., and Kovács, A.: A
Small Spot, Inert Gas, Ion Milling Process as a Complementary Technique to
Focused Ion Beam Specimen Preparation, Microsc. Microanal., 23, 782–793,
10.1017/S1431927617000514, 2017.
Follath, R., Schmidt, J. S., Weigand, M., Fauth, K., Garrett, R., Gentle,
I., Nugent, K., and Wilkins, S.: The X-ray microscopy beamline UE46-PGM2 at
BESSY, AIP Conference Proceedings, vol. 1234, 323–326, 2010.Fondell, M., Gorgoi, M., Boman, M., and Lindblad, A.: Surface modification of
iron oxides by ion bombardment – Comparing depth profiling by HAXPES and Ar
ion sputtering, J. Electron Spectros. Relat. Phenomena, 224, 23–26,
10.1016/j.elspec.2017.09.008, 2018.Fuggle, J. C. and Mårtensson, N.: Core-level binding energies in metals,
J. Electron Spectros. Relat. Phenomena, 21, 275–281,
10.1016/0368-2048(80)85056-0, 1980.Förster, J.-D. and Pöhlker, C.: Dataset for “Artifacts from manganese reduction in rock samples
prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy”, Max Planck Society, 10.17617/3.22, 2019.Garvie, L. A. J., Burt, D. M., and Buseck, P. R.: Nanometer-scale complexity,
growth, and diagenesis in desert varnish, Geology, 36, 215–218,
10.1130/G24409A.1, 2008.Giannuzzi, L. A., Geurts, R., and Ringnalda, J.: 2 keV Ga+ FIB Milling for
Reducing Amorphous Damage in Silicon, Microsc. Microanal., 11, 828–829,
10.1017/S1431927605507797, 2005.Gilbert, B., Frazer, B. H., Belz, A., Conrad, P. G., Nealson, K. H., Haskel,
D., Lang, J. C., Srajer, G., and De Stasio, G.: Multiple Scattering
Calculations of Bonding and X-ray Absorption Spectroscopy of Manganese
Oxides, J. Phys. Chem. A, 107, 2839–2847, 10.1021/jp021493s, 2003.
Glasauer, S. M., Langley, S., Beveridge, T. J., Fakra, S., Tyliszczak, T.,
Shuh, D., Boyanov, M., and Kemner, K.: The Internalization of Iron and
Manganese as Discrete Particles During the Bioreduction of Fe(III) and
Mn(IV) by a Dissimilatory Metal-Reducing Bacterium, AGU Fall Meet. Abstr.,
B13B–1095, 2006.Goldsmith, Y., Stein, M., and Enzel, Y.: From dust to varnish: Geochemical
constraints on rock varnish formation in the Negev Desert, Israel, Geochim.
Cosmochim. Acta, 126, 97–111, 10.1016/j.gca.2013.10.040, 2014.Gutierrez-Urrutia, I.: Analysis of FIB-induced damage by electron
channelling contrast imaging in the SEM, J. Microsc., 265, 51–59,
10.1111/jmi.12462, 2017.Guttmann, P. and Bittencourt, C.: Overview of nanoscale NEXAFS performed
with soft X-ray microscopes, Beilstein J. Nanotechnol., 6, 595–604,
10.3762/bjnano.6.61, 2015.Hapke, B.: Darkening of silicate rock powders by solar wind sputtering,
Moon, 7, 342–355, 10.1007/BF00564639, 1973.Henderson, R. and Glaeser, R. M.: Quantitative analysis of image contrast in
electron micrographs of beam-sensitive crystals, Ultramicroscopy, 16,
139–150, 10.1016/0304-3991(85)90069-5, 1985.Henke, B. L., Gullikson, E. M., and Davis, J. C.: X-Ray Interactions:
Photoabsorption, Scattering, Transmission, and Reflection at E = 50–30,000
eV, Z = 1–92, At. Data Nucl. Data Tables, 54, 181–342,
10.1006/adnd.1993.1013, 1993.Hitchcock, A. P.: Soft X-ray spectromicroscopy and ptychography, J. Electron
Spectros. Relat. Phenomena, 200, 49–63, 10.1016/j.elspec.2015.05.013,
2015.Hitchcock, A. P., Hitchcock, P., Jacobsen, C., Zimba, C., Loo, B.,
Rotenberg, E., Denlinger, J., and Kneedler, R.: aXis 2000 – Analysis of X-ray
images and spectra, available at:
http://unicorn.mcmaster.ca/axis/aXis2000-windows-pre-IDL8.3.html (last
access:
18 January 2019), 2018.Hoffman, A. and Paterson, P. J. K.: Electron stimulated reduction of
sapphire studied by electron energy loss and Auger spectroscopies, Surf.
Sci., 352–354, 993–997, 10.1016/0039-6028(95)01314-8, 1996.Hofmann, S. and Sanz, J. M.: Quantitative Evaluation of the Ion-Beam Effect
during Sputtering of Oxide Layers using AES and XPS, Fresenius' Zeitschrift
für Anal. Chemie, 314, 215–219, 10.1007/BF00516801, 1983.Holmes, J. L., Bachus, K. N., and Bloebaum, R. D.: Thermal effects of the
electron beam and implications of surface damage in the analysis of bone
tissue, Scanning, 22, 243–248, 10.1002/sca.4950220403, 2000.Ishitani, T. and Kaga, H.: Calculation of Local Temperature Rise in
Focused-Ion-Beam Sample Preparation, J. Electron Microsc. (Tokyo)., 44,
331–336, 10.1093/oxfordjournals.jmicro.a051185, 1995.
Jamison, R. B., Mardinly, A. J., Susnitzky, D. W., and Gronsky, R.: Effects
of Ion Species and Energy on the Amorphization of Si During FIB TEM Sample
Preparation as Determined by Computational and Experimental Methods,
Microsc. Microanal. – New York, 6, 526–527, 2000.Jiang, N.: Electron beam damage in oxides: a review, Reports Prog. Phys.,
79, 016501, 10.1088/0034-4885/79/1/016501, 2016.Joy, D. C. and Joy, C. S.: Low voltage scanning electron microscopy, Micron,
27, 247–263, 10.1016/0968-4328(96)00023-6, 1996.Kanaya, K., Ono, S., and Ishigaki, F.: Secondary electron emission from
insulators, J. Phys. D. Appl. Phys., 11, 2425–2437,
10.1088/0022-3727/11/17/015, 1978.Kelly, R.: Bombardment-induced compositional change with alloys, oxides,
oxysalts and halides III. The role of chemical driving forces, Mater. Sci.
Eng. A, 115, 11–24, 10.1016/0921-5093(89)90650-3, 1989.
Kilcoyne, A. L. D., Tyliszczak, T., Steele, W. F., Fakra, S., Hitchcock, P.,
Franck, K., Anderson, E., Harteneck, B., Rightor, E. G., Mitchell, G. E.,
Hitchcock, A. P., Yang, L., Warwick, T., and Ade, H.:
Interferometer-controlled scanning transmission X-ray microscopes at the
Advanced Light Source, J. Synchrotron Radiat., 10, 125–136, 2003.
Kim, M. J. and Carpenter, R. W.: Tem specimen heating during ion beam
thinning: microstructural instability, Ultramicroscopy, 21, 327–334, 1987.Knotek, M. L. and Feibelman, P. J.: Ion Desorption by Core-Hole Auger Decay,
Phys. Rev. Lett., 40, 964–967, 10.1103/PhysRevLett.40.964, 1978.
Krinsley, D., Dorn, R., and Tovey, N.: Nanometer-Scale Layering in Rock
Varnish: Implications for Genesis and Paleoenvironmental Interpretation, J.
Geol., 103, 106–113, 1995.Kuhlman, K. R., Sridharan, K., and Kvit, A.: Simulation of solar wind space
weathering in orthopyroxene, Planet. Space Sci., 115, 110–114,
10.1016/j.pss.2015.04.003, 2015.Kurata, H. and Colliex, C.: Electron-energy-loss core-edge structures in
manganese oxides, Phys. Rev. B, 48, 2102–2108,
10.1103/PhysRevB.48.2102, 1993.Lerotic, M., Jacobsen, C., Schäfer, T., and Vogt, S.: Cluster analysis of
soft X-ray spectromicroscopy data, Ultramicroscopy, 100, 35–57,
10.1016/j.ultramic.2004.01.008, 2004.Lerotic, M., Jacobsen, C., Gillow, J. B., Francis, A. J., Wirick, S., Vogt,
S., and Maser, J.: Cluster analysis in soft X-ray spectromicroscopy: Finding
the patterns in complex specimens, J. Electron Spectros. Relat. Phenomena,
144–147, 1137–1143, 10.1016/j.elspec.2005.01.158, 2005.Lerotic, M., Mak, R., Wirick, S., Meirer, F., and Jacobsen, C.: MANTiS: a
program for the analysis of X-ray spectromicroscopy data, J. Synchrotron
Radiat., 21, 1206–1212, 10.1107/S1600577514013964, 2014.
Li, J. and Liu, P.: Important Factors to Consider in FIB Milling of
Crystalline Materials, in: Characterization of Minerals, Metals, and
Materials 2017, edited by: Ikhmayies, S., Li, B., Carpenter, J. S., Li, J.,
Hwang, J.-Y., Monteiro, S. N., and Firrao, D., 329–336, Springer, Cham., 2017.Liu, T. and Dorn, R. I.: Understanding the Spatial Variability of
Environmental Change in Drylands with Rock Varnish Microlaminations, Ann.
Assoc. Am. Geogr., 86, 187–212, 10.1111/j.1467-8306.1996.tb01750.x,
1996.Macholdt, D. S., Jochum, K. P., Pöhlker, C., Stoll, B., Weis, U., Weber,
B., Müller, M., Kappl, M., Buhre, S., Kilcoyne, A. L. D., Weigand, M.,
Scholz, D., Al-Amri, A. M., and Andreae, M. O.: Microanalytical methods for
in-situ high-resolution analysis of rock varnish at the micrometer to
nanometer scale, Chem. Geol., 411, 57–68,
10.1016/j.chemgeo.2015.06.023, 2015.Macholdt, D. S., Jochum, K. P., Pöhlker, C., Arangio, A., Förster,
J.-D., Stoll, B., Weis, U., Weber, B., Müller, M., Kappl, M., Shiraiwa,
M., Kilcoyne, A. L. D., Weigand, M., Scholz, D., Haug, G. H., Al-Amri, A.,
and Andreae, M. O.: Characterization and differentiation of rock varnish
types from different environments by microanalytical techniques, Chem.
Geol., 459, 91–118, 10.1016/j.chemgeo.2017.04.009, 2017a.Macholdt, D. S., Herrmann, S., Jochum, K. P., Kilcoyne, A. L. D., Laubscher,
T., Pfisterer, J. H. K., Pöhlker, C., Schwager, B., Weber, B., Weigand,
M., Domke, K. F., and Andreae, M. O.: Black manganese-rich crusts on a Gothic
cathedral, Atmos. Environ., 171, 205–220,
10.1016/j.atmosenv.2017.10.022, 2017b.Mak, R., Lerotic, M., Fleckenstein, H., Vogt, S., Wild, S. M., Leyffer, S.,
Sheynkin, Y., and Jacobsen, C.: Non-negative matrix analysis for effective
feature extraction in X-ray spectromicroscopy, Faraday Discuss., 171,
357–371, 10.1039/C4FD00023D, 2014.Malherbe, J. B., Hofmann, S., and Sanz, J. M.: Preferential sputtering of
oxides: A comparison of model predictions with experimental data, Appl.
Surf. Sci., 27, 355–365, 10.1016/0169-4332(86)90139-X, 1986.Mardinly, J. and Susnitzky, D. W.: Transmission Electron Microscopy of
Semiconductor Based Products, MRS Proc., 523, 3–12,
10.1557/PROC-523-03, 1998.Mayer, J., Giannuzzi, L. A., Kamino, T., and Michael, J.: TEM Sample
Preparation and Damage, MRS Bull., 32, 400–407, 10.1557/mrs2007.63,
2007.McIntyre, N. S. and Zetaruk, D. G.: X-ray photoelectron spectroscopic
studies of iron oxides, Anal. Chem., 49, 1521–1529,
10.1021/ac50019a016, 1977.Michael, J. R.: Gallium Phase Formation in Cu During 30kV Ga+ FIB Milling,
Microsc. Microanal., 12, 1248–1249, 10.1017/S1431927606062015,
2006.Mikmeková, S., Matsuda, K., Watanabe, K., Ikeno, S., Müllerová,
I., and Ludek, F.: FIB Induced Damage Examined with the Low Energy SEM,
Mater. Trans., 52, 292–296, 10.2320/matertrans.MB201005, 2011.Mitchell, D. F., Sproule, G. I., and Graham, M. J.: Sputter reduction of
oxides by ion bombardment during Auger depth profile analysis, Surf.
Interface Anal., 15, 487–497, 10.1002/sia.740150808, 1990.MoberlyChan, W. J., Adams, D. P., Aziz, M. J., Hobler, G., and Schenkel, T.:
Fundamentals of Focused Ion Beam Nanostructural Processing: Below, At, and
Above the Surface, MRS Bull., 32, 424–432, 10.1557/mrs2007.66,
2007.
Moffet, R. C., Tivanski, A. V., and Gilles, M. K.: Scanning Transmission
X-ray Microscopy: Applications in Atmospheric Aerosol Research, in:
Fundamentals and Applications in Aerosol Spectroscopy, edited by:
Signorell, R. and Reid, J., CRC Press, 2011.Naguib, H. M. and Kelly, R.: On the increase in the electrical conductivity
of MoO3 and V2O5 following ion bombardment. Studies on bombardment-enhanced
conductivity-I, J. Phys. Chem. Solids, 33, 1751–1759,
10.1016/S0022-3697(72)80469-4, 1972.Nesbitt, H. W. and Banerjee, D.: Interpretation of XPS Mn(2p) spectra of Mn
oxyhydroxides and constraints on the mechanism of MnO 2 precipitation, Am.
Mineral., 83, 305–315, 10.2138/am-1998-3-414, 1998.Ohya, K. and Ishitani, T.: Target material dependence of secondary electron
images induced by focused ion beams, Surf. Coatings Technol., 158–159,
8–13, 10.1016/S0257-8972(02)00196-2, 2002.Ovchinnikov, V. V., Makhin'ko, F. F., and Solomonov, V. I.: Thermal-spikes
temperature measurement in pure metals under argon ion irradiation (E =
5–15 keV), J. Phys. Conf. Ser., 652, 012070,
10.1088/1742-6596/652/1/012070, 2015.Pallecchi, I., Pellegrino, L., Bellingeri, E., Siri, A. S., Marré, D.,
and Gazzadi, G. C.: Investigation of FIB irradiation damage in
La0.7Sr0.3MnO3 thin films, J. Magn. Magn. Mater., 320, 1945–1951,
10.1016/j.jmmm.2008.02.171, 2008.Pantano, C. G. and Madey, T. E.: Electron beam damage in Auger electron
spectroscopy, Appl. Surf. Sci., 7, 115–141,
10.1016/0378-5963(81)90065-9, 1981.
Parker, T. and Kelly, R.: Electrical and Structural Changes in Ion-Bombarded
TiO2 (Studies on bombardment-enhanced conductivity – II), in Ion
Implantation in Semiconductors and Other Materials, edited by: Crowder, B.
L., 551–566, The IBM Research Symposia Series, Springer, Boston, MA, 1973.
Pecher, K.: Charge state mapping of mixed valent iron and manganese mineral
particles using Scanning Transmission X-ray Microscopy (STXM), AIP
Conference Proceedings, vol. 507, 291–300, AIP, 2000.Pecher, K., McCubbery, D., Kneedler, E., Rothe, J., Bargar, J., Meigs, G.,
Cox, L., Nealson, K., and Tonner, B.: Quantitative charge state analysis of
manganese biominerals in aqueous suspension using scanning transmission
X-ray microscopy (STXM), Geochim. Cosmochim. Acta, 67, 1089–1098,
10.1016/S0016-7037(02)01229-2, 2003.
Perry, R. S. and Kolb, V. M.: From Darwin to Mars: desert varnish as a model
for preservation of complex (bio)chemical systems, edited by: Hoover, R. B.
and Rozanov, A. Y., 136 pp., 2004.Pieters, C. M. and Noble, S. K.: Space weathering on airless bodies, J.
Geophys. Res.-Planets, 121, 1865–1884, 10.1002/2016JE005128, 2016.Prenitzer, B. I., Giannuzzi, L. A., Newman, K., Brown, S. R., Irwin, R. B.,
Stevie, F. A., and Shofner, T. L.: Transmission electron microscope specimen
preparation of Zn powders using the focused ion beam lift-out technique,
Metall. Mater. Trans. A, 29, 2399–2406, 10.1007/s11661-998-0116-z,
1998.Prenitzer, B. I., Urbanik-Shannon, C. A., Giannuzzi, L. A., Brown, S. R.,
Irwin, R. B., Shofner, T. L., and Stevie, F. A.: The Correlation between Ion
Beam/Material Interactions and Practical FIB Specimen Preparation, Microsc.
Microanal., 9, 216–236, 10.1017/S1431927603030034, 2003.
Rajsiri, S., Kempshall, B. W., Schwarz, S. M., and Giannuzzi, L. A.: FIB
Damage in Silicon: Amorphization or Redeposition?, Microsc. Microanal.,
8, 50–51, 2002.Richards, F. J.: A Flexible Growth Function for Empirical Use, J. Exp. Bot.,
10, 290–301, 10.1093/jxb/10.2.290, 1959.Roof, S. and Callagan, C.:
The Climate of Death Valley, California, B. Am. Meteorol. Soc., 84,
1725–1740, 10.1175/BAMS-84-12-1725, 2003.Rubanov, S. and Munroe, P. R.: Investigation of the structure of damage
layers in TEM samples prepared using a focused ion beam, J. Mater. Sci.
Lett., 20, 1181–1183, 10.1023/A:1010950201525, 2001.Rubanov, S. and Munroe, P. R.: FIB-induced damage in silicon, J. Microsc.,
214, 213–221, 10.1111/j.0022-2720.2004.01327.x, 2004.Saifullah, M. S. M.: Sub-10 nm direct patterning of oxides using an electron
beam – a review, COSMOS, 5, 1–21, 10.1142/S0219607709000403, 2009.Schmied, R., Fröch, J. E., Orthacker, A., Hobisch, J., Trimmel, G., and
Plank, H.: A combined approach to predict spatial temperature evolution and
its consequences during FIB processing of soft matter, Phys. Chem. Chem.
Phys., 16, 6153–6158, 10.1039/c3cp55308f, 2014.Sezen, M., Plank, H., Fisslthaler, E., Chernev, B., Zankel, A.,
Tchernychova, E., Blümel, A., List, E. J. W., Groggera, W., and
Pölta, P.: An investigation on focused electron/ion beam induced
degradation mechanisms of conjugated polymers, Phys. Chem. Chem. Phys.,
13, 20235–20240, 10.1039/C1CP22406A, 2011.Sherman, D. M.: Electronic structures of iron(III) and manganese(IV)
(hydr)oxide minerals: Thermodynamics of photochemical reductive dissolution
in aquatic environments, Geochim. Cosmochim. Acta, 69, 3249–3255,
10.1016/j.gca.2005.01.023, 2005.Siemons, W., Beekman, C., Fowlkes, J. D., Balke, N., Tischler, J. Z., Xu,
R., Liu, W., Gonzales, C. M., Budai, J. D., and Christen, H. M.:
Focused-ion-beam induced damage in thin films of complex oxide BiFeO3, APL
Mater., 2, 022109, 10.1063/1.4866051, 2014.
Stojic, A. N. and Brenker, F. E.: Argon ion slicing (ArIS): a new tool to
prepare super large TEM thin films from Earth and planetary materials, Eur.
J. Mineral., 22, 17–21, 10.1127/0935-1221/2009/0022-2004, 2010.
Susnitzky, D. W. and Johnson, K. D.: Focused ion beam (FIB) milling damage
formed during TEM sample preparation of silicon, Microsc. Microanal – New
York, 4, 656–657, 1998.Süzer, Ş.: XPS Investigation of X-Ray-Induced Reduction of Metal
Ions, Appl. Spectrosc., 54, 1716–1718, 10.1366/0003702001948772,
2000.Tebo, B. M., Bargar, J. R., Clement, B. G., Dick, G. J., Murray, K. J.,
Parker, D., Verity, R., and Webb, S. M.: BIOGENIC MANGANESE OXIDES:
Properties and Mechanisms of Formation, Annu. Rev. Earth Planet. Sci.,
32, 287–328, 10.1146/annurev.earth.32.101802.120213, 2004.Tebo, B. M., Johnson, H. A., McCarthy, J. K., and Templeton, A. S.:
Geomicrobiology of manganese(II) oxidation, Trends Microbiol., 13,
421–428, 10.1016/j.tim.2005.07.009, 2005.Thiagarajan, N. and Lee, C. T. A., Trace-element evidence for the origin of
desert varnish by direct aqueous atmospheric deposition, Earth Planet.
Sc. Lett., 224, 131–141, 10.1016/j.epsl.2004.04.038, 2004.Tokunaga, T., Narushima, T., Yonezawa, T., Sudo, T., Okubo, S., Komatsubara,
S., Sasaki, K., and Yamamoto, T.: Temperature distributions of electron
beam-irradiated samples by scanning electron microscopy, J. Microsc.,
248, 228–233, 10.1111/j.1365-2818.2012.03666.x, 2012.Toner, B., Fakra, S., Villalobos, M., Warwick, T., and Sposito, G.: Spatially
Resolved Characterization of Biogenic Manganese Oxide Production within a
Bacterial Biofilm, Appl. Environ. Microbiol., 71, 1300–1310,
10.1128/AEM.71.3.1300-1310.2005, 2005.Volkert, C. A. and Minor, A. M.: Focused Ion Beam Microscopy and
Micromachining, MRS Bull., 32, 389–399, 10.1016/j.arth.2016.01.046,
2007.
Weigand, M.: Realization of a new Magnetic Scanning X-ray Microscope and
Investigation of Landau Structures under Pulsed Field Excitation, Culliver,
Göttingen, 2015.Wirth, R.: Focused Ion Beam (FIB): A novel technology for advanced
application of micro- and nanoanalysis in geosciences and applied
mineralogy, Eur. J. Mineral., 16, 863–876,
10.1127/0935-1221/2004/0016-0863, 2004.