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Title: Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy

Abstract

The spatial distribution oftransition metal valence states is of broad interest in the microanalysis ofgeological and environmental samples. An example is rock varnish, a naturalmanganese (Mn)-rich rock coating, whose genesis mechanism remains a subjectof scientific debate. We conducted scanning transmission X-ray microscopywith near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS)measurements of the abundance and spatial distribution of different Mnoxidation states within the nano- to micrometer thick varnish crusts. Suchmicroanalytical measurements of thin and hard rock crusts require samplepreparation with minimal contamination risk. Focused ion beam (FIB) slicingwas used to obtain ~100–1000 nm thin wedge-shaped slices of thesamples for STXM, using standard parameters. Yet, while this preparationis suitable for investigating element distributions and structures in rocksamples, we observed artifactual modifications of the Mn oxidation states atthe surfaces of the FIB slices. Our results imply that the preparationcauses a reduction of Mn 4+ to Mn 2+. We draw attention tothis issue, since FIB slicing, scanning electron microscopy (SEM) imaging,and other preparation and visualization techniques operating in thekilo-electron-volt range are well-established in geosciences, but researchersare often unaware of the potential for the reduction of Mn and possibly otherelements in the samples.

Authors:
 [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [2];  [3];  [1];  [1]; ORCiD logo [1]; ORCiD logo [4]
  1. Max Planck Society, Mainz (Germany)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
  3. Max Planck Society, Stuttgart (Germany)
  4. Max Planck Society, Mainz (Germany); King Saud Univ., Riyadh (Saudi Arabia)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1542389
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Geoscientific Instrumentation, Methods and Data Systems (Online)
Additional Journal Information:
Journal Name: Geoscientific Instrumentation, Methods and Data Systems (Online); Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2193-0864
Publisher:
European Geosciences Union
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES

Citation Formats

Macholdt, Dorothea S., Förster, Jan-David, Müller, Maren, Weber, Bettina, Kappl, Michael, Kilcoyne, A. L. David, Weigand, Markus, Leitner, Jan, Jochum, Klaus Peter, Pöhlker, Christopher, and Andreae, Meinrat O. Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy. United States: N. p., 2019. Web. doi:10.5194/gi-8-97-2019.
Macholdt, Dorothea S., Förster, Jan-David, Müller, Maren, Weber, Bettina, Kappl, Michael, Kilcoyne, A. L. David, Weigand, Markus, Leitner, Jan, Jochum, Klaus Peter, Pöhlker, Christopher, & Andreae, Meinrat O. Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy. United States. doi:10.5194/gi-8-97-2019.
Macholdt, Dorothea S., Förster, Jan-David, Müller, Maren, Weber, Bettina, Kappl, Michael, Kilcoyne, A. L. David, Weigand, Markus, Leitner, Jan, Jochum, Klaus Peter, Pöhlker, Christopher, and Andreae, Meinrat O. Thu . "Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy". United States. doi:10.5194/gi-8-97-2019. https://www.osti.gov/servlets/purl/1542389.
@article{osti_1542389,
title = {Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy},
author = {Macholdt, Dorothea S. and Förster, Jan-David and Müller, Maren and Weber, Bettina and Kappl, Michael and Kilcoyne, A. L. David and Weigand, Markus and Leitner, Jan and Jochum, Klaus Peter and Pöhlker, Christopher and Andreae, Meinrat O.},
abstractNote = {The spatial distribution oftransition metal valence states is of broad interest in the microanalysis ofgeological and environmental samples. An example is rock varnish, a naturalmanganese (Mn)-rich rock coating, whose genesis mechanism remains a subjectof scientific debate. We conducted scanning transmission X-ray microscopywith near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS)measurements of the abundance and spatial distribution of different Mnoxidation states within the nano- to micrometer thick varnish crusts. Suchmicroanalytical measurements of thin and hard rock crusts require samplepreparation with minimal contamination risk. Focused ion beam (FIB) slicingwas used to obtain ~100–1000 nm thin wedge-shaped slices of thesamples for STXM, using standard parameters. Yet, while this preparationis suitable for investigating element distributions and structures in rocksamples, we observed artifactual modifications of the Mn oxidation states atthe surfaces of the FIB slices. Our results imply that the preparationcauses a reduction of Mn4+ to Mn2+. We draw attention tothis issue, since FIB slicing, scanning electron microscopy (SEM) imaging,and other preparation and visualization techniques operating in thekilo-electron-volt range are well-established in geosciences, but researchersare often unaware of the potential for the reduction of Mn and possibly otherelements in the samples.},
doi = {10.5194/gi-8-97-2019},
journal = {Geoscientific Instrumentation, Methods and Data Systems (Online)},
number = 1,
volume = 8,
place = {United States},
year = {2019},
month = {3}
}

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Works referenced in this record:

Ion bombardment-induced decomposition of Li and Ba sulfates and carbonates studied by X-ray photoelectron spectroscopy
journal, January 1985

  • Contarini, Salvatore; Rabalais, J. Wayne
  • Journal of Electron Spectroscopy and Related Phenomena, Vol. 35, Issue 2
  • DOI: 10.1016/0368-2048(85)80056-6

Non-negative matrix analysis for effective feature extraction in X-ray spectromicroscopy
journal, January 2014

  • Mak, Rachel; Lerotic, Mirna; Fleckenstein, Holger
  • Faraday Discuss., Vol. 171
  • DOI: 10.1039/C4FD00023D

Transmission electron microscope specimen preparation of Zn powders using the focused ion beam lift-out technique
journal, September 1998

  • Prenitzer, B. I.; Giannuzzi, L. A.; Newman, K.
  • Metallurgical and Materials Transactions A, Vol. 29, Issue 9
  • DOI: 10.1007/s11661-998-0116-z

Ion beam heating of kinetically constrained nanomaterials
journal, March 2018


A combined approach to predict spatial temperature evolution and its consequences during FIB processing of soft matter
journal, January 2014

  • Schmied, Roland; Fröch, Johannes E.; Orthacker, Angelina
  • Physical Chemistry Chemical Physics, Vol. 16, Issue 13
  • DOI: 10.1039/c3cp55308f

Thermal effects of the electron beam and implications of surface damage in the analysis of bone tissue
journal, July 2000

  • Holmes, Jennifer L.; Bachus, Kent N.; Bloebaum, Roy D.
  • Scanning, Vol. 22, Issue 4
  • DOI: 10.1002/sca.4950220403

Soft X-ray spectromicroscopy and ptychography
journal, April 2015


A Flexible Growth Function for Empirical Use
journal, January 1959


Geomicrobiology of manganese(II) oxidation
journal, September 2005

  • Tebo, Bradley M.; Johnson, Hope A.; McCarthy, James K.
  • Trends in Microbiology, Vol. 13, Issue 9
  • DOI: 10.1016/j.tim.2005.07.009

Quantitative charge state analysis of manganese biominerals in aqueous suspension using scanning transmission X-ray microscopy (STXM)
journal, March 2003


Mechanisms of radiation damage in beam-sensitive specimens, for TEM accelerating voltages between 10 and 300 kV
journal, July 2012

  • Egerton, R. F.
  • Microscopy Research and Technique, Vol. 75, Issue 11
  • DOI: 10.1002/jemt.22099

Minimizing damage during FIB sample preparation of soft materials: FIB SAMPLE PREPARATION OF SOFT MATERIALS
journal, November 2011


Electron beam damage in oxides: a review
journal, December 2015


Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm
journal, March 2005


Quantitative Erfassung des Ionenstrahleinflusses beim Sputtering von Oxidschichten mit AES und XPS
journal, January 1983

  • Hofmann, S.; Sanz, J. M.
  • Fresenius' Zeitschrift für analytische Chemie, Vol. 314, Issue 3
  • DOI: 10.1007/BF00516801

MANTiS : a program for the analysis of X-ray spectromicroscopy data
journal, July 2014


An investigation on focused electron/ion beam induced degradation mechanisms of conjugated polymers
journal, January 2011

  • Sezen, Meltem; Plank, Harald; Fisslthaler, Evelin
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 45
  • DOI: 10.1039/c1cp22406a

Target material dependence of secondary electron images induced by focused ion beams
journal, September 2002


FIB-induced damage in silicon
journal, June 2004


Preferential sputtering of oxides: A comparison of model predictions with experimental data
journal, December 1986


Secondary electron emission from insulators
journal, December 1978


Core-level binding energies in metals
journal, January 1980

  • Fuggle, John C.; Mårtensson, Nils
  • Journal of Electron Spectroscopy and Related Phenomena, Vol. 21, Issue 3
  • DOI: 10.1016/0368-2048(80)85056-0

Darkening of silicate rock powders by solar wind sputtering
journal, January 1973


On the increase in the electrical conductivity of MoO3 and V2O5 following ion bombardment. Studies on bombardment-enhanced conductivity-I
journal, January 1972


Microanalytical methods for in-situ high-resolution analysis of rock varnish at the micrometer to nanometer scale
journal, September 2015


An XPS study of ion-induced dissociation on metal carbonate surfaces
journal, October 1981


Material damage induced by nanofabrication processes in manganite thin films
journal, February 2008


Ion Desorption by Core-Hole Auger Decay
journal, April 1978


Investigation of FIB irradiation damage in La0.7Sr0.3MnO3 thin films
journal, July 2008

  • Pallecchi, I.; Pellegrino, L.; Bellingeri, E.
  • Journal of Magnetism and Magnetic Materials, Vol. 320, Issue 13
  • DOI: 10.1016/j.jmmm.2008.02.171

Low voltage scanning electron microscopy
journal, June 1996


Trace-element evidence for the origin of desert varnish by direct aqueous atmospheric deposition
journal, July 2004

  • Thiagarajan, Nivedita; Aeolus Lee, Cin-Ty
  • Earth and Planetary Science Letters, Vol. 224, Issue 1-2
  • DOI: 10.1016/j.epsl.2004.04.038

A Small Spot, Inert Gas, Ion Milling Process as a Complementary Technique to Focused Ion Beam Specimen Preparation
journal, June 2017

  • Fischione, Paul E.; Williams, Robert E. A.; Genç, Arda
  • Microscopy and Microanalysis, Vol. 23, Issue 4
  • DOI: 10.1017/S1431927617000514

Cluster analysis of soft X-ray spectromicroscopy data
journal, July 2004


Spatial, temporal and geographic considerations of the problem of rock varnish diagenesis
journal, July 2011


Focused-ion-beam induced damage in thin films of complex oxide BiFeO 3
journal, February 2014

  • Siemons, W.; Beekman, C.; Fowlkes, J. D.
  • APL Materials, Vol. 2, Issue 2
  • DOI: 10.1063/1.4866051

Sputter reduction of oxides by ion bombardment during Auger depth profile analysis
journal, August 1990

  • Mitchell, D. F.; Sproule, G. I.; Graham, M. J.
  • Surface and Interface Analysis, Vol. 15, Issue 8
  • DOI: 10.1002/sia.740150808

Cluster analysis in soft X-ray spectromicroscopy: Finding the patterns in complex specimens
journal, June 2005

  • Lerotic, M.; Jacobsen, C.; Gillow, J. B.
  • Journal of Electron Spectroscopy and Related Phenomena, Vol. 144-147
  • DOI: 10.1016/j.elspec.2005.01.158

Sub-10 nm Direct Patterning of Oxides Using an Electron beam — a Review
journal, May 2009


An X-ray photoelectron spectroscopy study of the chemical changes in oxide and hydroxide surfaces induced by Ar+ ion bombardment
journal, August 1978


Nanometer-scale complexity, growth, and diagenesis in desert varnish
journal, January 2008

  • Garvie, Laurence A. J.; Burt, Donald M.; Buseck, Peter R.
  • Geology, Vol. 36, Issue 3
  • DOI: 10.1130/G24409A.1

Fundamentals of Focused Ion Beam Nanostructural Processing: Below, At, and Above the Surface
journal, May 2007

  • MoberlyChan, Warren J.; Adams, David P.; Aziz, Michael J.
  • MRS Bulletin, Vol. 32, Issue 5
  • DOI: 10.1557/mrs2007.66

Overview of nanoscale NEXAFS performed with soft X-ray microscopes
journal, January 2015

  • Guttmann, Peter; Bittencourt, Carla
  • Beilstein Journal of Nanotechnology, Vol. 6
  • DOI: 10.3762/bjnano.6.61

TEM Sample Preparation and FIB-Induced Damage
journal, May 2007

  • Mayer, Joachim; Giannuzzi, Lucille A.; Kamino, Takeo
  • MRS Bulletin, Vol. 32, Issue 5
  • DOI: 10.1557/mrs2007.63

Gallium Phase Formation in Cu During 30kV Ga+ FIB Milling
journal, July 2006


Space weathering on airless bodies: SPACE WEATHERING ON AIRLESS BODIES
journal, October 2016

  • Pieters, Carle M.; Noble, Sarah K.
  • Journal of Geophysical Research: Planets, Vol. 121, Issue 10
  • DOI: 10.1002/2016JE005128

Thermal-spikes temperature measurement in pure metals under argon ion irradiation (E = 5-15 keV)
journal, November 2015


FIB Induced Damage Examined with the Low Energy SEM
journal, January 2011


Surface modification of iron oxides by ion bombardment – Comparing depth profiling by HAXPES and Ar ion sputtering
journal, April 2018


X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
journal, July 1993

  • Henke, B. L.; Gullikson, E. M.; Davis, J. C.
  • Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342
  • DOI: 10.1006/adnd.1993.1013

X-ray photoelectron spectroscopic studies of iron oxides
journal, September 1977

  • McIntyre, N. S.; Zetaruk, D. G.
  • Analytical Chemistry, Vol. 49, Issue 11
  • DOI: 10.1021/ac50019a016

Interpretation of XPS Mn(2p) spectra of Mn oxyhydroxides and constraints on the mechanism of MnO 2 precipitation
journal, April 1998


Electron beam damage in Auger electron spectroscopy
journal, January 1981


Quantitative analysis of image contrast in electron micrographs of beam-sensitive crystals
journal, January 1985


Multiple Scattering Calculations of Bonding and X-ray Absorption Spectroscopy of Manganese Oxides
journal, April 2003

  • Gilbert, B.; Frazer, B. H.; Belz, A.
  • The Journal of Physical Chemistry A, Vol. 107, Issue 16
  • DOI: 10.1021/jp021493s

Electron-energy-loss core-edge structures in manganese oxides
journal, July 1993


Radiation damage in the TEM and SEM
journal, August 2004


Ligand field strengths and oxidation states from manganese L-edge spectroscopy
journal, October 1991

  • Cramer, S. P.; DeGroot, F. M. F.; Ma, Y.
  • Journal of the American Chemical Society, Vol. 113, Issue 21
  • DOI: 10.1021/ja00021a018

Transmission Electron Microscopy of Semiconductor Based Products
journal, January 1998


Analysis of FIB-induced damage by electron channelling contrast imaging in the SEM: ANALYSIS OF FIB INDUCED DAMAGE BY
journal, August 2016

  • Gutierrez-Urrutia, Ivan
  • Journal of Microscopy, Vol. 265, Issue 1
  • DOI: 10.1111/jmi.12462

2 keV Ga+ FIB Milling for Reducing Amorphous Damage in Silicon
journal, August 2005

  • Giannuzzi, L. A.; Geurts, R.; Ringnalda, J.
  • Microscopy and Microanalysis, Vol. 11, Issue S02
  • DOI: 10.1017/S1431927605507797

Simulation of solar wind space weathering in orthopyroxene
journal, September 2015

  • Kuhlman, Kimberly R.; Sridharan, Kumar; Kvit, Alexander
  • Planetary and Space Science, Vol. 115
  • DOI: 10.1016/j.pss.2015.04.003

XPS Investigation of X-Ray-Induced Reduction of Metal Ions
journal, November 2000


Electron stimulated reduction of sapphire studied by electron energy loss and Auger spectroscopies
journal, May 1996


The Correlation between Ion Beam/Material Interactions and Practical FIB Specimen Preparation
journal, May 2003

  • Prenitzer, B. I.; Urbanik-Shannon, C. A.; Giannuzzi, L. A.
  • Microscopy and Microanalysis, Vol. 9, Issue 3
  • DOI: 10.1017/S1431927603030034

Understanding the Spatial Variability of Environmental Change in Drylands with Rock Varnish Microlaminations
journal, June 1996


Characterization and differentiation of rock varnish types from different environments by microanalytical techniques
journal, May 2017


From dust to varnish: Geochemical constraints on rock varnish formation in the Negev Desert, Israel
journal, February 2014

  • Goldsmith, Yonaton; Stein, Mordechai; Enzel, Yehouda
  • Geochimica et Cosmochimica Acta, Vol. 126
  • DOI: 10.1016/j.gca.2013.10.040

Black manganese-rich crusts on a Gothic cathedral
journal, December 2017


BIOGENIC MANGANESE OXIDES: Properties and Mechanisms of Formation
journal, May 2004


The Climate of Death Valley, California
journal, December 2003

  • Roof, Steven; Callagan, Charlie
  • Bulletin of the American Meteorological Society, Vol. 84, Issue 12
  • DOI: 10.1175/BAMS-84-12-1725

In situ characterization of Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1
journal, August 2000


Rock varnish as a habitat for extant life on Mars
conference, February 2002

  • DiGregorio, Barry E.
  • International Symposium on Optical Science and Technology, SPIE Proceedings
  • DOI: 10.1117/12.454750

The X-ray microscopy beamline UE46-PGM2 at BESSY
conference, January 2010

  • Follath, R.; Schmidt, J. S.; Weigand, M.
  • SRI 2009, 10TH INTERNATIONAL CONFERENCE ON RADIATION INSTRUMENTATION, AIP Conference Proceedings
  • DOI: 10.1063/1.3463201

Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source
journal, February 2003

  • Kilcoyne, A. L. D.; Tyliszczak, T.; Steele, W. F.
  • Journal of Synchrotron Radiation, Vol. 10, Issue 2
  • DOI: 10.1107/S0909049502017739

Tem specimen heating during ion beam thinning: Microstructural instability
journal, January 1987


Nanometer-Scale Layering in Rock Varnish: Implications for Genesis and Paleoenvironmental Interpretation
journal, January 1995

  • Krinsley, David; Dorn, Ronald; Tovey, N. K.
  • The Journal of Geology, Vol. 103, Issue 1
  • DOI: 10.1086/629726

Charge state mapping of mixed valent iron and manganese mineral particles using Scanning Transmission X-ray Microscopy (STXM)
conference, January 2000

  • Pecher, K.
  • Sixth international conference on x-ray microscopy (XRM99), AIP Conference Proceedings
  • DOI: 10.1063/1.1291160

From Darwin to Mars: desert varnish as a model for preservation of complex (bio)chemical systems
conference, February 2004

  • Perry, Randall S.; Kolb, Vera M.
  • Optical Science and Technology, SPIE's 48th Annual Meeting, SPIE Proceedings
  • DOI: 10.1117/12.513383

FIB Damage in Silicon: Amorphization or Redeposition?
journal, August 2002

  • Rajsiri, S.; Kempshall, B. W.; Schwarz, S. M.
  • Microscopy and Microanalysis, Vol. 8, Issue S02
  • DOI: 10.1017/S1431927602101577