Spectroscopy and Diffraction

Molecular level solid-, liquid- and gas-interactions can be investigated through structural, chemical and compositional analysis with remarkable atomic scale spatial and high-energy resolution spectrometers and diffractometers for novel fundamental research.

Resources and Techniques

  • Electron spectroscopy
  • Electron backscatter diffraction
  • Atom probe tomography
  • Ion/molecular beam spectroscopy
  • 57Fe-Mössbauer spectroscopy
  • Optical spectroscopy
  • X-ray tomography and diffractometers

Additional Information

Capability Details

  • Electron spectrometers with high spatial and energy resolution in-situ and ex-situ x-ray photoelectron spectroscopy
  • Secondary ion mass spectrometers with single and cluster ion sources, and time-of-flight and magnetic mass analyzers
  • Electron microscopes with energy dispersive X-ray spectroscopy, electron energy loss spectroscopy and electron backscatter diffraction
  • Local Electrode Atom Probe tomography system with 355 nm UV laser and reflectron flight path for high mass resolution
  • Fourier transform infrared spectrometers with vacuum bench and variable temperature capability
  • Confocal-Raman, cryogenic time-resolved fluorescence, circular dichroism, stopped-flow absorbance, laser-induced breakdown and sum frequency generation optical tools
  • Variable temperature Mössbauer spectroscopy systems for bulk (transmission mode) and surface (emission) measures
  • X-ray diffraction instruments with sealed tube or rotating anode for analysis of powder, thin film and single crystal samples; point, CCD and image plate detection. X-ray computed tomography with 225- and 320-kV fixed, and 225-kV rotating target options using a 2000x2000 pixel area detector and state-of-the-art processing and visualization software

Electron spectroscopy – Achieving nanoscale spatial resolution, users can study elemental composition, structural properties, and chemical states of materials with applications to thin films, nanomaterials, catalysis, biological and environmental sciences, corrosion, and atmospheric aerosols.

Electron backscatter diffraction – Samples of microstructures in environmental and material science can be examined with three dimensional reconstruction and characterization using focused ion beam-electron backscatter diffraction analysis.

Atom probe tomography – Atom Probe Tomography (APT) provides comprehensive and accurate three dimensional chemical imaging for characterization of both metallic materials and low electrical conductivity materials, such as semiconductors, oxides, carbides, nitrides and composites.

Ion/molecular beam spectroscopy – Secondary ions and scattered ions from various materials are analyzed in straight, magnetic or time-of-flight mass spectrometers to investigate elemental, isotopic and molecular compositions through surface spectra, one dimensional depth profiling and two dimensional and three dimensional chemical imaging.

57Fe-Mössbauer spectroscopy – Using 57Fe (a versatile, highly sensitive, and stable isotope with natural abundance of 2.2%), users can obtain information about the valence state, coordination number and magnetic ordering temperatures for a wide range of Fe-containing samples; (e.g., Fe-organic matter complexes, sediments, catalysts, glass materials).

Optical spectroscopy – Fluorimetry, stopped-flow absorbance, FTIR and confocal-Raman tools enable analysis for biology, radiochemistry, and catalysis. Sum frequency generation-vibrational spectroscopy and second harmonic generation are available to study liquid, liquid and solid, and liquid interfaces.

X-ray tomography and diffractometers – X-ray computed tomography delivers images of microstructures (components, pore structure and connectivity) in biological and geological samples at tens of microns spatial resolution. General purpose and specialized x-ray diffraction systems, including single-crystal, microbeam and variable temperature powder capabilities, empower phase analysis of polycrystalline, epitaxial thin films, protein structure determination, and studies of problematic small inorganic molecules.

The atmospheric pressure reactor system is designed for testing the efficiency of various catalysts for the treatment of gas-phase pollutants. EMSL...
Custodian(s): Russell Tonkyn
The LEAP® 4000 XHR local electrode atom probe tomography instrument enabled the first-ever comprehensive and accurate 3-D chemical imaging studies...
The Bio-Logic® SFM-400/S is a 4-syringe stopped-flow system that offers the capability to carry out complex, multi-mixing experiments with the...
Custodian(s): Zheming Wang
EMSL's non-thermal interfacial reactions instrumentation is available for use in research directed toward understanding non-thermal interfacial...
Custodian(s): Greg Kimmel
EMSL's ultrahigh vacuum (UHV) surface chemistry-high-resolution electron energy loss spectroscopy (HREELS) system is designed to study the molecular...
Custodian(s): Mike Henderson
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different...
We have investigated the structure and dynamics of thin water films adsorbed on TiO2(110) using infrared reflection absorption spectroscopy (IRAS)...
The reactivity of zerovalent zinc (ZVZ) toward 1,2,3-trichloropropane (TCP) was evaluated under a variety of solution conditions, including deionized...
The ability to harness the metal-metal and metal-oxygen coordination structures of nanoalloy catalysts is critical for catalyzing the oxygen...
A novel write-once-read-many (WORM) optical stack on Mylar tape is proposed as a replacement for magnetic tape for archival data storage. This...
Posted: June 17, 2014
The Science Hexavalent chromium is a major environmental contaminant at several Department of Energy (DOE) sites as well as other sites around the...
Posted: April 08, 2014
The Science Uranium poses a serious risk of groundwater contamination at the Hanford Site. But most previous experimental studies addressing this...
Posted: March 12, 2014
The Science Lithium-sulfur batteries are promising options for electric vehicles and for storing renewable energy because they can store a lot of...
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The Science Biological material derived from plants represents a promising source for renewable and sustainable biofuel production, but there is a...
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The Science The release of wastes associated with nuclear reprocessing from storage facilities into the underlying sediments and groundwater is an...

Molecular level solid-, liquid- and gas-interactions can be investigated through structural, chemical and compositional analysis with remarkable atomic scale spatial and high-energy resolution spectrometers and diffractometers for novel fundamental research.

Resources and Techniques

  • Electron spectroscopy
  • Electron backscatter diffraction
  • Atom probe tomography
  • Ion/molecular beam spectroscopy
  • 57Fe-Mössbauer spectroscopy
  • Optical spectroscopy
  • X-ray tomography and diffractometers

Additional Information

Attachments: 

Probing the electronic structures of low oxidation-state uranium fluoride molecules UFx- (x=2-4) .

Abstract: 

We report the experimental observation of gaseous UFx- (x = 2-4) anions, which are investigated using photoelectron spectroscopy and relativistic quantum chemistry. Vibrationally resolved photoelectron spectra are obtained for all three species and the electron affinities of UFx (x = 2-4) are measured to be 1.16(3), 1.09(3), and 1.58(3) eV, respectively. Significant multi-electron transitions are observed in the photoelectron spectra of U(5f(3)7s(2)) F-2(-), as a result of strong electron correlation effects of the two 7s electrons. The U-F symmetric stretching vibrational modes are resolved for the ground states of all UFx (x = 2-4) neutrals. Theoretical calculations are performed to qualitatively understand the photoelectron spectra. The entire UFx- and UFx (x = 1-6) series are considered theoretically to examine the trends of U-F bonding and the electron affinities as a function of fluorine coordination. The increased U-F bond lengths and decreased bond orders from UF2- to UF4- indicate that the U-F bonding becomes weaker as the oxidation state of U increases from I to III. (C) 2013 AIP Publishing LLC.

Citation: 
Li WL, H Hu, T Jian, GV Lopez, J Su, J Li, and LS Wang.2013."Probing the electronic structures of low oxidation-state uranium fluoride molecules UFx- (x=2-4) ."Journal of Chemical Physics 139(24):Article No. 244303. doi:10.1063/1.4851475
Authors: 
Li WL
H Hu
T Jian
GV Lopez
J Su
J Li
LS Wang
Instruments: 
Publication year: 
2013

7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source.

Abstract: 

Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.

Citation: 
Pedrini B, CJ Tsai, G Capitani, C Padeste, M Hunter, NA Zatsepin, A Barty, H Benner, S Boutet, GK Feld, S Hau-Riege, R Kirian, C Kupitz, M Messerschmidt, JI Ogren, T Pardini, B Segelke, GJ Williams, JC Spence , R Abela, MA Coleman, JE Evans, G Schertler, M Frank, and XD Li.2014."7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source."Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 369(1647):Article No. 20130500. doi:10.1098/rstb.2013.0500
Authors: 
B Pedrini
CJ Tsai
G Capitani
C Padeste
M Hunter
NA Zatsepin
A Barty
H Benner
S Boutet
GK Feld
S Hau-Riege
R Kirian
C Kupitz
M Messerschmidt
JI Ogren
T Pardini
B Segelke
GJ Williams
JC Spence
R Abela
MA Coleman
JE Evans
G Schertler
M Frank
XD Li
Instruments: 
Publication year: 
2014

In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS.

Abstract: 

The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

Citation: 
Hua X, XY Yu, Z Wang, L Yang, B Liu, Z Zhu, AE Tucker, WB Chrisler, EA Hill, S Thevuthasan, Y Lin, S Liu, and MJ Marshall.2014."In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS."Analyst 139:1609-1613. doi:10.1039/C3AN02262E
Authors: 
X Hua
XY Yu
Z Wang
L Yang
B Liu
Z Zhu
AE Tucker
WB Chrisler
EA Hill
S Thevuthasan
Y Lin
S Liu
MJ Marshall
Instruments: 
Publication year: 
2014

Absorption Mode FT-ICR Mass Spectrometry Imaging.

Abstract: 

Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here we present the first use of absorption mode for Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image and then these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode ?Datacubes? for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.

Citation: 
Smith DF, DP Kilgour, M Konijnenburg, PB O'Connor, and RM Heeren.2013."Absorption Mode FT-ICR Mass Spectrometry Imaging."Analytical Chemistry 85(23):11180-11184. doi:10.1021/ac403039t
Authors: 
DF Smith
DP Kilgour
M Konijnenburg
PB O'Connor
RM Heeren
Instruments: 
Volume: 
85
Issue: 
23
Pages: 
11180-11184
Publication year: 
2013

Effect of Co-solutes on the Products and Solubility of Uranium(VI) Precipitated with Phosphate.

Abstract: 

Uranyl phosphate solids are often found with uranium ores, and their low solubility makes them promising target phases for in situ remediation of uranium-contaminated subsurface environments. The products and solubility of uranium(VI) precipitated with phosphate can be affected by the pH, dissolved inorganic carbon (DIC) concentration, and co-solute composition (e.g. Na+/Ca2+) of the groundwater. Batch experiments were performed to study the effect of these parameters on the products and extent of uranium precipitation induced by phosphate addition. In the absence of co-solute cations, chernikovite [H3O(UO2)(PO4)•3H2O] precipitated despite uranyl orthophosphate [(UO2)3(PO4)2•4H2O] being thermodynamically more favorable under certain conditions. As determined using X-ray diffraction, electron microscopy, and laser induced fluorescence spectroscopy, the presence of Na+ or Ca2+ as a co-solute led to the precipitation of sodium autunite ([Na2(UO2)2(PO4)2] and autunite [Ca(UO2)2(PO4)2]), which are structurally similar to chernikovite. In the presence of sodium, the dissolved U(VI) concentrations were generally in agreement with equilibrium predictions of sodium autunite solubility. However, in the calcium-containing systems, the observed concentrations were below the predicted solubility of autunite, suggesting the possibility of uranium adsorption to or incorporation in a calcium phosphate precipitate in addition to the precipitation of autunite.

Citation: 
Mehta V, F Maillot, Z Wang, JG Catalano, and DE Giammar.2014."Effect of Co-solutes on the Products and Solubility of Uranium(VI) Precipitated with Phosphate."Chemical Geology 364:66-75. doi:10.1016/j.chemgeo.2013.12.002
Authors: 
V Mehta
F Maillot
Z Wang
JG Catalano
DE Giammar
Instruments: 
Publication year: 
2014

Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses.

Abstract: 

Chemical durability is not a single material property that can be uniquely measured. Instead it is the response to a host of coupled material and environmental processes whose rates are estimated by a combination of theory, experiment, and modeling. High-level nuclear waste (HLW) glass is perhaps the most studied of any material yet there remain significant technical gaps regarding their chemical durability. The phenomena affecting the long-term performance of HLW glasses in their disposal environment include surface reactions, transport properties to and from the reacting glass surface, and ion exchange between the solid glass and the surrounding solution and alteration products. The rates of these processes are strongly influenced and are coupled through the solution chemistry, which is in turn influenced by the reacting glass and also by reaction with the near-field materials and precipitation of alteration products. Therefore, those processes must be understood sufficiently well to estimate or bound the performance of HLW glass in its disposal environment over geologic time-scales. This article summarizes the current state of understanding of surface reactions, transport properties, and ion exchange along with the near-field materials and alteration products influences on solution chemistry and glass reaction rates. Also summarized are the remaining technical gaps along with recommended approaches to fill those technical gaps.

Citation: 
Vienna JD, JV Ryan, S Gin, and Y Inagaki.2013."Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses."International Journal of Applied Glass Science 4(4):283-294. doi:10.1111/ijag.12050
Authors: 
JD Vienna
JV Ryan
S Gin
Y Inagaki
Instruments: 
Volume: 
4
Issue: 
4
Pages: 
283-294
Publication year: 
2013

In situ chemical probing of the electrode-electrolyte interface by ToF-SIMS.

Abstract: 

A portable vacuum interface allowing direct probing of the electrode-electrolyte interface was developed. A classical electrochemical system consisting of gold working electrode, platinum counter electrode, platinum reference electrode, and potassium iodide electrolyte was used to demonstrate real-time observation of the gold iodide adlayer on the electrode and chemical species as a result of redox reactions using cyclic voltammetry (CV) and the time-of-flight secondary ion mass spectrometry (ToF-SIMS, a vacuum-based surface analytical technique) simultaneously. This microfluidic electrochemical probe provides a new way to investigate the surface region with adsorbed molecules and region of diffused layer with chemical speciation in liquids in situ by surface sensitive techniques.

Citation: 
Liu B, XY Yu, Z Zhu, X Hua, L Yang, and Z Wang.2014."In situ chemical probing of the electrode-electrolyte interface by ToF-SIMS."Lab on a Chip 14(5):855-859. doi:10.1039/C3LC50971K
Authors: 
B Liu
XY Yu
Z Zhu
X Hua
L Yang
Z Wang
Instruments: 
Volume: 
14
Issue: 
5
Pages: 
855-859
Publication year: 
2014

An international initiative on long-term behavior of high-level nuclear waste glass.

Abstract: 

Nations producing borosilicate glass as an immobilization material for radioactive wastes resulting from spent nuclear fuel reprocessing have reinforced scientific collaboration to obtain consensus on mechanisms controlling the long-term dissolution rate of glass. This goal is deemed to be crucial for the development of reliable performance assessment models for geological disposal. The collaborating laboratories all conduct fundamental and/or applied research with modern materials science techniques. The paper briefly reviews the radioactive waste vitrification programmes of the six participant nations and summarizes the state-of-the-art of glass corrosion science, emphasizing common scientific needs and justifications for on-going initiatives.

Citation: 
Gin S, A Abdelouas, LJ Criscenti, WL Ebert, K Ferrand, T Geisler, MT Harrison, Y Inagaki, S Mitsui, KT Mueller, JC Marra, CG Pantano, EM Pierce, JV Ryan, JM Schofield, CI Steefel, and JD Vienna.2013."An international initiative on long-term behavior of high-level nuclear waste glass."Materials Today 16(6):243-248. doi:10.1016/j.mattod.2013.06.008
Authors: 
S Gin
A Abdelouas
LJ Criscenti
WL Ebert
K Ferr
T Geisler
MT Harrison
Y Inagaki
S Mitsui
KT Mueller
JC Marra
CG Pantano
EM Pierce
JV Ryan
JM Schofield
CI Steefel
JD Vienna
Instruments: 
Volume: 
16
Issue: 
6
Pages: 
243-248
Publication year: 
2013

Monte Carlo Simulations of the Corrosion of Aluminoborosilicate Glasses.

Abstract: 

Aluminum is one of the most common components included in nuclear waste glasses. Therefore, Monte Carlo (MC) simulations were carried out to investigate the influence of aluminum on the rate and mechanism of dissolution of sodium borosilicate glasses in static conditions. The glasses studied were in the compositional range (70-2x)% SiO2 x% Al2O3 15% B2O3 (15+x)% Na2O, where 0 ≤ x ≤ 15%. The simulation results show that increasing amounts of aluminum in the pristine glasses slow down the initial rate of dissolution as determined from the rate of boron release. However, the extent of corrosion - as measured by the total amount of boron release - initially increases with addition of Al2O3, up to 5 Al2O3 mol%, but subsequently decreases with further Al2O3 addition. The MC simulations reveal that this behavior is due to the interplay between two opposing mechanisms: (1) aluminum slows down the kinetics of hydrolysis/condensation reactions that drive the reorganization of the glass surface and eventual formation of a blocking layer; and (2) aluminum strengthens the glass thereby increasing the lifetime of the upper part of its surface and allowing for more rapid formation of a blocking layer. Additional MC simulations were performed whereby a process representing the formation of a secondary aluminosilicate phase was included. Secondary phase formation draws dissolved glass components out of the aqueous solution, thereby diminishing the rate of condensation and delaying the formation of a blocking layer. As a result, the extent of corrosion is found to increase continuously with increasing Al2O3 content, as observed experimentally. For Al2O3 < 10 mol%, the MC simulations also indicate that, because the secondary phase solubility eventually controls the aluminum content in the part of the altered layer in contact with the bulk aqueous solution, the dissolved aluminum and silicon concentrations at steady state are not dependent on the Al2O3 content of the pristine aluminoborosilicate glass.

Citation: 
Kerisit SN, JV Ryan, and EM Pierce.2013."Monte Carlo Simulations of the Corrosion of Aluminoborosilicate Glasses."Journal of Non-crystalline Solids 378:273-281. doi:10.1016/j.jnoncrysol.2013.07.014
Authors: 
SN Kerisit
JV Ryan
EM Pierce
Instruments: 
Publication year: 
2013

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