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
In this Environmental TEM (ETEM) study of supported Pt and Pd model catalysts, individual nanoparticles were tracked during heat treatments at...
Methanol synthesis from syngas (CO/CO2/H2) hydrogenation on the perfect Zn–terminated polar ZnO(0001) surface have been investigated using...
Silicon based nanowires have been grown from commercial silicon powders under conditions of differing oxygen and carbon activities. Nanowires grown...
Based on combined FTIR and XRD studies, we report here that H2O induces a morphological change of KNO3 species formed on model K2O/Al2O3 NOx storage-...
Localized zones or lenses of naturally reduced sediments have the potential to play a significant role in the fate and transport of redox-sensitive...
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...
Posted: March 02, 2014
The Science Biological material derived from plants represents a promising source for renewable and sustainable biofuel production, but there is a...
Posted: February 26, 2014
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: 

Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria.

Abstract: 

To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either aerobic or suboxic conditions. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily caused by differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Altered transcription levels appeared responsible for 26% of the protein changes, altered translational efficiency appeared responsible for 46% and a combination of both were responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part caused by altered tRNA pools, is a major determinant of regulated protein expression in bacteria.

Citation: 
Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley.2013."Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria."Integrative Biology 5(11):1393-1406. doi:10.1039/C3IB40120K
Authors: 
RC Taylor
BJM Webb-Robertson
LM Markillie
MH Serres
BE Linggi
JT Aldrich
EA Hill
MF Romine
MS Lipton
HS Wiley
Facility: 
Volume: 
5
Issue: 
11
Pages: 
1393-1406
Publication year: 
2013

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies .

Abstract: 

Characterization of geomicrobial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities and the role they play in regulating atmospheric CO2 levels and the Earth’s climate. A significant challenge in studying soil microbial proteins is their initial dissociation from the complex mixture of particles found in natural soil. Due to bias of the most robust cells, the removal of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in-situ lysis of bacterial cells leads to the expulsion of proteins to the soil surface, which can lead to potentially high levels of adsorption due to the physicochemical properties of both the protein and the soil. We investigated various compounds for their ability to block protein adsorption soil sites prior to in-situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding lysed Escherichia coli proteins to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil textures; use of an optimized desorption buffer further increases the number of identifications.

Citation: 
Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton.2013."Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ."Proteomics 13(18-19):2776-2785. doi:10.1002/pmic.201300003
Authors: 
CD Nicora
BJ Anderson
SJ Callister
AD Norbeck
SO Purvine
JK Jansson
OU Mason
M David
DD Jurelevicius
RD Smith
MS Lipton
Facility: 
Instruments: 
Volume: 
13
Pages: 
2776-2785
Publication year: 
2013

Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions

Abstract: 

Cultures of the cyanobacterial genus Cyanothece have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N2-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes and we performed quantitative proteome analysis of Cyanothece ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N2-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome c oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose-phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in Cyanothece ATCC 51142 in the presence of glycerol under H2 producing conditions, suggesting a competition between these sources of carbon. However, in Cyanothece PCC 7822, the Calvin cycle still played a role in cofactor recycling during H2 production. Our data comprise the first comprehensive profiling of proteome changes in Cyanothece PCC 7822, and allows an in-depth comparative analysis of major physiological and biochemical processes that influence H2-production in both the strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large scale H2 production.

Citation: 
Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman.2013."Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production."Applied and Environmental Microbiology 79(4):1070-1077. doi:10.1128/AEM.02864-12
Authors: 
UK Aryal
SJ Callister
S Mishra
X Zhang
JI Shutthanan
TE Angel
AK Shukla
ME Monroe
RJ Moore
DW Koppenaal
RD Smith
L Sherman
Facility: 
Instruments: 
Volume: 
79
Issue: 
4
Pages: 
1070-1077
Publication year: 
2013

Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface.

Abstract: 

The majority of in vitro studies characterizing the impact of engineered nanoparticles (NPs) on cells that line the respiratory tract were conducted in cells exposed to NPs in suspension. This approach introduces processes that are unlikely to occur during inhaled NP exposures in vivo, such as the shedding of toxic doses of dissolved ions. ZnO NPs are used extensively and pose significant sources for human exposure. Exposures to airborne ZnO NPs can induce adverse effects, but the relevance of the dissolved Zn2+ to the observed effects in vivo is still unclear. Our goal was to mimic in vivo exposures to airborne NPs and decipher the contribution of the intact NP from the contribution of the dissolved ions to airborne ZnO NP toxicity. We established the exposure of alveolar type II epithelial cells to aerosolized NPs at the air-liquid interface (ALI), and compared the impact of aerosolized ZnO NPs and NPs in suspension at the same cellular doses, measured as the number of particles per cell. By evaluating membrane integrity and cell viability 6 and 24 hours post exposure we found that aerosolized NPs induced toxicity at the ALI at doses that were in the same order of magnitude as doses required to induce toxicity in submersed cultures. In addition, distinct patterns of oxidative stress were observed in the two exposure systems. These observations unravel the ability of airborne ZnO NPs to induce toxicity without the contribution of dissolved Zn2+ and suggest distinct mechanisms at the ALI and in submersed cultures.

Citation: 
Xie Y, NG Williams, A Tolic, WB Chrisler, JG Teeguarden, BL Maddux, JG Pounds, A Laskin, and G Orr.2012."Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface."Toxicological Sciences 125(2):450-461. doi:10.1093/toxsci/kfr251
Authors: 
Y Xie
NG Williams
A Tolic
WB Chrisler
JG Teeguarden
BL Maddux
JG Pounds
A Laskin
G Orr
Facility: 
Volume: 
125
Issue: 
2
Pages: 
450-461
Publication year: 
2012

ISDD: A Computational Model of Particle Sedimentation, Diffusion and Target Cell Dosimetry for In Vitro Toxicity Studies.

Abstract: 

Background: The difficulty of directly measuring cellular dose is a significant obstacle to application of target tissue dosimetry for nanoparticle and microparticle toxicity assessment. As a consequence, the target tissue paradigm for dosimetry and hazard assessment of nanoparticles has largely been ignored in favor of using metrics of exposure (e.g. μg particle/mL culture medium, particle surface area/mL, particle number/mL). We have developed a computational model of solution particokinetics (sedimentation, diffusion) and dosimetry for non-interacting spherical particles and their agglomerates in monolayer cell culture systems. Particle transport to cells is calculated by simultaneous solution of Stokes Law (sedimentation) and the Stokes-Einstein equation (diffusion). Results: The In vitro Sedimentation, Diffusion and Dosimetry model (ISDD) was tested against measured transport rates or cellular doses for multiple sizes of polystyrene spheres (20-1100 nm), 35 nm amorphous silica, and large agglomerates of 30 nm iron oxide particles. Overall, without adjusting any parameters, model predicted doses were in close agreement with the experimental data, differing from as little as 5% to as much as three-fold, but in most cases approximately two-fold, within the limits of the accuracy of the measurement systems. Applying the model, we generalize the effects of particle size, particle density, agglomeration state and agglomerate characteristics on target cell dosimetry in vitro. Conclusions: Our results confirm our hypothesis that the dose-rates for all particles are not equal, but can vary significantly, in direct contrast to the assumption of dose-equivalency implicit in the use of mass-based media concentrations as metrics of exposure for dose-response assessment. The difference between equivalent nominal media concentration exposures on a μg/mL basis and target cell doses on a particle surface area or number basis can be as high as three to six orders of magnitude. As a consequence, in vitro hazard assessments utilizing mass-based exposure metrics have inherently high errors where particle number or surface areas target cells doses are believed to drive response. The gold standard for particle dosimetry for in vitro nanotoxicology studies should be direct experimental measurement of the cellular content of the studied particle. However, where such measurements are impractical, unfeasible, and before such measurements become common, particle dosimetry models such as ISDD provide a valuable, immediately useful alternative, and eventually an adjunct to such measurements.

Citation: 
Hinderliter PM, KR Minard, G Orr, WB Chrisler, BD Thrall, JG Pounds, and JG Teeguarden.2010."ISDD: A Computational Model of Particle Sedimentation, Diffusion and Target Cell Dosimetry for In Vitro Toxicity Studies."Particle and Fibre Toxicology 7(November):Article No. 36. doi:10.1186/1743-8977-7-36
Authors: 
PM Hinderliter
KR Minard
G Orr
WB Chrisler
BD Thrall
JG Pounds
JG Teeguarden
Facility: 
Publication year: 
2010

Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size

Abstract: 

In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled "universal reference" into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein "corona" that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.

Citation: 
Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu.2011."Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size."Proteomics 11(23):4569-4577. doi:10.1002/pmic.201100037
Authors: 
H Zhang
KE Burnum
ML Luna
BO Petritis
JS Kim
W Qian
RJ Moore
A Heredia-Langner
BJM Webb-Robertson
BD Thrall
DG Camp
II
RD Smith
JG Pounds
T Liu
Facility: 
Volume: 
11
Issue: 
23
Pages: 
4569-4577
Publication year: 
2011

Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A.

Abstract: 

The internalization of engineered nanoparticles (ENPs) into cells is known to involve active transport mechanisms, yet the precise biological molecules involved are poorly understood. We demonstrate that the uptake of amorphous silica ENPs (92 nm) by macrophage cells is strongly inhibited by silencing expression of scavenger receptor A (SR-A). In addition, ENP uptake is augmented by introducing SR-A expression into human cells that are normally non-phagocytic. Confocal fluorescent microscopy analyses show that the majority of single or small clusters of silica ENPs co-localize intracellularly with SR-A and are internalized through a pathway characteristic of clathrin-dependent endocytosis. In contrast, larger silica NP agglomerates (>500 nm) are poorly co-localized with the receptor, suggesting independent trafficking or internalization pathways are involved. SR-A silencing also caused decreased cellular secretion of pro-inflammatory cytokines in response to silica ENPs. As SR-A is expressed in macrophages throughout the reticulo-endothelial system, this pathway is likely an important determinant of the biodistribution of, and cellular response to ENPs.

Citation: 
Orr G, WB Chrisler, KJ Cassens, R Tan, BJ Tarasevich, LM Markillie, RC Zangar, and BD Thrall.2011."Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A."Nanotoxicology 5(3):296-311. doi:10.3109/17435390.2010.513836
Authors: 
G Orr
WB Chrisler
KJ Cassens
R Tan
BJ Tarasevich
LM Markillie
RC Zangar
BD Thrall
Facility: 
Volume: 
5
Issue: 
3
Pages: 
296-311
Publication year: 
2011

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

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