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

Description

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.

Instruments

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...
Custodian(s): Arun Devaraj, Daniel Perea
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

Publications

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5&...
Porous carbon nanofiber (CNF)-supported tin-antimony (SnSb) alloys is synthesized and applied as sodium ion battery anode. The chemistry and...
We report in this work detailed measurements on the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800...
Understanding hydrogen formation on TiO2 surfaces is of great importance as it could provide fundamental insight into water splitting for hydrogen...
A fully automated titration system with infrared detection was developed for investigating interfacial chemistry at high pressures. The apparatus...

Science Highlights

Posted: September 12, 2014
Green fluorescent proteins, or GFPs, are found in jellyfish and other marine animals and glow green when exposed to light. Scientists use GFPs use...
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...

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: 

Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs.

Abstract: 

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521.

Citation: 
Parenteau MN, LL Jahnke, JD Farmer, and SL Cady.2014."Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs."Astrobiology 14(6):, doi:10.1089/ast.2013.1122
Authors: 
MN Parenteau
LL Jahnke
JD Farmer
SL Cady
Instruments: 
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Structures and Stabilities of (MgO)n Nanoclusters.

Abstract: 

Global minima for (MgO)n structures were optimized using a tree growth−hybrid genetic algorithm in conjunction with MNDO/MNDO/d semiempirical molecular orbital calculations followed by density functional theory geometry optimizations with the B3LYP functional. New lowest energy isomers were found for a number of (MgO)n clusters. The most stable isomers for (MgO)n (n > 3) are 3-dimensional. For n < 20, hexagonal tubular (MgO)n structures are more favored in energy than the cubic structures. The cubic structures and their variations dominate after n = 20. For the cubic isomers, increasing the size of the cluster in any dimension improves the stability. The effectiveness of increasing the size of the cluster in a specific dimension to improve stability diminishes as the size in that dimension increases. For cubic structures of the same size, the most compact cubic structure is expected to be the more stable cubic structure. The average Mg−O bond distance and coordination number both increase as n increases. The calculated average Mg−O bond distance is 2.055 Å at n = 40, slightly smaller than the bulk value of 2.104 Å. The average coordination number is predicted to be 4.6 for the lowest energy (MgO)40 as compared to the bulk value of 6. As n increases, the normalized clustering energy ΔE(n) for the (MgO)n increases and the slope of the ΔE(n)vs n curve decreases. The value of ΔE(40) is predicted to be 150 kcal/mol, as compared to the bulk value ΔE(∞) = 176 kcal/mol. The electronic properties of the clusters are presented and the reactive sites are predicted to be at the corners.

Citation: 
Chen M, AR Felmy, and DA Dixon.2014."Structures and Stabilities of (MgO)n Nanoclusters."Journal of Physical Chemistry A 118(17):3136-3146. doi:10.1021/jp412820z
Authors: 
M Chen
AR Felmy
DA Dixon
Instruments: 
Volume: 
118
Issue: 
17
Pages: 
3136-3146
Publication year: 
2014

Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol.

Abstract: 

The size and thickness of organic aerosol particles collected by impaction in five field campaigns were compared to those of laboratory generated secondary organic aerosols (SOA). Scanning transmission x-ray microscopy (STXM) was used to measure the total carbon absorbance (TCA) by individual particles as a function of their projection areas on the substrate. Because they flatten less upon impaction, particles with higher viscosity and surface tension can be identified by a steeper slope on a plot of TCA vs. size. The slopes of the ambient data are statistically similar indicating a small range of average viscosities and surface tensions across five field campaigns. Steeper slopes were observed for the plots corresponding to ambient particles, while smaller slopes were indicative of the laboratory generated SOA. This comparison indicates that ambient organic particles have higher viscosities and surface tensions than those typically generated in laboratory SOA studies.

Citation: 
O'Brien RE, A Neu, SA Epstein, A MacMillan, B Wang, ST Kelly, S Nizkorodov, A Laskin, RC Moffet, and MK Gilles.2014."Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol."Geophysical Research Letters 41(2):4347-4353. doi:10.1002/2014GL060219
Authors: 
RE O'Brien
A Neu
SA Epstein
A MacMillan
B Wang
ST Kelly
S Nizkorodov
A Laskin
RC Moffet
MK Gilles
Facility: 
Volume: 
41
Issue: 
2
Pages: 
4347-4353
Publication year: 
2014

Oxidative Remobilization of Technetium Sequestered by Sulfide-Transformed Nano Zerovalent Iron.

Abstract: 

The dissolution of Tc(IV) sulfide and concurrent transformation of sulfidated ZVI during 2 oxidation were examined. Kinetic data obtained with 10 mL batch reactors showed that Tc(VII) 3 reduced by sulfidated nZVI has significantly slower reoxidation rates than Tc(VII) reduced by 4 nZVI only. In a 50 mL batch reactor, initial inhibition of Tc(IV) dissolution was apparent and 5 lasted until 120 hours at S/Fe = 0.112, presumably due to the redox buffer capacity of FeS. This 6 is evidenced by the parallel trends in oxidation-reduction potentials (ORP) and Tc dissolution 7 kinetics. Mӧssbauer spectra and micro X-ray diffraction of S/Fe = 0.112 suggested the 8 persistence of FeS after 24-h oxidation although X-ray photoelectron spectroscopy indicated 9 substantial surface oxidation. After 120-h oxidation, all characterizations showed complete 10 oxidation of FeS, which further indicates that FeS inhibits Tc oxidation. X-ray absorption 11 spectroscopy for S/Fe = 0.011 showed significantly increasing percentage of TcS2 in the solid 12 phase after 24-h oxidation, indicating TcS2 is more resistant to oxidation than TcO2. At S/Fe = 13 0.112, the XAS results revealed significant transformation of Tc speciation from TcS2 to TcO2 14 after 120-h oxidation at S/Fe = 0.112. Given that no apparent Tc dissolution occurred during this 15 period, the speciation transformation might play a secondary role in hindering Tc oxidation, 16 especially as redox buffer capacity approached depletion.

Citation: 
Fan D, R Anitori, BM Tebo, PG Tratnyek, JS Lezama Pacheco, RK Kukkadapu, L Kovarik, MH Engelhard, and ME Bowden.2014."Oxidative Remobilization of Technetium Sequestered by Sulfide-Transformed Nano Zerovalent Iron."Environmental Science & Technology 48(13):7409-7417. doi:10.1021/es501607s
Authors: 
D Fan
R Anitori
BM Tebo
PG Tratnyek
JS Lezama Pacheco
RK Kukkadapu
L Kovarik
MH Engelhard
ME Bowden
Instruments: 
Volume: 
48
Issue: 
13
Pages: 
7409-7417
Publication year: 
2014

Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams.

Abstract: 

High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification.

Citation: 
Debord JD, DF Smith, CR Anderton, RM Heeren, L Pasa-Tolic, RH Gomer, and FA Fernandez-Lima.2014."Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams."PLoS One 9(6):e99319. doi:10.1371/journal.pone.0099319
Authors: 
JD Debord
DF Smith
CR Anderton
RM Heeren
L Pasa-Tolic
RH Gomer
FA Fernez-Lima
Instruments: 
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Automated High-Pressure Titration System with In Situ Infrared Spectroscopic Detection.

Abstract: 

A fully automated titration system with infrared detection was developed for investigating interfacial chemistry at high pressures. The apparatus consists of a high-pressure fluid generation and delivery system coupled to a high-pressure cell with infrared optics. A manifold of electronically actuated valves is used to direct pressurized fluids into the cell. Precise reagent additions to the pressurized cell are made with calibrated tubing loops that are filled with reagent and placed in-line with the cell and a syringe pump. The cell’s infrared optics facilitate both transmission and attenuated total reflection (ATR) measurements to monitor bulk-fluid composition and solid-surface phenomena such as adsorption, desorption, complexation, dissolution, and precipitation. Switching between the two measurement modes is accomplished with moveable mirrors that direct radiation from a Fourier transform infrared spectrometer into the cell along transmission or ATR light paths. The versatility of the high-pressure IR titration system is demonstrated with three case studies. First, we titrated water into supercritical CO2 (scCO2) to generate an infrared calibration curve and determine the solubility of water in CO2 at 50 °C and 90 bar. Next, we characterized the partitioning of water between a montmorillonite clay and scCO2 at 50 °C and 90 bar. Transmission-mode spectra were used to quantify changes in the clay’s sorbed water concentration as a function of scCO2 hydration, and ATR measurements provided insights into competitive residency of water and CO2 on the clay surface and in the interlayer. Finally, we demonstrated how time-dependent studies can be conducted with the system by monitoring the carbonation reaction of forsterite (Mg2SiO4) in water-bearing scCO2 at 50 °C and 90 bar. Immediately after water dissolved in the scCO2, a thin film of adsorbed water formed on the mineral surface, and the film thickness increased with time as the forsterite began to dissolve. However, after approximately 2.5 hours, the trend reversed, and a carbonate precipitate began to form on the forsterite surface, exposing dramatic chemical changes in the thin-water film. Collectively, these applications illustrate how the high-pressure IR titration system can provide molecular-level information about the interactions between variably wet scCO2 and minerals relevant to underground storage of CO2 (geologic carbon sequestration). The apparatus could also be utilized to study high-pressure interfacial chemistry in other areas such as catalysis, polymerization, food processing, and oil and gas recovery.

Citation: 
Thompson CJ, PF Martin, J Chen, P Benezeth, HT Schaef, KM Rosso, AR Felmy, and JS Loring.2014."Automated High-Pressure Titration System with In Situ Infrared Spectroscopic Detection."Review of Scientific Instruments 85(4):Article No. 044102. doi:10.1063/1.4870411
Authors: 
CJ Thompson
PF Martin
J Chen
P Benezeth
HT Schaef
KM Rosso
AR Felmy
JS Loring
Instruments: 
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Molecular Hydrogen Formation from Proximal Glycol Pairs on TiO2(110).

Abstract: 

Understanding hydrogen formation on TiO2 surfaces is of great importance as it could provide fundamental insight into water splitting for hydrogen production using solar energy. In this work, hydrogen formation from glycols having different numbers of methyl end-groups have been studied using temperature pro-grammed desorption on reduced, hydroxylated, and oxidized TiO2(110) surfaces. The results from OD-labeled glycols demon-strate that gas-phase molecular hydrogen originates exclusively from glycol hydroxyl groups. The yield is controlled by a combi-nation of glycol coverage, steric hindrance, TiO2(110) order and the amount of subsurface charge. Combined, these results show that proximal pairs of hydroxyl aligned glycol molecules and subsurface charge are required to maximize the yield of this redox reaction. These findings highlight the importance of geometric and electronic effects in hydrogen formation from adsorbates on TiO2(110).

Citation: 
Chen L, Z Li, RS Smith, BD Kay, and Z Dohnalek.2014."Molecular Hydrogen Formation from Proximal Glycol Pairs on TiO2(110)."Journal of the American Chemical Society 136(15):5559-5562. doi:10.1021/ja500992b
Authors: 
L Chen
Z Li
RS Smith
BD Kay
Z Dohnalek
Facility: 
Volume: 
136
Issue: 
15
Pages: 
5559-5562
Publication year: 
2014

Intrinsic Chirality and Prochirality at Air/R-(+)- and S-(-)-Limonene Interfaces: Spectral Signatures with Interference Chiral

Abstract: 

We report in this work detailed measurements on the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800-3050cm-1) of the air/liquid interfaces of R-limonene and S-limonene, using the recently developed high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS). The achiral SFG spectra of R-limonene and S-limonene, as well as the equal amount (50/50) racemic mixture show that the enantiomers are with the same interfacial orientations. The interference chiral SFG spectra of the limonene enantiomers exhibit spectral signature from chiral response of the Cα-H stretching mode, and spectral signature from prochiral response of the CH2 asymmetric stretching mode, respectively. The chiral spectral feature of the Cα-H stretching mode changes sign from R-limonene to S-limonene, and disappears for the 50/50 racemic mixture. While the prochiral spectral feature of the CH2 asymmetric stretching mode is the same for R-limonene and S-limonene, and also surprisingly remains the same for the 50/50 racemic mixture. These results provided detail information in understanding the structure and chirality of molecular interfaces, and demonstrated the sensitivity and potential of SFG-VS as unique spectroscopic tool for chirality characterization and chiral recognition at the molecular interface.

Citation: 
Fu L, Y Zhang, Z Wei, and H Wang.2014."Intrinsic Chirality and Prochirality at Air/R-(+)- and S-(-)-Limonene Interfaces: Spectral Signatures with Interference Chiral Sum-Frequency Generation Vibrational Spectroscopy."Chirality 26(9):509-520. doi:10.1002/chir.22337
Authors: 
Fu L
Y Zhang
Z Wei
H Wang
Volume: 
26
Issue: 
9
Pages: 
509-520
Publication year: 
2014

Controlling SEI Formation on SnSb-Porous Carbon Nanofibers for Improved Na Ion Storage.

Abstract: 

Porous carbon nanofiber (CNF)-supported tin-antimony (SnSb) alloys is synthesized and applied as sodium ion battery anode. The chemistry and morphology of the solid electrolyte interphase (SEI) film and its correlation with the electrode performance are studied. The addition of fluoroethylene carbonate (FEC) in electrolyte significantly reduces electrolyte decomposition and creates a very thin and uniform SEI layer on the cycled electrode surface which could promote the kinetics of Na-ion migration/transportation, leading to excellent electrochemical performance.

Citation: 
Ji L, M Gu, Y Shao, X Li, MH Engelhard, BW Arey, W Wang, Z Nie, J Xiao, CM Wang, J Zhang, and J Liu.2014."Controlling SEI Formation on SnSb-Porous Carbon Nanofibers for Improved Na Ion Storage."Advanced Materials 26(18):2901-2908. doi:10.1002/adma.201304962
Authors: 
Ji L
M Gu
Y Shao
X Li
MH Engelhard
BW Arey
W Wang
Z Nie
J Xiao
CM Wang
J Zhang
J Liu
Facility: 
Instruments: 
Volume: 
26
Issue: 
18
Pages: 
2901-2908
Publication year: 
2014

Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates.

Abstract: 

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

Citation: 
Chaka AM, and AR Felmy.2014."Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates."Journal of Physical Chemistry A 118(35):7469-7488. doi:10.1021/jp500271n
Authors: 
AM Chaka
AR Felmy
Instruments: 
Volume: 
118
Issue: 
35
Pages: 
7469-7488
Publication year: 
2014

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