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. See a complete list of Spectroscopy and Diffraction instruments.

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 Physical Electronics Instruments (PHI) Quantum 2000 X-ray photoelectron spectrometer (XPS) is a unique system that uses a focused monochromatic...
Custodian(s): Mark Engelhard
Recently built and only available at EMSL, this customized SFG-VS spectrometer employs the synchronization of a 100-picosecond amplifier laser,...
Custodian(s): Hongfei Wang, Mark Bowden
EMSL offers a suite of instrumentation dedicated to understanding photoreactivity in the condensed phase, on surfaces, and at material interfaces....
Custodian(s): , Alan G Joly
EMSL offers a suite of instrumentation dedicated to understanding photoreactivity in the condensed phase, on surfaces, and at material interfaces....
Custodian(s): , Alan G Joly
This experimental facility couples an electrospray ionization source to a magnetic-bottle time-of-flight photoelectron spectrometer. It has been...
Custodian(s): Alan G Joly

Publications

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and...
Azulene is a non-alternant, non-benzenoid aromatic hydrocarbon with an intense blue colour, a dipole moment of 1.0 D,1 positive electron affinity,...
The adsorption, desorption, and displacement kinetics of H2O and CO2 on TiO2(110) are investigated using temperature programmed desorption (TPD) and...
We record sequences of Raman spectra at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated with 4,4’-...
Photosynthetic microbes are of emerging interest as production organisms in biotechnology because they can grow autotrophically using sunlight, an...

Science Highlights

Posted: February 27, 2015
The Science Geobacter bacterial species use metal reduction pathways to respire metals such as uranium, rendering it insoluble. This is of interest...
Posted: January 13, 2015
The Science Lithium (Li) metal has long been considered one of the most attractive anode materials, but large-scale application of high-energy...
Posted: November 21, 2014
The Science Carbon dioxide (CO2) sequestration in deep subsurface environments has received significant attention and investment as a way to reduce...
Posted: October 17, 2014
A multi-institutional team of researchers studied how and when cloud ice crystals form. Dust is usually a primary catalyst encouraging ice formation...
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...

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. See a complete list of Spectroscopy and Diffraction instruments.

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: 

Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2.

Abstract: 

Photosynthetic microbes are of emerging interest as production organisms in biotechnology because they can grow autotrophically using sunlight, an abundant energy source, and CO2, a greenhouse gas. Important traits for such microbes are fast growth and amenability to genetic manipulation. Here we describe Synechococcus elongatus UTEX 2973, a unicellular cyanobacterium capable of rapid autotrophic growth, comparable to heterotrophic industrial hosts such as yeast. Synechococcus 2973 can be readily transformed for facile generation of desired knockout and knock-in mutations. Genome sequencing coupled with global proteomics studies revealed that Synechococcus 2973 is a close relative of the widely studied cyanobacterium Synechococcus elongatus PCC 7942, an organism that grows more than two times slower. A small number of nucleotide changes are the only significant differences between the genomes of these two cyanobacterial strains. Thus, our study has unraveled genetic determinants necessary for rapid growth of cyanobacterial strains of significant industrial potential.

Citation: 
Yu J, ML Liberton, P Cliften, R Head, JM Jacobs, RD Smith, DW Koppenaal, JJ Brand, and HB Pakrasi.2015."Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2."Scientific Reports 5:8132. doi:10.1038/srep08132
Authors: 
Yu J
ML Liberton
P Cliften
R Head
JM Jacobs
RD Smith
DW Koppenaal
JJ Br
HB Pakrasi
Facility: 
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2015

Vibronic Raman Scattering at the Quantum Limit of Plasmons.

Abstract: 

We record sequences of Raman spectra at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated with 4,4’-dimercaptostilbene (DMS). A 2D correlation analysis of the recorded trajectories reveals that the observable vibrational states can be divided into sub-sets. The first set comprises the totally symmetric vibrations of DMS (ag) that are neither correlated with each other nor to the fluctuating background, which is assigned to the signature of charge transfer plasmons tunneling through DMS. The second set consists of bu vibrations, which are correlated both with each other and with the continuum. Our findings are rationalized on the basis of the charge-transfer theory of Raman scattering, and illustrate how the tunneling plasmons modulate the vibronic coupling term from which the intensities of the bu states are derived.

Citation: 
El-Khoury PZ, and WP Hess.2014."Vibronic Raman Scattering at the Quantum Limit of Plasmons."Nano Letters 14(7):4114-4118. doi:10.1021/nl501690u
Authors: 
PZ El-Khoury
WP Hess
Facility: 
Volume: 
14
Issue: 
7
Pages: 
4114-4118
Publication year: 
2014

Adsorption, Desorption, and Displacement Kinetics of H2O and CO2 on TiO2(110).

Abstract: 

The adsorption, desorption, and displacement kinetics of H2O and CO2 on TiO2(110) are investigated using temperature programmed desorption (TPD) and molecular beam techniques. The TPD spectra for both H2O and CO2 have well-resolved peaks corresponding to desorption from bridge-bonded oxygen (BBO), Ti, and oxygen vacancies (VO) sites in order of increasing peak temperature. Analysis of the saturated monolayer peak for both species reveals that the corresponding adsorption energies on all sites are greater for H2O and for CO2. Sequential dosing of H2O and CO2 reveals that, independent of the dose order, H2O molecules will displace CO2 in order to occupy the highest energy binding sites available. Isothermal experiments show that the displacement of CO2 by H2O occurs between 75 and 80 K. Further analysis shows that a ratio of 4 H2O to 3 CO2 molecules is needed to displace CO2 from the TiO2(110) surface.

Citation: 
Smith RS, Z Li, L Chen, Z Dohnalek, and BD Kay.2014."Adsorption, Desorption, and Displacement Kinetics of H2O and CO2 on TiO2(110)."Journal of Physical Chemistry B 118(28):8054-8061. doi:10.1021/jp501131v
Authors: 
RS Smith
Z Li
L Chen
Z Dohnalek
BD Kay
Volume: 
118
Issue: 
28
Pages: 
8054-8061
Publication year: 
2014

Poly(trifluoromethyl)azulenes: structures and acceptor properties.

Abstract: 

Azulene is a non-alternant, non-benzenoid aromatic hydrocarbon with an intense blue colour, a dipole moment of 1.0 D,1 positive electron affinity, and an “anomalous” emission from the second excited state in violation of Kasha’s rule.2,3 Azulene’s unique properties have potential uses in molecular switches,4,5 molecular diodes,6 organic photovoltaics,7 and charge transfer complexes.8-12 Introduction of electron-withdrawing groups to the azulenic core, such as CN,8,13,14 halogens,15-19 and CF3,20,21 can enhance certain electrical and photophysical properties. In this work, we report six new trifluoromethyl derivatives of azulene (AZUL), three isomers of AZUL(CF3)3 and three isomers of AZUL(CF3)4, and the first X-ray structure of a π-stacked donor-acceptor complex of a trifluoromethyl azulene with donor pyrene.

Citation: 
Clikeman TT, EV Bukovsky, IV Kuvychko, LK San, S Deng, XB Wang, YS Chen, SH Strauss, and OV Boltalina.2014."Poly(trifluoromethyl)azulenes: structures and acceptor properties."Chemical Communications 50(47):6263-6266. doi:10.1039/C4CC00510D
Authors: 
TT Clikeman
EV Bukovsky
IV Kuvychko
LK San
S Deng
XB Wang
YS Chen
SH Strauss
OV Boltalina
Volume: 
50
Issue: 
47
Pages: 
6263-6266
Publication year: 
2014

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations.

Abstract: 

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

Citation: 
Pierce EM, P Frugier, LJ Criscenti, KD Kwon, and SN Kerisit.2014."Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations."International Journal of Applied Glass Science 5(4):421-435. doi:10.1111/ijag.12077
Authors: 
EM Pierce
P Frugier
LJ Criscenti
KD Kwon
SN Kerisit
Volume: 
5
Issue: 
4
Pages: 
421-435
Publication year: 
2014

Microstructure of multistage annealed nanocrystalline SmCo2Fe2B alloy with enhanced magnetic properties.

Abstract: 

The microstructure and chemistry of SmCo2Fe2B melt-spun alloy after multistage annealing was investigated using high resolution transmission electron microscopy (HRTEM) and 3D atom probe tomography. The multistage annealing resulted in an increase in both the coercivity and magnetization. The presence of Sm(Co,Fe)4B (1:4:1) and Sm2(Co,Fe)17Bx (2:17:x) magnetic phases were confirmed using both techniques. Fe2B at a scale of ��5 nm was found by HRTEM precipitating within the 1:4:1 phase after the second-stage annealing. Ordering within the 2:17:x phase was directly identified both by the presence of antiphase boundaries observed by TEM and the interconnected isocomposition surface network found in 3D atom probe results in addition to radial distribution function analysis. The variations in the local chemistry after the secondary annealing were considered pivotal in improving the magnetic properties.

Citation: 
Jiang X, A Devaraj, B Balamurugan, J Cui, and JE Shield.2014."Microstructure of multistage annealed nanocrystalline SmCo2Fe2B alloy with enhanced magnetic properties."Journal of Applied Physics 15(6):Article No. 063902. doi:10.1063/1.4865298
Authors: 
X Jiang
A Devaraj
B Balamurugan
J Cui
JE Shield
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Formation of Interfacial Layer and Long-Term Cylability of Li-O-2 Batteries.

Abstract: 

Extended cycling of the Li-O2 battery under full discharge/charge conditions is achievable upon selection of appropriate electrode materials and cycling protocol. However, the decomposition of the side products also contribute to the observed good cycling behavior of high capacity Li-O2 batteries. Quantitative analyses of the discharge and charge products reveals a quick switch from the predominant formation of Li2O2 to the predominant formation of side products during the first a few cycles of the Li-O2 batteries. After the switch, cycling stabilizes with a repeatable formation of Li2O2/side products at ~1:2 ratio. CNTs/Ru composite electrodes exhibits lower charge voltage and deliver 50 full discharge-charge cycles without sharp capacity drop. Ru coated glass carbon electrode can lead to more than 500 cycles without change in its cycling profiles. The better understanding on Li-O2 reaction processes developed in this work may lead to the further improvement on the long term cycling behavior of high capacity Li-O2 batteries.

Citation: 
Nasybulin EN, W Xu, BL Mehdi, EC Thomsen, MH Engelhard, RC Masse, P Bhattacharya, M Gu, WD Bennett, Z Nie, CM Wang, ND Browning, and J Zhang.2014."Formation of Interfacial Layer and Long-Term Cylability of Li-O-2 Batteries."ACS Applied Materials & Interfaces 6(16):14141-14151. doi:10.1021/am503390q
Authors: 
EN Nasybulin
W Xu
BL Mehdi
EC Thomsen
MH Engelhard
RC Masse
P Bhattacharya
M Gu
WD Bennett
Z Nie
CM Wang
ND Browning
J Zhang
Facility: 
Instruments: 
Volume: 
6
Issue: 
16
Pages: 
14141-14151
Publication year: 
2014

Automated genome mining of ribosomal peptide natural products.

Abstract: 

Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic datasets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs and apply it for lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connection of multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 as the first natural product to be identified in an automated fashion by genome mining. The presented tool is available at cy-clo.ucsd.edu.

Citation: 
Mohimani H, R Kersten, W Liu, M Wang, SO Purvine, S Wu, HM Brewer, L Pasa-Tolic, N Bandeira, BS Moore, PA Pevzner, and PC Dorrestein.2014."Automated genome mining of ribosomal peptide natural products."ACS Chemical Biology 9(7):1545-1551. doi:10.1021/cb500199h
Authors: 
H Mohimani
R Kersten
W Liu
M Wang
SO Purvine
S Wu
HM Brewer
L Pasa-Tolic
N Beira
BS Moore
PA Pevzner
PC Dorrestein
Instruments: 
Volume: 
9
Issue: 
7
Pages: 
1545-1551
Publication year: 
2014

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