NMR and EPR

Molecular systems important to biology, environmental remediation and sustainability are studied using a suite of nuclear magnetic resonance (NMR) spectrometers with frequencies ranging from 300 to 850 MHz. A pair of electron paramagnetic resonance (EPR) spectrometers complement the capability. See a complete list of NMR and EPR instruments.

Description

Interfacial and in situ biology—Innovative NMR instrumentation and techniques for probing properties of macromolecular cellular assemblies and in situ and ex situ metabolic processes, as well as for exploring biological membrane proteins in the solid state. Unique EPR and variable-temperature NMR approaches to explore structure and properties of redox metal centers critical catalysis, environmental chemistry and cell biology.

Environmental chemistry— EMSL offers a unique NMR system for radiological studies. Users can perform magic angle spinning of highly radioactive samples with a novel hermetically sealed 3.2mm NMR probe. These tools allow users to apply NMR techniques to critical areas of radiological research, including the study of radioactive waste processing and storage.

Interfacial and in situ chemistry—Leading-edge solid-state NMR probe technology to analyze and quantify properties of advanced energy materials, fuel cells and real-time catalytic processes. High power pulsed field gradient diffusion capabilities for liquid and solid samples.

EMSL offers unique and custom NMR and EPR tools, including probes for specialized studies.

  • NMR spectrometers, ranging from 300 MHz to 850 MHz for high-field liquid-state, solid-state and micro-imaging techniques
  • W- and X-band pulsed EPR spectremeter for probing metal centers in biological and materials systems
  • NMR metabolomics capabilities
  • Extreme-temperature probes, both high and low temperatures
  • Virtual NMR tools for remote access to spectrometer systems.

Instruments

Highlighted Research Applications Structural biology Protein structure and dynamics Nuclei acid structure and dynamics. Metabolomics Eukaryotic and...
Custodian(s): Sarah D Burton, David Hoyt
Highlighted Research Applications Structural biology Protein structure and dynamics Nuclei acid structure and dynamics Metabolomics Eukaryotic and...
Custodian(s): David Hoyt, Nancy Isern
Highlighted Research Applications Characterization of quadrupolar nuclei for materials and biological samples In situ catalysis investigations via...
Research applications Samples containing paramagnetics Soils (SOM and NOM) Metal oxide materials for catalysis applications Researchers may operate...
Custodian(s): Nancy Washton, Sarah D Burton
Highlighted Research Applications Characterization of natural and soil organic matter (NOM and SOM) CO2 sequestration investigations via high-...
Custodian(s): Sarah D Burton, David Hoyt

Publications

Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in...
Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-...
We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002...
Shale formations play fundamental roles in large-scale geologic carbon sequestration (GCS) aimed primarily to mitigate climate change, and in smaller...
Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time,...

Science Highlights

Posted: March 27, 2015
Zeolites are widely used in industry as catalysts, but many of the characteristics of these materials are challenging to understand and predict. Led...
Posted: March 02, 2015
A new zinc-polyiodide redox flow battery developed at Pacific Northwest National Laboratory with EMSL resources uses an electrolyte with more than...
Posted: January 15, 2015
A team of scientists with Pacific Northwest National Laboratory, EMSL, Marine Biological Laboratory and The Pennsylvania State University grew two...
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: August 14, 2014
Industry uses zeolites as an ion exchange material and solid acid to catalyze a broad range of chemical reactions. Zeolites are also promising...

Instruments

There are no related projects at this time.

Molecular systems important to biology, environmental remediation and sustainability are studied using a suite of nuclear magnetic resonance (NMR) spectrometers with frequencies ranging from 300 to 850 MHz. A pair of electron paramagnetic resonance (EPR) spectrometers complement the capability. See a complete list of NMR and EPR instruments.

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

Abstract: 

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases are presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.

Citation: 
Wang Z, K Jin, Y Zhang, F Wang, and Z Zhu.2014."ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?"Surface and Interface Analysis 46(S1):257-260. doi:10.1002/sia.5419
Authors: 
Z Wang
K Jin
Y Zhang
F Wang
Z Zhu
Volume: 
46
Issue: 
0
Pages: 
257-260
Publication year: 
2014

1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen.

Abstract: 

Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in vivo and in vitro, little effort has been devoted to metabolic profiling of metastatic tumors in organs other than lymph nodes. In this work, NMR-based metabolomics combined with multivariate data analysis is used to study metastatic B16-F10 melanoma in C57BL/6J mouse spleen. Principal Component Analysis (PCA), an unsupervised multivariate data analysis method, is used to detect possible outliers, while Orthogonal Projection to Latent Structure (OPLS), a supervised multivariate data analysis method, is employed to find important metabolites responsible for discriminating the control and the melanoma groups. Two different strategies, i.e., spectral binning and spectral deconvolution, are used to reduce the original spectral data before statistical analysis. Spectral deconvolution is found to be superior for identifying a set of discriminatory metabolites between the control and the melanoma groups, especially when the sample size is small. OPLS results show that the melanoma group can be well separated from its control group. It is found that taurine, glutamate, aspartate, O-Phosphoethanolamine, niacinamide ,ATP, lipids and glycerol derivatives are decreased statistically and significantly while alanine, malate, xanthine, histamine, dCTP, GTP, thymidine, 2'-Deoxyguanosine are statistically and significantly elevated. These significantly changed metabolites are associated with multiple biological pathways and may be potential biomarkers for metastatic melanoma in spleen.

Citation: 
Wang X, MY Hu, J Feng, M Liu, and JZ Hu.2014."1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen."Metabolomics 10(6):1129-1144. doi:10.1007/s11306-014-0652-z
Authors: 
X Wang
MY Hu
J Feng
M Liu
JZ Hu
Volume: 
10
Issue: 
6
Pages: 
1129-1144
Publication year: 
2014

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater.

Abstract: 

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a major benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.

Citation: 
Wang YC, DK Schreiber, JJ Neeway, S Thevuthasan, JE Evans, JV Ryan, Z Zhu, and W Wei.2014."NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater."Surface and Interface Analysis 46(S1):233-237. doi:10.1002/sia.5585
Authors: 
YC Wang
DK Schreiber
JJ Neeway
S Thevuthasan
JE Evans
JV Ryan
Z Zhu
W Wei
Volume: 
46
Issue: 
Pages: 
233-237
Publication year: 
2014

In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide.

Abstract: 

Shale formations play fundamental roles in large-scale geologic carbon sequestration (GCS) aimed primarily to mitigate climate change, and in smaller-scale GCS targeted mainly for CO2-enhanced gas recovery operations. In both technologies, CO2 is injected underground as a supercritical fluid (scCO2), where interactions with shale minerals could influence successful GCS implementation. Reactive components of shales include expandable clays, such as montmorillonites and mixed-layer illite/smectite clays. In this work, we used in situ X-ray diffraction (XRD) and in situ infrared (IR) spectroscopy to investigate the swelling/shrinkage and water/CO2 sorption of a pure montmorillonite, Na-SWy-2, when the clay is exposed to variably hydrated scCO2 at 50 °C and 90 bar. Measured interlayer spacings and sorbed water concentrations at varying levels of scCO2 hydration are similar to previously reported values measured in air at ambient pressure over a range of relative humidities. IR spectra show evidence of both water and CO2 intercalation, and variations in peak shapes and positions suggest multiple sorbed types with distinct chemical environments. Based on the intensity of the asymmetric CO stretching band of the CO2 associated with the Na-SWy-2, we observed a significant increase in sorbed CO2 as the clay expands from a 0W to a 1W state, suggesting that water props open the interlayer so that CO2 can enter. However, as the clay transitions from a 1W to a 2W state, CO2 desorbs sharply. These observations were placed in the context of two conceptual models concerning hydration mechanisms for expandable clays and were also discussed in light of recent theoretical studies on CO2-H2O-clay interactions. The swelling/shrinkage of expandable clays could affect solid volume, porosity, and permeability of shales. Consequently, the results from this work could aid predictions of shale caprock integrity in large-scale GCS, as well as methane transmissivity in enhanced gas recovery operations.

Citation: 
Loring JS, ES Ilton, J Chen, CJ Thompson, PF Martin, P Benezeth, KM Rosso, AR Felmy, and HT Schaef.2014."In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide."Langmuir 30(21):6120-6128. doi:10.1021/la500682t
Authors: 
JS Loring
ES Ilton
J Chen
CJ Thompson
PF Martin
P Benezeth
KM Rosso
AR Felmy
HT Schaef
Volume: 
30
Issue: 
21
Pages: 
6120-6128
Publication year: 
2014

Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing.

Abstract: 

We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities which was manifested through the transcriptional upregulation of transport and catabolic pathways. While growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. On one hand, the production and excretion of specific amino acids (methionine and alanine) by the cyanobacterium correlated with the putative downregulation of the corresponding biosynthetic machinery of Shewanella W3-18-1. On the other hand, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation suggested increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

Citation: 
Beliaev AS, MF Romine, M Serres, HC Bernstein, BE Linggi, LM Markillie, NG Isern, WB Chrisler, LA Kucek, EA Hill, G Pinchuk, DA Bryant, HS Wiley, JK Fredrickson, and A Konopka.2014."Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing."The ISME Journal 8(11):2243-2255. doi:10.1038/ismej.2014.69
Authors: 
AS Beliaev
MF Romine
M Serres
HC Bernstein
BE Linggi
LM Markillie
NG Isern
WB Chrisler
LA Kucek
EA Hill
G Pinchuk
DA Bryant
HS Wiley
JK Fredrickson
A Konopka
Facility: 
Volume: 
8
Issue: 
11
Pages: 
2243-2255
Publication year: 
2014

Beyond the Active Site: The Impact of the Outer Coordination Sphere on Electrocatalysts for Hydrogen Production and Oxidation.

Abstract: 

Hydrogenase enzymes provide inspiration for investigations of molecular catalysts utilizing structural and functional mimics of the active site. However, the resulting active site mimics cannot match the combination of high rates and low overpotentials of the enzyme, suggesting that the rest of the protein scaffold, i.e., the outer coordination sphere, is necessary for the efficiency of hydrogenase. Therefore, inclusion of outer coordination sphere elements onto molecular catalysts may enable us to achieve and ultimately surpass the overall enzymatic efficiency. In an effort to identify and include the missing enzymatic features, there has been recent effort to understand the effect of outer coordination sphere elements on molecular catalysts for hydrogen oxidation and production. Our focus has been to utilize amino acid or peptide based scaffolds on an active functional mimic for hydrogen oxidation and production, [Ni(PR2NR’2)2]2+. This bottom-up approach, i.e, building an outer coordination sphere around a functional molecular catalyst, has allowed us to evaluate individual contributions to catalysis, including enhancing proton movement, concentrating substrate and introducing structural features to control reactivity. Collectively, these studies have resulted in catalysts that can operate faster, can operate at lower overpotentials, have enhanced water solubility, and/or can provide more stability to oxygen or extreme conditions such as strongly acidic or basic conditions than their unmodified parent complexes. Common mechanisms have yet to be defined to predictably control these processes but our growing knowledge in this area is essential for the eventual mimicry of enzymes for developing efficient molecular catalysts for practical use. This account reviews previously published work supported by the US DOE Basic Energy Sciences (BES), Physical Bioscience program, the Office of Science Early Career Research Program through the USDOE, BES, the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US DOE, Office of Science, Office of BES. Part of the research was conducted at the W.R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by U.S. DOE’s Office of Biological and Environmental Research program located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. Department of Energy.

Citation: 
Ginovska-Pangovska B, A Dutta, ML Reback, JC Linehan, and WJ Shaw.2014."Beyond the Active Site: The Impact of the Outer Coordination Sphere on Electrocatalysts for Hydrogen Production and Oxidation."Accounts of Chemical Research 47(8):2621-2630. doi:10.1021/ar5001742
Authors: 
B Ginovska-Pangovska
A Dutta
ML Reback
JC Linehan
WJ Shaw
Facility: 
Instruments: 
Volume: 
47
Issue: 
8
Pages: 
2621-2630
Publication year: 
2014

New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella

Abstract: 

An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

Citation: 
Xue J, NG Isern, RJ Ewing, AV Liyu, JA Sears, Jr, H Knapp, J Iversen, DR Sisk, BK Ahring, and PD Majors.2014."New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles."Applied Microbiology and Biotechnology 98(19):8367-8375. doi:10.1007/s00253-014-5847-8
Authors: 
J Xue
NG Isern
RJ Ewing
AV Liyu
JA Sears
Jr
H Knapp
J Iversen
DR Sisk
BK Ahring
PD Majors
Capabilities: 
Facility: 
Volume: 
98
Issue: 
19
Pages: 
8367-8375
Publication year: 
2014

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Dr. Washton is a key player in coupling solid-state NMR  (ssNMR) with computational chemistry for predictions of reaction site structure and kinetics, and to provide users with an integrated system for making predictions of NMR parameters based...