Toppling Raman shift in supercritical carbon dioxide: Vibrational mix shines new light on carbon sequestration measurements

Just as a wine glass vibrates and sometimes breaks when a diva sings the right note, carbon dioxide vibrates when light or heat serenades it. When it does, carbon dioxide exhibits a vibrational puzzle known as Fermi resonance. Now, researchers studying geologic carbon storage have learned a bit more about the nature of carbon dioxide.

The results provide clues to the nature of the Fermi resonance in other molecules, and will help researchers better understand details in chemical reactions. The team of researchers from the Department of Energy's Pacific Northwest National Laboratory report their findings in the February 28 issue of the journal in Physical Chemistry Chemical Physics.

"We're happy to be able to say something new about something so old," said PNNL chemist and author Charles Windisch, Jr. "We figured out how the different carbon dioxide molecules are vibrating at some of the Fermi resonance frequencies. And, of course, we can calibrate our data with more accuracy now."

"Even to this day, people mark Raman spectra incorrectly," said PNNL computational chemist Vassiliki-Alexandra Glezakou. "It helps to know what we are looking at, if we are going to use certain bands as guidelines to understand molecular interactions."

Carbon Dioxide Conundrum

The PNNL researchers did not set out to study again a phenomenon that dates back to the 1930s. Instead, they wanted to investigate what happens when carbon dioxide is stored underground as part of a national research effort to reduce carbon emissions from power generation. To do so, researchers plan to inject carbon dioxide in an unusual form of the gas that behaves like a liquid due to being under high pressure, called supercritical. To follow supercritical carbon dioxide in chemical reactions, researchers often use a technique called Raman spectroscopy.

Raman spectroscopy is a way of capturing a molecule's vibration. Simple molecules can vibrate in well-defined modes such as stretching and bending, which correspond to peak frequencies on a graph. These peaks are as unique and reproducible as a fingerprint.

The number and position of these peaks in a spectrum can be predicted by quantum mechanics, but Fermi resonances result in unanticipated peaks due to a combination of two different vibrations, such as stretching and bending. First recognized in carbon dioxide and explained by Enrico Fermi in 1931, scientists agree that the Fermi peaks are the result of the mixing of the two vibrational modes, but they often label one of them as 'stretch' and the other as 'bend'. This labeling became a problem when PNNL researchers observed a 'flip' in the Raman spectrum of supercritical carbon dioxide.

Shift or Flip?

To follow reactions, researchers often use different versions of elements called isotopes. Normally, carbon dioxide contains carbon plus the isotope oxygen-16, the most common form of oxygen. By using a heavier isotope of oxygen with its own fingerprint, oxygen-18, PNNL researchers can track the fate of carbon dioxide when it reacts with minerals, particularly when there are other sources of oxygen present such as water.

In the Raman spectra of the lighter supercritical carbon dioxide, the pair of Fermi peaks included a weaker one at a lower frequency and a stronger one at higher frequency. When they replaced all of the oxygens with the heavier isotope, however, the peaks seemed to flip, with the stronger one appearing at a lower frequency instead.

At first, it was not clear how the two sets of Fermi peaks related to each other -- whether the peaks were really a mirror image or if the stronger oxygen-16 peak somehow morphed into a weaker peak when heavy oxygen-18 was introduced. Typically, a heavier isotope will shift peaks to lower frequencies, although different modes are not necessarily affected by the same amount.

The researchers needed to unambiguously identify the peaks and to figure out how much bending and stretching modes contributed to each one. To do so, the team decided to simulate the carbon dioxide molecules with different oxygen isotopes on a computer and see if they could recreate the Raman spectra they saw in their experiments.

To the Computer

Using computing resources at EMSL, DOE's Environmental Molecular Sciences Laboratory at PNNL, Glezakou simulated carbon dioxide in supercritical conditions similar to those in the experiment. The molecules were "made" with either oxygen-16 or oxygen-18.

They analyzed the motion of the molecules to produce computational spectra that echoed the real spectra. In this way, the team was able to determine the percent of bending and stretching modes expected in each peak.

The results showed that with oxygen-16, the stronger peak at the higher frequency is due mostly to the stretching mode, while the weaker peak at the lower frequency is due mostly to the bending mode.

Oxygen-18, however, told a different story. The results with heavy carbon dioxide showed unequivocally that the light- and heavy-oxygen peaks were not exactly mirror images of each other. Carbon dioxide is mostly a linear molecule, so the bending motion is much less affected than the stretch when the oxygen-16 is replaced by its heavier isotope. As a result, the composition of the peaks does not remain the same.

"The heavier oxygen doesn't just shift the peaks. It changes their identity," said Glezakou. "And the bigger effects are on the stretching, because the peak with the most stretching has the biggest frequency shift."

Windisch added that the experimental results matched the computational ones nicely, in spite of the difficulty. "Our colleague Paul Martin here at PNNL had to build equipment so we could do these experiments at the pressures we needed. Not easy," he said.

Having nailed down the vibrational pedigree of these carbon dioxide molecules, they plan to use these results to understand better other reactions between carbon dioxide and a variety of minerals.

This work was supported by the U.S. Department of Energy, Office of Fossil Energy.

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The above story is reprinted from materials provided by Pacific Northwest National Laboratory, via Newswise.

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Journal Reference:

Charles F. Windisch, Vassiliki-Alexandra Glezakou, Paul F. Martin, B. Peter McGrail, Herbert T. Schaef. Raman spectrum of supercritical C18O2 and re-evaluation of the Fermi resonance. Physical Chemistry Chemical Physics, 2012; 14 (8): 2560 DOI: 10.1039/C1CP22349F

Chemical measurements confirm official estimate of Gulf oil spill rate

By combining detailed chemical measurements in the deep ocean, in the oil slick, and in the air, NOAA scientists and academic colleagues have independently estimated how fast gases and oil were leaking during the 2010 Deepwater Horizon oil spill in the Gulf of Mexico.

The new chemistry-based spill rate estimate, an average of 11,130 tons of gas and oil compounds per day, is close to the official average leak rate estimate of about 11,350 tons of gas and oil per day (equal to about 59,200 barrels of liquid oil per day).

"This study uses the available chemical data to give a better understanding of what went where, and why," said Thomas Ryerson, Ph.D., a NOAA research chemist and lead author of the study. "The surface and subsurface measurements and analysis provided by our university colleagues were key to this unprecedented approach to understanding an oil spill."

The NOAA-led team did not rely on any of the data used in the original estimates, such as video flow analysis, pipe diameter and fluid flow calculations. "We analyzed a completely separate set of chemical measurements, which independently led us to a very similar leak estimate," Ryerson said.

The new study, Chemical data quantify Deepwater Horizon hydrocarbon flow rate and environmental distribution, was published online January 9 in the journal Proceedings of the National Academy of Sciences.

The new analysis follows on another NOAA-led study published last year, in which Ryerson and colleagues estimated a lower limit to the Deepwater Horizon leak rate based on two days of airborne data collected during the spill and the chemical makeup of the reservoir gas and oil determined before the spill. The new analysis adds in many other sources of data, including subsurface and surface samples taken during six weeks of the spill and including a direct measure of the makeup of the gas and oil actually leaking into the Gulf.

Ryerson and his colleagues found that the leaking gas and oil quickly separated into three major pools: the underwater plume about 3,300-4,300 feet below the surface, the visible surface slick, and an airborne plume of evaporating chemicals. Each pool had a very different chemical composition.

The underwater plume was enhanced in gases known to dissolve readily in water, the team found. This included essentially all of the lightweight methane (natural gas) and benzene (a known carcinogen) present in the spilling reservoir fluid. The surface oil slick was dominated by the heaviest and stickiest components, which neither dissolved in seawater nor evaporated into the air. And the airborne plume of chemicals contained a wide mixture of intermediate-weight components of the spilled gas and oil.

The visible surface slick represented about 15 percent of the total leaked gas and oil; the airborne plume accounted for about another 7 percent. About 36 percent remained in a deep underwater plume, and 17 percent was recovered directly to the surface through a marine riser. The location of the balance, about 25 percent of the total, is not directly accounted for by the chemical data.

This information about the transport and fate of different components of the spilled gas and oil mixture could help resource managers and others trying to understand environmental exposure levels.

The chemical measurements made from mid-May through June showed that the composition of the atmospheric plume changed very little, suggesting little change in the makeup of the leaking gas and oil.

The team of researchers also used the detailed chemical measurements to calculate how much gas and oil, in total, was spilling from the breached reservoir deep underwater. The new chemistry-based estimate of 11,130 tons per day has an estimated range of 8,900 to 13,300 tons per day. By comparison, the official estimated range was 10,000 to 12,700 tons per day.

 

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The above story is reprinted from materials provided by National Oceanic and Atmospheric Administration.

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Nanotechnology: Nanomechanical measurements of unprecedented resolution made on protein molecules

UCLA physicists have made nanomechanical measurements of unprecedented resolution on protein molecules.

The new measurements, by UCLA physics professor Giovanni Zocchi and former UCLA physics graduate student Yong Wang, are approximately 100 times higher in resolution than previous mechanical measurements, a nanotechnology feat which reveals an isolated protein molecule, surprisingly, is neither a solid nor a liquid.

"Proteins are the molecular machines of life, the molecules we are made of," Zocchi said. "We have found that sometimes they behave as a solid and sometimes as a liquid.

"Solids have a shape while liquids flow -- for simple materials at low stresses. However, for complex materials, or large stresses, the behavior can be in-between. Subjected to mechanical forces, a material might be elastic and store mechanical energy (simple solid), viscous and dissipate mechanical energy (simple fluid), or visco-elastic and both store and dissipate mechanical energy (complex solid, complex fluid). The viscoelastic behavior characteristic of more complex matter had not been clearly seen before on isolated proteins because mechanical measurements tend to destroy the proteins."

Zocchi and Wang's new nanotechnology method allowed them to apply stresses and probe the mechanics of the protein without destroying it. Wang, now a physics postdoctoral fellow at the University of Illinois in Urbana-Champaign, and Zocchi discovered a "transition to a viscoelastic regime in the mechanical response" of the protein.

"Below the transition, the protein responds elastically, like a spring," Zocchi said. "Above the transition, the protein flows like a viscous liquid. However, the transition is reversible if the stress is removed. Functional conformational changes of enzymes (changes in the shape of the molecule) must typically operate across this transition."

The measurements were performed on the enzyme guanylate kinase, or GK, a member of an essential class of enzymes called kinases. Specifically, GK transfers a phosphate group from ATP (the universal "fuel" of the cell) to GMP, producing GDP, an essential metabolic component, Zocchi said.

The study on the characterization of the "visco-elastic transition" is reported this month in the online journal PLoS ONE, a publication of the Public Library of Science. The research was federally funded by the National Science Foundation's division of materials research and by a grant from the University of California Lab Research Program.

Zocchi and Wang published related findings earlier this year in the journal Europhysics Letters, a publication of the European Physical Society, and the journal Physical Review Letters.

In previous research, Zocchi and colleagues reported a significant step in controlling chemical reactions mechanically last year, made a significant step toward a new approach to protein engineering in 2006, created a mechanism at the nanoscale to externally control the function and action of a protein in 2005, and created a first-of-its-kind nanoscale sensor using a single molecule less than 20 nanometers long in 2003. A nanometer is roughly 2,000 times smaller than the width of a human hair.

The above story is reprinted from materials provided by University of California - Los Angeles. The original article was written by Stuart Wolpert.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Yong Wang, Giovanni Zocchi. Viscoelastic Transition and Yield Strain of the Folded Protein. PLoS ONE, 2011; 6 (12): e28097 DOI: 10.1371/journal.pone.0028097

Note: If no author is given, the source is cited instead.

Gulf oil spill: Airborne chemistry measurements assess flow rate, fate of spilled gases and oil

NOAA scientists and academic partners have found a way to use air chemistry measurements taken hundreds of feet above last year's BP Deepwater Horizon oil spill to estimate how fast gases and oil were leaking from the reservoir thousands of feet underwater. The scientists also determined the fate of most of those gas and oil compounds using atmospheric chemistry data collected from the NOAA WP-3D research aircraft overflights in June.

The study, accepted for publication in Geophysical Research Letters, a publication of the American Geophysical Union, is available online as a paper in press.

"We present a new method for understanding the fate of most of the spilled gases and oil," said Tom Ryerson, lead author of the report, from NOAA's Earth System Research Laboratory in Boulder, CO. "We found that the spilled gases and oil (spilled fluid) obeyed a simple rule: whether a compound can dissolve or evaporate determines where it goes in the marine environment. That simple rule, and the methods we lay out in this paper, could enable airborne evaluation of the magnitude of future spills."

Knowing where the spilled gas and oil mixture ended up could also help resource managers and others trying to understand environmental exposure levels.

Using the atmospheric measurements and information about the chemical makeup of the leaking reservoir fluid, Ryerson and his colleagues calculated that at least 32,600-47,700 barrels of liquid gases and oil poured out of the breached reservoir on June 10. This range, determined independently of previous estimates presents a lower limit. "Although we accounted for gases that dissolved before reaching the surface, our atmospheric data are essentially blind to gases and oil that remain trapped deep underwater," Ryerson said. Comparison of the new result with official estimates is not possible because this airborne study could not measure that trapped material.

Not including that trapped material, atmospheric measurements combined with reservoir composition information showed that about one-third (by mass) of the oil and gas dissolved into the water column on its way to the surface. The team found another 14 percent by mass (570,000 lbs per day) was lost quickly to the atmosphere within a few hours after surfacing, and an additional 10 percent was lost to the atmosphere over the course of the next 24 to 48 hours.

Among the study's other key findings:

Some compounds evaporated essentially completely to the atmosphere, which allowed scientists to make an estimate of flow rate based solely on atmospheric measurements and reservoir composition information.Airborne instruments picked up no enhanced levels of methane, the lightest-weight hydrocarbon in the leaking reservoir fluid, showing that it dissolved essentially completely in the water column.Benzene -- a known human carcinogen -- and ethane were found in only slightly elevated concentrations in the air, meaning they dissolved nearly completely in the water.A number of slightly heavier carbon compounds ended up in both the air and water, with the precise fraction depending on the compound. Based on these data, the team inferred different exposure risks of mid- and shallow-water marine species to elevated levels of potentially toxic compounds.

A portion of oil and gas was "recovered" by response activities and piped from the leaking wellhead to the Discoverer Enterprise drill ship on the ocean surface. The research team calculated this recovered fraction by measuring emissions from natural gas flaring aboard the recovery ship. They calculated a recovery rate of 17,400 barrels of reservoir fluid (liquid gas and oil) for June 10, and which accounted for approximately one-third to one-half of the group's total estimate of 32,600-47,700 barrels of fluid per day.

Ryerson and his colleagues concluded that the technique they developed could be applied to future oil spills, whether in shallow or deep water. The Gulf research flights were possible only because a NOAA WP-3D research aircraft had already been outfitted with sensitive chemistry equipment for deployment to California for an air quality and climate study and was redeployed to the Gulf. NOAA's Gulf flights were in support of the Unified Area Command's effort to observe and monitor the environmental effects of the spill.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by National Oceanographic and Atmospheric Administration.

Journal Reference:

Ryerson, T.B., K.C. Aikin, W.M. Angevine, E.L. Atlas, D.R. Blake, C.A. Brock, F.C. Fehsenfeld, R.-S. Gao, J.A. de Gouw, D.W. Fahey, J.S. Holloway, D.A. Lack, R.A. Lueb, S. Meinardi, A.M. Middlebrook, D.M. Murphy, J.A. Neuman, J.B. Nowak, D. D. Parrish, J. Peischl, A.E. Perring, I.B. Pollack, A. R. Ravishankara, J. M. Roberts, J. P. Schwarz, J. R. Spackman, H. Stark, C. Warneke, L. A. Watts. Atmospheric emissions from the Deepwater Horizon spill constrain air-water partitioning, hydrocarbon fate, and leak rate. Geophysical Research Letters, 2011; DOI: 10.1029/2011GL046726

Multiplexed capillary isoelectric focusing increases efficiency in protein measurements

The Springer journal Analytical and Bioanalytical Chemistry (ABC) has chosen Oluwatosin O. Dada (34) as the recipient of its Best Paper Award 2010. Dada is the lead author of a paper in ABC on capillary isoelectric focusing. The award, accompanied by 1,000 euros, was created by Springer to help exceptional young scientists establish their research careers. The ABC Best Paper Award has been given since 2005.

Capillary isoelectric focusing is an interesting technique for the characterization of proteins. However, multiplexing capillary isoelectric focusing is a daunting task. Dr. Dada's significant contribution to this technology is the development of a state-of-the-art tool for high-throughput capillary isoelectric focusing. The performance of this technology is stunning: It provides the highest throughput isoelectric focusing analysis ever reported, the highest sensitivity ever reported for a high-throughput instrument, and the highest resolution separation ever reported for capillary isoelectric focusing. The technology will find wide application, including characterization of recombinant and therapeutic proteins, the diagnosis of disease, and the study of systems biology.

Dr. Dada received his BSc in industrial chemistry in 2001 from Olabisi Onabanjo University in Nigeria. He moved to the United States in 2004, where he received his PhD in analytical chemistry from Utah State University in 2008. He then spent two years at the University of Washington in Seattle as a postdoctoral research associate. Currently, he holds a research assistant professor position at the University of Notre Dame, USA, where he continues his research on capillary electrophoresis with laser-induced fluorescence and photothermal instrumentation for bioanalysis.

Prof. Aldo Roda, Editor of Analytical and Bioanalytical Chemistry, said, "There is a highly competitive effort underway in the scientific community to improve the analytical performance of isoelectric focusing (IEF) as a tool for protein separation and concentration. Several groups have investigated the miniaturization of cIEF and the integration of cIEF to a microchip format. With this paper, Dada and co-workers offer us new analytical approaches to resolving the ongoing problem of time-consuming procedures."

More information: The article "Capillary array isoelectric focusing with laser-induced fluorescence detection" is freely available online on SpringerLink at http://www.springe … 71l58435h58/

Provided by Springer