Monday, August 29, 2011

Flexibility: The key to carbon capture

From power plants that capture their own carbon dioxide emissions to vehicles powered by hydrogen, clean energy applications often demand materials that can selectively adsorb large volumes of harmful gases. Materials known as porous coordination polymers (PCPs) have great gas-trapping potential, and now their adsorptive properties can be boosted using a new technique developed by a research team in Japan.

The key to the development is making PCPs that can flex, since it allows the team to tune the gas-adsorbing properties of these materials—whether it is to improve the ability to selectively adsorb one from a mixture or to fine-tune the pressure at which the gas is captured and released. 

While structural flexibility in PCPs is not new, team member Ryotaro Matsuda from the RIKEN SPring-8 Center, Harima, explains that he and his colleagues successfully incorporated this flexibility into a PCP built from molecular components known as secondary building units (SBUs). At the molecular scale, PCPs consist of vast networks of tiny interlinked cages, inside which gas molecules can sit. SBUs are made from clusters of metal atoms that can be used to form the corner of each cage. Their use gives materials scientists great control over the structure of a cage, but they can also lock the structure.

Matsuda and colleagues overcame the rigidity problem by connecting the cage corners into cubes using long, slim carbon-based linkers. In the absence of , these slender linkers allow the cage framework to collapse into a non-porous solid; but in the presence of a gas, the material expands—a behavior known as gate-opening adsorption (Fig. 1). 

It is a behavior that could prove useful, Matsuda explains. “Gate-opening-type adsorption, which is induced by the structural transformations from a non-porous structure to a porous structure at a certain pressure of gas, would provide a way to enhance the efficiency of pressure swing adsorption,” he says. Pressure-swing adsorption is being investigated as a way to capture from . The concept relies on finding materials that will release the gas in response to a drop in pressure, so that it can be piped away for long-term, underground storage.

The researchers are now looking to improve the performance of their material. “We are currently trying to tune the soft porosity of the prototype PCP to separate mixtures of gases,” says Matsuda. “We have also been working to reveal the relationship between the structure, adsorption property and separation ability of [other] PCPs.”

More information: Seo, J. et al. Soft secondary building unit: dynamic bond rearrangement on multinuclear core of porous coordination polymers in gas media. Journal of the American Chemical Society 133, 9005–9013 (2011).

Provided by RIKEN (news : web)

Deep recycling in the Earth faster than thought

 The recycling of the Earth's crust in volcanoes happens much faster than scientists have previously assumed. Rock of the oceanic crust, which sinks deep into the earth due to the movement of tectonic plates, reemerges through volcanic eruptions after around 500 million years. Researchers from the Max Planck Institute for Chemistry in Mainz obtained this result using volcanic rock samples. Previously, geologists thought this process would take about two billion years.

Virtually all of the ocean islands are volcanoes. Several of them, such as Hawaii, originate from the lowest part of the mantle. This geological process is similar to the movement of coloured liquids in a lava lamp: hot rock rises in cylindrical columns, the so-called mantle plumes, from a depth of nearly 3,000 kilometers. Near the surface, it melts, because the pressure is reduced, and forms volcanoes. The plume originates from former ocean crust which early in the Earth's history sank to the bottom of the mantle. Previously, scientists had assumed that this recycling took about two billion years.

The chemical analysis of tiny glassy inclusions in olivine crystals from basaltic lava on Mauna Loa volcano in Hawaii has now surprised geologists: the entire recycling process requires at most half a billion years, four times faster than previously thought.

The microscopically small inclusions in the volcanic rock contain trace elements originally dissolved in seawater, and this allows the recycling process to be dated. Before the old ocean crust sinks into the mantle, it soaks up seawater, which leaves tell-tale trace elements in the rock. The age is revealed by the isotopic ratio of strontium which changes with time. Strontium is a chemical element, which occurs in trace amounts in sea water. The isotopes of chemical elements have the same number of protons but different numbers of neutrons. Mainz scientists developed a special laser mass spectrometry method which allowed the detection of isotopes of strontium in extremely small quantities.

To their surprise, the Max Planck researchers found residues of sea water with an unexpected strontium isotope ratio in the samples, which suggested an age of less than 500 million years for the inclusions. Therefore the rock material forming the Hawaiian basalts must be younger.

"Apparently strontium from sea water has reached deep in the Earth's mantle, and reemerged after only half a billion years, in Hawaiian volcano lavas," says Klaus Peter Jochum, co-author of the publication. "This discovery was a huge surprise for us."

Another surprise for the scientists was the tremendous variation of strontium isotope ratios found in the melt inclusions in olivine from the single lava sample. “This variation is much larger than the known range for all Hawaiian lavas”, says Alexander Sobolev. “This finding suggests that the mantle is far more chemically heterogeneous on a small spatial scale than we thought before.” This heterogeneity is preserved only by melt inclusions but is completely obliterated in the lavas because of their complete mixing.

Sobolev, Jochum and their colleagues expect to obtain similar results for other volcanoes and therefore be able to determine the recycling age the ocean crust more precisely.

Original publication:
Alexander V. Sobolev, Albrecht W. Hofmann, Klaus Peter Jochum, Dmitry V. Kuzmin & Brigitte Stoll; A young source for the Hawaiian plume; Nature, 10. August 2011

Light unlocks fragrance in laboratory

In Anna Gudmundsdottir's laboratory at the University of Cincinnati, dedicated researchers endeavor to tame the extremely reactive chemicals known as radicals.

Highly reactive radicals are atoms, molecules or frantically trying to become something else. Their lifetimes are measured in fractions of seconds and typically occur in the middle of a chain of . They are also known as reactive intermediates. Much of Gudmundsdottir's work has focused on a family of radicals known as triplet nitrenes.

"Triplet nitrenes are reactive intermediates with high spin," Gudmundsdottir said. "You have a nitrogen molecule that has two unpaired on it. We discovered they were actually very stable for intermediates. They live for milliseconds and that's when we got into this idea can we make them stable enough for various investigations."

The potential uses of relatively stable radicals have excited interest from industry. The high spin Gudmundsdottir describes suggests that triplet nitrenes, for example, might be ideal candidates for creating organic magnets that are lighter, more flexible and energy-intensive than conventional metal or ceramic magnets. Gudmundsdottir's research suggests that radicals, including triplet nitrenes, may show a pathway to materials with many magnetic, electrical and .

"I talk a lot about radicals," Gudmundsdottir said. "Nitrenes are radicals. We study the of the precursors to the nitrenes. We are looking at how you use the excited state of molecules to form specific radicals."

One line of inquiry, presented by Gudmundsdottir to a recent Gordon Research Conference, described how her team used radicals to create a specific trap for a fragrance, which is then slowly released when exposed to light.

"The question was, can you actually tether a fragrance to something so that it will release slowly?" Gudmundsdottir said. "It turned out that a precursor similar to the ones we used to form the nitrenes could be used it as a photoremovable protecting group."

The "photoprotectant" acts as a sort of cap, containing the fragrance until the cap is pried off by a photon of light. For this particular purpose, Gudmundsdottir said it was important to design a photoprotectant "cap" that was somewhat difficult to pry off. For household products, such as a scented cleaning fluid, consumers want fragrance to be released slowly over a long period of time. That requires what is known as a low "quantum yield." In other words, how much fragrance gets released by how many photons.

The difficulty, Gudmundsdottir said, is that different applications need different rates of release. For medical uses, doctors might want a higher quantum yield, by which a little bit of light releases a lot of medicine.

"There are all kinds of applications for photoreactions," she said, "from household goods, perfumes, sun-protection, drug delivery and a variety of biologically reactive molecules. So we just decided, OK, we are very fundamental chemists, we'll design different systems and see if we can manipulate the rate of release."

Gudmundsdottir's research group studies the release mechanism, locates where there are limitations, and tries to determine what controls the rate. They also consider environmental factors, including how the delivery systems react with oxygen.

"We do very fundamental work to get the knowledge here before can take it into specific directions," she said. "If we don't understand it, we can't design where to take it next."

Much of this understanding develops from watching how radicals form and decay. Gudmundsdottir's group uses a laser flash photolysis system to fire a laser into a sample and to track the spectrum of radiated light as the radicals decay.

"What I like about transient spectroscopy is actually seeing the intermediates we work with on nanosecond, microsecond and millisecond timescales," she said.

The team also uses computer modeling, but the chemical operations of these short-lived and rapidly reacting chemicals are difficult to model, so Gudmundsdottir has tapped into the resources of the Ohio Supercomputer Center.

"Calculating excited states takes up quite a bit of computer resources and that's why we use the supercomputer," she said. "That's a really nice resource to have available. I can sit anywhere or my students can sit anywhere and we can do the calculations to model reactions."

Gudmundsdottir said the questions raised by applications leads to helpful fundamental questions that can be tackled through basic research.

"Going forward, we probably want to do more applied study with our photo protective groups, to collaborate with someone to see them in some other applications," she said. "I'm interested in how they act inside cells."

Provided by University of Cincinnati (news : web)

Clustering is key to lighting up the dark proteome

Clustering is key to lighting up the dark proteome


Most mass spectrometry studies attempt to identify Peptide-Spectrum Matches (PSMs) and often ignore Spectrum-Spectrum Matches (SSMs), especially if PSMs for these SSMs are not established. However, SSMs also are useful when the corresponding peptide is not identified, because they allow a researcher to cross-reference spectra generated by different researchers and to query all spectra ever generated against a single repository. Spectral libraries are essentially databases of PSMs, while spectral archives are databases of both PSMs and SSMs. Although construction of PSMs (via tandem mass spectrometry database search) is a well-studied topic, construction of all SSMs represents a formidable clustering problem. The figure reveals similarities and highlights differences between construction (left) and use (right) of spectral libraries and spectral archives. With an archive, researchers first cluster, then search the clusters against a protein database to generate Peptide-Cluster Matches (PCMs). In turn, these PCMs get propagated to all spectra in the identified clusters to generate PSMs. With the library, researchers first search the spectra against a protein database to generate PSMs, group PSMs corresponding to the same peptide, and finally deposit the curated consensus PSM in the spectral library. Then, the spectral library can be used to identify spectra from new spectral datasets.

A new approach that organizes previously unused mass spectra from proteomics studies gives scientists the ability to use these spectra to gain more information about proteins in a wide range of organisms. Scientists from the University of California-San Diego and Pacific Northwest National Laboratory have created a vast spectral archive from more than a billion mass spectra acquired at PNNL between 2001 and 2009. They describe their approach in the July issue of Nature Methods.

In recent years, the volume of tandem mass spectrometry data generated from proteomics experiments has increased dramatically. Multiple, nearly identical mass spectra of the same are routinely measured by various laboratories. Scientists compare the spectra with peptides residing in a database of known . They then evaluate the resulting matches using various scoring methods to assign an identity to the peptide spectrum. Large sets of spectra can be organized into spectral libraries where other spectra can be brought for comparison, leading to increasing effectiveness in peptide assignments used for protein identifications.

But what about those spectra not identified; that is, those not associated with a known peptide? Typically, unidentified spectra are ignored or discarded, as they have limited value to the researchers because the protein is unidentified. As a result, a significant fraction of the proteins remain unidentified, constituting an effective "dark " of unknown content.

Shedding light on the dark proteome is where the UCSD/PNNL team comes in. While spectral libraries discard unidentified spectra, spectral archives use all mass spectra—identified or unidentified-as clusters (see "Spectral Archives Complement Spectral Libraries"). The scientists not only showed the feasibility of constructing large archives and their basic utility for run-of-the-mill peptide identification, they developed new applications now possible because a diverse collection of datasets can be analyzed as a whole.

"We believe that spectral archives could change the nature of proteomics by motivating researchers who are analyzing seemingly unrelated data to share this data," said senior author Dr. Pavel Pevzner, UCSD. "Doing so improves the quality of the interpretations of both of their spectral datasets."

With archives, a researcher can identify clusters of spectra from different organisms. Besides indicating that such spectra are interesting—as they are likely to indicate proteins occurring over multiple species—this fact can be used to reduce the effective protein database size, leading to new, confident peptide and protein identifications. The team also showed that short peptides (shorter than 7 amino acids) could be confidently identified, which is much more difficult with typically used approaches.

The PNNL mass spectra data used by the team included samples taken from a diverse set of more than 100 organisms, including humans, the common house mouse, and the metal-reducing bacterium Shewanella oneidensis. The research team developed a clustering tool, MS-Cluster, that generated a spectral archive from the ~1.18 billion spectra from PNNL. This archive greatly exceeds the size of existing spectral repositories.

To evaluate whether spectral archives can increase peptide identifications, the researchers selected a subset of 14.5 million spectra from the microorganism S. oneidensis and constructed an archive with them. They did this by breaking the dataset into five sets of ~2.9 million spectra then incrementally adding each set of spectra to the archive. At each stage they compared the number of protein and unique peptide identifications made by searching the clusters in the archive with the number that could be obtained with conventional database search approaches.

The archive consistently yielded more unique peptide and protein identifications. With the archive, the scientists also were able to identify many more spectra through their cluster membership. At different stages, they identified 50-75% more spectra through cluster membership than via a regular database search.

This study also highlights the large number of spectra for which peptide and protein identifications are not achieved, opening the door for use of experimental and computational approaches to identify the significant numbers of peptides effectively ignored by proteomics studies to date.

More information: Frank AM, et al. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8(7):587-591. DOI:10.1038/nmeth.1609

Provided by Pacific Northwest National Laboratory (news : web)