The origin of organic magnets

 A theoretical model for the unusual occurrence of magnetism in organic molecules may help develop this class of material for electronics applications.

Electrical engineers are starting to consider materials made from organic molecules -- including those made from carbon atoms -- as an intriguing alternative to the silicon and metals used currently in electronic devices, since they are easier and cheaper to produce. A RIKEN-led research team has now demonstrated the origin of magnetism in organic molecules1, a property that is rarely found in this class of material, but is vital if a full range of organic electronic devices is to be created.

The permanent magnetic properties of materials such as iron stem from an intrinsic mechanism called ferromagnetism. Ferromagnetism in organic materials is rare because their atomic structure is fundamentally different from metals. One of the few examples identified to date is called TDAE-C60: a compound comprising spherical carbon cages attached to an organic molecule known as tetrakis-dimethylamino-ethylene. Since its identification in 1991, many theoretical and experimental studies have provided some insight into the mechanism driving this unexpected ferromagnetism, but the explanation was not definitive. A full understanding would help materials scientists to develop more advanced magnetic materials in the future. "A precise model for organic magnetism could aid the design of high-density recording materials for use in next-generation memories," says team member Hitoshi Yamaoka from the RIKEN SPring-8 Center, Harima.

Materials scientists are particularly interested in understanding the electronic structure of TDAE-C60 and how this relates to its ferromagnetic properties. To this end, Yamaoka and his colleagues from research institutes across Japan studied this material using a powerful technique known as photoelectron spectroscopy (PES). They fired x-rays at a single crystal of TDAE-C60, and this radiation excited electrons in the crystal, which then escaped from the surface. The researchers measured the number and the kinetic energy of these electrons from which they could infer information about the electronic structure.

"From these experiments on a single crystal we could establish an exact theoretical model for organic magnetism," explains Yamaoka. "We propose that the transfer of one electron from the TDAE to the C60 causes the magnetic properties of TDAE-C60." The existence of the resulting positively charge TDAE state was also supported by the team's theoretical calculations.

With this thorough understanding of organic magnetism, the next step will be to apply the material to practical applications. "The problem with the TDAE-C60 organic magnet, however, is that the magnetism only appears at temperatures below 16 kelvin," says Yamaoka. "The next step will be to raise this transition point."

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The above story is reprinted from materials provided by RIKEN, via ResearchSEA.

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Avalanche of reactions at the origin of life

Volcanic-hydrothermal flow channels offer a chemically unique environment, which at first glance appears hostile to life. It is defined by cracks in the crust of the earth, through which water flows, laden with volcanic gases are contacting a diversity of minerals. And yet – it is precisely this extreme environment, where the two mechanisms could have emerged, which are at the root of all life: The multiplication of biomolecules (reproduction) and the emergence of new biomolecules on the basis of previously formed biomolecules (evolution).

At the outset of this concatenation of reactions that led eventually to the formation of cellular forms of life there are only a few amino acids, which are formed from volcanic gases by mineral catalysis. Akin to a domino stone that triggers a whole avalanche, these first biomolecules stimulate not only their own further synthesis but also the production of wholly new biomolecules. "In this manner life begins by necessity in accordance with pre-established laws of chemistry and in a pre-determined direction", declares Günter Wächtershäuser, honorary professor for evolutionary biochemistry at the University of Regensburg. He developed the mechanism of a self-generating metabolism – theoretically, alas, an experimental demonstration has been lacking so far.

Now, scientists around Claudia Huber and Wolfgang Eisenreich, at the Chair of Biochemistry in the Department of Chemistry at the TUM in close cooperation with Wächtershäuser, managed for the first time to demonstrate experimentally the possibility of such a self-stimulating mechanism. A catalyst consisting of compounds of the transition metals nickel, cobalt or iron has the lead role in these reactions. It provides not only for the formation of the first biomolecules, but it also initiates the concatenation of reactions. The reason: The biomolecules just newly formed from the volcanic gases engage the center of the transition metal catalyst to enable further chemical reactions bringing forth wholly new biomolecules. "This coupling between the catalyst and an organic reaction product is the first step", explains Wächtershäuser. "Life arises, if subsequently a whole cascade of further couplings takes place, and this primordial life leads eventually to the formation of genetic material and of the first cells".

The scientists simulated in their experiments the conditions of volcanic-hydrothermal flow channels and established an aqueous-organometallic system that produces a whole suite of different biomolecules, among them the amino acids glycin and alanin. Here the carbon source was provided by a cyano compound and the reducing agent by carbon monoxide. Nickel compounds turned out to be the most effective catalysts in these experiments. The scientists then added the products glycin and alanin to another system, that generated again two new biomolecules. The result: The two amino acids increased the productivity oft he second system by a factor of five.

In future experiments the scientists intend to recreate more precisely the conditions of volcanic-hydrothermal systems, wherein life could have arisen billions of years ago. "For this purpose we simulate first certain stages in the development of a volcanic-hydrothermal flow system in order to determine essential parameters", explains Wächtershäuser. "Only thereafter we may engage in a rational construction of a flow reactor".

The results of the scientists around Wächtershäuser and Eisenreich show that an origin and evolution of life in hot water of volcanic flow ducts is feasible. The results reveal advantages of the theory compared to other approaches. Within the flow ducts temperature, pressure and pH change along the flow path, and thereby a graded spectrum of conditions is offered that is appropriate for all stages of early evolution up to the formation of genetic material (RNA/DNA).

The most important property of the system is its autonomy: As opposed to the notion of a cool prebiotic both, the first metabolism was not dependent on accidental events or an accumulation of essential components over thousands of years. As soon as the first domino stone is toppled, the others will follow automatically. The origin of life proceeds along definite trajectories, pre-established by the rules of chemistry – a chemically determined process giving rise to the tree of all forms of life.

More information: Elements of metabolic evolution. C. Huber, F. Kraus, M. Hanzlik, W. Eisenreich, G. Wächtershäuser, Chemistry – A European Journal, advanced online publication: 13 Jan 2012 – DOI: 10.1002/chem.201102914

Provided by Technische Universitaet Muenchen

New study sheds light on evolutionary origin of oxygen-based cellular respiration

As the central process by which cells capture and store the chemical energy they need to survive, cellular respiration is essential to all life on this planet. While most of us are familiar with one form of respiration, whereby oxygen is used to transform nutrients into molecules of adenosine triphosphate (ATP) for use as energy ("aerobic respiration"), many of the world's organisms breathe in a different way. At the bottom of the ocean and in other places with no oxygen, organisms get their energy instead using substances such as nitrate or sulfur to synthesize ATP, much the way organisms did many billions of years ago ("anaerobic respiration").

While less well-known, this latter type of cellular respiration is no less important, fuelling the production of most of the world's nitrous oxide (N2O), an ozone depleting and greenhouse gas 310 times more potent than carbon dioxide. As the enzyme responsible for catalyzing the reactions underlying anaerobic respiration, nitric oxide reductase (NOR) has attracted increasing attention in environmental circles. The mystery of NOR's catalyzing mechanism, however – which accounts for a staggering 70% of the planet's N2O production – remains largely unsolved.

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This is a schematic representation of the proton transfer pathways for the NO reduction reaction in cNOR and qNOR, and the proton pumping pathway in COX. The direction of the proton transfer is denoted by red dotted arrows. cNOR has a proton transfer pathway from the outside of the cell to the catalytic site for the NO reduction reaction. In sharp contrast to this, there is no proton transfer pathway from the outside of the cell in qNOR. Unexpectedly, however, we identified a proton transfer pathway from the inside of the cell to the catalytic site in qNOR. In COX, protons are pumped from the inside to the outside of the cell through the catalytic site. The location of the proton transfer pathway we identified in qNOR (pink color) is similar to a part of the proton pumping pathway in COX. Credit: RIKEN

With their latest research, the team sought an answer to this mystery in the origin of an evolutionary innovation known as the "proton pump". To accelerate ATP-synthesis, aerobic organisms harness the potential of an electrochemical concentration gradient across the cell, created by "pumping" protons out using energy from an oxygen reduction reaction. The enzyme powering this mechanism, cytochrome oxidase (COX), is genetically and structurally similar to NOR, suggesting a common ancestor. No evidence of any "pump", however, has been detected in anaerobic organisms.

That is, until now. Using radiation from the RIKEN SPring-8 facility in Harima, Japan, the world's largest synchrotron radiation facility, the researchers probed the 3D structure of qNOR and discovered a channel acting as a proton transfer pathway for a key catalytic reaction. While not itself a proton pump, the position and function of this pathway suggest it is an ancestor of the proton pump found in COX. The finding thus establishes first-ever evidence for a proton pump in anaerobic organisms, shedding light onto the mysterious mechanisms governing the production of nitrogen oxide and the evolutionary path that led to their emergence.

Provided by RIKEN (news : web)

Products of biotechnological origin using vegetable and fruit by-products generated by the industry

Through the TRANSBIO project, Tecnalia will be implementing biotechnological solutions, like fermention and enzymatic processes to obtain new, high-value products of biotechnological origin in the form of new materials offering the potential to replace current plastics, foodstuffs and enzymes for applications in detergents using the materials not taken advantage of in the fruit and vegetable processing industry. This way, the global sustainability of the biomass production and processing industry will be improved, and the competitiveness of the European biotechnology industry will be enhanced through new applications.

As a result of these processes, new and more sustainable plastic materials will be obtained to be used in food packaging application, enzymes for producing detergents, and other biotechnological products for application in foodstuff.

In parallel, and in order to achieve the total use of the by-products employed in the project, those that may not be suited for use in biotechnological processes and the waste materials coming from fermentation processes will be tested to assess their use as raw material for the production of biogas.

The consortium participating in the TRANSBIO project comprises various partners from the ambit of industry and the academic sector with experience in complementary fields. The combination of these synergies allows all the links in the value chain to be taken into consideration, from the reprocessing of by-products, fermentation, and right up to the processing of the final product.

Tecnalia is coordinating this international consortium that has 16 partners from nine countries and two continents (Latin America and Europe) to look into the potential of new biotechnological solutions for obtaining bioproducts that, in practice, will signify the cutting of the environmental impact of food-producing activities.

Provided by Elhuyar Fundazioa

Study builds on plausible scenario for origin of life on Earth

A relatively simple combination of naturally occurring sugars and amino acids offers a plausible route to the building blocks of life, according to a paper published in Nature Chemistry co-authored by a professor at the University of California, Merced.

The study, "A Route to Enantiopure RNA Precursors from Nearly Racemic Starting Materials," shows how the precursors to RNA could have formed on Earth before any life existed. It was authored by Jason E. Hein, Eric Tse and Donna G. Blackmond, a team of researchers with the Scripps Research Institute. Hein is now a chemistry professor with UC Merced. The paper was published online Sunday.

Biological molecules, such as RNA and proteins, can exist in either a natural or unnatural form, called enantiomers. By studying the chemical reactions carefully, the research team found that it was possible to generate only the natural form of the necessary RNA precursors by including simple amino acids.

"These amino acids changed how the reactions work and allowed only the naturally occurring RNA precursors to be generated in a stable form," said Hein. "In the end, we showed that an amazingly simple result emerged from some very complex and interconnected chemistry."

The natural enantiomer of the RNA precursor molecules formed a crystal structure visible to the naked eye. The crystals are stable and avoid normal chemical breakdown. They can exist until the conditions are right for them to change into RNA.

More information: DOI: 10.1038/NCHEM.110

Provided by University of California - Merced

Pinpointing the origin of corpses, fingering fake cheese and more -- with 'isoscapes'

An emerging field of science termed "isoscapes" is making it possible to pinpoint the geographical origins of illegal drugs, trafficked endangered animals, dismembered human body parts at crime scenes, and even pricey scotch whiskey and cheese, according to an article in the current edition of Chemical & Engineering News (C&EN), the American Chemical Society's weekly newsmagazine.

In the article, Sarah Everts, C&EN European correspondent, explains how isoscapes has even led to development of one of the newest and most unusual maps of the world. It is a map showing the isotope contours of the world, which scientists and others are using in tracking the geographical origins of objects, and even in research on global climate change. Isoscape is a combination of the words "isotope" and "landscapes," where isotopes are atoms of an element that differ slightly in the number of subatomic particles called neutrons that they possess.

Identification by isoscapes is based on the discovery that the tissue in a person's body and composition of drugs, whiskey, and other objects contains a distinctive isotope ratio "fingerprint." That fingerprint stems from the isotope ratios of food, water, and air where the person, whiskey and other objects originated. And those isotope ratios vary with geography that can be plotted on a map. The article explains how the isotope-based map can help convict murderers and authenticate the origins of fancy foods.

More information: “Isotopes Impart Geographical Clues”: http://pubs.acs.or … 926sci1.html

Provided by American Chemical Society (news : web)

Evidence of a natural origin for banned drug that plumps up livestock

There may be a natural solution to the mystery of how small amounts of a banned drug that disrupts thyroid function and plumps up livestock gets into their bodies — and the bodies of humans, scientists are reporting. Their study, which appears in ACS' Journal of Agricultural and Food Chemistry, reports the first evidence that the substance can form naturally in feed and food.

Julie Vanden Bussche and colleagues explain that thiouracil is a drug that increases the weight of livestock by making them retain water. Some regulatory agencies have banned its use because the extra weight cheats consumers, who buy water for the price of meat, and because of potential adverse health effects. To keep an eye on compliance, government agencies test animals for thiouracil. For example, both the U.S. Department of Agriculture and the European Union Reference Laboratories developed sensitive tests to detect thiouracil. Perhaps because these tests are so sensitive, the drug is now showing up often but at low levels — levels that are lower than expected if the animals were purposely doped. Hence, some scientists speculated that thiouracil may also have a natural origin. To settle the controversy, the researchers analyzed livestock feed and other food for the presence of thiouracil.

They found that plants in the family called Brassicaceae — which includes cruciferous vegetables, such as broccoli and cauliflower, and other plants, such as rapeseed and feeding cabbage, that are used as animal feed — had small amounts of thiouracil in them naturally. "To the best of our knowledge this study is the first to report the presence of naturally occurring thiouracil in feed and food samples, hereby elucidating and acknowledging a natural origin for the low-level residues detected in urine of various species," say the researchers.

More information: “Feed or Food Responsible for the Presence of Low-Level Thiouracil in Urine of Livestock and Humans?” J. Agric. Food Chem., 2011, 59 (10), pp 5786–5792 DOI: 10.1021/jf200556x

Abstract
In recent years, questions have been raised on the possible semi-endogenous status of the alleged xenobiotic thyreostatic drug thiouracil; thiouracil has been detected in the urine of various animals (livestock and domesticated) at concentrations between 1 and 10 µg L–1 and also in human urine. Although several studies suggest Brassicaceae-derived feed as potential origin, no traces of thiouracil have been detected in feed so far. Therefore, the aim of this study was to elucidate the origin of thiouracil in the urine of livestock and humans. To this purpose various Brassicaceae feed and food sources (e.g., rapeseed, rapeseed coarse meal, cabbage, cauliflower, broccoli) were investigated for the presence of thiouracil. In addition, the impact of the Brassicaceae-related ß-thioglucosidase enzyme was evaluated. This myrosinase enzyme appeared to be crucial, because without its catalyzed hydrolysis no thiouracil could be detected in the various Brassicaceae-derived samples. Therefore, a sample pretreatment with incorporated enzymatic hydrolysis was developed after ensuring the quality performance of the extracted myrosinase mixture with a single-point glucose assay. Upon enzymatic hydrolysis and LC-MS2 analysis, thiouracil was successfully detected in samples of traditional rapeseed, rapeseed-‘00’ variety coarse meal (values of erucic acid <2% and glucosinolates <25 µmol g–1), and rapeseed cake at 1.5, 1.6, and 0.4 µg kg–1, respectively. As for the food samples, broccoli and cauliflower displayed thiouracil concentrations of 6.0 and <1.0 µg kg–1, respectively. To the best of the authors' knowledge this study is the first to report the presence of naturally occurring thiouracil in feed and food samples. Future research should investigate the pathway of thiouracil formation and identify its possible precursors.

Provided by American Chemical Society (news : web)

'Lost' samples from famous origin of life researcher could send search for first life in new direction

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Preserved samples from a 1958 experiment done by "primordial soup" pioneer Stanley Miller contain amino acids created by the experiment. The samples had not undergone analysis until recently when Miller's former student Jeffrey Bada and colleagues discovered a wide range of amino acids. The find could be an important step toward understanding how life on Earth could have originated. The vials have been relabeled but the boxes are marked with Miller's original notes. Credit: Scripps Institution of Oceanography, UC San Diego

(PhysOrg.com) -- Stanley Miller gained fame with his 1953 experiment showing the synthesis of organic compounds thought to be important in setting the origin of life in motion. Five years later, he produced samples from a similar experiment, shelved them and, as far as friends and colleagues know, never returned to them in his lifetime.

More 50 years later, Jeffrey Bada, Miller's former student and a current Scripps Institution of Oceanography, UC San Diego professor of marine chemistry, discovered the samples in Miller's laboratory material and made a discovery that represents a potential breakthrough in the search for the processes that created Earth's first life forms.

Former Scripps undergraduate student Eric Parker, Bada and colleagues report on their reanalysis of the samples in the March 21 issue of Proceedings of the National Academy of Sciences. Miller's 1958 experiment in which the gas hydrogen sulfide was added to a mix of gases believed to be present in the atmosphere of early Earth resulted in the synthesis of sulfur amino acids as well as other amino acids. The analysis by Bada's lab using techniques not available to Miller suggests that a diversity of organic compounds existed on early planet Earth to an extent scientists had not previously realized.

 

Scripps Oceanography professor of Marine Chemistry Jeffrey Bada holds a preserved sample from a 1958 experiment done by "primordial soup" pioneer Stanley Miller. The residue in the sample contains amino acids created by the experiment. The samples had not undergone analysis until recently when Bada and colleagues discovered a wide range of amino acids using modern detection methods. Credit: Scripps Institution of Oceanography, UC San Diego

The new findings support the case that volcanoes — a major source of atmospheric hydrogen sulfide today — accompanied by lightning converted simple gases into a wide array of amino acids, which are were in turn available for assembly into early proteins.

Bada also found that the amino acids produced in Miller's experiment with hydrogen sulfide are similar to those found in meteorites. This supports a widely-held hypothesis that processes such as the ones in the laboratory experiments provide a model of how organic material needed for the origin of life are likely widespread in the universe and thus may provide the extraterrestrial seeds of life elsewhere.

Successful creation of the sulfur-rich amino acids would take place in the labs of several researchers, including Miller himself, but not until the 1970s.

"Unbeknownst to him, he'd already done it in 1958," said Bada.

Miller's initial experiments in the 1950s with colleague Harold Urey used a mixture of gases such as methane, ammonia, water vapor and hydrogen and electrically charged them as lightning would. The experiment, which took place in a closed chamber meant to simulate conditions on early Earth, generated several simple amino acids and other organic compounds in what became known as "primordial soup."

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This is a photo of Stanley Miller in his UC San Diego lab in 1970. Credit: Scripps Institution of Oceanography Archives

With the gases and electrical energy they produce, many geoscientists believe the volcanoes on a young planet covered much more extensively by water than today's served as oases of raw materials that allowed prebiotic matter to accumulate in sufficient quantities to assemble into more complex material and eventually into primitive life itself. Bada had already begun reanalyzing Miller's preserved samples and drawing conclusions about the role of volcanoes in sparking early life when he came across the previously unknown samples. In a 2008 analysis of samples left from Miller's more famous experiment, Bada's team had been able to detect many more amino acids than his former mentor had thanks to modern techniques unavailable to Miller.

Miller, who became a chemistry professor at UCSD in 1960, conducted the experiments while a faculty member at Columbia University. He had collected and catalogued samples from the hydrogen sulfide mix but never analyzed them. He only casually mentioned their existence late in his life and the importance of the samples was only realized shortly before his death in 2007, Bada said. It turned out, however, that his 1958 mix more closely resembled what geoscientists now consider early Earth conditions than did the gases in his more famous previous experiment.

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The original box containing archived spark discharge samples prepared by Stanley Miller in 1958. For unknown reasons, Miller never analyzed these even though this is his first experiment using hydrogen sulfide. The label shows Miller?s original writing: p 114 refers to his notebook. Credit: Jeffrey Bada and Robert Benson/Scripps Institution of Oceanography, University of California at San Diego

"This really not only enhances our 2008 study but goes further to show the diversity of compounds that can be produced with a certain gas mixture," Bada said.

The Bada lab is gearing up to repeat Miller's classic experiments later this year. With modern equipment including a miniaturized microwave spark apparatus, experiments that took the elder researcher weeks to carry out could be completed in a day, Bada said.

Provided by University of California - San Diego (news : web)