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  • richardmitnick 5:20 pm on February 23, 2015 Permalink | Reply
    Tags: , Chemistry,   

    From DOE Pulse: “NETL invents improved oxygen carriers” 

    pulse

    DOE NETL
    National Energy Technology Lab

    February 23, 2015
    Linda Morton, 304.285.4543,
    Linda.morton@netl.doe.gov

    1
    Oxygen carriers are similar in texture to
    sand. The oxygen carrier pictured here
    blends magnesium oxide and hematite.

    One of the keys to the successful deployment of chemical looping technologies is the development of affordable, high performance oxygen carriers. One potential solution is the naturally-occurring iron oxide, hematite. “Hematite is pretty cheap,” says Doug Straub, Technical Coordinator for the National Energy Technology Laboratory’s Chemical Looping Combustion (CLC) projects and the just-completed Industrial Carbon Management Initiative (ICMI). “You just dig it out of the ground and run it through a screen.” That affordability makes hematite attractive as an oxygen-carrier material, but high performance at the conditions imposed by the chemical looping process is also important. Researchers at the DOE lab are investigating how to enhance hematite-based oxygen carriers so they can stand up to high reactor temperatures. Oxygen carriers also need to be resilient in the face of frequent impacts with reactor walls, with each other, and (in coal-burning reactors) with coal particles. Researchers are also improving oxygen carriers so that they more completely combust the fuel.

    Their work has paid off. Dr. Ranjani Siriwardane (who leads the CLC oxygen carrier research) and Dr. Duane Miller (a chemical engineer at NETL) have invented an oxygen carrier that pairs magnesium oxide with hematite. During a pilot-scale run through NETL’s fluidized bed reactor last year, their carrier showed better performance than carriers that contained just natural hematite.

    What’s next? In the words of Dr. Siriwardane, “this is a big scale-up problem,” and that scale-up can be difficult. The quantities of carriers used at the laboratory scale are small, and techniques for preparing them are easier to control. But, as Dr. Siriwardane explains, “some of the techniques we use for lab-scale preparations are not practical for large-scale preparations, where different techniques and equipment are used. Finding the proper production techniques for our carriers that still deliver the required performance is a big challenge.” However NETL researchers are clearly up to the challenge: when Drs. Siriwardane and Miller applied for the patent for their magnesium-oxide-and-hematite carrier, they had about 100 grams of material, just enough for a lab-scale run. Since then, they have worked with NexTech Materials, a commercial materials vendor, to prepare a 400-pound batch of the carrier for the pilot-scale test.

    In addition to the hematite-based carrier, NETL is also exploring alternative carrier materials, with the goal of optimizing carrier performance and affordability for specific chemical looping applications. A second carrier developed by Drs. Siriwardane and Hanjing Tian (formerly of NETL but now a West Virginia University faculty member) relies on manmade materials instead of natural hematite. Made of copper oxide, iron oxide, and alumina, it too is ready for pilot-scale testing.

    The oxygen carriers that NETL invents to enable CLC could have applications beyond electricity generation. CLC is also useful in industrial steam production, says Dr. Miller, and can be used for the production of hydrogen or syngas from methane. NETL scientists continue research to discover and develop carriers for such real-world applications with the expectation that the energy technologies they enable will one day be very green and very, very affordable.

    See the full article here.

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    DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

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  • richardmitnick 3:41 am on February 18, 2015 Permalink | Reply
    Tags: , Chemistry,   

    From New Scientist: “Half a dozen molecules cause vital acid break-up” 

    NewScientist

    New Scientist

    12 February 2015
    Rachel Ehrenberg

    It sounds like a bad physics joke: how many water molecules does it take to change an acid? At some point the acid breaks apart, giving up a proton to the water. But exactly when enough water is present to cause the break-up has been hard to pin down. New experiments may not only tell us the answer, but also shed light on questions in fields from atmospheric science to biochemistry.

    Precisely how an acid molecule falls apart when surrounded by a handful of water molecules is a long-standing mystery, even though it’s a common and important interaction. “This is fundamental,” says chemist Ken Leopold of the University of Minnesota in Minneapolis. “Proton transfer is ubiquitous; it’s the simplest chemical reaction.”

    Previous work was largely theoretical and probed water-acid mixes only at exceedingly low temperatures. So physicist Vitaly Kresin of the University of Southern California in Los Angeles and colleagues decided to study the less unearthly temperature of 200 kelvin (-73.15 °C).

    The team blasted hot water vapour through a pinhole a mere 75 micrometres wide and added hydrochloric acid to the spray. The spray of water-acid clusters was then passed through an electric field, which deflected the clusters certain distances. Previous work suggested that the distribution of positive and electric charges in the clusters changes when the acid splits apart, and this knowledge, combined with the measured deflections, allowed the team to deduce how many water molecules it took to spur the acid into ditching its proton.

    Communal proton

    The simplest scenario is that just one water molecule in the cluster is the lucky recipient. But the team also did some modelling that hints at quantum effects kicking in once there are half a dozen or so water molecules. In this scenario, the proton is shared, bouncing freely around the cluster. “Protons are very small and mobile, they can bounce all over the place,” says Kresin, “and each water molecule can spin and very easily change shape.”

    There’s a third possibility: perhaps the experiment wasn’t seeing the acid splitting at all. In this scenario, the water molecules in the clusters redistribute their charges, leading to the deflections the team saw. If that’s the case, then more water is needed to make the acid break apart, and some other experiment will have to be devised to see it happening.

    Whatever the case, a better understanding of proton transfer will shed light on biochemical reactions, and on atmospheric processes in which acids and water form aerosols that affect the climate and human health.

    Journal reference: Physical Review Letters, DOI: 10.1103/PhysRevLett.114.043401

    See the full article here.

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  • richardmitnick 5:32 pm on February 13, 2015 Permalink | Reply
    Tags: , , Chemistry, , , ,   

    From SLAC: “Scientists Get First Glimpse of a Chemical Bond Being Born” 


    SLAC Lab

    February 12, 2015

    Scientists have used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to get the first glimpse of the transition state where two atoms begin to form a weak bond on the way to becoming a molecule.

    1
    This illustration shows atoms forming a tentative bond, a moment captured for the first time in experiments with an X-ray laser at SLAC National Accelerator Laboratory. The reactants are a carbon monoxide molecule, left, made of a carbon atom (black) and an oxygen atom (red), and a single atom of oxygen, just to the right of it. They are attached to the surface of a ruthenium catalyst, which holds them close to each other so they can react more easily. When hit with an optical laser pulse, the reactants vibrate and bump into each other, and the carbon atom forms a transitional bond with the lone oxygen, center. The resulting carbon dioxide molecule detaches and floats away, upper right. The Linac Coherent Light Source (LCLS) X-ray laser probed the reaction as it proceeded and allowed the movie to be created. (SLAC National Accelerator Laboratory)

    This fundamental advance, reported Feb. 12 in Science Express and long thought impossible, will have a profound impact on the understanding of how chemical reactions take place and on efforts to design reactions that generate energy, create new products and fertilize crops more efficiently.

    “This is the very core of all chemistry. It’s what we consider a Holy Grail, because it controls chemical reactivity,” said Anders Nilsson, a professor at the SLAC/Stanford SUNCAT Center for Interface Science and Catalysis and at Stockholm University who led the research. “But because so few molecules inhabit this transition state at any given moment, no one thought we’d ever be able to see it.”


    Anders Nilsson, a professor at SLAC and at Stockholm University, explains how scientists used an X-ray laser to watch atoms form a tentative bond, and why that’s important.

    The experiments took place at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. Its brilliant, strobe-like X-ray laser pulses are short enough to illuminate atoms and molecules and fast enough to watch chemical reactions unfold in a way never possible before.

    Researchers used LCLS to study the same reaction that neutralizes carbon monoxide (CO) from car exhaust in a catalytic converter. The reaction takes place on the surface of a catalyst, which grabs CO and oxygen atoms and holds them next to each other so they pair up more easily to form carbon dioxide.

    In the SLAC experiments, researchers attached CO and oxygen atoms to the surface of a ruthenium catalyst and got reactions going with a pulse from an optical laser. The pulse heated the catalyst to 2,000 kelvins – more than 3,000 degrees Fahrenheit – and set the attached chemicals vibrating, greatly increasing the chance that they would knock into each other and connect.

    The team was able to observe this process with X-ray laser pulses from LCLS, which detected changes in the arrangement of the atoms’ electrons – subtle signs of bond formation – that occurred in mere femtoseconds, or quadrillionths of a second.

    “First the oxygen atoms get activated, and a little later the carbon monoxide gets activated,” Nilsson said. “They start to vibrate, move around a little bit. Then, after about a trillionth of a second, they start to collide and form these transition states.”

    ‘Rolling Marbles Uphill’

    The researchers were surprised to see so many of the reactants enter the transition state – and equally surprised to discover that only a small fraction of them go on to form stable carbon dioxide. The rest break apart again.

    “It’s as if you are rolling marbles up a hill, and most of the marbles that make it to the top roll back down again,” Nilsson said. “What we are seeing is that many attempts are made, but very few reactions continue to the final product. We have a lot to do to understand in detail what we have seen here.”

    Theory played a key role in the experiments, allowing the team to predict what would happen and get a good idea of what to look for. “This is a super-interesting avenue for theoretical chemists. It’s going to open up a completely new field,” said report co-author Frank Abild-Pedersen of SLAC and SUNCAT.

    A team led by Associate Professor Henrik Öström at Stockholm University did initial studies of how to trigger the reactions with the optical laser. Theoretical spectra were computed under the leadership of Stockholm Professor Lars G.M. Pettersson, a longtime collaborator with Nilsson.

    Preliminary experiments at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), another DOE Office of Science User Facility, also proved crucial. Led by SSRL’s Hirohito Ogasawara and SUNCAT’s Jerry LaRue, they measured the characteristics of the chemical reactants with an intense X-ray beam so researchers would be sure to identify everything correctly at the LCLS, where beam time is much more scarce. “Without SSRL this would not have worked,” Nilsson said.

    The team is already starting to measure transition states in other catalytic reactions that generate chemicals important to industry.

    “This is extremely important, as it provides insight into the scientific basis for rules that allow us to design new catalysts,” said SUNCAT Director and co-author Jens Nørskov.

    Researchers from LCLS, Helmholtz-Zentrum Berlin for Materials and Energy, University of Hamburg, Center for Free Electron Laser Science, University of Potsdam, Fritz-Haber Institute of the Max Planck Society, DESY and University of Liverpool also contributed to the research. The research was funded by the DOE Office of Science, the Swedish National Research Council, the Knut and Alice Wallenberg Foundation, the Volkswagen Foundation and the German Research Foundation (DFG) Center for Ultrafast Imaging.

    See the full article here.

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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 2:25 pm on February 12, 2015 Permalink | Reply
    Tags: , , Chemistry,   

    From APS: “Viewpoint: Making Waves with DNA” 

    AmericanPhysicalSociety

    American Physical Society

    February 9, 2015
    Irving R. Epstein

    Strands of DNA can be used to generate waves of chemical reactions with programmable shape and velocity.

    1
    Figure 1 Schematic view of the system studied by Zadorin et al. A single-stranded DNA (A) binds to one of the two complementary ends of the DNA template T. The resulting A:T complex uses the polymerase enzyme (pol) to generate another molecule of A on the template. A second enzyme (nick) facilitates the splitting of the two A molecules and their detachment from T. The net result is an “autocatalytic” reaction in which A catalyzes its own production: A+T+monomers→2A+T. By varying the concentration of DNA strands and enzymes, the authors were able to generate waves of chemical reactions with controllable shape and velocity.

    Research in chemistry can be roughly divided into two categories: analysis—the measurement of existing objects and phenomena—and synthesis—the construction of those objects and phenomena from simpler pieces. Typically, synthesis lags behind analysis: one first determines the formula of a molecule (and often its structure) before attempting to make it. However, as chemistry advances, investigators are increasingly attempting to synthesize first, designing chemical systems that realize desired phenomena. A team led by André Estevez-Torres at CNRS in France and co-workers has demonstrated an experimental toolkit that could be used for the rational engineering of nonlinear chemical effects in solution. Using DNA strands moving in a narrow channel and reacting under the action of enzymes, the authors are able to create chemical waves whose shapes and velocity can be finely controlled. Their setup could be programmed to yield a broad spectrum of other nonlinear phenomena in systems governed by a combination of chemical reactivity and molecular diffusion (“reaction-diffusion” systems).

    Nonlinear chemical dynamics characterizes many natural and industrial processes and is a quintessential feature of living organisms: most of their chemistry occurs far from equilibrium, has a nonlinear dependence on parameters like molecular concentrations, and may exhibit temporal oscillations (many biological functions are, for instance, synchronized to a 24-hour cycle). Researchers have applied a number of algorithms to design systems featuring such nonlinear behavior, engineering chemical oscillators (reactions in which the concentration of one or more components exhibits periodic changes), propagating reaction fronts or “Turing patterns” —spatial patterns of concentrations that, as Alan Turing proposed, might be related to biological morphogenesis (e.g., the formation of leopard spots or zebra stripes).

    But design algorithms are severely limited by the realities imposed by nature. One may write down a set of equations that generates a desired phenomenon, e.g., spatiotemporal chaos, for a set of reaction rates and diffusion coefficients. There is, however, no guarantee that an actual collection of molecules can be found that realizes the theorized behavior. For example, over the past several decades, researchers have successfully engineered, through systematic studies, new chemical oscillators with desired parameters for a variety of applications. These efforts have resulted in the discovery of several oscillators, but none of these oscillators “by design” has attained the importance of the Belousov-Zhabotinsky (BZ) reactions, a family of oscillating reactions (discovered serendipitously) that remains the most versatile and reliable chemical oscillator for most applications.

    Most efforts to design reaction-diffusion phenomena have utilized small inorganic molecules, largely because these substances are cheap, easy to work with, and produce visible color changes when they undergo reduction and oxidation (redox) reactions. Unfortunately, these reaction mixtures are typically not biocompatible, and they cannot be used in applications that place them in contact with components of living systems like proteins. The BZ reaction, for example, only works at acidity levels lethal to most biological cells.

    A solution may be offered by oligonucleotides (short single strands of DNA or RNA), which have been utilized as versatile building blocks for oscillators, computational elements, and structures with arbitrary shapes. In their new work, Estevez-Torres et al. have focused on dynamical aspects: They demonstrated that DNA strands can be used to realize an experimental model for reaction-diffusion systems whose spatiotemporal dynamics is fully controllable by programming three key elements of the system: the reaction rates, the diffusion coefficients, and the topology of the chemical reaction network (i.e., which reactions are linked to each other in ways that generate positive or negative feedback).

    Figure 1 shows a schematic of the authors’ setup: a linear channel in which they are able to generate traveling waves of chemical concentrations whose velocity can be precisely controlled. A single strand of DNA (A) can attach to either half of a complementary strand (T) to form a complex (A:T). In the presence of an enzyme (pol), the A:T complex serves as a template for growth of an additional A strand from monomeric precursors in the solution. A second “nicking” enzyme (nick) causes the two A molecules to detach from the T strand. The net result is an “autocatalytic” reaction in which A acts as a catalyst of its own production: A+T+monomers→2A+T

    It is known that autocatalytic reactions can generate chemical waves that travel with a characteristic velocity (ν) depending on the effective rate constant (k) for the reaction and the diffusion coefficient (D) of the autocatalyst (A in this case): ν=(kD)1/2. This idea has been exploited to generate a family of propagating acidity fronts in inorganic reactions, where the hydrogen ion (H+) was the autocatalyst. It was not possible, however, to control the velocity of those fronts, because the reaction rate depends on diffusion and the diffusion coefficient of H+ in water is fixed. Here, the authors are instead able to tune the effective rate constant k by varying the concentration of either the template or the enzyme. They can also control D, the effective diffusion rate of A (which depends on the diffusion rate of A relative to the A:T complex). By binding a heavy but chemically inert group C to T, they can reduce its diffusion rate and that of the complex without affecting its affinity to A. In other words, by choosing the concentrations of T, C, and pol, they can act on the two independent “control knobs” of the diffusion coefficient and the reaction rate constant. In this way, they can generate reaction waves with velocities that vary by as much as 3 orders of magnitude.

    What is exciting about this approach is that it is not limited to the generation of chemical waves. The scheme could be extended to generate any desired reaction-diffusion phenomenon for which one can write a set of elementary reactions. Turing patterns, for example, could be produced, as suggested by a previous study, by picking a slightly different reaction network, including an activator (like A in this case) but also an inhibitor that diffuses 1 order of magnitude faster than A. The “toolbox” employed by Estevez-Torres’ team, in which the activator species (A) can be slowed down by the massive inert group (C), already contains all elements needed to achieve the necessary range for diffusion coefficients.

    Approaches like the one explored by the authors, building on eons of evolution in the ability to control nucleic acids, suggest a bright future for this research line. The fact that DNA-based reactions are inherently biocompatible makes them attractive for potential applications, in particular if the system can be coupled to mechanical forces, as has been done for the BZ reaction. For example, one could envision inserting an anticancer drug into a DNA shell designed to undergo a mechanical deformation and release the drug when it encounters a molecule with a characteristic shape on the tumor surface.

    This research is published in Physical Review Letters.

    See the full article here.

    For those who are interested, the original article has a complete list of references and a numeric key for those references.

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    American Physical Society
    Physicists are drowning in a flood of research papers in their own fields and coping with an even larger deluge in other areas of physics. How can an active researcher stay informed about the most important developments in physics? Physics highlights a selection of papers from the Physical Review journals. In consultation with expert scientists, the editors choose these papers for their importance and/or intrinsic interest. To highlight these papers, Physics features three kinds of articles: Viewpoints are commentaries written by active researchers, who are asked to explain the results to physicists in other subfields. Focus stories are written by professional science writers in a journalistic style and are intended to be accessible to students and non-experts. Synopses are brief editor-written summaries.

     
  • richardmitnick 8:12 am on February 3, 2015 Permalink | Reply
    Tags: , Chemistry, ,   

    From PNNL: “Duets by Molecules and Plasmons” 


    PNNL Lab

    January 2015

    Scientists examine the information content in nanoscale chemical images

    Physical Sciences Division
    Research Highlights

    January 2015

    1
    Frequency resolved TERS images of the laser-irradiated region, reconstructed using four different Raman-allowed vibrations of DMS. The representative images are obtained from the same pass of the AFM probe through the laser-illuminated region of the substrate. Namely, this is the same image, reconstructed at four different energies. The 2D contours have a color bar starting at white (brightest signals), passing through yellow to black (lowest signals). Copyright 2014: American Chemical Society. Enlarge/expand Image.

    Results: Light waves trapped on a metal’s surface can interrogate the nearby molecules about their chemical identity through the molecule’s characteristic vibrations, which act as fingerprints. Scientists at Pacific Northwest National Laboratory (PNNL) “saw” the interaction between the molecules and the trapped light waves or surface plasmons. Their fundamental endeavor could lead to breakthroughs in interpreting ultrasensitive chemical images for characterizing new materials with potential uses in catalysis and energy conversion.

    The article is featured in the American Chemical Society (ACS) Editors’ Choice collection. The decision was made by the journal editors, who select one article a day from across the 55 ACS journals to appear in this special collection. As such, it was made freely available to the public. The article was the editors’ choice for November 12, 2014.

    Why It Matters: To detect only a few molecules, researchers using ultrasensitive spectroscopic and microscopic techniques rely on localized surface plasmons. This is particularly the case when the molecular identity must be determined. These plasmons are essentially light waves trapped at the surface of nanoscale noble metal structures. In surface plasmon-enhanced vibrational spectroscopy, the recorded optical signals result from the interaction between molecular and plasmonic states. This was revealed by PNNL scientists, who set out to understand the information content encoded in nanoscale chemical images, recorded by taking advantage of the unique properties of localized surface plasmons. They found that each pixel in their recorded images reports on the distinct local environments in which each probed molecule resides.

    “This is really fundamental science that takes us a step closer to understanding what one actually measures with this type of spectroscopy,” said Dr. Patrick El-Khoury, a PNNL chemical physicist who carried out the measurements.

    User Facility: EMSL

    Research Team: Patrick Z. El-Khoury, Dehong Hu, and Wayne P. Hess, Pacific Northwest National Laboratory; Tyler W. Ueltschi and Amanda L. Mifflin, University of Puget Sound

    See the full article here.

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    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 8:02 am on January 27, 2015 Permalink | Reply
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    From AAAS: “How Earth’s earliest life overcame a genetic paradox” 

    AAAS

    AAAS

    26 January 2015
    Tim Wogan

    1
    The unique temperature conditions of hydrothermal vents like this one could have favored the evolution of complex life.

    On ancient Earth, the earliest life encountered a paradox. Chains of RNA—the ancestor of DNA—were floating around, haphazardly duplicating themselves. Scientists know that eventually, these RNA chains must have become longer and longer, setting the stage for the evolution of complex life forms like amoebas, worms, and eventually humans. But under all current models, shorter RNA molecules, having less material to copy, would have reproduced faster, favoring the evolution of primitive organisms over complex ones. Now, new research offers a potential solution: Longer RNA chains could have hidden out in porous rocks near volcanic sites such as hydrothermal ocean vents, where unique temperature conditions might have helped complex organisms evolve.

    Hydrothermal vents are fissures in Earth’s crust that pump out superheated water. They would have been common on early Earth, which was more tectonically active than the planet is today, says Dieter Braun, an experimental biophysicist at Ludwig Maximilian University in Munich, Germany. The water in hydrothermal vents is particularly rich in nutrients, making them promising sites for the origin of life.

    To figure out if hydrothermal vents could have given the evolution of complex life a boost, Braun and his colleagues examined the physics of a theoretical single pore in the rock surrounding a vent. The pore is open at the top and at the bottom and filled with a dilute solution of RNA molecules of various lengths. The solution on the hot side—the one closer to the stream of superheated water—would become less dense and rise up through the pore. Some of it would escape at the top, to be replenished by more nutrient-rich fluid entering at the bottom. The remainder would diffuse across to the cold side of the pore and drop back down. A complex physical effect called thermophoresis causes charged molecules in a solution to accumulate in colder water, and the longer chains, having more charge, would do this more often than shorter chains. Therefore, the shorter RNA chains would be more likely to escape out of the top of the pore, whereas the longer ones would stay trapped inside where, continually fed by nutrients, they could reproduce. Better still, Braun says, the continuous temperature cycling could actually help split the RNA double helix apart, making it easier for it to reproduce.

    To test this elaborate hypothesis, Braun and his colleagues constructed a simulated piece of porous rock from a network of tiny glass capillary tubes heated on one side. They allowed dissolved fragments of DNA to be washed into the tubes from the bottom. Ideally, they would have used RNA, but Braun explains that there’s no good way to reproduce RNA in a lab, whereas it’s easy to reproduce DNA with a standard laboratory process called PCR. “All the thermophoresis and the characteristics of the trapping mechanism are the same for DNA and RNA,” he says. Once they let the experiment run, the researchers found that longer chains of DNA were more likely to accumulate inside the tubes than shorter chains were. As a result, the longer strands reproduced much better inside the pores and their populations grew, whereas the shorter strands were diluted so much that they went extinct, the team reports online today in Nature Chemistry.

    It’s “nice chemistry,” says marine chemist Jeffrey Bada of the University of California (UC), San Diego, but he is not convinced that hydrothermal vents, or any other likely habitat on early Earth, could have provided the conditions created in the lab: “The processes outlined are not likely to take place on a significant scale on the Earth or elsewhere.” Biochemist Irene Chen of UC Santa Barbara disagrees and even thinks the research opens a door to studying environments beyond just volcanic ones. She suggests rock pores hotter on one side than the other could result from solar, as well as hydrothermal, heating, expanding the types of environments that could have favored the evolution of complex life. A physical environment that could plausibly have existed on the early Earth “actually selects for longer RNA sequences,” she says. “The extra length is basically room for biological creativity.”

    See the full article here.

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  • richardmitnick 12:59 pm on January 18, 2015 Permalink | Reply
    Tags: , , Chemistry, Institut d'Astrophysique Spatiale   

    From Institut d’Astrophysique Spatiale: “Detection of sugars in a laboratory simulation of interstellar and pre-cometary organic matter produced from the photo/thermos chemistry of ices” 

    Institut d'Astrophysique Spatiale bloc

    Institut d’Astrophysique Spatiale

    13/01/2015
    No Writer Credit

    Ten aldehydes, including two sugars potentially important for prebiotic chemistry, have for the first time been identified in organic residues issued from photochemistry of interstellar ice analogues, produced in the laboratory by the IAS MICMOC/SUGARS experiment.

    The MICMOC experiment (Matière Interstellaire et Cométaire: Molécules Organiques Complexes) has a variant (Chiral-MICMOC on the SOLEIL synchrotron) which investigates the spatial conformation (left, L, or right D) of the amino acids produced under the photochemical action of ultraviolet circularly polarized light. The aim of this experiment is to propose an astrophysical scenario for the origin of homochirality observed in biological molecules on the Earth. The MICMOC/SUGARS experiment is another variant of the initial set-up. This fully interdisciplinary approach assembles astrophysicists, molecular physicists, and chemists. It mixes an experimental approach including a strong astrophysical background with the simulation of the evolution of interstellar ice analogues in the laboratory and sophisticated analytical chemistry methods for the detection of molecules of prebiotic interest.

    The detection of numerous amino acids in the organic residues produced by the photo/thermo-chemistry of ices has been reported, in part thanks to our collaboration between IAS (Orsay) and INC (Nice). The overall quality of the samples produced by the IAS team « Astrochimie et Origines » has been attested by the use of 13C atoms markers in the original ice samples to avoid any confusion with possible contamination of the samples during manipulation.

    Recently, a change in the analytical procedure has allowed the detection of a new family of molecules: the aldehydes. Among them are the two sugars glycolaldehyde and glyceraldehyde, potentially important for prebiotic chemistry. According to a recent study, these molecules may be considered as possible precursors of ribonucleotides (constituents of RNA), in the same manner that amino acids (which are detected within the same experimental protocol) are key molecules for the early formation of proteins. The detection of these molecules in our samples strengthens the scenario of an exogenous delivery of organic molecules essential for starting prebiotic chemistry at the surface of the early Earth.

    Finally, if glycolaldehyde is indeed detected in the interstellar medium, that is not the case yet for glyceraldehyde, which can be seen now as a potential target for large modern radioastronomy instruments such as ALMA. Glyceraldehyde could also be proposed for detection in primitive carbonaceous meteorites.

    Research paper: P. de Marcellus et al. (2015). Aldehydes and sugars from evolved precometary ice analogues: Importance of ices in astrochemical and prebiotic evolution.
    PNAS. DOI : 10.1073/pnas.1418602112 10.1073/pnas.1418602112

    2

    Left: UV source for astrochemistry experiments at IAS (picture : P. de Marcellus). Right: the “Pillars of Creation” (in the Eagle nebula) seen by the Hubble Space Telescope (HST, NASA).

    See the full article here.

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    The Institut d’Astrophysique Spatiale (IAS) is a laboratory of the National Center of Scientific Research (CNRS) and of the University of Paris-Sud 11. in addition to having the status of Observatory.The IAS comprises 140 scientists, engineers, technicians, administrators and graduate students.

     
  • richardmitnick 4:13 pm on January 14, 2015 Permalink | Reply
    Tags: , , Chemistry, U Wisconsin   

    From U Wisconsin: “Chemical dial controls attraction between water-repelling molecules” 

    U Wisconsin

    University of Wisconsin

    Jan. 14, 2015
    Chris Barncard

    Fear of water may seem like an irrational hindrance to humans, but on a molecular level, it lends order to the world.

    Some substances — lots of greasy, oily ones in particular — are hydrophobic. They have no attraction to water, and essentially appear repelled by the stuff.

    s
    Sam Gellman

    Combine hydrophobic pieces in a molecule with parts that are instead attracted to water, and sides are taken. Structure appears, as in the membranes that encircle living cells.

    “Those membranes are formed by molecules that are mostly greasy, and that pack together to avoid interacting with water,” says Sam Gellman, a University of Wisconsin–Madison chemistry professor. “The hydrophilic parts point in one direction — toward water — and the hydrophobic parts in the other, and the result is molecular organization that forms a wall.”

    And with it, all the things of life that require the wall’s protection.

    “It’s arguably one of the most important interactions between molecules, because it occurs in water where biology and so much technology happens,” says Nicholas Abbott, a UW–Madison chemical and biological engineering professor.

    Abbott, Gellman and a group of University of Wisconsin–Madison researchers have provided new insights on hydrophobic interactions within complex systems. In a study published today in the journal Nature, the researchers show how the nearby presence of polar (water-attracted, or hydrophilic) substances can change the way the nonpolar hydrophobic groups want to stick to each other.

    The team built simple molecules with stable structures that incorporated hydrophobic and hydrophilic groups in precisely determined patterns. Then they used an atomic force microscope, a tool that allowed them to probe the surface of the molecules by tugging hydrophobic units apart and measuring the stickiness between them.

    n
    Nicholas Abbott

    “We show that if you have two nonpolar groups, and they are going to interact through water, the way they interact depends on their neighbors,” Abbott says. “It’s just like a pair of friends having a conversation. The way in which they interact will depend on who is standing close enough to hear.”

    It’s been theorized that the bonds between hydrophobic particles would indeed change in the presence of charged, water-loving molecules. The researchers’ experiments demonstrated those effects, and noticed also that as the chemical structure of charged hydrophilic groups change, so does the magnitude of their impact on the stickiness between hydrophobic groups.

    “That sticky interaction is defined by the hydrophobic effect,” Gellman says. “And our measurements show that it’s possible to place polar groups in a way that can dial up or dial down the adhesion between two hydrophobic surfaces in water.”

    This level of control could offer a new way to design all sorts of molecules that perform useful functions in water, such as ointments based on emulsions, food products, detergents and more.

    “You can imagine new designs of switchable materials, smart materials, and maybe drug delivery systems that can release an active agent in a controlled manner by manipulating this interaction,” Abbott says.

    The collaborators’ work, which was supported by the National Science Foundation and sparked by a partnership made possible through UW–Madison’s Nanoscale Science and Engineering Center, may also sharpen the way biologists view changes in proteins.

    Proteins that catalyze reactions and pass information at the molecular level in living cells are often very complex combinations of hydrophobic and hydrophilic groups. The qualities of their component parts that attract or repel water play a role in the way proteins fold up, which then determines whether and how they perform their intended tasks.

    After proteins are synthesized and fold up in their proper shapes, biological processes begin to modify their structure — adding here or replacing there.

    “Another implication of our research,” Gellman says, “is that those changes can have profound effects that have not previously been understood.”

    See the full article here.

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    In achievement and prestige, the University of Wisconsin–Madison has long been recognized as one of America’s great universities. A public, land-grant institution, UW–Madison offers a complete spectrum of liberal arts studies, professional programs and student activities. Spanning 936 acres along the southern shore of Lake Mendota, the campus is located in the city of Madison.

     
  • richardmitnick 1:05 pm on December 30, 2014 Permalink | Reply
    Tags: , Chemistry, , ,   

    From phys.org: “Gummy bears under antiparticle fire” 

    physdotorg
    phys.org

    This article has the distinction of having been recommended by Dr. Don Lincoln, physicist extraordinaire at FNAL

    Dec 29, 2014
    Technical University Munich

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    Gummy bear on the experimental set-up. Credit: Wenzel Schürmann / TUM

    Gelatin is used in the pharmaceutical industry to encapsulate active agents. It protects against oxidation and overly quick release. Tiny pores in the material have a significant influence on this, yet they are difficult to investigate. In experiments on gummy bears, researchers at Technische Universität München (TUM) have now transferred a methodology to determine the free volume of gelatin preparations.

    o
    Redox example
    Sodium and fluorine bonding ionically to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions are then attracted to each other. The sodium is oxidized, and the fluorine is reduced.

    Custom-tailored gelatin preparations are widely used in the pharmaceutical industry. Medications that do not taste good can be packed into gelatin capsules, making them easier to swallow. Gelatin also protects sensitive active agents from oxidation. Often the goal is to release the medication gradually. In these cases slowly dissolving gelatin is used.

    Nanopores in the material play a significant role in all of these applications. “The larger the free volume, the easier it is for oxygen to penetrate it and harm the medication, but also the less brittle the gelatin,” says PD Dr. Christoph Hugenschmidt, a physicist at TU München.

    However, characterizing the size and distribution of these free spaces in the unordered biopolymer is difficult. A methodology adapted by the Garching physicists Christoph Hugenschmidt and Hubert Ceeh provides relief. “Using positrons as highly mobile probes, the volume of the nanopores can be determined, especially also in unordered systems like netted gelatins,” says Christoph Hugenschmidt.

    Positrons are the antiparticles corresponding to electrons. They can be produced in the laboratory in small quantities, as in this experiment, or in large volumes at the Heinz Maier Leibnitz Research Neutron Source (FRM II) of the TU München. If a positron encounters an electron they briefly form an exotic particle, the so-called positronium. Shortly after it annihilates to a flash of light.

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    Gummy bears under antiparticle fire
    The experimental set-up with a fixated gummy bear. Credit: Wenzel Schürmann / TUM

    To model gelatin capsules that slowly dissolve in the stomach, the scientists bombarded red gummy bears in various drying stages with positrons. Their measurements showed, that in dry gummy bears the positroniums survive only 1.2 nanoseconds on average while in soaked gummy bears it takes 1.9 nanoseconds before they are annihilated. From the lifetime of the positroniums the scientists can deduce the number and size of nanopores in the material.

    g2
    Gummy bears under antiparticle fire
    The experimental set-up with a fixated gummy bear. Credit: Wenzel Schürmann / TUM

    See the full article here.

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    About Phys.org in 100 Words

    Phys.org™ (formerly Physorg.com) is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004, Phys.org’s readership has grown steadily to include 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

     
  • richardmitnick 6:43 pm on December 29, 2014 Permalink | Reply
    Tags: , Chemistry, ,   

    From Brookhaven Lab: “Microscopy Reveals how Atom-High Steps Impede Oxidation of Metal Surfaces” 

    Brookhaven Lab

    December 29, 2014
    Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174

    Rust never sleeps. Whether a reference to the 1979 Neil Young album or a product designed to protect metal surfaces, the phrase invokes the idea that corrosion from oxidation.—the more general chemical name for rust and other reactions of metal with oxygen—is an inevitable, persistent process. But a new study performed at the Center for Functional Nanomaterials (CFN) at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory reveals that certain features of metal surfaces can stop the process of oxidation in its tracks.

    n
    Low-energy electron microscopy images of the nickel-aluminum surface before and after oxidation. The faint lines before oxidation indicate the atom-high steps that separate flat terrace sections of the crystal surface. As oxidation begins at a point on one terrace, the oxide spreads in elongated stripes along that terrace, pushing steps out of the way and bunching them closer and closer together. Eventually the bunching of steps stops the growth of the oxide stripe and another begins to form, often at right angles, to produce a grid-like pattern.

    “As the oxide stripes grow … one ends up with these patterns of blocks and lines that are reminiscent of the grid-based paintings by Mondrian.”
    — Peter Sutter

    The findings, published in the Proceedings of the National Academy of Sciences, could be relevant to understanding and perhaps controlling oxidation in a wide range of materials—from catalysts to the superalloys used in jet engine turbines and the oxides in microelectronics.

    The experiments were performed by a team led by Guangwen Zhou of Binghamton University, in collaboration with Peter Sutter of the CFN, a DOE Office of Science User Facility. The team used a low-energy electron microscope (LEEM) to capture changes in the surface structure of a nickel-aluminum alloy as “stripes” of metal oxide formed and grew under a range of elevated temperatures.

    “These microscopes are not that frequently found in ordinary research labs; there are only a handful around the U.S.,” Sutter said. “We have a pretty lively ‘user community’ of scientists who come to the CFN just to use this type of instrument.”

    p
    Peter Sutter with one of the low-energy electron microscopes at Brookhaven Lab’s Center for Functional Nanomaterials.

    The metal Zhou wanted to study, nickel-aluminum, has a characteristic common to all crystal surfaces: a stepped structure composed of a series of flat terraces at different heights. The steps between terraces are only one atom high, but they can have a significant effect on material properties. Being able to see the steps and how they change is essential to understanding how the surface will behave in different environments, in this case in response to oxygen, Sutter said.

    Said Zhou, “The acquisition of this kind of knowledge is essential for gaining control over the response of a metal surface to the environment.”

    Scientists have known for a while that the atoms at the edges of atomic steps are especially reactive. “They are not as completely surrounded as the atoms that are part of the flat terraces, so they are more free to interact with the environment,” Sutter said. “That plays a role in the material’s surface chemistry.”

    The new study showed that the aluminum atoms involved in forming aluminum oxide stripes came exclusively from the steps, not the terraces. But the LEEM images revealed even more: The growing oxide stripes could not “climb” up or down the steps, but were confined to the flat terraces. To continue to grow, they had to push the steps away as oxygen continued to grab aluminum atoms from the edges. This forced the steps to bunch closer and closer together, eventually slowing the rate of oxide stripe growth, and then completely stopping it.

    “For the first time we show that atomic steps can slow surface oxidation at the earliest stages,” Zhou said.
    Guangwen Zhou

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    Guangwen Zhou at Binghamton University’s Analytical and Diagnostics Laboratory. Photo credit: Jonathan Cohen, Binghamton University

    However, as one stripe stops growing, another begins to form. “As the oxide stripes grow along the two possible directions on the crystal, which are at right angles to one another, one ends up with these patterns of blocks and lines that are reminiscent of the grid-based paintings by Mondrian,” Sutter said. “They are quite beautiful…” and persistent after all.

    In fact, scientists who’ve studied a different “cut,” or facet, of the crystalline nickel-aluminum alloy have observed that steps on that surface had no effect on oxide growth. In addition, on that surface, aluminum atoms throughout the bulk of the crystal could participate in the formation of aluminum oxide, and the oxide stripes could overrun the steps, Zhou said.

    Still the details and differences of the two types of surfaces could offer new ways scientists might attempt to control oxidation depending on their purpose.

    “Oxides are not all bad,” Sutter said. “They form as a protective layer against corrosion attack. They play important roles in chemistry, for example in catalysis. Silicon oxide is the insulating material on microelectronic circuits, where it plays a central role in directing the flow of current.”

    Knowing which kind of surface a material has and its effects on oxidation—or how to engineer surfaces with desired properties—might improve the design of these and other materials.

    This work was supported by the DOE Office of Science.

    sic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

    See the full article here.

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    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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