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  • richardmitnick 4:51 am on July 1, 2014 Permalink | Reply
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    From Berkeley Lab: “News Center Up in Flames: Evidence Confirms Combustion Theory” 

    Berkeley Logo

    Berkeley Lab

    June 30, 2014
    Kate Greene

    Berkeley Lab and University of Hawaii research outlines the story of soot, with implications for cleaner-burning fuels.

    Researchers at the Department of Energy’s Lawrence Berkeley National Lab (Berkeley Lab) and the University of Hawaii have uncovered the first step in the process that transforms gas-phase molecules into solid particles like soot and other carbon-based compounds.

    The finding could help combustion chemists make more-efficient, less-polluting fuels and help materials scientists fine-tune their carbon nanotubes and graphene sheets for faster, smaller electronics. In addition, the results could have implications for the burgeoning field of astrochemistry, potentially establishing the chemical process for how gaseous outflows from stars turn into carbon-based matter in space.

    flame
    Graphical representation of the chemistry in the early stages of soot formation. The mechanism to the right was demonstrated by experiment, while the one on the left was not. Credit: Dorian Parker, University of Hawaii

    “When you burn a flame, you start with a gas-phase reactant and then analyze the products, which include soot,” says Musahid Ahmed, scientist in the Chemical Sciences Division at Berkeley Lab. “But there is no direct evidence for the chemical bonds that break and form in the process.” For more than 30 years, scientists have developed computational models of combustion to explain how gas molecules form soot, but now Ahmed and his colleagues have data to confirm one long-standing theory in particular. “Our paper presents the first direct observation of this process,” he says.

    While the research is relevant to a number of disciplines—combustion science, materials science, and astrochemistry—it’s combustion science that could see the most direct impact the soonest, says Ahmed. Specifically, the fundamental chemistry discovery could be used to find or design fuels that burn cleaner and don’t produce as much soot.

    Think about your car engine. If the combustion process were perfect, only carbon dioxide and water would come out of the tailpipe. Instead, we see fumes and particulates like soot, a visible macromolecule made up of sheets of carbon.

    Theoretically, there are hundreds of different ways molecules can combine to create these dirty emissions. But there has been one popular class of mechanisms that outlines possible early steps for bond making and bond breaking during combustion. Called hydrogen abstraction-acetylene addition, or HACA, it was developed by Michael Frenklach professor of mechanical engineering at the University of California Berkeley in 1991.

    One version of HACA works like this: during the high-temperature, high-pressure environment of combustion, a simple ring of six carbon and six hydrogen atoms, called benzene, would lose one of its hydrogen atoms, allowing another two-carbon molecule called acetylene, to attach to the ring, giving it a kind of tail. Then the acetylene tail would lose one of its hydrogen atoms so another acetylene could link up in, doubling the carbon atoms in the tail to four.

    Next, the tail would curl around and attach to the original ring, creating a double-ring structure called naphthalene. Link by link, ring by ring, these molecules would continue to grow in an unwieldy, crumpled way until they became the macromolecules that we recognize as soot.

    To test the first step of the theoretical HACA mechanism, Ahmed and collaborators from the University of Hawaii used a beamline at the Advanced Light Source (ALS) at Berkeley Lab specifically outfitted to study chemical dynamics. The ALS, a DOE Office of Science user facility, produces numerous photons over a wide range of energies, allowing researchers to probe a variety of molecules produced in this chemical reaction with specialized mass spectrometry analysis.

    two
    Musa Ahmed and Tyler Troy at the Advanced Light Source (ALS) Beamline 9.0.2 where the chemical dynamics experiments on combustion take place. Credit: Roy Kaltschmidt

    Unique to this experimental setup, Ahmed’s team used a so-called hot nozzle, which recreates combustion environment in terms of pressure and temperature. The group started with a gaseous mix of nitrosobenzene (a benzene ring with a molecule of nitrogen and oxygen attached) and acetylene, and pumped it through a heated tube at a pressure of about 300 torr and a temperature of about 750 degrees Celsius. The molecules that came out the other end were immediately skimmed into a mass spectrometer that made use of the synchrotron light for analysis.

    The researchers found two molecules predominantly emerged from the process. The more abundant kind was the carbon ring with a short acetylene tail on it, called phenylacetylene. But they also saw evidence for the double ring, naphthalene. These results, says Ahmed, effectively rule out one HACA mechanism—that a carbon ring would gain two separate tails and those tails would bond to form the double ring—and confirm the most popular HACA mechanism where a long tail curls around to form naphthalene.

    Ahmed’s local team included Tyler Troy, postdoctoral fellow at Berkeley Lab, and this work was performed with long-term collaborator Ralf Kaiser, professor of physical chemistry at the University of Hawaii at Manoa, and Dorian Parker, postdoctoral fellow also at Hawaii. The research was published June 20 online in the journal Angewandte Chemie.

    “Having established the route to naphthalene, the simplest polycyclic aromatic hydrocarbon, the next step will be to unravel the pathways to more complex systems,” says Kaiser.

    Further experiments will investigate these follow-up mechanisms. It’s a tricky feat, explains Ahmed, because the molecular possibilities quickly multiply. The researchers will add infrared spectroscopy to their analysis in order to catch the variety of molecules that form during these next phases of combustion.

    This research was funded by the DOE Office of Science and the National Science Foundation.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 9:10 am on June 9, 2014 Permalink | Reply
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    From D.O.E Pulse: “Nanoscope to probe chemistry on the molecular scale” 

    pulse

    D.O.E. Pulse

    June 9, 2014
    Kate Greene, 510.486.4404, kgreene@lbl.gov

    For years, scientists have had an itch they couldn’t scratch. Even with the best microscopes and spectrometers, it’s been difficult to study and identify molecules at the so-called mesoscale, a region of matter that ranges from 10 to 1000 nanometers in size. Now, with the help of broadband infrared light from the Advanced Light Source (ALS) synchrotron at DOE’s Lawrence Berkeley National Laboratory (Berkeley Lab), researchers have developed a broadband imaging technique that looks inside this realm with unprecedented sensitivity and range.

    sheet

    This peptoid nanosheet, produced by Gloria Olivier and Ron Zuckerman at Berkeley Lab, is less than 8 nanometers thick at points. SINS makes it possible to acquire spectroscopic images of these ultra-thin nanosheets for the first time.

    By combining atomic force microscopy with infrared synchrotron light, researchers from Berkeley Lab and the University of Colorado have improved the spatial resolution of infrared spectroscopy by orders of magnitude, while simultaneously covering its full spectroscopic range, enabling the investigation of variety of nanoscale, mesoscale, and surface phenomena that were previously difficult to study.

    The new technique, called Synchrotron Infrared Nano-Spectroscopy or SINS, will enable in-depth study of complex molecular systems, including liquid batteries, living cells, novel electronic materials and stardust.

    “The big thing is that we’re getting full broadband infrared spectroscopy at 100 to 1000 times smaller scale,” says Hans Bechtel, principal scientific engineering associate at Berkeley Lab. “This is not an incremental achievement. It’s really revolutionary.”

    In a Proceedings of the National Academy of Sciences paper published May 6 online, titled Ultra-broadband infrared nano-spectroscopic imaging, Berkeley Lab’s Bechtel and Michael Martin, a Berkeley Lab staff scientist, and colleagues from Markus Raschke’s group at the University of Colorado at Boulder describe SINS. They demonstrate the nanoscope’s ability to capture broadband spectroscopic data over a variety of samples, including a semiconductor-insulator system, a mollusk shell, proteins, and a peptoid nanosheet. Martin says these demonstrations just “scratch the surface” of the potential of the new technique.

    Synchronizing Scopes

    SINS combines two pre-existing infrared technologies: a newer technique called infrared scattering-scanning near-field optical microscopy (IR s-SNOM) and an old laboratory standby, known even to college chemistry students, called Fourier Transform Infrared Spectroscopy (FTIR). A clever melding of these two tools, combined with the intense infrared light of the synchrotron at Berkeley Lab gives the researchers the ability to identify clusters of molecules sized as small as 20 to 40 nanometers.

    Experimental setup for SINS that includes the synchrotron light source, an atomic force microscope, a rapid-scan Fourier transform infrared spectrometer, a beamsplitter, mirrors and a detector.

    The new approach overcomes long-standing barriers with pre-existing microscopy techniques that often involve demanding technical and sample preparation requirements. Infrared spectroscopy uses low-energy light, is minimally invasive, and is applicable under ambient conditions, making it an excellent tool for chemical and molecular identifications in systems that are static as well as those that are living and dynamic. The technique works by shining low-energy infrared light onto a molecular sample. Molecules can be thought of as systems of balls (atoms) and springs (bonds between atoms) that vibrate with characteristic wiggles; they absorb infrared radiation at frequencies that correspond to their natural vibrating modes. The output from this absorption is a spectrum, often called a fingerprint, which shows distinctive peaks and dips, depending on the bonds and atoms present in the sample.

    But infrared spectroscopy has its challenges too. While it works well for bulk samples, traditional infrared spectroscopy can’t resolve molecular composition below about 2000 nanometers. The major hurdle is the diffraction limit of light, which is the fundamental barrier that determines the smallest focus spot of light and is particularly troublesome for the large wavelengths of infrared light. In recent years, though, the diffraction limit has been overcome by a technique called scattering-scanning near-field optical microscopy, or s-SNOM, which involves shining light onto a metallic tip. The tip acts as an antenna for the light, directing it to a tiny region at its apex just tens of nanometers wide.

    This trick is what’s used in IR s-SNOM, where infrared light is coupled to a metallic tip. The challenge with IR s-SNOM, however, is that researchers have been relying on infrared light produced by lasers. Lasers emit a large number of photons needed for the technique, but because they operate in a narrow wavelength band, they can only probe a narrow range of molecular vibrations. In other words, laser light simply can’t give you the flexibility to explore a spectrum of mixed molecules.

    A spectral-linescan of a blue mussel shell, which transitions from calcite to aragonite, illustrates the spatial resolution and spectroscopic range capabilities of the SINS technique. The image shows two simultaneously acquired vibrational modes across the transition region.

    Bechtel, Martin and Raschke’s team saw the opportunity to use Berkeley Lab’s ALS to overcome the laser limitation. The lab’s synchrotron produces broadband infrared light with a high-photon count that can be focused to the diffraction limit. The researchers coupled the synchrotron light to a metallic tip with an apex of about 20 nanometers, focusing the infrared beam onto the samples. The resulting spectrum is analyzed with a modified FTIR instrument.

    “This is actually one of very few examples where synchrotron light has been coupled to scanning probe microscopy,” says Raschke. “Moreover, the implementation of the technique at the synchrotron brings chemical nano-spectroscopy and -imaging out of the lab of a few laser science experts and makes it available for a broader scientific community at a user facility.”

    From mollusks to moon rocks

    The team demonstrated the technique by confirming the spectroscopic signature of silicon dioxide on silicon and by illustrating the sharp chemical transition that occurs within the shells of the blue mussel (M. edulis). Additionally, the researchers looked at proteins and a peptoid nanosheet, an engineered, ultra-thin film of proteins with medical and pharmacological applications.

    Martin is excited for the potential of SINS, which is available for researchers from any institution to use. In particular he’s interested in a closer look at battery systems, with the hope that understanding battery chemistry on the mesoscale could provide insight into better performance. Further out, he expects SINS to be useful for a range of biochemistry as well. “This hints at a dream I’ve had in my mind, to look at the surface of a cell, inside the bi-layer membrane, the channels, and receptors,” says Martin. “If we could put a SINS tip on a living cell, we could watch biochemistry happen in real time.”

    Bechtel, for his part, is intrigued by the possibility of using SINS for the study of lunar rocks, meteorites and stardust. These extraterrestrial materials have a molecular diversity that is difficult to resolve on the nanoscale, particularly in a non-destructive manner for these rare samples. A better understanding of the makeup of moon rocks and dust from space could provide clues to the formation of the planets and solar system.

    Raschke is using the technique to study the processes that limit the performance of organic solar cells. He is looking to further improve the flexibility of the technique such that it can be applied under variable and controlled atmospheric and low-temperature conditions. Among other tweaks, he plans to increase the sensitivity of the technique with the ultimate goal of performing singe-molecule chemical spectroscopy.
    This research was supported by the DOE’s Office of Science.

    See the full article here.

    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 7:38 pm on May 8, 2014 Permalink | Reply
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    From Berkeley Lab: “Berkeley Lab Develops Nanoscope to Probe Chemistry on the Molecular Scale” 


    Berkeley Lab

    May 07, 2014
    Kate Greene 510-486-4404 kgreene@lbl.gov

    For years, scientists have had an itch they couldn’t scratch. Even with the best microscopes and spectrometers, it’s been difficult to study and identify molecules at the so-called mesoscale, a region of matter that ranges from 10 to 1000 nanometers in size. Now, with the help of broadband infrared light from the Advanced Light Source (ALS) synchrotron at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), researchers have developed a broadband imaging technique that looks inside this realm with unprecedented sensitivity and range.

    pep
    This peptoid nanosheet, produced by Gloria Olivier and Ron Zuckerman at Berkeley Lab, is less than 8 nanometers thick at points. SINS makes it possible to acquire spectroscopic images of these ultra-thin nanosheets for the first time.

    By combining atomic force microscopy with infrared synchrotron light, researchers from Berkeley Lab and the University of Colorado have improved the spatial resolution of infrared spectroscopy by orders of magnitude, while simultaneously covering its full spectroscopic range, enabling the investigation of variety of nanoscale, mesoscale, and surface phenomena that were previously difficult to study.

    The new technique, called Synchrotron Infrared Nano-Spectroscopy or SINS, will enable in-depth study of complex molecular systems, including liquid batteries, living cells, novel electronic materials and stardust.

    “The big thing is that we’re getting full broadband infrared spectroscopy at 100 to 1000 times smaller scale,” says Hans Bechtel, principal scientific engineering associate at Berkeley Lab. “This is not an incremental achievement. It’s really revolutionary.”

    In a Proceedings of the National Academy of Sciences paper published May 6 online, titled Ultra-broadband infrared nano-spectroscopic imaging, Berkeley Lab’s Bechtel and Michael Martin, a Berkeley Lab staff scientist, and colleagues from Markus Raschke’s group at the University of Colorado at Boulder describe SINS. They demonstrate the nanoscope’s ability to capture broadband spectroscopic data over a variety of samples, including a semiconductor-insulator system, a mollusk shell, proteins, and a peptoid nanosheet. Martin says these demonstrations just “scratch the surface” of the potential of the new technique.

    Synchronizing Scopes

    SINS combines two pre-existing infrared technologies: a newer technique called infrared scattering-scanning near-field optical microscopy (IR s-SNOM) and an old laboratory standby, known even to college chemistry students, called Fourier Transform Infrared Spectroscopy (FTIR). A clever melding of these two tools, combined with the intense infrared light of the synchrotron at Berkeley Lab gives the researchers the ability to identify clusters of molecules sized as small as 20 to 40 nanometers.

    exp
    Experimental setup for SINS that includes the synchrotron light source, an atomic force microscope, a rapid-scan Fourier transform infrared spectrometer, a beamsplitter, mirrors and a detector.

    micro
    Atomic force microscope (AFM/MFM) on the left with controlling computer on the right.

    The new approach overcomes long-standing barriers with pre-existing microscopy techniques that often involve demanding technical and sample preparation requirements. Infrared spectroscopy uses low-energy light, is minimally invasive, and is applicable under ambient conditions, making it an excellent tool for chemical and molecular identifications in systems that are static as well as those that are living and dynamic. The technique works by shining low-energy infrared light onto a molecular sample. Molecules can be thought of as systems of balls (atoms) and springs (bonds between atoms) that vibrate with characteristic wiggles; they absorb infrared radiation at frequencies that correspond to their natural vibrating modes. The output from this absorption is a spectrum, often called a fingerprint, which shows distinctive peaks and dips, depending on the bonds and atoms present in the sample.

    But infrared spectroscopy has its challenges too. While it works well for bulk samples, traditional infrared spectroscopy can’t resolve molecular composition below about 2000 nanometers. The major hurdle is the diffraction limit of light, which is the fundamental barrier that determines the smallest focus spot of light and is particularly troublesome for the large wavelengths of infrared light. In recent years, though, the diffraction limit has been overcome by a technique called scattering-scanning near-field optical microscopy, or s-SNOM, which involves shining light onto a metallic tip. The tip acts as an antenna for the light, directing it to a tiny region at its apex just tens of nanometers wide.

    This trick is what’s used in IR s-SNOM, where infrared light is coupled to a metallic tip. The challenge with IR s-SNOM, however, is that researchers have been relying on infrared light produced by lasers. Lasers emit a large number of photons needed for the technique, but because they operate in a narrow wavelength band, they can only probe a narrow range of molecular vibrations. In other words, laser light simply can’t give you the flexibility to explore a spectrum of mixed molecules.

    spec
    A spectral-linescan of a blue mussel shell, which transitions from calcite to aragonite, illustrates the spatial resolution and spectroscopic range capabilities of the SINS technique. The image shows two simultaneously acquired vibrational modes across the transition region.

    Bechtel, Martin and Raschke’s team saw the opportunity to use Berkeley Lab’s ALS to overcome the laser limitation. The lab’s synchrotron produces broadband infrared light with a high-photon count that can be focused to the diffraction limit. The researchers coupled the synchrotron light to a metallic tip with an apex of about 20 nanometers, focusing the infrared beam onto the samples. The resulting spectrum is analyzed with a modified FTIR instrument.

    “This is actually one of very few examples where synchrotron light has been coupled to scanning probe microscopy,” says Raschke. “Moreover, the implementation of the technique at the synchrotron brings chemical nano-spectroscopy and -imaging out of the lab of a few laser science experts and makes it available for a broader scientific community at a user facility.”

    From mollusks to moon rocks

    The team demonstrated the technique by confirming the spectroscopic signature of silicon dioxide on silicon and by illustrating the sharp chemical transition that occurs within the shells of the blue mussel (M. edulis). Additionally, the researchers looked at proteins and a peptoid nanosheet, an engineered, ultra-thin film of proteins with medical and pharmacological applications.

    Martin is excited for the potential of SINS, which is available for researchers from any institution to use. In particular he’s interested in a closer look at battery systems, with the hope that understanding battery chemistry on the mesoscale could provide insight into better performance. Further out, he expects SINS to be useful for a range of biochemistry as well. “This hints at a dream I’ve had in my mind, to look at the surface of a cell, inside the bi-layer membrane, the channels, and receptors,” says Martin. “If we could put a SINS tip on a living cell, we could watch biochemistry happen in real time.”

    mm
    Berkeley Lab’s Michael Martin

    Bechtel, for his part, is intrigued by the possibility of using SINS for the study of lunar rocks, meteorites and stardust. These extraterrestrial materials have a molecular diversity that is difficult to resolve on the nanoscale, particularly in a non-destructive manner for these rare samples. A better understanding of the makeup of moon rocks and dust from space could provide clues to the formation of the planets and solar system.

    Raschke is using the technique to study the processes that limit the performance of organic solar cells. He is looking to further improve the flexibility of the technique such that it can be applied under variable and controlled atmospheric and low-temperature conditions. Among other tweaks, he plans to increase the sensitivity of the technique with the ultimate goal of performing singe-molecule chemical spectroscopy.

    This research was supported by the DOE Office of Science.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 7:03 am on February 25, 2014 Permalink | Reply
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    From Berkeley Lab: “On the Road to Mottronics…” 


    Berkeley Lab

    Researchers at the Advanced Light Source Find Key to Controlling the Electronic and Magnetic Properties of Mott Thin Films

    February 24, 2014
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    Mottronics” is a term seemingly destined to become familiar to aficionados of electronic gadgets. Named for the Nobel laureate Nevill Francis Mott, Mottronics involve materials – mostly metal oxides – that can be induced to transition between electrically conductive and insulating phases. If these phase transitions can be controlled, Mott materials hold great promise for future transistors and memories that feature higher energy efficiencies and faster switching speeds than today’s devices. A team of researchers working at Berkeley Lab’s Advanced Light Source (ALS) have demonstrated the conducting/insulating phases of ultra-thin films of Mott materials can be controlled by applying an epitaxial strain to the crystal lattice.

    balls
    Epitaxial mismatches in the lattices of nickelate ultra-thin films can be used to tune the energetic landscape of Mott materials and thereby control conductor/insulator transitions. No image credit.

    “Our work shows how an epitaxial mismatch in the lattice can be used as a knot to tune the energetic landscape of Mott materials and thereby control conductor/insulator transitions,” says Jian Liu, a post-doctoral scholar now with Berkeley Lab’s Materials Sciences Division, who is the lead author on a paper describing this work in the journal Nature Communications. “Through epitaxial strain, we forced nickelate films containing only a few atomic layers into different phases with dramatically different electronic and magnetic properties. While some of these phases are not obtainable in conventional ways, we were able to produce them in a form that is ready for device development.”

    The Nature Communications paper is titled Heterointerface engineered electronic and magnetic phases of NdNiO3 thin films. The corresponding author is Jak Chakhalian, a professor of physics at the University of Arkansas. Co-authors are Mehdi Kargarian, Mikhail Kareev, Ben Gray, Phil Ryan, Alejandro Cruz, Nadeem Tahir, Yi-De Chuang, Jinghua Guo, James Rondinelli, John Freeland and Gregory Fiete.

    two
    Jinghua Guo (left) and Yi-De Chuang at Beamline 8.0.1 of the Advanced Light Source were part of a team that discovered a key to controlling the electronic and magnetic properties of Mott materials. (Photo by Roy Kaltschmidt)

    Nickel-based rare-earth perovskite oxides, or “nickelates,” are considered to be an ideal model for the study of Mott materials because they display strongly correlated electron systems that give rise to unique electronic and magnetic properties. Liu and his co-authors studied thin films of neodymium nickel oxide using ALS beamline 8.0.1, a high flux undulator beamline that produces x-ray beams optimized for the study of nanoscale materials and strongly correlated physics.

    “ALS beamline 8.0.1 provides the high photon flux and energy range that are critical when dealing with nanoscale samples,” Liu says. “The state-of-the-art Resonant X-ray Scattering endstation has a high-speed, high-sensitivity CCD camera that makes it feasible to find and track diffraction peaks off a thin film that was only six nanometers thick.”

    The transition between the conducting and insulating phases in nickelates is determined by various microscopic interactions, some of which favor the conducting phase, some which favor the insulating phase. The energetic balance of these interactions determines how easily electricity is conducted by electrons moving between the nickel and oxygen ions. By applying enough epitaxial strain to alter the space between these ions, Liu and his colleagues were able to tune this energetic balance and control the conducting/insulating transition. In addition, they found strain could also be used to control the nickelate’s magnetic properties, again by exploiting the lattice mismatch.

    “Magnetism is another hallmark of Mott materials that often goes hand-in-hand with the insulating state and is used to distinguish Mott insulators,” says Liu. “The challenge is that most Mott insulators, including nickelates, are antiferromagnets that macroscopically behave as non-magnetic materials. “At ALS beamline 8.0.1, we were able to directly track the magnetic evolution of our thin films while tuning the metal-to-insulator transition. Our findings give us a better understanding of the physics behind the magnetic properties of these nickelate films and point to potential applications for this magnetism in novel Mottronics devices.”

    This research was primarily supported the U.S. Department of Energy’s Office of Science.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 7:25 pm on February 21, 2014 Permalink | Reply
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    From Berkeley Lab: “Tracking Catalytic Reactions in Microreactors” 


    Berkeley Lab

    See the full article here.

    February 21, 2014

    Infrared Technique at Berkeley Lab’s Advanced Light Source Could Help Improve Flow Reactor Chemistry for Pharmaceuticals and Other Products

    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    A pathway to more effective and efficient synthesis of pharmaceutical drugs and other flow reactor chemical products has been opened by a study in which for the first time the catalytic reactivity inside a microreactor was mapped in high resolution from start-to-finish. The results not only provided a better understanding of the chemistry behind the catalytic reactions, they also revealed opportunities for optimization, which resulted in better catalytic performances. The study was conducted by a team of scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley.

    Working at Berkeley Lab’s Advanced Light Source (ALS), the team, which was led by chemists Dean Toste and Gabor Somorjai, both of whom hold joint appointments with Berkeley Lab and UC Berkeley, used tightly focused beams of infrared and x-ray light to track the evolution of a catalytic reaction with a spatial resolution of 15 microns.

    graph
    Infrared microspectroscopy scans can track the formation of different chemical products as reactants flow through a microreactor.

    “The formation of different chemical products during the reactions was analyzed using in situ infrared micro-spectroscopy, while the state of the catalyst along the flow reactor was determined using in situ x-ray absorption microspectroscopy,” says Toste, a faculty scientist with Berkeley Lab’s Chemical Sciences Division. “Our results show that using infrared microspectroscopy to monitor the evolution of reactants into a desired product could be an invaluable tool for optimizing pharmaceutical-related synthetic processes that take place in flow reactors.”

    two
    Dean Toste (left) and Elad Gross led a team that developed a technique which allows the catalytic reactivity inside a microreactor to be mapped in high resolution from start-to-finish. (Photo by Roy Kaltschmidt)

    Toste and Somorjai are the corresponding authors of a paper in the Journal of the American Chemical Society (JACS) titled In-situ IR and X-ray high spatial-resolution microspectroscopy measurements of multistep organic transformation in flow microreactor catalyzed by Au nanoclusters. Elad Gross, a post-doctoral scholar with the corresponding authors, is the lead author. Other co-authors are Xing-Zhong Shu, Selim Alayoglu, Hans Bechtel and Michael Martin.

    Catalysts – substances that speed up the rates of chemical reactions without themselves being chemically changed – are used to initiate virtually every manufacturing process that involves chemistry. There are two basic modes of catalytic reactors – batch, in which a final chemical product is produced over a series of separate stages; and flow, in which chemical reactions run in a continuously flowing stream to yield a final product. With the implementation of microreactors, the pharmaceutical industry aims to make the switch from batch mode to flow mode, as flow reactors provide a highly recyclable, scalable and efficient setup that enhances the sustainability and performance of catalysts. However, the synthesis of pharmaceutical drugs is a multiphase, complex process that needs to be carefully monitored. Until now, there has been no capability to follow the multistep production process of pharmaceutical drugs in flow reactors without perturbing the flow reaction.

    “Our method allows us to watch an entire catalytic movie, from reactants into products formation, instead of only snapshots of the catalytic process,” says Gross. “In most cases before, chemists had to extrapolate information on the reaction process based on analysis of the final product. With our technique, we don’t have to guess what happened in the first scene based on what we saw in the final scene, since now we’re able to directly watch a high-resolution movie of the entire process.”

    For this study, Gross and his colleagues used a heterogeneous catalyst of gold nanoclusters loaded onto a silica support to produce dihydropyran, an organic compound whose formation involves multiple reactant steps. Each of these reactants shows a distinguishable infrared signature, allowing their evolution into the final product to be precisely monitored with an infrared beam. The infrared microspectroscopy was performed at ALS beamline 1.4.

    “ALS beamline 1.4 provides a bright infrared beam with a diameter of less than 10 micrometers,” Gross says. “The small diameter of the beam enabled us to draw a map of the flow reactor with high spatial resolution of up to 15 micrometers. Without this high resolution imaging, we would not be able to track and understand key processes in the catalytic reaction.”

    map
    A combination of in situ infrared micro-spectroscopy and in situ x-ray absorption microspectroscopy allows catalytic reactivity inside a microreactor to be mapped in high resolution from start-to-finish.

    In following the reaction kinetics step-by-step, the Berkeley researchers discovered that the catalytic reaction they were observing is completed within the first five-percent of the flow reactor’s volume, which meant that the remaining 95-percent of the reactor, though packed with catalyst did not contribute to the catalytic process.

    “Based on this result, we were able to minimize the volume of the flow reactor and the amount of catalyst by an order of magnitude without deteriorating the catalytic reactivity,” Gross says.

    While the infrared microspectroscopy technique employed in this study allowed one-dimensional mapping of a catalytic reaction along the path of the flow reactor, the actual flow reactor is three-dimensional. Gross and Toste along with Michael Martin and Hans Bechtel, beam-scientists at the ALS infrared beamline, are now exploring techniques that would permit two- and three-dimensional mapping of catalytic reactions.

    “Multidimensional imaging will give us the ability to know where exactly inside the volume of the flow reactor the catalytic reaction takes place,” Gross says. “This will provide us advanced tools for better understanding and optimization of the catalytic reaction.”

    This research was supported by the DOE Office of Science.

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  • richardmitnick 6:19 pm on February 6, 2014 Permalink | Reply
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    From Berkeley Lab: “New Insight into an Emerging Genome-Editing Tool” 


    Berkeley Lab

    Berkeley Researchers Show Expanded Role for Guide RNA in Cas9 Interactions with DNA

    February 06, 2014
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    The potential is there for bacteria and other microbes to be genetically engineered to perform a cornucopia of valuable goods and services, from the production of safer, more effective medicines and clean, green, sustainable fuels, to the clean-up and restoration of our air, water and land. Cells from eukaryotic organisms can also be modified for research or to fight disease. To achieve these and other worthy goals, the ability to precisely edit the instructions contained within a target’s genome is a must. A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9, which plays a critical role in the bacterial immune system. Cas9 should become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape by researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley.

    dna
    The crystal structure of SpyCas9 features a nuclease domain lobe (red) and an alpha-helical lobe (gray) each with a nucleic acid binding cleft that becomes functionalized when Cas9 binds to guide RNA.

    binding
    Upon binding with guide RNA, the two structural lobes of Cas9 reorient so that the two nucleic acid binding clefts face each other, forming a central channel that interfaces with target DNA.

    Biochemist Jennifer Doudna and biophysicist Eva Nogales, both of whom hold appointments with Berkeley Lab, UC Berkeley, and the Howard Hughes Medical Institute (HHMI), led an international collaboration that used x-ray crystallography to produce 2.6 and 2.2 angstrom (Å) resolution crystal structure images of two major types of Cas9 enzymes. The collaboration then used single-particle electron microscopy to reveal how Cas9 partners with its guide RNA to interact with target DNA. The results point the way to the rational design of new and improved versions of Cas9 enzymes for basic research and genetic engineering.

    “The combination of x-ray protein crystallography and electron microscopy single-particle analysis showed us something that was not anticipated,” says Nogales. “The Cas9 protein, on its own, exists in an inactive state, but upon binding to the guide RNA, the Cas9 protein undergoes a radical change in its three-dimensional structure that enables it to engage with the target DNA.”

    “Because we now have high-resolution structures of the two major types of Cas9 proteins, we can start to see how this family of bacterial enzymes has evolved,” Doudna says. “We see that the two structures are quite different from each other outside of their catalytic domains, suggesting an interesting structural plasticity that could explain how Cas9 is able to use different kinds of guide RNAs. Also, the differences in the two structures suggest that it may be possible to engineer smaller Cas9 variants and still retain function, an important goal for some genome engineering applications.”

    two
    Eva Nogales (left) and Jennifer Doudna led a study that produced the first detailed look at the 3D structure of the Cas9 enzyme and how it partners with guide RNA. (Photo by Roy Kaltschmidt)

    Doudna and Nogales are the corresponding authors, along with Martin Jinek of the University of Zurich, of a paper in Science that describes this research. The paper is titled Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Co-authors are Fuguo Jiang, David Taylor, Samuel Sternberg, Emine Kaya, Enbo Ma, Carolin Anders, Michael Hauer, Kaihong Zhou, Steven Lin, Mattias Kaplan, Anthony Iavarone and Emmanuelle Charpentier.

    See the full article here.

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  • richardmitnick 5:01 pm on February 3, 2014 Permalink | Reply
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    From Berkeley Lab: “How a Shape-shifting DNA-repair Machine Fights Cancer” 


    Berkeley Lab

    February 03, 2014
    Dan Krotz 510-484-5956 dakrotz@lbl.gov

    Maybe you’ve seen the movies or played with toy Transformers, those shape-shifting machines that morph in response to whatever challenge they face. It turns out that DNA-repair machines in your cells use a similar approach to fight cancer and other diseases, according to research led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab).

    mre
    One protein complex, two very different shapes and functions: In the top image, the scientists created an Mre11-Rad50 mutation that speeds up hydrolysis, yielding an open state that favors a high-fidelity way to repair DNA. In the bottom image, the scientists slowed down hydrolysis, resulting in a closed ATP-bound state that favors low-fidelity DNA repair. (Credit: Tainer lab)

    As reported in a pair of new studies, the scientists gained new insights into how a protein complex called Mre11-Rad50 reshapes itself to take on different DNA-repair tasks.

    Their research sheds light on how this molecular restructuring leads to different outcomes in a cell. It could also guide the development of better cancer-fighting therapies and more effective gene therapies.

    As reported in a pair of new studies, the scientists gained new insights into how a protein complex called Mre11-Rad50 reshapes itself to take on different DNA-repair tasks.

    Their research sheds light on how this molecular restructuring leads to different outcomes in a cell. It could also guide the development of better cancer-fighting therapies and more effective gene therapies.

    Mre11-Rad50’s job is the same in your cells, your pet’s cells, or any organism’s. It detects and helps fix the gravest kind of DNA breaks in which both strands of a DNA double helix are cut. The protein complex binds to the broken DNA ends, sends out a signal that stops the cell from dividing, and uses its shape-shifting ability to choose which DNA repair process is launched to fix the broken DNA. If unrepaired, double strand breaks are lethal to the cell. In addition, a repair job gone wrong can lead to the proliferation of cancer cells.

    Little is known about how the protein’s Transformer-like capabilities relate to its DNA-repair functions, however.

    To learn more, the scientists modified the protein complex in ways that were designed to affect just one of the many activities it undertakes. They then used structural biology, biochemistry, and genomic tools to study the impacts of these modifications.

    “By targeting a single activity, we can make the protein complex go down a different pathway and learn how its dynamic structure changes,” says John Tainer of Berkeley Lab’s Life Sciences Division. He conducted the research with fellow Berkeley Lab scientist Gareth Williams and scientists from several other institutions.

    Adds Williams, “In some cases, we sped up or slowed down the protein complex’s movements, and by doing so we changed its biological outcomes.”

    sybll
    Much of the research was conducted at the SIBYLS beamline at the Advanced Light Source. SIBYLS stands for Structurally Integrated Biology for Life Sciences.

    Much of the research was conducted at the Advanced Light Source (ALS), a synchrotron located at Berkeley Lab that generates intense X-rays to probe the fundamental properties of substances. They used an ALS beamline called SYBILS, which combines X-ray scattering with X-ray diffraction capabilities. It yields atomic-resolution images of the crystal structures of proteins. It can also watch the transformation of the protein as it undergoes conformational changes.

    In one study published in the journal Molecular Cell, the scientists studied Mre11 from microbial cells. They developed two molecular inhibitors that block Mre11’s ability to cut DNA, a critical initial step in the repair process.

    They tested the effect of these inhibitors in human cells. They found that Mre11 first makes a nick away from the broken DNA strand it is repairing. Mre11 then works back toward the broken end. Previously, scientists thought that Mre11 always starts at the broken DNA end. They also found that when Mre11 cuts in the middle of a DNA strand, it initiates a high-precision DNA-repair pathway called homologous recombination repair.

    In another study published in EMBO Journal, the scientists created Rad50 mutations that either promote or destabilize the shape formed when the Rad50 subunit binds with ATP, a chemical that fuels the protein complex’s movements.

    Biochemical and functional assays conducted by Tanya Paull of the University of Texas at Austin revealed how these changes affect microbial, yeast, and human Mre11-Rad50 activities. Paul Russell at the Scripps Research Institute helped the scientists learn how these Rad50 mutations affect yeast cells.

    They found that some mutations slowed down ATP hydrolysis, which is how Rad50 and other enzymes use ATP as fuel. Other mutations sped it up. Both changes affected Mre11-Rad50’s workflow, and its biological outcomes, in a big way.

    “When we slowed down hydrolysis and favored the ATP-bound state, Rad50 favored a non-homologous end joining pathway, which is a low-fidelity way to repair DNA,” says Williams. “When we sped it up, the subunit favored homologous repair, which is the high-fidelity pathway.”

    This approach, in which scientists start with a specific protein mechanism and learn how it affects the entire organism, will help researchers develop a predictive understanding of how Mre11-Rad50 works.

    “It’s a ‘bottom up’ way to study proteins such as Mre11-Rad50, and it could guide the development of better cancer therapies and other applications,” says Tainer.

    See the full article, with further material, here.

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  • richardmitnick 4:27 pm on November 22, 2013 Permalink | Reply
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    From Berkeley Lab: “An Inside Look at a MOF in Action” 


    Berkeley Lab

    Berkeley Lab Researchers Probe Into Electronic Structure of MOF May Lead to Improved Capturing of Greenhouse Gases

    November 22, 2013
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    A unique inside look at the electronic structure of a highly touted metal-organic framework (MOF) as it is adsorbing carbon dioxide gas should help in the design of new and improved MOFs for carbon capture and storage. Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have recorded the first in situ electronic structure observations of the adsorption of carbon dioxide inside Mg-MOF-74, an open metal site MOF that has emerged as one of the most promising strategies for capturing and storing greenhouse gases.

    Working at Berkeley Lab’s Advanced Light Source (ALS), a team led by Jeff Kortright of Berkeley Lab’s Materials Sciences Division, used the X-ray spectroscopy technique known as Near Edge X-ray Absorption Fine Structure (NEXAFS) to obtain what are believed to be the first ever measurements of chemical and electronic signatures inside of a MOF during gas adsorption.

    “We’ve demonstrated that NEXAFS spectroscopy is an effective tool for the study of MOFs and gas adsorption,” Kortright says. “Our study shows that open metal site MOFs have significant X-ray spectral signatures that are highly sensitive to the adsorption of carbon dioxide and other molecules.”

    Kortright is the corresponding author of a paper describing these results in the Journal of the American Chemical Society (JACS). The paper is titled Probing Adsorption Interactions In Metal-Organic Frameworks Using X-ray Spectroscopy. Co-authors are Walter Drisdell, Roberta Poloni, Thomas McDonald, Jeffrey Long, Berend Smit, Jeffrey Neaton and David Prendergast.

    spec
    Mg-MOF-74 is an open metal site MOF whose porous crystalline structure could enable it to serve as a storage vessel for capturing and containing the carbon dioxide emitted from coal-burning power plants. (National Academy of Sciences)

    See the full article here.

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  • richardmitnick 6:35 pm on November 18, 2013 Permalink | Reply
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    From Berkeley Lab: “A Superconductor-Surrogate Earns Its Stripes” 


    Berkeley Lab

    November 18, 2013
    Berkeley Lab Study Reveals Origins of an Exotic Phase of Matter

    Alison Hatt 510-486-7154 ajhatt@lbl.gov

    Understanding superconductivity – whereby certain materials can conduct electricity without any loss of energy – has proved to be one of the most persistent problems in modern physics. Scientists have struggled for decades to develop a cohesive theory of superconductivity, largely spurred by the game-changing prospect of creating a superconductor that works at room temperature, but it has proved to be a tremendous tangle of complex physics.

    Now scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have teased out another important tangle from this giant ball of string, bringing us a significant step closer to understanding how high- temperature superconductors work their magic. Working with a model compound, the team illuminated the origins of the so-called “stripe phase” in which electrons become concentrated in stripes throughout a material, and which appears to be linked to superconductivity.

    image
    Ultrafast changes in the optical properties of strontium-doped lanthanum nickelate throughout the infrared spectrum expose a rapid dynamics of electronic localization in the nickel-oxide plane, shown at left. This process, illustrated on the right, comprises the first step in the formation of ordered charge patterns or “stripes.”

    “We’re trying to understand nanoscale order and how that determines material properties such as superconductivity,” said Robert Kaindl, a physicist in Berkeley Lab’s Materials Sciences Division. “Using ultrafast optical techniques, we are able to observe how charge stripes start to form on a time scale of hundreds of femtoseconds.” A femtosecond is just one millionth of one billionth of a second.

    Electrons in a solid material interact extremely quickly and on very short length scales, so to observe their behavior researchers have built extraordinarily powerful “microscopes” that zoom into fast events using short flashes of laser light. Kaindl and his team brought to bear the power of their ultrafast-optics expertise to understand the stripe phase in strontium-doped lanthanum nickelate (LSNO), a close cousin of high-temperature superconducting materials.

    “We chose to work with LSNO because it has essential similarities to the cuprates (an important class of high-temperature superconductors), but its lack of superconductivity lets us focus on understanding just the stripe phase,” said Giacomo Coslovich, a postdoctoral researcher at Berkeley Lab working with Kaindl.

    “With science, you have to simplify your problems,” Coslovich continued. “If you try to solve them all at once with their complicated interplay, you will never understand what’s going on.”

    two
    Giacomo Coslovich (left) and Robert Kaindl (right) next to the laser setup that generates extremely short pulses of light at “mid-infrared” wavelengths, far beyond the spectrum perceptible by the human eye.

    Beyond the ultrafast measurements, the team also studied X-ray scattering and the infrared reflectance of the material at the neighboring Advanced Light Source, to develop a thorough, cohesive understanding of the stripe phase and why it forms.

    Said Kaindl, “We took advantage of our fortunate location in the national lab environment, where we have both these ultrafast techniques and the Advanced Light Source. This collaborative effort made this work possible.”

    See the full article here.

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  • richardmitnick 2:06 pm on July 10, 2013 Permalink | Reply
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    From Berkeley Lab: “Of Aging Bones and Sunshine” 


    Berkeley Lab

    Study at Berkeley Lab’s Advanced Light Source Links Vitamin D Deficiency to Accelerated Aging of Bones

    July 10, 2013
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    “Everyone knows that as we grow older our bones become more fragile. Now a team of U.S. and German scientists led by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley has shown that this bone-aging process can be significantly accelerated through deficiency of vitamin D – the sunshine vitamin.

    Vitamin D deficiency is a widespread medical condition that has been linked to the health and fracture risk of human bone on the basis of low calcium intake and reduced bone density. However, working at Berkeley Lab’s Advanced Light (ALS), a DOE national user facility, the international team demonstrated that vitamin D deficiency also reduces bone quality.

    ‘The assumption has been that the main problem with vitamin D deficiency is reduced mineralization for the creation of new bone mass, but we’ve shown that low levels of vitamin D also induces premature aging of existing bone,’ says Robert Ritchie, who led the U.S. portion of this collaboration. Ritchie holds joint appointments with Berkeley Lab’s Materials Sciences Division and the University of California (UC) Berkeley’s Materials Science and Engineering Department.

    bones
    These 3D reconstructions of crack paths show in the normal bone (left) pronounced crack deflection by splitting along the interfaces of the osteons accompanied by the formation of crack bridges. In vitamin D–deficient sample, the crack takes a tortuous breaking path across the osteons with no crack bridging. (Courtesy of Ritchie and Bale)

    ‘Unraveling the complexity of human bone structure may provide some insight into more effective ways to prevent or treat fractures in patients with vitamin D deficiency,’ says Björn Busse, of the Department of Osteology and Biomechanics at the University Medical Center in Hamburg, Germany, who led the German portion of the team.”

    See the full article here.

    Ritchie and Busse have reported their findings in the journal Science Translational Medicine.

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