From Livermore Lab: “Lawrence Livermore scientists discover new materials to capture methane”

Lawrence Livermore National Laboratory

04/16/2013
Anne M Stark, LLNL, (925) 422-9799, stark8@llnl.gov

“Scientists at Lawrence Livermore National Laboratory (LLNL) and UC Berkeley and have discovered new materials to capture methane, the second highest concentration greenhouse gas emitted into the atmosphere.

Methane capture in zeolite SBN. Blue represents adsorption sites, which are optimal for methane (CH4) uptake. Each site is connected to three other sites (yellow arrow) at optimal interaction distance.

Methane is a substantial driver of global climate change, contributing 30 percent of current net climate warming. Concern over methane is mounting, due to leaks associated with rapidly expanding unconventional oil and gas extraction, and the potential for large-scale release of methane from the Arctic as ice cover continues to melt and decayed material releases methane to the atmosphere. At the same time, methane is a growing source of energy, and aggressive methane mitigation is key to avoiding dangerous levels of global warming.

The research team, made up of Amitesh Maiti, Roger Aines and Josh Stolaroff of LLNL and Professor Berend Smit, researchers Jihan Kim and Li-Chiang Lin at UC Berkeley and Lawrence Berkeley National Lab, performed systematic computer simulation studies on the effectiveness of methane capture using two different materials – liquid solvents and nanoporous zeolites (porous materials commonly used as commercial adsorbents).

While the liquid solvents were not effective for methane capture, a handful of zeolites had sufficient methane sorption to be technologically promising. The research appears in the April 16 edition of the journal, Nature Communications.”

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From ORNL: “ORNL microscopy uncovers “dancing” silicon atoms in graphene”

April 3, 2013
Morgan McCorkle

“Jumping silicon atoms are the stars of an atomic scale ballet featured in a new Nature Communications study from the Department of Energy’s Oak Ridge National Laboratory.

Oak Ridge National Laboratory researchers used electron microscopy to document the ‘dancing’ motions of silicon atoms, pictured in white, in a graphene sheet.

The ORNL research team documented the atoms’ unique behavior by first trapping groups of silicon atoms, known as clusters, in a single-atom-thick sheet of carbon called graphene. The silicon clusters, composed of six atoms, were pinned in place by pores in the graphene sheet, allowing the team to directly image the material with a scanning transmission electron microscope.

The ‘dancing’ movement of the silicon atoms was caused by the energy transferred to the material from the electron beam of the team’s microscope.

‘It’s not the first time people have seen clusters of silicon,’ said coauthor Juan Carlos Idrobo. ‘The problem is when you put an electron beam on them, you insert energy into the cluster and make the atoms move around. The difference with these results is that the change that we observed was reversible. We were able to see how the silicon cluster changes its structure back and forth by having one of its atoms ‘dancing’ between two different positions.’”

See the full article here.

ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.

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From PNNL Lab: “A New Method for Measuring the Viscosity of Nanoparticles”

First direct determination of the chemical diffusivity and viscosity of secondary organic aerosols

March 2013
Suraiya Farukhi
Christine Sharp

“Results: For the first time, scientists measured the chemical diffusivity and viscosity of atmospheric organic particles, thanks to a new approach from scientists at Pacific Northwest National Laboratory, University of Washington, and Imre Consulting. The team doped atmospherically important organic nanoparticles, known as secondary organic aerosols (SOAs), with tracer molecules and measured their diffusion rate as they slowly worked their way out of the particles. Knowing the diffusion rate, the scientists calculated the particle’s viscosity.

‘Over the past two years, we have shown that long-standing assumptions about the most fundamental properties of SOA particles — phase and volatility — are wrong. Here, for the first time, we quantify chemical diffusivity in SOA particles and show that SOA viscosity is larger — a million times higher than assumed,’ said lead author Dr. Alla Zelenyuk, physical chemist at Pacific Northwest National Laboratory.

Determining the viscosity of tar-like secondary organic aerosols, ubiquitous atmospheric particles, is now possible thanks to a new method developed by scientists at Pacific Northwest National Laboratory, University of Washington, and Imre Consulting.

Why It Matters: Convenient, but unsubstantiated, assumptions have haunted atmospheric scientists studying SOAs for years, making it impossible to model how the particles affect climate and human health. With the development of new approaches and precise characterization instruments, scientists have disproved the common assumption. With this current study, Zelenyuk and her colleagues have given atmospheric modelers and others data that are invaluable for accurately portraying the particles and their effects in different scenarios, such as new regulations.”

See the full article here.

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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From PNNL Lab: “Striking While the Iron Is Hot”

Chromatography combined with database search strategy identifies hard-to-find heme proteins

March 2013
Suraiya Farukhi
Christine Sharp

“Results: Heme c is an important iron-containing post-translational modification found in many proteins. It plays an important role in respiration, metal reduction, and nitrogen fixation, especially anaerobic respiration of environmental microbes. Such bacteria and their c-type cytochromes are studied extensively because of their potential use in bioremediation, microbial fuel cells, and electrosynthesis of valuable biomaterials.

Heme C

Until recently, these modifications were hard to find using traditional proteomic methods. Scientists at Pacific Northwest National Laboratory combined a heme c tag protein affinity purification strategy called histidine affinity chromatography (HAC) with enhanced database searching. This combination confidently identified heme c peptides in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments-by as much as 100-fold in some cases.”

Why It Matters: Iron is a critical part of many biological processes; however, it is often not biologically available or it can be toxic in high quantities. So, biological systems have developed intricate methods to use and store iron. Many environmentally important microbes and microbial communities are rich in c-type cytochromes. Combining HAC and data analysis tailored to the unique properties of heme c peptides should enable more detailed study of the role of c-type cytochromes in these microbes and microbial communities.

‘Several proteomics studies have analyzed the expression of c-type cytochromes under various conditions,’ said PNNL postdoctoral researcher Dr. Eric Merkley, and lead author of a paper that appeared in the Journal of Proteome Research. ‘A shared feature of these studies is that the cytochrome-rich fractions, the cell envelope or extracellular polymeric substance, were purified and explicitly analyzed to efficiently detect cytochromes. Analyses of large-scale proteomics datasets have typically suggested that c-type cytochromes, particularly the heme c peptides, are under-represented.’”

See the full article here.

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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From Livermore Lab: “Boron chemistry reported in Chemical Reviews”

Lawrence Livermore National Laboratory

03/28/2013
Anne M Stark

“Livermore researchers have described in detail the properties of the room temperature form of the element boron.

A ball-and-stick structural model of rhombohedral boron is shown in the foreground and a picture of Badwater Basin in California is shown in the background. The Badwater Basin salt flats contain high concentrations of evaporative minerals such as borax, an important boron-containing compound. Photo by Tadashi Ogitsu; image by Liam Krauss/Livermore Computing.

In the periodic table, boron occupies a peculiar, transitional position. It sits on the first row, and has metallic elements to its left, and non-metals to its right. Furthermore, it is the only non-metal in the third column of the periodic table.

The bonding orbitals (red and blue surfaces) in B-boron demonstrate how vacancies and self-interstitials can stabilize the structure. Left: Part of the stable form of boron called the B28 unit (gold ball-and-stick) has a local instability that leads to the introduction of B13 vacancies with unoccupied orbitals (red surfaces). Right: The system is stabilized as two interstitials boronatoms (B17 and B18) are introduced as a pair, which transforms the unoccupied orbitals (red surfaces on the left) to nearly complete chemical bonds (blue surfaces on the right nearby the B17 and B18 interstitials).

It is not surprising that the crystallographic structure and topology of boron’s stable form at room temperature (β-boron) are not shared by any other element, and are extremely complex. The formidable intricacy of β-boron, characterized by interconnecting icosahedra (a regular polyhedron with 20 identical equilateral triangular faces) partially occupied sites, and an unusually large number of atoms per unit cell (more than 300), has been known for more than 40 years.

Boron remains the only element purified in macroscopic quantities for which the ground state geometry has not been completely determined by experiments. Theoretical progress over the last decade has shed light on numerous properties of elemental boron, leading to a thorough characterization of its structure at ambient conditions, as well as of its electronic and thermodynamic properties.

In the March 8 online edition of Chemical Reviews, LLNL researchers Tadashi Ogitsu and Eric Schwegler along with Giulia Galli of University of California, Davis, discuss in detail starting from the history of boron research, and the properties of β-boron, as inferred from experiments and the ab-initio theories developed over the last decade.”

See the full article here.

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From M.I.T.: “New solar-cell design based on dots and wires”

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MIT researchers improve efficiency of quantum-dot photovoltaic system by adding a forest of nanowires.

March 25, 2013
David L. Chandler

“Using exotic particles called quantum dots as the basis for a photovoltaic cell is not a new idea, but attempts to make such devices have not yet achieved sufficiently high efficiency in converting sunlight to power. A new wrinkle added by a team of researchers at MIT — embedding the quantum dots within a forest of nanowires — promises to provide a significant boost.”

Scanning Electron Microscope images show an array of zinc-oxide nanowires (top) and a cross-section of a photovoltaic cell made from the nano wires, interspersed with quantum dots made of lead sulfide (dark areas). A layer of gold at the top (light band) and a layer of indium-tin-oxide at the bottom (lighter area) form the two electrodes of the solar cell.
Images courtesy of Jean, et al/Advanced Materials

See the full article here.

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From Argonne APS: "Shedding Light on Chemistry with a Biological Twist"

News from Argonne National Laboratory

MARCH 14, 2013
David Bradley

“Many of life’s processes rely on light to trigger a chemical change. Photosynthesis, vision, the movement of light-seeking or light-avoiding bacteria, for instance, all exploit photochemistry. Discovering exactly how living things absorb and convert light energy into a form that can change the molecules involved in such processes would not only help scientists understand them but could lead to ways to mimic such processes for more efficient solar energy conversion, for instance. A clearer understanding of how light can drive biological processes has emerged from x-ray diffraction studies carried out on beamlines at the U.S. Department of Energy Office of Science’s Advanced Photon Source (APS) at Argonne, and the European Synchrotron Radiation Facility (ESRF). This work will help science shed a brighter light on some of life’s most critical processes.”

The isomerization of a small molecule caged inside a photoactive protein recorded by time-resolved x-ray crystallography reveals a detailed sequence of events (represented by dominos) composed of a short-lived intermediate (red) whose reaction trajectory bifurcates along bicycle-pedal (left) and hula-twist (right) pathways. No image credit.

See the full article here.

Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security.

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From Berkeley Lab: “In the Blink of an Eye: X-ray Imaging on the Attosecond Timescale”

Berkeley Lab

March 07, 2013
Lynn Yarris

“In the blink of an eye, more attoseconds have expired than the age of Earth measured in – minutes. A lot more. To be precise, an attosecond is one billionth of a billionth of a second. The attosecond timescale is where you must go to study the electron action that is the starting point of all of chemistry. Not surprisingly, chemists are most eager to explore it with X-rays, the region of the electromagnetic spectrum that can probe the core electrons of atoms, the electrons that uniquely identify atomic species.

Berkeley Lab’s Ali Belkacem

Ali Belkacem, a chemist with the Lawrence Berkeley National Laboratory, has been using powerful laboratory-scale lasers to test whether multidimensional nonlinear x-ray spectroscopy on the attosecond timescale is practical for the light sources of the future – and just what combination of beam characteristics is needed to define them.

Heralded as the science of the 21st century by Science and The Economist, attosecond science is a new frontier of molecular and material science. It is expected to catalyze novel applications in a wide range of fields such as nanotechnology and life sciences, based on the ultimate visualization and control of the quantum nature of the electron.”

See the full article here.

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

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From Berkeley Lab: “Searching for the Solar System’s Chemical Recipe”

Berkeley Lab

Berkeley Lab’s Chemical Dynamics Beamline points to why isotope ratios in interplanetary dust and meteorites differ from Earth’s

February 20, 2013
Paul Preuss

“By studying the origins of different isotope ratios among the elements that make up today’s smorgasbord of planets, moons, comets, asteroids, and interplanetary ice and dust, Mark Thiemens and his colleagues hope to learn how our solar system evolved. Thiemens, Dean of the Division of Physical Sciences at the University of California, San Diego, has worked on this problem for over three decades.

The protosun evolved in a hot nebula of infalling gas and dust that formed an accretion disk (green) of surrounding matter. Visible and ultraviolet light poured from the sun, irradiating abundant clouds of carbon monoxide, hydrogen sulfide, and other chemicals. Temperatures near the sun were hot enough to melt silicates and other minerals, forming the chondrules found in early meteoroids (dashed black circles). Beyond the “snowline” (dashed white curves), water, methane, and other compounds condensed to ice. Numerous chemical reactions contributed to the isotopic ratios seen in relics of the early solar system today.

In recent years his team has found the Chemical Dynamics Beamline of the Advanced Light Source (ALS) at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) to be an invaluable tool for examining how photochemistry determines the basic ingredients in the solar system recipe.

‘Mark and his colleagues Subrata Chakraborty and Teresa Jackson wanted to know if photochemistry could explain some of the differences in isotope ratios between Earth and what’s found in meteorites and interplanetary dust particles,’ says Musahid (Musa) Ahmed of Berkeley Lab’s Chemical Sciences Division, a scientist at the Chemical Dynamics Beamline who works with the UC San Diego team. ‘They needed a source of ultraviolet light powerful enough to dissociate gas molecules like carbon monoxide, hydrogen sulfide, and nitrogen. That’s us: our beamline basically provides information about gas-phase photodynamics.’”

At this point, I direct you to the full article. There is a lot going on here.

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

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From NASA Chandra: “Chemistry and the Universe”

NASA Chandra

Chemistry, the study of the intricate dances and bondings of low-energy electrons to form the molecules that make up the world we live in, may seem far removed from the thermonuclear heat in the interiors of stars and the awesome power of supernovas. Yet, there is a fundamental connection between them.

To illustrate this connection, the familiar periodic table of elements—found in virtually every chemistry class—has been adapted to show how astronomers see the chemical Universe. What leaps out of this table is that the simplest elements, hydrogen and helium, are far and away the most abundant.

Periodic Table alteration

The Periodic Table

The Universe started out with baryonic matter in its simplest form, hydrogen. In just the first 20 minutes or so after the Big Bang, about 25% of the hydrogen was converted to helium. In essence, the chemical history of the Universe can be divided into two mainphases: one lasting 20 minutes, and the rest lasting for 13.7 billion years and counting.

One of the principal scientific accomplishments of the Chandra X-ray Observatory has been to help unravel how the chemical enrichment by stellar winds and supernovas works on a galactic and intergalactic scale.

Cassiopeia A (Cas A, for short), the youngest supernova remnant in the Milky Way.Credit: NASA/CXC/MIT/UMass Amherst/M.D.Stage et al.

Chandra images and spectra of individual supernova remnants reveal clouds of gas rich in elements such as oxygen, silicon, sulfur, calcium and iron, and track the speed at which these elements have been ejected in the explosion. The Chandra image of the Cas A supernova remnant shows iron rich ejecta outside silicon-rich ejecta, thus indicating that turbulent mixing and an aspherical explosion turned much of the original star inside out. Observations of Doppler-shifted emission lines for Cas A and other supernova remnants are providing three-dimensional information on the distribution and velocity of the supernova ejecta which will help to constrain models for the explosion.

See the full article here.

Chandra X-ray Center, Operated for NASA by the Smithsonian Astrophysical Observatory

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