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: “Seeing the Messages Microbes Send”

Novel chemical imaging instrument shows how bacteria support diverse, nearby colonies

March 2013
Suraiya Farukhi
Christine Sharp

“Results: With a novel technique that noninvasively analyzes microbes, scientists at Pacific Northwest National Laboratory profiled, for the first time, the chemicals that a cyanobacterium makes available to others. Over 4 days, Synechococcus sp. PCC 7002 steadily secretes two molecules that could be used as resources by other bacteria that are nearby. The technique that chemically profiles the microbial communities in both space and time is Nanospray Desorption Ionization Electrospray Mass Spectrometry, or nano-DESI. This instrument was built by Dr. Julia Laskin and her team at Pacific Northwest National Laboratory. This research graced the cover of Analyst.

Scientists at Pacific Northwest National Laboratory used the nano-DESI to show how bacteria support other colonies. No image credit.

‘This is a tool that will help microbiologists identify molecules that promote or inhibit growth of microbial communities,’ said Lab Fellow Laskin. ‘It also gives us much better control for studying interactions between microbial communities.’

Why It Matters: Understanding microbial ecology — how bacteria, algae and other microbes influence each other — could provide basic answers needed to advance sustainable energy. For example, Synechococcus sp. PCC 7002 uses carbon dioxide and sunlight to produce sugars that fuel the colony. Knowing how to best grow and modify these bacteria to mass-produce fuels could increase our nation’s energy independence. Here, nano-DESI provides key data for sustainable energy, but the opportunities stretch much farther.

‘Any place where there are microbes and you have a format where nano-DESI could be applied, you can study that ecology,’ said Dr. Allan Konopka, a biologist and Lab Fellow at PNNL who worked on the study. ‘This opens doors to a host of applications, such as understanding how bacteria associated with plant roots affect a plant.’”

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: “Synthetic molecule first electricity-making catalyst to use iron to split hydrogen gas”

February 17, 2013
Mary Beckman

“To make fuel cells more economical, engineers want a fast and efficient iron-based molecule that splits hydrogen gas to make electricity. Online Feb. 17 at Nature Chemistry, researchers report such a catalyst. It is the first iron-based catalyst that converts hydrogen directly to electricity. The result moves chemists and engineers one step closer to widely affordable fuel cells.

Burning hydrogen in a fuel cell generates an electrical current. A new iron-based catalyst might help make those fuel cells less expensive.

‘A drawback with today’s fuel cells is that the platinum they use is more than a thousand times more expensive than iron,’ said chemist R. Morris Bullock, who leads the research at the Department of Energy’s Pacific Northwest National Laboratory.

His team at the Center for Molecular Electrocatalysis has been developing catalysts that use cheaper metals such as nickel and iron. The one they report here can split hydrogen as fast as two molecules per second with an efficiency approaching those of commercial catalysts. The center is one of 46 Energy Frontier Research Centers established by the DOE Office of Science across the nation in 2009 to accelerate basic research in energy.

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.”

See the full article here.

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: “Proton Delivery and Removal Can Speed or Distract Common Catalyst”

Placing protons in the right spot lets catalysts avoid wasting time and energy on profligate reactions

February 2013
Suraiya Farukhi
Christine Sharp

“Results: Proton delivery and removal determines if a well-studied catalyst takes its highly productive form or twists into a less useful structure, according to scientists at Pacific Northwest National Laboratory. The catalyst takes two protons and forms molecular hydrogen, or it can split the hydrogen. The team showed that the most productive isomer, endo/endo, has the key nitrogen-hydrogen bonds pushed close to the nickel center. If the catalyst is in the endo/endo form, the reaction occurs in a fraction of a second. If the catalyst is stuck in another form, the reaction takes days to complete.

While one configuration (endo/endo) of a popular nickel catalyst can produce thousands of hydrogen molecules a second, the other forms that place the proton farther from the center are slower and less efficient. No image credit

‘When we started on the research, there was the belief that breaking or forming hydrogen was the crucial step,’ said Dr. Simone Raugei, a PNNL theoretician. ‘It isn’t. It is putting protons in the right spot on the catalyst. Once you have them in the right spot, everything goes very quickly.’

Why It Matters: The fundamental chemical questions around how protons move underlie a host of energy challenges, including fuels and fertilizer production. Agricultural waste and other fuel feedstocks are packed with oxygen that needs to be replaced with hydrogen. Adding hydrogen to nitrogen to create ammonia for fertilizer uses about 1% of the world’s energy. Improving these reactions and those that result in the widespread use of fuel cells requires understanding the basics of how protons move.

‘The catalyst we studied is the fastest of its type with hydrogen, but it still isn’t fast enough to put in a fuel cell and drive down the road,’ said Dr. Wendy Shaw, a biophysical chemist at PNNL. ‘To get the catalysts to achieve their full potential, we need to understand all of the bottlenecks and how to overcome them.’”

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: “Seeing a Common Catalyst with New Eyes”

Chemical imaging microscope shows corrugated gamma-alumina surface
January 2013
Suraiya Farukhi
Christine Sharp

“Results: Neither smooth nor disordered, gamma-alumina nanoparticles are corrugated with tiny pores inside, according to scientists at Pacific Northwest National Laboratory. Using a powerful transmission electron microscope, the team obtained ultrahigh-resolution images and chemical data about the particle’s surface. They found that the particles were covered with ridges made from a more open, yet symmetrical, arrangement of atoms. The open arrangement on the surfaces, notated as (110), covers 70% of the nanoparticle.

The surface of the plate-like particles is far from smooth, according to a new transmission electron microscopy study conducted by Pacific Northwest National Laboratory and the FEI Company.

By understanding the structure and function of tiny gamma-alumina particles, scientists are taking crucial steps to optimizing and realizing new useful properties for these materials. ‘If we can learn about the surfaces, then we can tailor them and make them more efficient in catalytic applications,’ said Dr. Libor Kovarik, who led the imaging study as part of PNNL’s Chemical Imaging Initiative.

Why It Matters: Reducing refineries’ energy demands or car and truck emissions requires efficient catalysts on durable support materials. The supporting material must withstand severe temperature and pressure changes. Gamma-alumina has been studied extensively, but its atomic arrangement has not been established because of the challenge of getting a detailed view of this complex material. Accurately describing the atomic structure is crucial for understanding and taking advantage of the best properties of gamma-alumina.

‘Catalytic research demands this type of state-of-the-art chemical imaging research,’ said Dr. Charles Peden, a heterogeneous catalysis scientist who worked on the study, and an Associate Director of PNNL’s Institute for Integrated Catalysis. ‘Dr. Kovarik’s outstanding new images from this powerhouse microscope have yielded unprecedented new information about a catalyst material of enormous practical utility.’”

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: “An Unexpected Pairing of Frustrated Molecules”

Scientists at PNNL explain how separated molecules get together to split hydrogen

January 2013
No Writer Credit

“Results: While their shapes frustrate traditional bonding, two unreactive molecules come together and surround themselves within a solvent cage to create a reactive environment to split hydrogen, according to two new studies by scientists at Pacific Northwest National Laboratory. Splitting a hydrogen molecule into a proton and a hydride ion (H-), known as activating the hydrogen, is vital for sustainable energy production and storage. The pair of molecules is called a frustrated Lewis pair or FLP.

At Pacific Northwest National Laboratory, researchers built simulations showing how two molecules combine to activate hydrogen, shedding new light on a reaction that could, one day, support hydrogenation of biofuels.(No image credit)

Why It Matters: Turning plant material or other renewable resources into fuels requires adding hydrogen with minimal use of external energy. This demands an effective catalyst. The studies provide fundamental insights into the processes that could one day be used to optimize that catalyst.

‘This is very fundamental research,’ said Dr. Shawn Kathmann, a PNNL theoretician on the project. ‘It is advancing our struggle to understand more complex catalyzed reactions.’”

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: “Metabolomics Key to Identifying Disease Pathway”

Research reveals lactic acid’s role in lung disease

January 2013
Suraiya Farukhi
Christine Sharp

“Results:Expertise at Pacific Northwest National Laboratory contributed to the understanding of the role of cellular metabolism in the pathogenesis of a currently untreatable lung disease. This research, reported in the American Journal of Respiratory and Critical Care Medicine, highlights the importance of PNNL’s nuclear magnetic resonance (NMR) metabolomics in the field of biomedicine.

Top: Lactic acid concentrations were measured in whole lung homogenates using ¹H-PASS nuclear magnetic resonance (NMR) spectroscopy obtained from patients with idiopathic pulmonary fibrosis (IPF) and compared with healthy control subjects. Bottom: Lactate dehydrogenase-5 (LDH5) expression is elevated in fibroblasts and lung tissue from IPF patients. LDH5 is responsible for the generation of lactic acid. Immunohistochemistry is shown for LDH5 performed on lung tissue sections from a healthy control subject (left) and a patient with IPF (right). LDH5 expression, shown as the reddish-brown stained area, is increased in the lung tissue of patients with IPF.

Why It Matters: Scientists increasingly recognize that dysregulated, or impaired, cellular metabolism impacts disease processes. However, they know little about the role of cellular metabolism as it relates to lung disease. Greater understanding of the dysregulated processes in human diseases will help in developing improved diagnostic and treatment strategies.”

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: “A Pathway for Protons”

Efficient delivery to material’s center turns oxygen cleanly into water

January 2013
No Writer Credit

Results : Pushing protons around may sound like a small task, but it is a big part of energy independence for the United States. Moving four relatively large protons to where they are needed is easier if you build a path, as is being done by scientists at the Center for Molecular Electrocatalysis. The research team has built two iron-based compounds that help protons move from the exterior to where they are needed. Once delivered, the protons bond with molecular oxygen, O2, and create water. In previous compounds, the protons often don’t arrive in time or go to the wrong place, which leads to forming the unwanted byproduct hydrogen peroxide (H2O2). The new compounds direct the protons in ways that help separate the two oxygen atoms in O2, and thereby drives the reaction to completion.

‘While water is the end product, it is not the goal of our work. These studies show that we can take the knowledge that the Center for Molecular Electrocatalysis has learned for reactions that move two protons and apply that knowledge to the challenge of relaying four protons,’ said Dr. James Mayer, an expert in proton-coupled electron transfer reactions and a professor at the University of Washington, who led this research.

Why It Matters: Understanding how to move protons efficiently lets scientists design new materials that can turn electrons generated by wind turbines and solar farms into fuels, creating easily transported, use-any-time alternatives to coal and oil.

‘We want to generate as much power as we can when the conditions are right and store the energy,’ said Dr. Monte Helm, Deputy Director for the Center for Molecular Electrocatalysis. ‘This research is directly related to storing that energy in chemical bonds, so we can get the energy out at a future time, when necessary.’”

Scientists from the Center for Molecular Electrocatalysis have built two iron-based compounds that help protons move from the exterior to where they are needed. Once delivered, the protons bond with molecular oxygen and create water. No image credit

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: “Carbon dioxide reveals a predilection for tumbling alone and lining up together”

Pacific Northwest National Laboratory

Carbon Dioxide emissions are very important, so this research is very important.

December 2012
Suraiya Farukhi
Christine Sharp

“Results: Crowded together on a titanium dioxide surface, carbon dioxide molecules relinquish their free-tumbling ways to form crooked lines and cling to molecules in nearby lines, according to scientists at Pacific Northwest National Laboratory. Bringing together a trio of instruments and a supercomputer, the team joined experiments and theory to understand carbon dioxide’s behavior.

‘We want to build our understanding from the ground up,’ said Dr. Zdenek Dohnalek, an experimental chemist on the study. ‘We want to understand the interaction of carbon dioxide with well-known models of oxides, such as titanium dioxide.’

Carbon dioxide diffuses on titanium rows by a tumbling mechanism. Once bound to a titanium atom, the carbon dioxide’s axis tilts. No image credit.

Why It Matters: Understanding how carbon dioxide molecules behave is basic science needed by the energy sector to facilitate carbon sequestration and fuel production. Sequestration stores carbon dioxide emissions from power plants underground. Fuel production uses the carbon dioxide as a building block to create fuels.

‘While titanium dioxide is a model material that will likely not be used to sequester carbon dioxide or serve as a catalyst for fuel conversion, the fundamental aspects of carbon dioxide reactivity revealed in our study are very intriguing,’ said Dr. Xiao Lin, a Linus Pauling Postdoctoral Fellow at PNNL, who proposed this research as part of his fellowship.”

See the full article here.

“Located in Richland, Washington, PNNL is one among ten U.S. Department of Energy (DOE) national laboratories managed by DOE’s Office of Science. Our research strengthens the U.S. foundation for innovation, and we help find solutions for not only DOE, but for the U.S. Department of Homeland Security, the National Nuclear Security Administration, other government agencies, universities and industry.”

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From PNNL Lab: “New Protein Discovered Gives Insights to Iron’s Fate Underground”

August 2012
Christine Sharp
Suraiya Farukhi

Scientists identify molecule that steals electrons, leaving iron stuck in the mud

Results: It’s almost an evil twin story; a protein that steals electrons from iron in one microbe looks a lot like one that adds electrons in another microbe, according to scientists at Pacific Northwest National Laboratory and the University of East Anglia. Their survey of the genes of common groundwater bacterium Sideroxydans lithotrophicus ES-1, which removes electrons from iron, revealed that it contained genes in common with Shewanella oneidensis MR-1, which adds electrons to iron.

Proposed roles of MtoAB and CymAES-1 in Sideroxydans lithotrophicus ES-1-mediated extracellular Fe(II) oxidation. Decaheme c-Cyt MtoA, which is inserted into the porin-like, outer membrane (OM) protein MtoB, oxidizes Fe(II) directly on the bacterial surface and transfers the released electrons across the OM to the periplasmic proteins that have yet to be identified. The periplasmic proteins relay the electrons through the periplasm (PS) to the tetraheme c-Cyt CymAES-1. CymAES-1, located in the cytoplasmic or inner membrane (IM), reduces quinone to quinol. c-Cyts are labeled in red, and the direction of electron transfer is indicated by a yellow arrows. No image credit

Their results contribute to understanding of the molecular mechanisms by which microorganisms change the electron configuration of iron and, thus, change its mobility. The research was published in Frontiers in Microbiological Chemistry.

‘Recent studies indicate that aerobic Fe(II)-oxidizing bacteria, FeOB, would play a key role in niches having low levels of oxygen concentration, where microbial Fe(II)-oxidation can compete with the chemical oxidation of Fe(II),’ said PNNL biogeochemist Dr. Juan Liu, first author of the study paper.

Why It Matters: Science has realized the importance of microorganisms in research on processes such as carbon sequestration, the generation of new energy sources, and the movement and ultimate resting place of contaminants. Scientists are interested in the oxidation state, or loss of electrons, of iron because it dramatically affects the metal’s solubility in water, in which electron transfer proteins play critical roles. In contrast to Fe(II), trivalent iron, Fe(III), is not water soluble.

The difference in solubility between Fe(II) and Fe(III) also means that iron acquisition tends to be much more of a problem for organisms that use oxygen than for those that don’t, because anaerobic environments favor the more soluble Fe(II).

‘We have shown the generality of these reaction mechanisms in metal oxidizing and reducing bacteria,’ said Dr. Liang Shi, a PNNL microbiologist who led the study. ‘Whether it’s Fe(II) or Fe(III), iron’s solubility affects its accessibility to microorganisms. To access these different phases of Fe, some microorganisms seem to adopt a common mechanism.’”

See the full article here.

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