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  • richardmitnick 3:40 pm on September 22, 2015 Permalink | Reply
    Tags: , Chemistry,   

    From ETH Zürich: “Chemistry for the methanol economy” 

    ETH Zurich bloc

    ETH Zürich

    Fabio Bergamin

    Unstable crude oil prices and limited oil resources have made the production of petrochemicals from methanol increasingly popular – above all in China. Scientists at ETH Zurich have now deciphered the complex chemistry behind the start of this process.

    The Shenhua Baotou production plant in north China converts coal into so-called olefins since 2010. It is the first industrial plant of its kind worldwide. (Photo: Syn Energy Technology Co. Ltd.)

    Ethylene is produced in greater amounts than any other basic chemical in the world. The small molecule consisting of two carbon atoms and four hydrogen atoms, it is a basic building block in the manufacture of a wide range of basic chemicals, polymers and plasticisers. The packaging material polyethylene (PE) is just one popular application among many. Today ethylene is primarily manufactured from crude oil in a process known as cracking, but the ongoing price volatility and the finite availability of crude oil have caused a surge for an alternative manufacturing approach: its synthesis from methanol in the so-called methanol-to-olefins (MTO) process. Now a team of scientists at ETH Zurich and ENS Lyon has worked out in detail how the reaction begins.

    Chemists developed the MTO process in the late 1970s, and today there are manufacturing plants all over the world. China has more MTO plants than any other country: five large-scale facilities are currently in operation and a further thirteen are planned. The reason for this is simple: China has a huge demand for petrochemicals with limited access to oil deposits. What the country does have is large coal reserves, and methanol can be manufactured quite easily by gasifying coal. In addition, methanol can be made from natural gas. Consequently, Chinese investors are planning to manufacture methanol in the United States for export to China, drawing on the U.S.’s plentiful shale gas reserves.

    Where does the carbenium ion come from?

    For the MTO reaction to occur, methanol is brought together with so-called zeolites at 400 degrees Celsius. These zeolites are porous, granular aluminosilicate minerals facilitating the reaction as catalysts. For a long time, chemists were unable to exactly explain the MTO reaction. 20 years ago scientists postulated that other molecules had to be involved: positively charged cyclic hydrocarbon molecules in which five to six carbon atoms are bonded together, also known as cyclic carbenium ions. Such species actually react with methanol: They stitch two methanol molecules together and form a carbon-carbon bond, before producing ethylene.

    However, if these cyclic carbenium ions are involved and necessary for the reaction to start, the question is where do they come from? Many scientists proposed that these ions must be present as adventitious contaminants in methanol.

    Now the Franco-Swiss research team has proposed a different explanation. “We have shown that alumina, which is always present in zeolites, can easily transform methanol into ethylene and other hydrocarbons, which can then be converted into carbenium ions in the pores of the zeolite catalyst,” explains Christophe Copéret, Professor of Surface and Interface Chemistry at ETH Zurich and one of the authors of the study. “While the MTO process is up and running at industrial scale, this work shades new light on how the process starts. And it shows that simple oxide materials like alumina can trigger carbon-carbon bond formation from methanol derivatives, thus opening new avenues for the upgrading of methanol into long chain hydrocarbons.”

    See the full article here .

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    ETH Zurich campus
    ETH Zurich is one of the leading international universities for technology and the natural sciences. It is well known for its excellent education, ground-breaking fundamental research and for implementing its results directly into practice.

    Founded in 1855, ETH Zurich today has more than 18,500 students from over 110 countries, including 4,000 doctoral students. To researchers, it offers an inspiring working environment, to students, a comprehensive education.

    Twenty-one Nobel Laureates have studied, taught or conducted research at ETH Zurich, underlining the excellent reputation of the university.

  • richardmitnick 8:52 am on August 11, 2015 Permalink | Reply
    Tags: , Chemistry,   

    From Princeton: “Nozomi Ando: Breaking free with a love of chemistry” 

    Princeton University
    Princeton University

    August 10, 2015
    Tien Nguyen, Department of Chemistry

    The research of Nozomi Ando (above), a Princeton University assistant professor of chemistry, pushes the limits of using X-ray-based methods to unravel the structure of enzymes, which could help scientists understand how these incredibly complex molecules are central to biological processes such as cellular metabolism and DNA replication. Photos by Todd Reichart, Department of Chemistry

    At two in the morning, Princeton University’s Frick Chemistry Laboratory appears quiet and cavernous. But if you listen closely, faint drumbeats might be heard coming from the lab of Nozomi Ando as she and her students work to their favorite late-night band, Queen.

    “The hours aren’t required — we’ve just been driven by excitement about the science,” said Ando, an assistant professor in chemistry who joined the Princeton faculty in 2014. Almost a year later, Ando said the lab is still in the fun phase, energized by the constant collection of new data: “For me, it’s brain candy.”

    The Ando lab has already attracted two postdoctoral researchers, a graduate student and five undergraduates, all of them eager to be involved in her ambitious research program. These projects aim to push the limits of using X-ray-based methods in structural enzymology, which is the study of the structure of enzymes such as those responsible for cellular metabolism and DNA replication. Unraveling the structure of these incredibly complex molecules helps scientists understand how the enzymes operate in these biological processes.

    In a common application of X-ray methods, known as X-ray crystallography, scientists shoot X-rays at a crystalline sample and use the beam’s scattering patterns to produce a model of the compound’s structure. In one project the Ando group has termed “hacking crystallography,” Ando proposed that instead of collecting the X-ray scattering patterns in the experiment, they gather the background data, which can be an intricate and unruly set of data.

    Because the atoms in the sample are moving slightly, if the researchers can find a way to interpret this data, they could construct a molecular movie instead of a snapshot. The way enzymes change position reveals information about their function, as enzymes often must adopt specific conformations to carry out their jobs. Only 10 or so articles have been published around this challenging concept, but Ando said she hopes to create a “renaissance” in this area.

    Garnet Chan, the Hepburn Professor of Theoretical Chemistry at Princeton, said that with Ando’s unique application of X-ray techniques, she would be at the forefront of a new class of discoveries. “I see her contributing in a big way to the development of the department,” he said.

    With X-ray crystallography, scientists typically model a compound’s structure by shooting a light beam at a crystalline sample of the compound and recording how the beams scatter. In one project, Ando proposed instead collecting the background data, which can be used to create a molecular movie instead of a snapshot. The X-ray image above is visualized as a topographical map that shows sharp diffraction peaks as well as weak, noisy signals, all of which form a comprehensive view of a compound’s structure. (Data visualization courtesy of Nozomi Ando, Department of Chemistry)

    Developing a laser focus

    Ando has always been very independent, said her father Teichii Ando, a professor of materials science at Northeastern University. He recounted how she became interested in singing as a teen, and sought out lessons on her own, paying with her earnings from tutoring. Ando’s passion for classical singing continued well into her graduate studies at Cornell University, and she even performed operatic arias during site visits from the National Science Foundation (NSF) to Cornell’s High Energy Synchrotron Source, where her Ph.D. adviser, Sol Gruner, was director.

    As a physics graduate student in Gruner’s lab, Ando became an expert on small-angle X-ray scattering (SAXS), a specialized technique for studying the structure of proteins in solution. The X-ray beams used in her experiments were generated by the Cornell synchrotron, which is a massive underground particle accelerator that shoots subatomic particles around a half-mile-long circular track at close to the speed of light. Attached to the ring are laboratory spaces crowded with computers, fumehoods for prepping samples and a large metal box where the beam enters the room. “It felt like walking through a spaceship,” Ando said.

    Because there are only five synchrotrons in the United States, researchers must apply for time at these Department of Energy or NSF-funded facilities. During the Ando lab’s first trip to Cornell’s synchrotron last October, they collected months’ worth of data over the course of four sleepless nights — and afterward emerged with their shared appreciation for Queen.

    Ando works with chemistry major and rising senior Emily Adler to interpret scattering images from an experiment conducted on a synchrotron, which is a massive underground particle accelerator that shoots subatomic particles around a half-mile-long circular track at close to the speed of light.

    “It’s definitely a team effort to get everything done,” said Kate Davis, a postdoctoral researcher in the Ando lab. She described the lab environment as incredibly positive and non-judgmental, a particularly beneficial characteristic because the group members all come from different scientific backgrounds.

    “It’s an atmosphere where it’s OK to say ‘I don’t know,’ but then of course we apply ourselves to learning the answer,” said Buz Barstow, a Burroughs Wellcome Fund CASI Fellow at Princeton and Ando’s husband. His research is focused on engineering biological processes to store renewable energy. Barstow and Ando’s research teams work together closely and share scientific expertise at joint group meetings.

    To ensure the researchers develop a solid grasp on the fundamentals of the work, Ando and Barstow have rotating group members present chapters of a physical biochemistry textbook. “Being able to explain something simply is really important — it’s the ultimate indicator of understanding,” Ando said.

    Ando is herself a gifted communicator, colleagues said.

    “It’s rare to find someone who can hold a meaningful back-and-forth with biologists, biochemists and physicists,” said Ando’s postdoctoral adviser, Catherine Drennan, a professor of chemistry and biology at the Massachusetts Institute of Technology and the Howard Hughes Medical Institute. “It’s one of the things that makes her special.”

    Rising junior and chemistry major Isao Anzai inoculates cultures in Ando’s laboratory. Since joining Princeton’s faculty in 2014, Ando has already attracted two postdoctoral researchers, a graduate student and five undergraduates with her ambitious research program.

    As a postdoctoral researcher, Ando brought her skills in small-angle X-ray scattering to a project that involved three lab groups. The goal was to elucidate the structure of ribonucleotide reductase (RNR), a key enzyme for DNA replication and repair, using a combination of strategies. The team had modeled possible structures using electron microscopy, crystallography and small-angle X-ray scattering techniques that didn’t make sense. They expected to see a ring structure but instead their model looked like a crazy lattice, Ando said.

    Drennan recalled how Ando gathered the whole team around the computer so that they could look at it as a group. Upon tweaking the color scheme, they realized that they were actually looking at not one ring, but two interlocking rings. In this ring configuration, RNR was essentially inactive and unable to participate in electron transfer. Their findings provided a vital connection between the enzyme’s conformation and activity, and were reported in the journal Proceedings of the National Academy of Sciences in 2011.

    Ando also is promoting scientific collaboration at Princeton. She has begun working with researchers in the laboratory of Mohammad Seyedsayamdost, an assistant professor of chemistry, who shares Ando’s interest in complex enzymes. “It was very clear from Nozomi’s interview that with her skill set she would be the focal point of many different collaborations,” Seyedsayamdost said.

    Ando brings people together even beyond the lab bench. When she coordinated the Drennan lab’s participation in the competitive departmental Halloween group costume contest at MIT, they won dressed as free radicals by donning Che Guevara-esque berets and T-shirts that Ando had designed with chemical structures of radical molecules.

    When preparing to start her assistant professorship at Princeton, Ando said she briefly pondered adopting a more conservative style, but decided against it. “Have I ever liked being conventional?” she said, reflecting on her personal and professional decisions. “No.”

    See the full article here.

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    Princeton University Campus

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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  • richardmitnick 2:21 pm on August 3, 2015 Permalink | Reply
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    From NYU: NYU Scientists bring order, and color, to microparticles” 


    New York University

    August 3, 2015
    No Writer Credit

    A team of New York University scientists has developed a technique that prompts microparticles to form ordered structures in a variety of materials. The advance offers a method to potentially improve the makeup and color of optical materials used in computer screens along with other consumer products. (c) iStock/dolphfyn

    A team of New York University scientists has developed a technique that prompts microparticles to form ordered structures in a variety of materials. The advance, which appears in the Journal of the American Chemical Society (JACS) as an “Editors’ Choice” article, offers a method to potentially improve the makeup and color of optical materials used in computer screens along with other consumer products.

    The work is centered on enhancing the arrangement of colloids—small particles suspended within a fluid medium. Colloidal dispersions are composed of such everyday items such as paint, milk, gelatin, glass, and porcelain, but their potential to create new materials remains largely untapped.

    Notably, DNA-coated colloids offer particular promise because they can be linked together, with DNA serving as the glue to form a range of new colloidal structures. However, previous attempts have produced uneven results, with these particles attaching to each other in ways that produce chaotic or inflexible configurations.

    The NYU team developed a new method to apply DNA coating to colloids so that they crystallize—or form new compounds—in an orderly manner. Specifically, it employed a synthetic strategy—click chemistry—introduced more than a decade ago that is a highly efficient way of attaching DNA. Here, scientists initiated a chemical reaction that allows molecular components to stick together in a particular fashion—a process some have compared to connecting Legos.

    In a previous paper, published earlier this year in the journal Nature Communications, the research team outlined the successful execution of this technique. However, the method, at that point, could manipulate only one type of particle. In the JACS study, the research team shows the procedure can handle five additional types of materials—and in different combinations.

    The advance, the scientists say, is akin to a builder having the capacity to construct a house using glass, metal, brick, and concrete—rather than only wood.

    “If you want to program and create structures at microscopic levels, you need to have the ability for a particle to move around and find its optimal position,” explains David Pine, a professor of physics at NYU and chair of the Chemical and Bioengineering Department at NYU Polytechnic School of Engineering. “Our research shows that this be done and be achieved with multiple materials, all resulting in several different types of compounds.”

    The work was conducted by researchers at NYU’s Molecular Design Institute and Center for Soft Matter Research and at South Korea’s Sungkyunkwan University. The paper’s other authors were: Yufeng Wang of the Center for Soft Matter Research and Molecular Design Institute; Yu Wang and Xiaolong Zheng of the Molecular Design Institute; Etienne Ducrot of the Center for Soft Matter Research; Myung-Goo Lee and Gi-Ra Yi of Sungkyunkwan University’s School of Chemical Engineering; and Marcus Weck of the Molecular Design Institute.

    The research was supported, in part, by grants from the U.S. Army Research Office (W911NF- 510 10-1-0518), the National Research Foundation of Korea (NRF-2014S1A2A2028608), and by the National Science Foundation’s Materials Research Science and Engineering Center (MRSEC) Program (DMR-0820341).

    NYU’s center is one of 24 MRSECs in the country. These NSF-backed centers support interdisciplinary and multidisciplinary materials research to address fundamental problems in science and engineering.

    For more on the NYU MRSEC, click here.

    See the full article here..

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    More than 175 years ago, Albert Gallatin, the distinguished statesman who served as secretary of the treasury under Presidents Thomas Jefferson and James Madison, declared his intention to establish “in this immense and fast-growing city … a system of rational and practical education fitting for all and graciously opened to all.” Founded in 1831, New York University is now one of the largest private universities in the United States. Of the more than 3,000 colleges and universities in America, New York University is one of only 60 member institutions of the distinguished Association of American Universities.

  • richardmitnick 9:31 am on July 30, 2015 Permalink | Reply
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    From livescience: “Origin-of-Life Story May Have Found Its Missing Link” 


    June 06, 2015
    Jesse Emspak

    A field of geysers called El Tatio located in northern Chile’s Andes Mountains. Credit: Gerald Prins

    How did life on Earth begin? It’s been one of modern biology’s greatest mysteries: How did the chemical soup that existed on the early Earth lead to the complex molecules needed to create living, breathing organisms? Now, researchers say they’ve found the missing link.

    Between 4.6 billion and 4.0 billion years ago, there was probably no life on Earth. The planet’s surface was at first molten and even as it cooled, it was getting pulverized by asteroids and comets. All that existed were simple chemicals. But about 3.8 billion years ago, the bombardment stopped, and life arose. Most scientists think the “last universal common ancestor” — the creature from which everything on the planet descends — appeared about 3.6 billion years ago.

    But exactly how that creature arose has long puzzled scientists. For instance, how did the chemistry of simple carbon-based molecules lead to the information storage of ribonucleic acid, or RNA?

    A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). Note that this is a single strand of RNA that folds back upon itself.

    The RNA molecule must store information to code for proteins. (Proteins in biology do more than build muscle — they also regulate a host of processes in the body.)

    The new research — which involves two studies, one led by Charles Carter and one led by Richard Wolfenden, both of the University of North Carolina — suggests a way for RNA to control the production of proteins by working with simple amino acids that does not require the more complex enzymes that exist today. [7 Theories on the Origin of Life on Earth]

    Missing RNA link

    This link would bridge this gap in knowledge between the primordial chemical soup and the complex molecules needed to build life. Current theories say life on Earth started in an “RNA world,” in which the RNA molecule guided the formation of life, only later taking a backseat to DNA, which could more efficiently achieve the same end result.

    The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structure of two base pairs are shown in the bottom right.

    Like DNA, RNA is a helix-shaped molecule that can store or pass on information. (DNA is a double-stranded helix, whereas RNA is single-stranded.) Many scientists think the first RNA molecules existed in a primordial chemical soup — probably pools of water on the surface of Earth billions of years ago. [Photo Timeline: How the Earth Formed]

    The idea was that the very first RNA molecules formed from collections of three chemicals: a sugar (called a ribose); a phosphate group, which is a phosphorus atom connected to oxygen atoms; and a base, which is a ring-shaped molecule of carbon, nitrogen, oxygen and hydrogen atoms. RNA also needed nucleotides, made of phosphates and sugars.

    The question: How did the nucleotides come together within the soupy chemicals to make RNA? John Sutherland, a chemist at the University of Cambridge in England, published a study in May in the journal Nature Chemistry that showed that a cyanide-based chemistry could make two of the four nucleotides in RNA and many amino acids.

    That still left questions, though. There wasn’t a good mechanism for putting nucleotides together to make RNA. Nor did there seem to be a natural way for amino acids to string together and form proteins. Today, adenosine triphosphate (ATP) does the job of linking amino acids into proteins, activated by an enzyme called aminoacyl tRNA synthetase. But there’s no reason to assume there were any such chemicals around billions of years ago.

    Also, proteins have to be shaped a certain way in order to function properly. That means RNA has to be able to guide their formation — it has to “code” for them, like a computer running a program to do a task.

    Carter noted that it wasn’t until the past decade or two that scientists were able to duplicate the chemistry that makes RNA build proteins in the lab. “Basically, the only way to get RNA was to evolve humans first,” he said. “It doesn’t do it on its own.”

    Perfect sizes

    In one of the new studies, Carter looked at the way a molecule called “transfer RNA,” or tRNA, reacts with different amino acids.

    They found that one end of the tRNA could help sort amino acids according to their shape and size, while the other end could link up with amino acids of a certain polarity. In that way, this tRNA molecule could dictate how amino acids come together to make proteins, as well as determine the final protein shape. That’s similar to what the ATP enzyme does today, activating the process that strings together amino acids to form proteins.

    Carter told Live Science that the ability to discriminate according to size and shape makes a kind of “code” for proteins called peptides, which help to preserve the helix shape of RNA.

    “It’s an intermediate step in the development of genetic coding,” he said.

    In the other study, Wolfenden and colleagues tested the way proteins fold in response to temperature, since life somehow arose from a proverbial boiling pot of chemicals on early Earth. They looked at life’s building blocks, amino acids, and how they distribute in water and oil — a quality called hydrophobicity. They found that the amino acids’ relationships were consistent even at high temperatures — the shape, size and polarity of the amino acids are what mattered when they strung together to form proteins, which have particular structures.

    “What we’re asking here is, ‘Would the rules of folding have been different?'” Wolfenden said. At higher temperatures, some chemical relationships change because there is more thermal energy. But that wasn’t the case here.

    By showing that it’s possible for tRNA to discriminate between molecules, and that the links can work without “help,” Carter thinks he’s found a way for the information storage of chemical structures like tRNA to have arisen — a crucial piece of passing on genetic traits. Combined with the work on amino acids and temperature, it offers insight into how early life might have evolved.

    This work still doesn’t answer the ultimate question of how life began, but it does show a mechanism for the appearance of the genetic codes that pass on inherited traits, which got evolution rolling.

    The two studies are published in the June 1 issue of the journal Proceedings of the National Academy of Sciences.

    See the full article here.

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  • richardmitnick 7:34 am on July 29, 2015 Permalink | Reply
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    From Princeton: “New chemistry makes strong bonds weak” 

    Princeton University
    Princeton University

    July 28 2015
    Tien Nguyen

    Researchers at Princeton have developed a new chemical reaction that breaks the strongest bond in a molecule instead of the weakest, completely reversing the norm for reactions in which bonds are evenly split to form reactive intermediates.

    Catalytic alkene carboamination enabled by oxidative proton-coupled electron transfer

    Published on July 13 in the Journal of the American Chemical Society, the non-conventional reaction is a proof of concept that will allow chemists to access compounds that are normally off-limits to this pathway. The team used a two-component catalyst system that works in tandem to selectively activate the strongest bond in the molecule, a nitrogen-hydrogen (N-H) bond, through a process known as proton-coupled electron transfer (PCET).

    “This PCET chemistry was really interesting to us. In particular, the idea that you can use catalysts to modulate an intrinsic property of a molecule allows you to access chemical space that you couldn’t otherwise,” said Robert Knowles, an assistant professor of chemistry who led the research.

    Using PCET as a way to break strong bonds is seen in many essential biological systems, including photosynthesis and respiration, he said. Though this phenomenon is known in biological and inorganic chemistry settings, it hasn’t been widely applied to making new molecules—something Knowles hopes to change.

    Given the unexplored state of PCET catalysis, Knowles decided to turn to theory instead of the trial and error approach usually taken by synthetic chemists in the initial stages of reaction development. Using a simple mathematical formula, the researchers calculated, for any pair of catalysts, the pair’s combined “effective bond strength,” which is the strength of the strongest bond they could break. Because both molecules independently contribute to this value, the research team had a high degree of flexibility in designing the catalyst system.

    When they tested the catalyst pairs in the lab, the researchers observed a striking correlation between the “effective bond strength” and the reaction efficiency. While effective bond strengths that were lower or higher than the target N-H bond strength gave low reaction yields, the researchers found that matching the strengths promoted the reaction in very high yield.

    “To see this formula actually working was really inspiring,” said Gilbert Choi, a graduate student in the Knowles lab and lead author on the work. Once he identified a successful catalyst system, he explored the scope of the reaction and its mechanism.

    Proposed catalytic cycle

    The researchers think that the reaction starts with one of the catalysts, a compound called dibutylphosphate, tugging on a hydrogen atom, which lengthens and weakens the N-H bond. At the same time, the other catalyst, known as a light-activated iridium complex, targets the weakened bond and plucks off one electron from the two-electron bond, slicing it down the middle.

    Once the bond is split, the reactive nitrogen intermediate goes on to form a new carbon-nitrogen bond, giving rise to structurally complex products. This finding builds on work the Knowles lab published earlier this year also in the Journal of the American Chemical Society on a similar reaction that used a more sensitive catalyst system.

    Their research has laid a solid foundation for PCET catalysis as a platform for developing new reactions. “My sincere view is that ideas are a lot more valuable than reactions,” Knowles said. “I’m optimistic that people can use these ideas and do things that we hadn’t even considered.”

    See the full article here.

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    Princeton University Campus

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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  • richardmitnick 3:55 pm on July 27, 2015 Permalink | Reply
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    From SLAC: “New ‘Molecular Movie’ Reveals Ultrafast Chemistry in Motion” 

    SLAC Lab

    June 22, 2015

    This video describes how the Linac Coherent Light Source, an X-ray free-electron laser at SLAC National Accelerator Laboratory, provided the first direct measurements of how a ring-shaped gas molecule unravels in the millionths of a billionth of a second after it is split open by light. The measurements were compiled in sequence to form the basis for computer animations showing molecular motion. (SLAC National Accelerator Laboratory)

    Scientists for the first time tracked ultrafast structural changes, captured in quadrillionths-of-a-second steps, as ring-shaped gas molecules burst open and unraveled. Ring-shaped molecules are abundant in biochemistry and also form the basis for many drug compounds. The study points the way to a wide range of real-time X-ray studies of gas-based chemical reactions that are vital to biological processes.

    This illustration shows shape changes that occur in quadrillionths-of-a-second intervals in a ring-shaped molecule that was broken open by light. The molecular motion was measured using SLAC’s Linac Coherent Light Source X-ray laser. The colored chart shows a theoretical model of molecular changes that syncs well with the actual results. The squares in the background represent panels in an LCLS X-ray detector. (SLAC National Accelerator Laboratory)

    Researchers working at the Department of Energy’s SLAC National Accelerator Laboratory compiled the full sequence of steps in this basic ring-opening reaction into computerized animations that provide a “molecular movie” of the structural changes.

    Conducted at SLAC’s Linac Coherent Light Source, a DOE Office of Science User Facility, the pioneering study marks an important milestone in precisely tracking how gas-phase molecules transform during chemical reactions on the scale of femtoseconds. A femtosecond is a millionth of a billionth of a second.

    “This fulfills a promise of LCLS: Before your eyes, a chemical reaction is occurring that has never been seen before in this way,” said Mike Minitti, a SLAC scientist who led the experiment in collaboration with Peter Weber at Brown University. The results are featured in the June 22 edition of Physical Review Letters.

    “LCLS is a game-changer in giving us the ability to probe this and other reactions in record-fast timescales,” Minitti said, “down to the motion of individual atoms.” The same method can be used to study more complex molecules and chemistry.

    The free-floating molecules in a gas, when studied with the uniquely bright X-rays at LCLS, can provide a very clear view of structural changes because gas molecules are less likely to be tangled up with one another or otherwise obstructed, he added. “Until now, learning anything meaningful about such rapid molecular changes in a gas using other X-ray sources was very limited, at best.”

    New Views of Chemistry in Action

    The study focused on the gas form of 1,3-cyclohexadiene (CHD), a small, ring-shaped organic molecule derived from pine oil. Ring-shaped molecules play key roles in many biological and chemical processes that are driven by the formation and breaking of chemical bonds. The experiment tracked how the ringed molecule unfurls after a bond between two of its atoms is broken, transforming into a nearly linear molecule called hexatriene.

    “There had been a long-standing question of how this molecule actually opens up,” Minitti said. “The atoms can take different paths and directions. Tracking this ultimately shows how chemical reactions are truly progressing, and will likely lead to improvements in theories and models.”

    The Making of a Molecular Movie

    In the experiment, researchers excited CHD vapor with ultrafast ultraviolet laser pulses to begin the ring-opening reaction. Then they fired LCLS X-ray laser pulses at different time intervals to measure how the molecules changed their shape.

    Researchers compiled and sorted over 100,000 strobe-like measurements of scattered X-rays. Then, they matched these measurements to computer simulations that show the most likely ways the molecule unravels in the first 200 quadrillionths of a second after it opens. The simulations, performed by team member Adam Kirrander at the University of Edinburgh, show the changing motion and position of its atoms.

    Each interval in the animations represents 25 quadrillionths of a second ­– about 1.3 trillion times faster than the typical 30-frames-per-second rate used to display TV shows.

    “It is a remarkable achievement to watch molecular motions with such incredible time resolution,” Weber said.

    A gas sample was considered ideal for this study because interference from any neighboring CHD molecules would be minimized, making it easier to identify and track the transformation of individual molecules. The LCLS X-ray pulses were like cue balls in a game of billiards, scattering off the electrons of the molecules and onto a position-sensitive detector that projected the locations of the atoms within the molecules.

    A Successful Test Case for More Complex Studies

    “This study can serve as a benchmark and springboard for larger molecules that can help us explore and understand even more complex and important chemistry,” Minitti said.

    Additional contributors included scientists at Brown and Stanford universities in the U.S. and the University of Edinburgh in the U.K. The work was supported by the DOE Office of Basic Energy Sciences.

    See the full article here.

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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 9:31 am on July 24, 2015 Permalink | Reply
    Tags: , , Chemistry, , Vitamin B3   

    From NASA Goddard: “NASA Researchers Find “Frozen” Recipe for Extraterrestrial Vitamin” 

    NASA Goddard Banner
    Goddard Space Flight Center

    July 23, 2015
    Bill Steigerwald
    ​NASA Goddard Space Flight Center

    This is an artist’s concept of a protoplanetry disk surrounding a forming star that is ejecting jets of material (yellow beams). Such disks contain countless tiny dust grains, many of which become incorporated into asteroids, comets, and planets. Credits: NASA Goddard

    Vitamin B3 could have been made on icy dust grains in space, and later delivered to Earth by meteorites and comets, according to new laboratory experiments by a team of NASA-funded researchers. Vitamin B3, also known as niacin or nicotinic acid, is used to build NAD (nicotinamide adenine dinucleotide), which is essential to metabolism and probably ancient in origin. The result supports a theory that the origin of life may have been assisted by a supply of biologically important molecules produced in space and brought to Earth by comet and meteor impacts.

    The new work builds on earlier research by the team in which they analyzed carbon-rich meteorites and discovered that vitamin B3 was present at concentrations ranging from about 30 to 600 parts-per-billion. In that work, the team performed preliminary laboratory experiments that showed vitamin B3 could be made from a simpler building-block organic molecule called pyridine in carbon dioxide ice under conditions that simulated the environment in space.

    The new experiments made the simulation more realistic by adding water ice to the mixture and using amounts closer to what is expected for interstellar ices and comets. The team found that even with the addition of water, the vitamin could be made under a wide variety of scenarios where the water ice abundance varied by up to ten times.

    “We found that the types of organic compounds in our laboratory-produced ices match very well to what is found in meteorites,” said Karen Smith of NASA’s Goddard Space Flight Center in Greenbelt, Maryland. “This result suggests that these important organic compounds in meteorites may have originated from simple molecular ices in space. This type of chemistry may also be relevant for comets, which contain large amounts of water and carbon dioxide ices. These experiments show that vitamin B3 and other complex organic compounds could be made in space and it is plausible that meteorite and comet impacts could have added an extraterrestrial component to the supply of vitamin B3 on ancient Earth.”

    Smith, who is lead author of a paper on this research published online June 17, 2015 in Chemical Communications, performed the work with her team at NASA Goddard, including her postdoctoral research advisor, Perry Gerakines of NASA Goddard. “This work is part of a broad research program in the field of Astrobiology at NASA Goddard,” Gerakines said. “We are working to understand the origins of biologically important molecules and how they came to exist throughout the Solar System and on Earth. The experiments performed in our laboratory demonstrate an important possible connection between the complex organic molecules formed in cold interstellar space and those we find in meteorites.”

    Exploding stars (supernovae) and the winds from red giant stars near the end of their lives produce vast clouds of gas and dust. Solar systems are born when shock waves from stellar winds and other nearby supernovae compress and concentrate a cloud of ejected stellar material until dense clumps of that cloud begin to collapse under their own gravity, forming a new generation of stars and planets.

    These clouds contain countless dust grains. Just as frost forms on car windows during cold, humid nights, carbon dioxide, water, and other gases form a layer of frost on the surface of these grains. Radiation in space powers chemical reactions in this frost layer to produce complex organic molecules, possibly including vitamin B3. The icy grains become incorporated into comets and asteroids, some of which impact young planets like ancient Earth, delivering the organic molecules contained within them.

    This is an artist’s concept of a nebula containing gas, dust, and asteroids that will later form stars and planets. Credits: NASA Goddard

    The researchers tested this theory by simulating the space environment in the Cosmic Ice Laboratory at NASA Goddard. An aluminum plate cooled to around minus 423 degrees Fahrenheit (minus 253 Celsius) was used to represent the frigid surface of an interstellar dust grain. The plate was chilled in a vacuum chamber to replicate space conditions, and gases containing water, carbon dioxide, and pyridine were released into the chamber, where they froze onto the plate. The plate was then bombarded with protons at about 1 million volts from a particle accelerator to simulate space radiation.

    A picture of the aluminum plate with a chemical deposit on it. Credits: Karen Smith/NASA Goddard

    The team performed an initial analysis of the contents of the frozen layer by shining infrared light on it to identify absorption patterns – certain molecules absorb infrared light at specific colors, or frequencies. The plate was then heated to room temperature so the ice residue could be analyzed in greater detail at Goddard’s Astrobiology Analytical Laboratory. The team found that this experiment produced a variety of complex organic molecules, including vitamin B3.

    Observations from the European Space Agency’s Rosetta mission, now in orbit around Comet 67P/Churyumov-Gerasimenko, might add more support to the theory that comets brought organic matter to Earth.

    ESA Rosetta spacecraft

    “Rosetta could help validate these experiments if it finds some of the same complex organic molecules in the gases released by the comet or in the comet’s nucleus,” said Smith.

    This work was supported by a NASA Postdoctoral Program Fellowship administered by Oak Ridge Associated Universities through a contract with NASA, the NASA Astrobiology Institute (NAI) via the Goddard Center for Astrobiology (GCA), and the NASA Cosmochemistry Program. NASA’s Ames Research Center in Mountain View, California, administers the NAI.

    See the full article here.

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    NASA’s Goddard Space Flight Center is home to the nation’s largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe.

    Named for American rocketry pioneer Dr. Robert H. Goddard, the center was established in 1959 as NASA’s first space flight complex. Goddard and its several facilities are critical in carrying out NASA’s missions of space exploration and scientific discovery.

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  • richardmitnick 3:05 pm on July 20, 2015 Permalink | Reply
    Tags: , Chemistry,   

    From U Arizona: “UA Researchers Reveal Elusive Molecule “ 

    U Arizona bloc

    University of Arizona

    July 13, 2015
    Daniel Stolte

    A long-standing chemistry puzzle has been solved, with potential implications ranging from industrial processes to atmospheric chemistry.

    Andrei Sanov, a professor in the UA Department of Chemistry and Biochemistry, and students Andrew Dixon (in red), a doctoral student, and Tian Xue, an undergraduate majoring in chemistry, have captured proof of a long sought-after four-atom compound that has eluded researchers for the last century. (Photo: John de Dios/UANews)

    Scientists at the University of Arizona have discovered a mysterious molecule with a structure simple enough to make it into high school textbooks, yet so elusive that chemists have argued for more than a century over whether it even exists.

    And, like so many important discoveries in science, this one started out with a neglected flask sitting in a storage fridge, in this case in the lab of Andrei Sanov, a professor in the UA’s Department of Chemistry and Biochemistry.

    Sanov and two of his students report the first definitive observation and spectroscopic characterization of ethylenedione, or “OCCO,” representing two carbon monoxide molecules chemically bound together. According to the researchers, the interest in this deceptively “simple” compound is fueled by many reasons: from its assumed role as a fleeting intermediate in a flurry of chemical reactions to its alleged properties as a wonder drug.

    Forgoing the past synthetic strategies that relied on the manipulation of neutral species, two students in Sanov’s laboratory created OCCO from its negatively charged ion and used a highly advanced technique called photoelectron imaging spectroscopy to analyze the product. This technique uses laser pulses to eject electrons from molecules, effectively yielding “a portrait of the molecule viewed from within,” as Sanov put it.

    The results confirm the existence of the elusive species and reveal its important fundamental properties, with implications not only for the basic understanding of so-called radical molecular species, but also industrial processes and potentially even atmospheric chemistry and climate modeling.

    Andrei Sanov and his doctoral student Andrew Dixon redirect laser from the Nd: yittrium aluminum garnet laser and into the Negative Ion Photo Electron Imaging Spectrometer, the custom-made instrument the team used to isolate and document the elusive ethylenedione. Undergraduate Tian Xue stayed close to the laser’s console, making sure everything was working properly. (Photo: John de Dios/UANews)

    Molecule Has Vexed Generations

    Chemists have pursued the OCCO molecule off and on since 1913, when its existence was first suggested. In the 1940s, at a particularly controversial turn in OCCO’s history, it was claimed to be the active component of Glyoxylide, a purported antidote for a long list of afflictions, from exhaustion to cancer. The claims were classified as fraud by the U.S. Food and Drug Administration, because the wonder drug proved to be nothing but water. Nonetheless, to this day the myth of Glyoxylide as a “lost” cancer remedy continues to be perpetuated on the Internet.

    According to Sanov, one of the motivations for pursuing ethylenedione is the elegant fundamental puzzle that the molecule presents: Most students with elementary chemistry education can draw the straightforward structure, O=C=C=O. Over the years, the anticipated existence of OCCO also has been backed by predictions of sophisticated theory. However, all past studies failed to provide conclusive experimental evidence that ethylenedione exists — and therein lay the puzzle.

    “We are not talking about some complex compound here,” Sanov said. “This is a small molecule with only four atoms and an ‘obvious’ structure. Shouldn’t modern science be able to tackle it?”

    The key to the mystery is the unstable nature of the OCCO, which tends to split into two carbon monoxide (CO) fragments after half a nanosecond or so. OCCO is what chemists call a diradical. Radicals and diradicals play exceptionally important roles in controlling the mechanisms and outcomes of chemical reactions, involved in all aspects of life, industry, technology and environment.

    “Radicals and diradicals are all around us,” Sanov said. “Think of them as molecules with unpaired electrons that are ‘underemployed’ and looking for action. This means that they are eager to react, because the making and breaking of chemical bonds is controlled by electrons. A radical is a molecule that has one such ‘underemployed’ electron. A diradical has two.”

    From a spectroscopist’s point of view, OCCO’s properties leave the molecule with no reason to evade detection, he explained.

    “And yet, it had never been observed, neither as a substance nor as a transient species, despite a century-long history of attempts,” Sanov said.

    A Nearly Forgotten Flask

    Until now. More precisely, until the day when Andrew Dixon, a soon-to-be fifth-year doctoral student in Sanov’s lab and the lead author of the paper, opened the fridge and spotted a flask labeled “Glyoxal.”

    “We started with a general interest in diradical systems and as part of those experiments, we decided to purchase some glyoxal, a precursor that is widely used in industrial applications but has not been explored as a potential synthesis molecule because its high water content makes it very difficult to work with,” Dixon said. “Once we had bought it, we looked at it and I remember thinking, ‘Oh man, this has 60 percent water. Let’s figure this out some other day.'”

    During a conversation with a colleague, Dixon became aware of a compound that functions as a “molecular sieve,” stripping the glyoxal solution of its high water content.

    “Once we had it in the gas phase so we could analyze it in our mass spectrometer, it turned out to be a good sample to work with, giving nice signal intensity,” Dixon said. “We tried to find a name for the molecule that we were making, and a Wikipedia search pulled up ethylenedione. That’s when we noticed it was something new.”

    “We tried to rule out every other possible solution,” said co-author Tian Xue, who will be a senior undergraduate student in the fall, “to make sure it wasn’t some other anion that could pose as OCCO.”

    To snap a “portrait” of the elusive species, they then unleashed lasers of short duration and precisely defined energies onto the molecules they produced.

    “We can create a beam of ions, and as they travel into the mass spectrometer, different molecules travel at different speeds, which allow us to separate out our ion of interest,” Dixon explained. “In our window of interest, we can pulse the laser right when the expected OCCO anion is passing through.”

    Using the laser pulses, Dixon and Xue were able to shoot off excess electrons from the stable anion of ethylenedione. They then captured photoelectron images of the quantum states of the resulting neutral OCCO at the very beginning of the molecule’s lifespan, which lasts only about half a nanosecond.

    “This seems very short by human standards, but is in fact a long lifetime in the molecular realm,” Sanov said.

    ‘Unknown Player’ in Atmosphere?

    In light of the fact that glyoxal, OCCO’s precursor molecule, plays a big role in atmospheric chemistry, Dixon speculates on the possibility that OCCO itself might also play a role, with potential implications for the modeling of atmospheric processes.

    “Given that glyoxal, its precursor, is a known pollutant and byproduct of combustion processes, whether man-made or natural, and given that OCCO seems to be a trivial molecule to create in our methodology, it is possible that it too could result from such processes, which, if true, could make it an unknown player in the atmosphere,” Dixon said. “And if you don’t know there is a species that you should be accounting for, your model will never be completely correct.”

    “One important result of our work is the end of the long-standing controversy surrounding the existence of this molecule,” Sanov said. “The theoretical predictions were correct — the transient OCCO diradical does exist. We have finally found it.”

    See the full article here.

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    U Arizona campus

    The University of Arizona (UA) is a place without limits-where teaching, research, service and innovation merge to improve lives in Arizona and beyond. We aren’t afraid to ask big questions, and find even better answers.

    In 1885, establishing Arizona’s first university in the middle of the Sonoran Desert was a bold move. But our founders were fearless, and we have never lost that spirit. To this day, we’re revolutionizing the fields of space sciences, optics, biosciences, medicine, arts and humanities, business, technology transfer and many others. Since it was founded, the UA has grown to cover more than 380 acres in central Tucson, a rich breeding ground for discovery.

    Where else in the world can you find an astronomical observatory mirror lab under a football stadium? An entire ecosystem under a glass dome? Visit our campus, just once, and you’ll quickly understand why the UA is a university unlike any other.

  • richardmitnick 4:48 pm on July 12, 2015 Permalink | Reply
    Tags: , , Chemistry, ICE, Northern Arizona University,   

    From Space.com: “Ice Lab Plays It Cool for Pluto Flyby” 

    space-dot-com logo


    July 11, 2015
    Sarah Lewin

    Researchers in an Arizona ice lab spend long hours making crystal-clear ice from mixes of methane, nitrogen and even carbon monoxide — and now, with data from the New Horizons mission to Pluto arriving soon, the lab’s time has come.

    The surface of Pluto is likely covered in a coarse mixture of ices that don’t resemble anything found naturally on Earth. The bitter cold on icy dwarf planets like Pluto and Eris, discovered in 2005, crystallizes blends of substances that on Earth occur more commonly as gases: mainly nitrogen, with a heaping dose of methane and a smattering of other molecules mixing things up.

    To understand the composition of a planet like Pluto from a distance, researchers measure the wavelengths of light that bounce off of the planet’s surface, by telescope or (when possible) much closer up, by spacecraft. Those distinctive wavelengths create a sort of fingerprint for different substances, and by comparing the fingerprints to a database of ice measurements back home, researchers hope to figure out the molecular compositions, temperatures and phases of matter covering Pluto’s surface.

    Temp 0
    Northern Arizona University’s ice lab researchers Matt Bovyn (left), Stephen Tegler (center) and Will Grundy (right) modify the machinery they use to generate exotic ices like those found on Pluto. Credit: Stephen Tegler

    The ice lab at Northern Arizona University has been focusing on creating and measuring ices with different proportions of methane and nitrogen in preparation for the incoming Pluto data. They’ve also begun to incorporate some of the other molecules observed on Pluto to create ices of even greater complexity, Will Grundy, an investigator at the lab, astronomer at the Lowell Observatory and co-investigator on the New Horizons mission, told Space.com.

    Any new ice observations from Pluto’s surface that can’t be found in the database that Grundy and his colleagues have created will mean another trip to the lab to try and match those measurements.

    “We’re going to be getting observations from Pluto with New Horizons that are going to light a fire under our butts,” Grundy said.

    “Our role here in the ice lab has been sort of a support role to try and understand how ice spectra behave under different circumstances,” Stephen Tegler, the chair of Northern Arizona University’s physics and astronomy department and researcher in the ice lab, explained to Space.com. “Then, armed with that broad view, you can take all that information, knowledge and experience, and say, ‘OK, we have this particular fingerprint pattern. How does it relate to what we see in the ice lab?'”

    Temp 1
    A methane ice sample ready for investigation by Northern Arizona University’s ice lab. The methane is visible in the lower half of the cell. Credit: Stephen Tegler

    To measure the “fingerprinting” of a given ice sample, the researchers fire infrared light through the ices they create as they cool down. They track how the changes in temperature and phase of the ice affect which wavelengths of light are absorbed. Many people think “phase” refers to solid, liquid or gas — but it’s much more complicated where these nonwater ices are concerned. They go through several different solid transitions: At certain temperatures, the already-solid ices will suddenly rearrange into a new crystalline setup. (Nitrogen, for instance, suddenly changes from a hexagonal to cubic crystal as it cools past 35.6 degrees Kelvin.)

    Add combinations of different elements into the mix, which change at different temperatures, and it gets complicated fast. “Every combination, it’s almost like we’ve got to come up with a new recipe to grow that very clear ice,” Tegler said. Adding carbon monoxide, another gas present on Pluto, makes the recipes even more devilishly difficult — but also more useful to pinpointing the conditions on different parts of Pluto’s surface, which might have the molecules in different proportions and temperatures.

    “From the point of view of doing remote sensing, anything that changes is something that you could hope to detect from a telescope or from a spacecraft, so that’s a valuable thing to know about,” Grundy said.

    Any unexpected, strange or inexplicable measurements will require new ices and new analysis to interpret. The lab has only scratched the surface on the gases the probe might encounter, say the team members.

    “There are some things I haven’t worked up the courage to try,” Grundy said. “Another species that’s on Pluto is hydrogen cyanide, which is even more toxic [than carbon monoxide] — and worse, it can be explosive as well,” Grundy said.

    See the full article here.

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  • richardmitnick 10:40 am on May 8, 2015 Permalink | Reply
    Tags: , , , Chemistry,   

    From AAAS: “Electron microscopes close to imaging individual atoms” 



    7 May 2015
    Robert F. Service

    This composite image of the protein β-galactosidase shows the progression of cryo-EM’s ability to resolve a protein’s features from mere blobs (left) a few years ago to the ultrafine 0.22-nanometer resolution today (right). Veronica Falconieri/ Subramaniam Lab/CCR/ NCI/ NIH

    Today’s digital photos are far more vivid than just a few years ago, thanks to a steady stream of advances in optics, detectors, and software. Similar advances have also improved the ability of machines called cryo-electron microscopes (cryo-EMs) to see the Lilliputian world of atoms and molecules. Now, researchers report that they’ve created the highest ever resolution cryo-EM image, revealing a druglike molecule bound to its protein target at near atomic resolution. The resolution is so sharp that it rivals images produced by x-ray crystallography, long the gold standard for mapping the atomic contours of proteins. This newfound success is likely to dramatically help drugmakers design novel medicines for a wide variety of conditions.

    “This represents a new era in imaging of proteins in humans with immense implications for drug design,” says Francis Collins, who heads the U.S. National Institutes of Health in Bethesda, Maryland. Collins may be partial. He’s the boss of the team of researchers from the National Cancer Institute (NCI) and the National Heart, Lung, and Blood Institute that carried out the work. Still, others agree that the new work represents an important milestone. “It’s a major advance in the technology,” says Wah Chiu, a cryo-EM structural biologist at Baylor College of Medicine in Houston, Texas. “It shows [cryo-EM] technology is here.”

    Cryo-EM has long seemed behind the times—an old hand tool compared with the modern power tools of structural biology. The two main power tools, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, enable researchers to pin down the position of protein features to less than 0.2 nanometers, good enough to see individual atoms. By contrast, cryo-EM has long been limited to a resolution of 0.5 nm or more.

    Cryo-EM works by firing a beam of electrons at a thin film containing myriad copies of a protein that have been instantly frozen in place by plunging them in liquid nitrogen. Detectors track the manner in which electrons scatter off different atoms in the protein. When an image is taken, the proteins are strewn about in random orientations. So researchers use imaging software to do two things; first, they align their images of individual proteins into a common orientation. Then, they use the electron scattering data to reconstruct the most likely position of all the protein’s amino acids and—if possible—its atoms.

    Cryo-EM has been around for decades. But until recently its resolution hasn’t even been close to crystallography and NMR. “We used to be called the field of blob-ology,” says Sriram Subramaniam, a cryo-EM structural biologist at NCI, who led the current project. But steady improvements to the electron beam generators, detectors, and imaging analysis software have slowly helped cryo-EM inch closer to the powerhouse techniques. Earlier this year, for example, two groups of researchers broke the 0.3-nm-resolution benchmark, enough to get a decent view of the side arms of two proteins’ individual amino acids. Still, plenty of detail in the images remained fuzzy.

    For their current study, Subramaniam and his colleagues sought to refine their images of β-galactosidase, a protein they imaged last year at a resolution of 0.33 nm. The protein serves as a good test case, Subramaniam says, because researchers can compare their images to existing x-ray structures to check their accuracy. Subramaniam adds that the current advance was more a product of painstaking refinements to a variety of techniques—including protein purification procedures that ensure each protein copy is identical and software improvements that allow researchers to better align their images. Subramaniam and his colleagues used some 40,000 separate images to piece together the final shape of their molecule. They report online today in Science that these refinements allowed them to produce a cryo-EM image of β-galactosidase at a resolution of 0.22 nm, not quite sharp enough to see individual atoms, but clear enough to see water molecules that bind to the protein in spots critical to the function of the molecule.

    That level of detail is equal to the resolution of many structures using x-ray crystallography, Chiu says. That’s vital, he adds, because for x-ray crystallography to work, researchers must produce millions of identical copies of a protein and then coax them to align in exactly the same orientation as they solidify into a crystal. But many proteins resist falling in line, making it impossible to determine their x-ray structure. NMR spectroscopy doesn’t require crystals, but it works only on small proteins. Cryo-EM represents the best of both worlds: It can work with massive proteins, but it doesn’t require crystals.

    As a result, the new advances could help structural biologists map vast numbers of new proteins they’ve never mapped before, Chiu says. That, in turn, could help drug developers design novel drugs for a multitude of conditions associated with different proteins. But one thing the technique has already shown is crystal clear, that in imaging, as well as biology, slow, evolutionary advances over time can produce big results.

    See the full article here.

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

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