Researchers use neutrons to spy on the elusive hydronium ion

A Los Alamos National Laboratory research team has harnessed neutrons to view for the first time the critical role that an elusive molecule plays in certain biological reactions. The effort could aid in treatment of peptic ulcers or acid reflux disease, or allow for more efficient conversion of woody waste into transportation fuels.

In a paper appearing this week in Angewandte Chemie International Edition, Los Alamos researchers join an international team in describing the role played by the elusive hydronium ion in the transfer of protons during enzyme-catalyzed reactions.

Prior to this research, no one has ever directly witnessed the role of the hydronium ion, a water molecule bound to an additional hydrogen ion, in macromolecular catalysts—the catalytic mechanisms of enzymes.

Researchers took an interest in an enzyme that has the potential to allow conversion of sugars in woody biomass into alcohol, a potential alternative fuel, because the enzyme loses its effectiveness when the pH value of the milieu is lowered—a common occurrence in the interior of industrial yeast cells fermenting alcohol. As it turns out, this biochemical reaction also has ramifications for the activation of proton pumps in the stomach, which produces excess acid in those afflicted by gastric diseases.

The scientists sought to figure out the mechanism behind these reactions. Neutrons from the Los Alamos Neutron Science Center provided a possible tool for unveiling the secret agent at the heart of the chemistry.

Hydronium ions had not been seen before by researchers who attempted to use X-rays to understand the chemical mechanism of enzymes. This is because tiny hydrogen atoms are essentially invisible under X-rays. To help make things visible, the researchers substituted hydrogen in their enzyme samples with deuterium, an isotope of hydrogen that behaves chemically identical to its nonisotopic counterpart. Deuterium yields a clear signal when bombarded with neutrons. Therefore, neutrons provided a perfect method for uncloaking the elusive hydronium ions, which appeared as a pyramid-shaped mass in the enzyme's active site where the chemical reaction occurs.

The researchers discovered a crucial change as the system they were studying fell into the acidic range of the pH scale (below 6). The hydronium ion that could be seen facilitating the binding of a metal ion cofactor crucial to the conversion of the sugar molecule into its fermentable form suddenly became dehydrated—think of water, H2O, being removed from hydronium, H3O+. The space occupied by the relatively large hydronium ion collapsed into a tiny volume occupied by the remaining proton (a positively charged hydrogen ion, H+). This spatial change in the molecular structure prevented the sugar from being attacked by the enzyme.

The observed phenomenon provided an answer about why pH plays such an important role in the process and renders the enzyme inactive under acidic conditions. More important, it definitively illustrated that the hydronium ion plays a key role in the transport of protons in these types of biochemical systems.

"This is something that has never been seen before," said Los Alamos researcher Andrey Kovalevsky, principal author of the paper. "This proves that hydronium is the active chemical agent in our studies of the catalytic mechanism of enzymes."

The research has broad implications for the possible role of hydronium ions in other biological systems. In addition to acid reflux disease, the research may help provide a better understanding of metabolic transfer of energy in living cells or living organisms.

More information: Angewandte Chemie International Edition Volume 50, Issue 33, pages 7520–7523, August 8, 2011 DOI: 10.1002/anie.201101753

Provided by DOE/Los Alamos National Laboratory

A bit of boron, a pinch of palladium: One-stop shop for the Suzuki reaction

ScienceDaily (Aug. 2, 2011) — Thanks to a team of chemists from Ludwig-Maximilians-Universitaet (LMU) in Munich, a crucial type of intermediate in the so-called Suzuki reaction can now be synthesized using an economical “one-pot” strategy. These compounds are used on an industrial scale to make the carbon scaffolds that form the basis of useful drugs and innovative materials.

Carbon-containing compounds are at the heart of organic chemistry, and carbon is the basis of all living matter. However, the so-called Suzuki reaction provides a simple means of creating carbon-carbon bonds to form compounds that can serve as the starting points for the synthesis of an infinite variety of organic molecules. A team of researchers led by LMU chemist Professor Paul Knochel has recently developed a practical and general method for the synthesis of a class of intermediates that readily undergo the Suzuki reaction.

"The new method is broadly applicable to diverse starting compounds and is very economical because it produces very few unwanted byproducts," says Knochel. "It should also be of great interest in an industrial setting, where Suzuki reactions are used in the development of medicinal compounds and novel materials such as liquid crystals for display screens."

The Suzuki reaction -- which involves the use of palladium to catalyze the cross-coupling of organoboron compounds with organic halogen-containing molecules -- makes it possible to link carbon atoms together in a very straightforward way. The products of the reaction can then be utilized for the construction of a virtually unlimited number of organic substances. The Suzuki reaction thus forms the basis for the synthesis of novel drugs and innovative materials. Akira Suzuki was awarded the Nobel Prize in Chemistry for his discovery of the reaction that bears his name.

Knochel and his team were hoping to extend the applicability of the reaction by finding an easy, economical and general way to synthesize the necessary organoboron compounds so that they could be used in Suzuki reactions without further purification. "We were able to optimize the process in such a way that the boronates can be made in a one-pot reaction," says Christoph Sämann, who made a major contribution to the study. "The method works well under very mild conditions, is compatible with many different functional groups and can therefore be applied to a wide range of compounds."

In contrast to the organoboronates that have been used so far, the products generated via the new synthetic route have two organic groups attached to the boron atom, and both can be transferred, without loss, in the course of the subsequent Suzuki reaction. "This significantly improves overall yields, making the reaction much more economical," says Knochel. "The new reaction also produces less waste, which is an especially important consideration in industrial applications."

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Ludwig-Maximilians-Universitaet Muenchen (LMU).

Journal Reference:

Benjamin A. Haag, Christoph Sämann, Anukul Jana, Paul Knochel. Practical One-Pot Preparation of Magnesium Di(hetero)aryl- and Magnesium Dialkenylboronates for Suzuki-Miyaura Cross-Coupling Reactions. Angewandte Chemie International Edition, 2011; 50 (32): 7290 DOI: 10.1002/anie.201103022

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

One box of Girl Scout Cookies worth $15 billion: Lab shows troop how any carbon source can become valuable graphene

Scientists can make graphene out of just about anything with carbon -- even Girl Scout Cookies.

Graduate students in the Rice University lab of chemist James Tour proved it when they invited a troop of Houston Girl Scouts to their lab to show them how it's done.

The work is part of a paper published online by ACS Nano. Rice scientists described how graphene -- a single-atom-thick sheet of the same material in pencil lead -- can be made from just about any carbon source, including food, insects and waste.

The cookie gambit started on a dare when Tour mentioned at a meeting that his lab had produced graphene from table sugar.

"I said we could grow it from any carbon source -- for example, a Girl Scout cookie, because Girl Scout Cookies were being served at the time," Tour recalled. "So one of the people in the room said, 'Yes, please do it. ... Let's see that happen.'"

Members of Girl Scouts of the United States of America Troop 25080 came to Rice's Smalley Institute for Nanoscale Science and Technology to see the process. Rice graduate students Gedeng Ruan, lead author of the paper, and Zhengzong Sun calculated that at the then-commercial rate for pristine graphene -- $250 for a two-inch square -- a box of traditional Girl Scout shortbread cookies could turn a $15 billion profit.

"That's a lot of cash!" said an amazed Sydney Shanahan, a member of the troop.

A sheet of graphene made from one box of shortbread cookies would cover nearly three football fields, Sun said.

The experiment was a whimsical way to make a serious point: that graphene -- touted as a miracle material for its toughness and conductivity since its discovery by Nobel Prize-winning scientists Andre Geim and Konstantin Novoselov in 2004 -- can be drawn from many sources.

To demonstrate, the researchers subsequently tested a range of materials, as reported in the new paper, including chocolate, grass, polystyrene plastic, insects (a cockroach leg) and even dog feces (compliments of lab manager Dustin James' miniature dachshund, Sid Vicious).

In every case, the researchers were able to make high-quality graphene via carbon deposition on copper foil. In this process, the graphene forms on the opposite side of the foil as solid carbon sources decompose; the other residues are left on the original side. Typically, this happens in about 15 minutes in a furnace flowing with argon and hydrogen gas and turned up to 1,050 degrees Celsius.

Tour expects the cost of graphene to drop quickly as commercial interests develop methods to manufacture it in bulk. Another new paper by Tour and his Rice colleagues described a long-sought way to make graphene-based transparent electrodes by combining graphene with a fine aluminum mesh. The material may replace expensive indium tin oxide as a basic element in flat-panel and touch-screen displays, solar cells and LED lighting.

The experiment the Girl Scouts witnessed "has a lot to do with current research topics in academia and in industry," said Tour, Rice's T.T. and W.F. Chao Chair in Chemistry as well as a professor of mechanical engineering and materials science and of computer science. "They learned that carbon -- or any element -- in one form can be inexpensive and in another form can be very expensive."

Diamonds are a good example, he said. "You could probably get a very large diamond out of a box of Girl Scout Cookies."

Zhiwei Peng a graduate student in Tour's group, is a co-author of the paper.

Sandia National Laboratory, the Air Force Office of Scientific Research and the Office of Naval Research MURI program funded the research.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Rice University.

Journal Reference:

Gedeng Ruan, Zhengzong Sun, Zhiwei Peng, James M. Tour. Growth of Graphene from Food, Insects and Waste. ACS Nano, 2011; 110729113834087 DOI: 10.1021/nn202625c

First opal-like crystals discovered in meteorite

 Scientists have found opal-like crystals in the Tagish Lake meteorite, which fell to Earth in Canada in 2000. This is the first extraterrestrial discovery of these unusual crystals, which may have formed in the primordial cloud of dust that produced the sun and planets of our solar system 4.6 billion years ago, according to a report in the Journal of the American Chemical Society.

Katsuo Tsukamoto and colleagues say that colloidal crystals such as opals, which form as an orderly array of particles, are of great interest to for their potential use in new electronics and optical devices. Surprisingly, the crystals in the meteorite are composed of magnetite, which scientists thought could not assemble into such a crystal because magnetic attractions might pack the atoms together too tightly. "We believe that, if synthesized, magnetite colloidal crystals have promising potential as a novel functional material," the article notes.

The formation of colloidal crystals in the meteorite implies that several conditions must have existed when they formed. "First, a certain amount of solution water must have been present in the meteorite to disperse the colloidal particles," the report explains. "The solution water must have been confined in small voids, in which colloidal crystallization takes place. These conditions, along with evidence from similar meteorites, suggest that the crystals may have formed 4.6 billion years ago."

The authors acknowledge funding from the Japan Society for the Promotion of Science, the Tohoku University Global COE Program, and the Center for Interdisciplinary Research Tohoku University.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by American Chemical Society.

Journal Reference:

Jun Nozawa, Katsuo Tsukamoto, Willem van Enckevort, Tomoki Nakamura, Yuki Kimura, Hitoshi Miura, Hisao Satoh, Ken Nagashima, Makoto Konoto. Magnetite 3D Colloidal Crystals Formed in the Early Solar System 4.6 Billion Years Ago. Journal of the American Chemical Society, 2011; 133 (23): 8782 DOI: 10.1021/ja2005708

Note: If no author is given, the source is cited instead.

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Meteorites: Tool kits for creating life on Earth

 Meteorites hold a record of the chemicals that existed in the early solar system and that may have been a crucial source of the organic compounds that gave rise to life on Earth. Since the 1960s, scientists have been trying to find proof that nucleobases, the building blocks of our genetic material, came to Earth on meteorites. New research, being published in the Proceedings of the National Academy of Sciences, indicates that certain nucleobases do reach Earth from extraterrestrial sources, by way of certain meteorites, and in greater diversity and quantity than previously thought.

Extensive research has shown that amino acids, which string together to form proteins, exist in space and have arrived on our planet piggybacked on a type of organic-rich meteorite called carbonaceous chondrites. But it has been difficult to similarly prove that the nucleobases found on meteorite samples are not due to contamination from sources on Earth.

The research team, which included Jim Cleaves of Carnegie's Geophysical Laboratory, used advanced spectroscopy techniques to purify and analyze samples from 11 different carbonaceous chondrites and one ureilite, a very rare type of meteorite with a different type of chemical composition. This was the first time all but two of these meteorites had been examined for nucleobases.

Two of the carbonaceous chondrites contained a diverse array of nucleobases and compounds that are structurally similar, so-called nucleobase analogs. Especially telling was the fact that three of these nucleobase analogs are very rare in terrestrial biology. What's more, significant concentrations of these nucleobases were not found in soil and ice samples from the areas near where the meteorites were collected.

"Finding nucleobase compounds not typically found in Earth's biochemistry strongly supports an extraterrestrial origin," Cleaves said.

The team tested their conclusion with experiments to reproduce nucleobases and analogs using chemical reactions of ammonia and cyanide, which are common in space. Their lab-synthesized nucleobases were very similar to those found in the carbonaceous chondrites, although the relative abundances were different. This could be due to chemical and thermal processing that the meteorite-origin nucleobases underwent while traveling through space.

These results have far-reaching implications. The earliest forms of life on Earth may have been assembled from materials delivered to Earth by meteorites.

"This shows us that meteorites may have been molecular tool kits, which provided the essential building blocks for life on Earth," Cleaves said.

Funding for various portions of this work was provided by the NASA Postdoctoral Program administered through Oak Ridge Associated Universities, the Goddard Center for Astrobiology, the NASA Astrobiology Institute, NASA Astrobiology: Exobiology and Evolutionary Program. Meteorites were provided by the NASA Johnson Space Center, the Smithsonian Museum of Natural History, P. Ehrenfreund, P. Jenniskens and M. Shaddad, the University of Melbourne Australia, and the 2006 ANSMET team.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by Carnegie Institution.