Archive for the ‘Chemistry’ Category

Proton Grease: An Acid Accelerated Molecular Rotor

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A molecular rotor was designed that rotates 7 orders of magnitude faster upon protonation. The quinoline rotor is based on a rigid N-arylimide framework that displays restricted rotation due to steric interaction between the quinoline nitrogen and imide carbonyls. At rt (23 °C), the rotor rotates slowly (t1/2 = 26 min, ΔG = 22.2 kcal/mol).

However, upon addition of 3.5 equiv of acid the rotor rotates rapidly (t1/2 = 2.0 × 10–4 s, ΔG = 12.9 kcal/mol). Mechanistic studies show that this dramatic acid catalyzed change is due to stabilization of the planar transition state by the formation of an intramolecular hydrogen bond between the protonated quinoline nitrogen (N+—H) and an imide carbonyl (O═C). The acid catalyzed acceleration is reversible and can be stopped by addition of base.

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April 12, 2012 at 8:44 pm

Posted in Chemistry

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H3+: the Molecule that Made the Universe

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In a study that pushed quantum mechanical theory and research capabilities to the limit, UA researchers have found a way to see the molecule that likely made the universe – or at least the hot and fiery bits of it.

The molecule known as H3+ is believed to have had a vital role in cooling down the first stars of the universe, and may still play an important part in the formation of current stars. Above, new stars burst into being in the star-forming nebula Messier 78, imaged by NASA's Spitzer Space Telescope. (Image credit: NASA/JPL-Caltech)

Lurking in the vast, chilly regions between stars, the unassuming molecule known as a triatomic hydrogen ion, or H3+, may hold secrets of the formation of the first stars after the Big Bang.

At the University of Arizona, then doctoral candidate Michele Pavanello spent months doing painstaking calculations to find a way to spot H3+ and unveil its pivotal role in astronomy and spectroscopy, supervised by Ludwik Adamowicz, a professor in the UA’s department of  hemistry and biochemistry. The groundbreaking results have been published in a recent edition of Physical Review Letters.

“Most of the universe consists of hydrogen in various forms,” said Adamowicz, “but the H3+ ion is the most prevalent molecular ion in interstellar space. It’s also one of the most important molecules in existence.”

Believed to be critical to the formation of stars in the early days of the universe, H3+ also is the precursor to many types of chemical reactions, said Adamowicz, including those leading to compounds such as water or carbon, which are essential for life…..
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April 11, 2012 at 6:37 pm

Red Wine, Tartaric Acid And The Secret Of Superconductivity

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Last year, physicists discovered that red wine can turn certain materials into superconductors. Now they’ve found that Beaujolais works best and think they know why

Last year, a group of Japanese physicists grabbed headlines around the world by announcing that they could induce superconductivity in a sample of iron telluride by soaking it in red wine. They found that other alcoholic drinks also worked–white wine, beer, sake and so on–but red wine was by far the best.

The question, of course, is why. What is it about red wine that does the trick?

Today, these guys provide an answer, at least in part. Keita Deguchi at the National Institute for Materials Science in Tsukuba, Japan, and a few buddies, say the mystery ingredient is tartaric acid and have the experimental data to show that it plays an important role in the process.

First, some background. Iron-based superconductors were discovered in 2008 and have since become the focus of intense interest. Deguchi and co study iron telluride which does not superconduct unless some of the telluride atoms are replaced with sulphur, forming FeTeS.

But even then, FeTeS doesn’t superconduct unless it goes through a final processing stage; heating it in water, for example.

Nobody knows what this process does or how it can convert an ordinary material into a superconductor. But some liquids are better than others, as determined by the fraction of the sample they convert into a superconductor.

This is the stage Deguchi and co have been puzzling over. Their approach is to make a sample of FeTeS, cut it up into slices and then heat each slice in a different liquid.

Water works quite well but whiskey, shochu and beer are all better. And of course, red wine is the best of all.

Now Deguchi and co have repeated the experiment with different types of red wine to see which works best. They’ve used wines made with a single grape variety including gamay, pinot noir, merlot, carbernet sauvignon and sangiovese.

It turns out that the best performer is a wine made from the gamay grape–for the connoisseurs, that’s a 2009 Beajoulais from the Paul Beaudet winery in central France.

They then analysed the wines to see which ingredient correlated best with superconducting performance and settled on tartaric acid as the likely culprit. The Beaujolais has the highest tartaric acid concentration.

Finally, they repeated the experiment using a mixture of water and tartaric acid to find out how well it performed.

Interestingly, they found that the solution performed better than water alone but not as well as the Beaujolais.

So while tartaric acid is clearly part of the answer, there must be another component of red wine that somehow encourages the transition to a superconducting state.

That’s a useful step forward for a team clearly dedicated to unravelling the mysterious powers of alcohol. On that basis alone, the work must be applauded.

However, there are still plenty of unanswered questions here, not least of which is how the superconducting transition process occurs at all in the presence of these liquids.

Corkscrews on standby.

Ref: Tartaric Acid In Red Wine As One Of The Key Factors To Induce Superconductivity In FeTe0.8S0.2
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March 22, 2012 at 4:33 pm

A Surprising New Kind of Proton Transfer

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Berkeley Lab scientists and their colleagues have discovered an unsuspected way that protons can move among molecules – revealing new opportunities for research in biology, environmental science, and green chemistry

When a proton – the bare nucleus of a hydrogen atom – transfers from one molecule to another, or moves within a molecule, the result is a hydrogen bond, in which the proton and another atom like nitrogen or oxygen share electrons. Conventional wisdom has it that proton transfers can only happen using hydrogen bonds as conduits, “proton wires” of hydrogen-bonded networks that can connect and reconnect to alter molecular properties.

Hydrogen bonds are found everywhere in chemistry and biology and are critical in DNA and RNA, where they bond the base pairs that encode genes and map protein structures. Recently a team of researchers using the Advanced Light Source (ALS) at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) discovered to their surprise that in special cases protons can find ways to transfer even when hydrogen bonds are blocked. The team’s results appear in Nature Chemistry.

Stacking the odd molecules

A group led by Musahid Ahmed, a senior scientists in Berkeley Lab’s Chemical Sciences Division (CSD), has long collaborated with a theoretical research group at the University of Southern California (USC) headed by Anna Krylov. In recent work to understand how bases are bonded in staircase-like molecules like DNA and RNA, Krylov’s group made computer models of paired, ring-shaped uracil molecules, and investigated what might happen to these doubled forms (dimers) when they were subjected to ionization – the removal of one or more electrons with resulting net positive charge.

Uracil is one of the four nucleobases of RNA, whose structure is similar to DNA except that, while both use the bases adenine, cytosine, and guanine, in DNA the fourth base is thymine and in RNA it’s uracil. The USC group used a uracil dimer labeled 1,3-dimethyluracil – “a strange creature that doesn’t necessarily exist in nature,” says CSD’s Amir Golan, who led the Berkeley Lab team at the ALS. The purpose of this strange creature, Golan says, is to block hydrogen bonding of the two identical monomers of the uracil dimer by attaching a methyl group to each, “because methyl groups are poison to hydrogen bonds.”

The uracils could still bond in the vertical direction by means of pi bonds, which are perpendicular to the usual plane of bonding among the flat rings of uracil and other nucleobases. “Pi stacking” is important in the configuration of DNA and RNA, in protein folding, and in other chemical structures as well, and pi stacking was what interested the USC researchers. They brought their theoretical calculations to Berkeley Lab for experimental testing at the ALS’s Chemical Dynamics beamline 9.0.2.

To examine how the molecules were bonded, Golan and his colleagues first created a gaseous molecular beam of real methylated uracil monomers and dimers, then ionized them with a beam of energetic ultraviolet light from the ALS synchrotron. The resulting species were weighed in a mass spectrometer to see how the uracil had responded to the extra boost of energy.

Uracil is one of the four bases of RNA (carbon atoms are brown, nitrogen purple, oxygen red, hydrogen white). Because methyl groups discourage hydrogen bonding, methylated uracil should be incapable of proton transfer. But after ionization of methylated uracil dimers, a proton moves by a different route, from one monomer to the other.

“Uracils could be joined by hydrogen bonds or by pi bonds, but these uracils had been methylated to block hydrogen bonds. So what we expected to see when we ionized them was that if they were bonded, they would have to be stacked on top of each other,” Golan says. Instead of holding together by pi bonds, however, when ionized some uracil dimers had fallen apart into monomers that carried an extra proton.

Where the protons come from

“What we did not expect to see was proton transfer,” Golan says. “Surprising as this was, we needed to find where the protons were coming from. The methyl groups consist of a single carbon atom and three hydrogen atoms, but methylated uracil has other hydrogens too. Still, the methyl groups were the natural suspects.”

To test this hypothesis, the researchers invited colleagues from Berkeley Lab’s Molecular Foundry to join the collaboration. They created methyl groups in which the hydrogen atoms – which like most hydrogen had single protons as their nuclei – were replaced by deuterium atoms, “heavy hydrogen” atoms with nuclei consisting of a proton and a neutron of virtually the same mass.

The molecular beam experiment was repeated at the ALS, and once again some of the methylated uracil dimers fell apart into monomers upon ionization. This time, however, the tell-tale monomers were not simply protonated, they were deuterated.

Says Golan, “By looking at the mass of the fragments we could see that instead of uracil plus one” – the mass of a single proton – “they were uracil plus two” – a proton and neutron, or deuteron. “This proved that indeed the transferred protons came from the methyl groups.”

The experiment showed that proton transfer in this case followed a very different route from the usual process of hydrogen bonding. Here the transfer involved not just an attraction between molecular arrangements that were slightly positively charged and others that were slightly negatively charged, as in a hydrogen bond. Instead it required significant rearrangements of the two uracil dimer fragments, to allow protons of hydrogen atoms in the methyl group on one monomer to move closer to an oxygen atom in the other. Theoretical calculations of the new pathway were led by USC’s Krylov and Ksenia Bravaya.

The moral of the story, says Golan, is that methyl groups do not always kill proton transfer. “Granted, this was a model system – what we did was ionize the uracil systems in the gas phase instead of in solution, as would be the case in a living organism,” he says. “Nevertheless, we showed that proton transfer is possible without hydrogen-bonding networks. Which means there could be unsuspected pathways for proton transfer in RNA and DNA and other biological processes – especially those that involve pi-stacking – as well as in environmental chemistry and in purely chemical processes like catalysis.”

The next step: a range of new experiments to directly map proton transfer rates and gain structural insight into the transfer mechanism, with the goal of visualizing these unexpected new pathways for proton transfer….
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Written by physicsgg

March 19, 2012 at 5:01 pm

Posted in BIOLOGY, Chemistry

Image or mirror image?

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Chiral recognition by femtosecond laser

It is not always easy to distinguish between images and mirror images of molecules, but this knowledge is important when one image of a molecule is a drug and the mirror image is toxic. One new approach to this may be chiral recognition in the gas phase. This involves using synchrotron radiation (highly energetic photons from a particle accelerator) to eject electrons from the molecules and analyzing their trajectories. In the journal Angewandte Chemie, German researchers have now demonstrated that such experiments also work with a compact laser system.
The trick is to replace the individual high-energy photon with three laser photons that excite the molecule through intermediate levels until it releases an electron (this method is known as REMPI, Resonance-Enhanced Multi-Photon Ionization). “It is thus possible to eject electrons with less energetic but more intense light,” explains Thomas Baumert of the University of Kassel.
For the measurements, the light must be circularly polarized. What does this mean? “Ordinary” light consists of waves that oscillate in all spatial directions perpendicular to their direction of travel. If light is linearly polarized, the light waves oscillate exclusively in one plane. When light is circularly polarized, the light wave oscillates in a helical form, because its amplitude describes a circle around the axis of travel – either to the right or the left.
Molecules in the gas phase are randomly oriented and thus encounter the laser light from all possible angles; the ejected electrons also fly off in every possible direction as they leave the molecule. By using both a special configuration for measurement and special calculation processes, the team is able to determine the distribution of the angles of the electrons’ flight paths. In the case of linearly polarized light, the distribution is symmetrical. “However, when the electrons are ejected by circularly polarized light, we find a distinct asymmetry to the angles at which the free electrons are found in relation to the laser beam,” reports Baumert. “This asymmetry is inverted if left circularly polarized light is used instead of right, an effect known as photoelectron circular dichroism. We observe the same effect when we keep the circular polarization the same but change from the “right handed” to the “left handed” structure of the chiral molecule being observed.” The researchers were able to demonstrate this with the chiral compounds camphor and fenchone.
“This circular dichroism effect has previously only been observed with synchrotron radiation. In contrast, our procedure uses a compact laser system, so that this method is not limited to basic laboratory research but, because of the magnitude of the observed effects, may also find its way into analysis,” according to Baumert…..
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March 9, 2012 at 4:14 pm

Posted in Chemistry

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The chemistry of exploding stars

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Meteorite contains evidence of formation of sulfur molecules derived from the ejecta of a supernova explosion

Fundamental chemical processes in predecessors of our solar system are now a bit better understood: An international team led by Peter Hoppe, researcher at the Max Planck Institute for Chemistry in Mainz, has now examined dust inclusions of the 4.6 billion years old Murchison, meteorite, which had been already found in 1969, using a very sensitive method. The stardust grains originate from a supernova, and are older than our solar system. The scientists discovered chemical isotopes, which indicate that sulfur compounds such as silicon sulfide originate from the ejecta of exploding stars. Sulfur molecules are central to many processes and important for the emergence of life.

Star dust from a supernova. The electron microscopic image shows a silicon carbide grain from the meteorite Murchinson. The approximately one micrometre small grains originate from a supernova as an isotopic analysis has shown. Isotopes are forms of an element with different weights. Picture: Peter Hoppe, Max Planck Institute for Chemistry © Peter Hoppe, MPI for Chemistry

Models already predicted the formation of sulfur molecules in the ejecta of exploding stars – the supernovae. Scientists from Germany, Japan and the U.S. now provided evidence to substantiate the theory with the help of isotope analyses of stardust from meteorites.

The team around the Mainz Max Planck researcher Peter Hoppe initially isolated thousands of about 0.1 to 1 micrometre-sized silicon carbide stardust grains from the Murchison meteorite, which was already found on Earth in 1969. The stardust grains originate from a supernova, and are older than our solar system. The researchers then determined with a highly sensitive spectrometer, the so-called NanoSIMS, the isotopic distribution of the samples. With this technique an ion beam is shot onto the individual stardust grains and releases atoms from the surface. The spectrometer then separates them according to their mass and measures the isotopic abundances. Isotopes of a chemical element have the same number of protons but different numbers of neutrons.

In five silicon carbide samples the astrophysicists found an unusual isotopic distribution: They measured a high amount of heavy silicon and a low amount of heavy sulfur isotopes, a result that does not fit with current models of isotope abundances in stars. At the same time they were able to detect the decay products of radioactive titanium which can be produced only in the innermost zones of a supernova. This proves that the stardust grains indeed derive from a supernova.

A proof for the model of the chemistry of the ejecta of supernovae

“The stardust grains we found are extremely rare. They represent only about the 100 millionth part of the entire meteorite material. That we have found them is very much a coincidence – especially since we were actually looking for silicon carbide stardust with isotopically light silicon,” says Peter Hoppe. “The signature of isotopically heavy silicon and light sulfur can only be plausibly explained if silicon sulfide molecules were formed in the innermost zones in the ejecta of a supernova.” Afterwards, the sulfide molecules were enclosed in the condensing silicon carbide crystals. These crystals then reached the solar nebula around 4.6 billion years ago and were subsequently incorporated into the forming planetary bodies. They finally reach the Earth in meteorites which are fragments of asteroids.

Carbon monoxide and silicon monoxide were already detected in infrared spectra of the ejecta of supernova explosions. Although models predicted the formation of sulfur molecules, it has not yet been possible to prove this. The measurements on silicon carbide stardust now provide support to the predictions that silicon sulfide molecules arise a few months after the explosion at extreme temperatures of several thousand degrees Celsius in the inner zones of supernova ejecta.

The meteorite studied was named after the Australian city of Murchison, where it was found in 1969. For astronomers, it is an inexhaustible diary about the formation of our solar system, as it has remained almost unaltered since its formation. Besides the stardust inclusions from the ejecta of a supernova Murchison also transported dust to the Earth which has been formed in the winds of giant red stars. Through further analyses, the researchers hope to learn more about the origin of their parent stars.

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January 20, 2012 at 4:10 pm

Nobel prizewinning quasicrystal fell from space

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It came from outer space (Image: Luca Bindi and Paul Steinhardt)

A Nobel prizewinning crystal has just got alien status. It now seems that the only known sample of a naturally occurring quasicrystal fell from space, changing our understanding of the conditions needed for these curious structures to form….
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Read also: The quasicrystal from outer space

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January 3, 2012 at 5:04 pm

Posted in Chemistry, SPACE

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‘New metal type’ at Earth’s core

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The precise chemistry of metals within the Earth's interior will dictate the nature of its magnetic field

The composition of the Earth’s core remains a mystery. Scientists know that the liquid outer core consists mainly of iron, but it is believed that small amounts of some other elements are present as well. Oxygen is the most abundant element in the planet, so it is not unreasonable to expect oxygen might be one of the dominant “light elements” in the core. However, new research from a team including Carnegie’s Yingwei Fei shows that oxygen does not have a major presence in the outer core. This has major implications for our understanding of the period when the Earth formed through the accretion of dust and clumps of matter. Their work is published Nov. 24 in Nature.

According to current models, in addition to large amounts of iron, the Earth’s liquid outer core contains small amounts of so-called light elements, possibly sulfur, oxygen, silicon, carbon, or hydrogen. In this research, Fei, from Carnegie’s Geophysical Laboratory, worked with Chinese colleagues, including lead author Haijun Huang from China’s Wuhan University of Technology, now a visiting scientist at Carnegie. The team provides new experimental data that narrow down the identity of the light elements present in Earth’s outer core.

With increasing depth inside the Earth, the pressure and heat also increase. As a result, materials act differently than they do on the surface. At Earth’s center are a liquid outer core and a solid inner core. The light elements are thought to play an important role in driving the convection of the liquid outer core, which generates the Earth’s magnetic field.

Scientists know the variations in density and speed of sound as a function of depth in the core from seismic observations, but to date it has been difficult to measure these properties in proposed iron alloys at core pressures and temperatures in the laboratory.

“We can’t sample the core directly, so we have to learn about it through improved laboratory experiments combined with modeling and seismic data,” Fei said.

High-speed impacts can generate shock waves that raise the temperature and pressure of materials simultaneously, leading to melting of materials at pressures corresponding to those in the outer core. The team carried out shock-wave experiments on core materials, mixtures of iron, sulfur, and oxygen. They shocked these materials to the liquid state and measured their density and speed of sound traveling through them under conditions directly comparable to those of the liquid outer core.

By comparing their data with observations, they conclude that oxygen cannot be a major light element component of the Earth’s outer core, because experiments on oxygen-rich materials do not align with geophysical observations. This supports recent models of core differentiation in early Earth under more ‘reduced’ (less oxidized) environments, leading to a core that is poor in oxygen.

“The research revealed a powerful way to decipher the identity of the light elements in the core. Further research should focus on the potential presence of elements such as silicon in the outer core,” Fei said. –

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December 20, 2011 at 9:07 pm

Posted in Chemistry, GEOLOGY

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