Science News

Scientists Capture First Images of Molecules Before and After Reaction

May 30, 2013 — Every chemist's dream -- to snap an atomic-scale picture of a chemical before and after it reacts -- has now come true, thanks to a new technique developed by chemists and physicists at the University of California, Berkeley.

Using a state-of-the-art atomic force microscope, the scientists have taken the first atom-by-atom pictures, including images of the chemical bonds between atoms, clearly depicting how a molecule's structure changed during a reaction. Until now, scientists have only been able to infer this type of information from spectroscopic analysis.

"Even though I use these molecules on a day to day basis, actually being able to see these pictures blew me away. Wow!" said lead researcher Felix Fischer, UC Berkeley assistant professor of chemistry. "This was what my teachers used to say that you would never be able to actually see, and now we have it here."

The ability to image molecular reactions in this way will help not only chemistry students as they study chemical structures and reactions, but will also show chemists for the first time the products of their reactions and help them fine-tune the reactions to get the products they want. Fischer, along with collaborator Michael Crommie, a UC Berkeley professor of physics, captured these images with the goal of building new graphene nanostructures, a hot area of research today for materials scientists because of their potential application in next-generation computers.

"However, the implications go far beyond just graphene," Fischer said. "This technique will find application in the study of heterogeneous catalysis, for example," which is used widely in the oil and chemical industries. Heterogeneous catalysis involves the use of metal catalysts like platinum to speed reactions, as in the catalytic converter of a car.

"To understand the chemistry that is actually happening on a catalytic surface, we need a tool that is very selective and tells us which bonds have actually formed and which ones have been broken," he added. "This technique is unique out there right now for the accuracy with which it gives you structural information. I think it's groundbreaking."

"The atomic force microscope gives us new information about the chemical bond, which is incredibly useful for understanding how different molecular structures connect up and how you can convert from one shape into another shape," said Crommie. "This should help us to create new engineered nanostructures, such as bonded networks of atoms that have a particular shape and structure for use in electronic devices. This points the way forward."

Fischer and Crommie, along with other colleagues at UC Berkeley, in Spain and at the Lawrence Berkeley National Laboratory (LBNL), published their findings online May 30 in the journal Science Express.

From shadow to snapshot

Traditionally, Fischer and other chemists conduct detailed analyses to determine the products of a chemical reaction, and even then, the actual three-dimensional arrangement of atoms in these products can be ambiguous.

"In chemistry you throw stuff into a flask and something else comes out, but you typically only get very indirect information about what you have," Fischer said. "You have to deduce that by taking nuclear magnetic resonance, infrared or ultraviolet spectra. It is more like a puzzle, putting all the information together and then nailing down what the structure likely is. But it is just a shadow. Here we actually have a technique at hand where we can look at it and say this is exactly the molecule. It's like taking a snapshot of it."

Fischer is developing new techniques for making graphene nanostructures that display unusual quantum properties that could make them useful in nano-scale electronic devices. The carbon atoms are in a hexagonal arrangement like chicken wire. Rather than cutting up a sheet of pure carbon -- graphene -- he hopes to place a bunch of smaller molecules onto a surface and induce them to zip together into desired architectures. The problem, he said, is how to determine what has actually been made.

That's when he approached Crommie, who uses atomic force microscopes to probe the surfaces of materials with atomic resolution and even move atoms around individually on a surface. Working together, they devised a way to chill the reaction surface and molecules to the temperature of liquid helium -- about 4 Kelvin, or 270 degrees Celsius below zero -- which stops the molecules from jiggling around. They then used a scanning tunneling microscope to locate all the molecules on the surface, and zeroed in on several to probe more finely with the atomic force microscope. To enhance the spatial resolution of their microscope they put a single carbon monoxide molecule on the tip, a technique called non-contact AFM first used by Gerhard Meyer and collaborators at IBM Zurich to image molecules several years ago.

After imaging the molecule -- a "cyclic" structure with several hexagonal rings of carbon that Fischer created especially for this experiment -- Fischer, Crommie and their colleagues heated the surface until the molecule reacted, and then again chilled the surface to 4 Kelvin and imaged the reaction products.

"By doing this on a surface, you limit the reactivity but you have the advantage that you can actually look at a single molecule, give that molecule a name or number, and later look at what it turns into in the products," he said.

"Ultimately, we are trying to develop new surface chemistry that allows us to build higher ordered architectures on surfaces, and these might lead into applications such as building electronic devices, data storage devices or logic gates out of carbon materials."

The research is coauthored by Dimas G. de Oteyza, Yen-Chia Chen, Sebastian Wickenburg, Alexander Riss, Zahra Pedramrazi and Hsin-Zon Tsai of UC Berkeley's Department of Physics; Patrick Gorman and Grisha Etkin of the Department of Chemistry; and Duncan J. Mowbray and Angel Rubio from research centers in San Sebastián, Spain. Crommie, Fischer, Chen and Wickenburg also have appointments at Lawrence Berkeley National Laboratory.

The work is sponsored by the Office of Naval Research, the Department of Energy and the National Science Foundation.

How a mosquito survives a raindrop hit

A raindrop hitting a mosquito in flight is like a midair collision between a human and a bus. Except that the mosquito survives.

New experiments show how the insect’s light weight works in its favor, says engineer David Hu of the Georgia Institute of Technology in Atlanta. In essence, the (relatively) huge, fast drop doesn’t transfer much of its momentum to a little wisp of an insect. Instead the falling droplet sweeps the insect along on the downward plunge. As Hu puts it, the mosquito “just rides the drop.”

The trick is breaking away from that drop before it and the insect splash into the ground. Mosquitoes that separate themselves in time easily survive a raindrop strike, Hu and his colleagues report online June 4 in the Proceedings of the National Academy of Sciences.

Such studies help reveal how animals evolved to take advantage of flight, says biologist Tyson Hedrick of the University of North Carolina at Chapel Hill. Mosquito tricks may also inspire engineers designing swarms of tiny flying robots, or interest physicists and mathematicians studying complex fluid dynamics at this scale.

Plenty of lab work has investigated how flying animals recover from disturbances, but there’s little work on raindrops because those collisions are very hard to study, Hu says. To mimic raindrop speed of about 9 meters per second, he and his colleagues tried dripping water off the third floor of a building toward ground-level mosquitoes. “It’s the worst game of darts you can imagine,” he says. “You have no hope of hitting them.”

Finally, Hu sprayed streams of water from a pump at caged lab mosquitoes and then refined the process by spraying mosquito-sized beads. His team found that mosquitoes hit with water survived using an insect version of tai chi: Move with the blow instead of resisting it. A raindrop can reach 50 times the mass of a mosquito, and after colliding, “the mosquito becomes a stowaway,” Hu says.

The wild ride comes with danger. Mosquitoes hitchhiking on water experience acceleration 100 to 300 times the force of Earth’s gravity, the researchers found. The previous champs for surviving acceleration had been jumping fleas, at a mere 130 times Earth’s gravity.

Such studies suggest insects are making tradeoffs, Hedrick says. Mosquitoes’ small mass might allow them fly through raindrops but leave them more vulnerable to other menaces, such as wind. Larger and heavier horseflies “should have no problem with wind but might be more disturbed by raindrop impacts,” he says.

Scientists who work in the field know how readily mosquitoes can survive wet weather. “I’ve worked in the field many rainy nights,” says entomologist Nathan Burkett-Cadena of the University of South Florida in Tampa, “and received zero respite from mosquitoes during even heavy rains.”

Smile please: New tech takes pain out of fillings

Now, Metal Crown Is Slipped Over Decayed Tooth

London: A new technique for treating tooth decay could put an end to painful fillings that prevent millions of people from going to the dentist. Experts are testing a pain-free way of dealing with rotten teeth that dispenses with the dentist’s drill. It is also done without the need for anaesthetic jabs and appears to be more effective than a conventional filling. 
    The results of pilot studies have been so promising that the NHS has pumped $3million into a nationwide study of the technique which involves sealing decay in, rather than scraping it out, the Daily Mail reported. However, the technique is only suitable for milk teeth and so for children, rather than adults. 
    Normally, having a filling involves being given an injection of local anaesthetic. The rotten part of the tooth is then removed using the drill and the hole packed with filling. Under the Hall technique, named after Aberdeenshire dentist Norna (CORR) Hall, no effort is made to remove the decayed part of the tooth. Instead, a metal crown is simply slipped over the tooth and cemented in place. 
    No anaesthetic is needed and, starved of bacteria and oxygen, the decay stops or slows down to such a rate that it doesn’t cause any pain. The crown stays in place until it falls out naturally with the tooth at around the age of ten. 
    Nicola Innes, a lecturer in paediatric dentistry at Dundee University, has carried out two studies into the ‘child-friendly’ technique. “The Hall Technique is now taught as a standard part of the undergraduate dental programme in almost all dental schools now,” she said. 
    In a two-year trial of 132 children aged between three and ten, children, parents and dentists all preferred the Hall technique. 
    Teeth treated this way also caused fewer problems in the future. The NHS-funded trial will study almost 1,500 children treated at 50 dental practices in the north of England, inner-city London and Scotland and Wales. ANI

Chimpanzees are genetically more diverse than us

London: Groups of chimpanzees within central Africa are more different genetically than humans living on different continents, a study has found. The Oxford Universityled study, published in the journal PLoS Genetics, suggests that genomics can provide a valuable new tool for use in chimpanzee conservation. 

    It has the potential to identify the population of the origin of an individual chimpanzee or the provenance of a sample of bush meat, a university of Oxford release said. 

    Common chimpanzees in equatorial Africa have long been recognized as falling into three distinct populations or sub-species: western, central and eastern chimpanzees. 

    A fourth group, the Cameroonian chimpanzee, has been proposed to live in southern Nigeria and western Cameroon, but there is controversy as to whether it constitutes a distinct group. 

    Oxford University researchers, along with scientists from other major universities examined DNA from 54 chimpanzees. They compared the DNA at 818 positions across the genome that varied between individuals. 

    Their analysis showed that Cameroonian chimpanzees are distinct from the other, well-established groups and previous conclusions that Cameroonian and western chimpanzees are most closely related were shown to be untrue. 

    The researchers also contrasted the levels of genetic variation between the chimpanzee groups with that seen in humans from different populations. Surprisingly, even though all the chimpanzees live in relatively close proximity, chimpanzees from different populations were substantially more different genetically than humans living on different continents. PTI

New discovery: Oxygen detected on Saturn’s moon

Washington: Planetary scientists claim to have for the first time detected presence of oxygen in the atmosphere of Saturn’s moon Dione. 

    An international team, led by Los Alamos National Laboratory, says it has discovered molecular oxygen ions in the upper-most atmosphere of Dione, one of the 62 known moons orbiting Saturn, thanks to Nasa’s Cassini spacecraft, the ‘Geophysical Research Letters’ journal reported. 

    Dione — discovered in 1684 by astronomer Giovanni Cassini (after whom the spacecraft was named) — orbits Saturn at roughly the same distance as our own moon orbits Earth. The tiny moon is a mere 700 miles wide and appears to be a thick, pockmarked layer of water ice surrounding a smaller rock core. 

    As it orbits Saturn every 2.7 days, Dione is bombarded by charged particles (ions) emanating from Saturn’s very strong magnetosphere. 

    These ions slam into the surface of Dione, displacing molecular oxygen ions into Dione’s thin atmosphere through a process called sputtering. 

    Molecular oxygen ions are then stripped from Dione’s exosphere by Saturn’s strong magnetosphere, says the team. A sensor aboard the Cassini spacecraft called the Cassini Plasma Spectrometer detected the oxygen ions in Dione’s wakeduring a flyby of the moon in 2010. Now, the team confirmed the presence of oxygen in the ringed planet's moon. 

    Team leader Robert Tokar said, “The concentration of oxygen in Dione’s atmosphere is roughly similar to what you would find in Earth's atmosphere at an altitude of 300 miles. It’s not enough to sustain life, but — together with similar observations of other moons around Saturn and Jupiter — these are definitive examples of a process by which a lot of oxygen can be produced in icy celestial bodies that are bombarded by charged particles or photons from the Sun or whatever light source happens to be nearby.” PTI

Saturn Moons spied from the side

Titan, Saturn’s largest moon, hovers in front of the planet’s rings like a holiday ornament in this natural color photo snapped by the Cassini spacecraft and released on December 22. The hazy orange moon looms large next to bright, icy Dione – Saturn’s third-largest satellite – against the shadows of Saturn’s rings.

Titan looks murky because of its atmosphere – a puffy, blue-rimmed nitrogen shroud. The cloudy cover is darker at the moon’s north pole and slightly flattened at the moon’s south pole (see this Casssini image also released December 22). Organic compounds within the smoggy layer form clouds of ethane and methane that seasonally rain down upon Titan’s surface.

Dione – essentially a spherical ice cube with a rocky core — is heavily cratered, cut with canyons, and home to icy cliffs. In this image, Dione is 3.2 million kilometers away from Cassini; Titan is 2.3 million kilometers away.

First Earth-sized Planets Netted

The newest exo-apples of the planet-hunting Kepler space telescope’s unblinking eye are two rocky, Earth-sized planets hovering around Kepler-20, a sunlike star 950 light-years away.

Though snuggled too close to their star to be habitable, these first Earth-sized worlds confirmed by the Kepler team are another big step forward for the planet hunters, who recently found a planet somewhat larger than Earth orbiting a sunlike star at a distance hospitable to life. Finding habitable distant worlds — Earth-sized planets at the right distance from their stars to allow the presence of liquid water — is the team’s ultimate goal.

"The hunt is on to find a planet that combines the best of both of these worlds — a true Earth twin," says David Charbonneau, an astronomer at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., and a coauthor of a study describing the small planets that appears online December 20 in Nature.

One of the planets, the pragmatically named Kepler-20e, is a bit smaller than Venus — 0.87 times as wide as Earth — and completes a trip around the star every 6.1 days. The other, Kepler-20f, is 1.03 times as wide as Earth, and a year on that planet would last just 19.6 days. Because the planets are so small, they’re probably made of ingredients similar to Earth’s.

Depending on where and how it formed, Kepler-20f could even have developed a water vapor atmosphere, says planetary scientist Jonathan Fortney of the University of California, Santa Cruz. “If it started out with the amount of water we had on Earth and Venus, it’s probably long gone — just like it is on Venus,” he says. “But if that planet had a tremendous amount more water, then it might have some left over.”

The Kepler-20 system is a quintet comprising three large planets (Kepler-20b, c and d) and the two Earth-sized ones, all tucked in nearer to their star than Mercury is to the sun. Moving out from Kepler-20, the five spheres alternate in size, with the runts of the planetary litter bracketed on either side by their bigger siblings.

“It’s one of the most shocking architectures we’ve seen,” Charbonneau says. “Exoplanets have had a lot of surprises, but this is going to be very difficult to explain.”

The strange — but stable — configuration is encoded in the blips and blinks the planets produce as they pass in front of their sun, which is one of more than 150,000 in a field of stars the telescope stares at. Different-sized blips correspond to different-sized planets, and watching the star for long enough reveals how frequently each planet completes its journey.

Currently set to wrap up at the end of 2012, the mission could be extended for several more years if limited budgets allow. More observing time will let scientists monitor Kepler’s starry patch for long enough to detect Earth-sized planets in longer, habitable orbits.

“The spacecraft doesn't know about politics and financial difficulties — it will continue to beam data back to Earth until at least 2015, even if no one is listening,” says astronomer Debra Fischer of Yale University. “You just have to keep the lights on, and keep the science team intact. The next three years are where they’re going to detect the Earths at habitable distances.”