Chemistry Newsblast

Power of the Pyramid

From starting ingredients to final product, the path of a chemical reaction often includes multiple intermediate steps. These intermediate steps form chemical compounds that may only exist briefly and in tiny concentrations. Yet despite their fleeting presence, these intermediates can have a profound impact on the outcome of a reaction. Not surprisingly, researchers would like to know more about these intermediates, but trapping them for further study, particularly in an aqueous environment, has proven tricky.

Enter the pyramid. Chemists Ken Raymond (ACS ’64) and Robert Bergman (ACS ’63), both at the University of California, Berkeley, had previously developed water-soluble pyramid-shaped assemblies, or tetrahedra, that have a strong propensity for trapping cations within their hydrophobic cavities. The researchers decided to see if these ion-trapping tetrahedra could capture and stabilize the reactive iminium cations that form during the chemical reaction between amines and ketones.

In fact, Raymond, Bergman, and their collaborators found that the iminium cation-capturing tetrahedra formed spontaneously in water from a mix of gallium ions, amines, and ketones. These tetrahedra immediately and effectively encapsulated iminium cations within their cavities. NMR spectroscopy showed that anywhere from 30 to 90% of the tetrahedral cavities trapped iminium cations, depending upon the size of the amine and ketone molecules in the pyramids.

“Once encapsulated, the iminium ions remained stable for months at room temperature,” says Bergman. “This technique should provide us with the ability to study the reactions of individual molecules in isolated and controlled environments.”

The pyramid-based encapsulation technique developed by Raymond and Bergman has many of the same essential features as enzymatic catalysis, including the creation of cavities that allow for the recognition and control of molecular asymmetry in reactions. Such asymmetric capabilities are essential for preparing compounds that have biological activity. With this technique, it may also be possible to develop chemical reactions that could not previously have been done in aqueous solution.

Building Magnetic Polymers with Hydrogen Bonds

Researchers at Argonne National Laboratory have pioneered a new approach for making magnetic polymers that are held together with strong hydrogen bonds. These polymers contain an innovative bifluoride building block, HF2 – , that helps create magnetically ordered regions within the polymer. The development may help lead to new techniques for faster and more versatile computer chips, among other applications.

“Nature uses hydrogen bonds to do all kinds of things, including holding the DNA double helix together, and is important in a wide range of biological processes,” says chemist John Schlueter. “When making molecular materials, strong bonds are needed to fabricate the molecular building blocks. Weaker bonds, including hydrogen bonds, act as the glue to hold the blocks together.” It’s this phenomenon that allowed the creation of the first fully organic superconductor, discovered at Argonne a decade ago.

The magnetic polymer, which forms as beautiful deep blue crystals, is produced when copper ions bind to pyrazine molecules, creating a sheet-like structure. Like a Tinkertoy building block, the bifluoride ion acts as a bridge to hold the planes together. The product is a three-dimensional coordination polymer that forms under mild synthetic conditions. The exceptionally simple structure is held together by one of the strongest hydrogen bonds known, making this a thermally stable material.

The researchers studied the magnetic properties of the material with a technique that uses muons as mini-magnetometers. Muons are subatomic particles that are heavier than electrons but have the same charge and magnetic spin. The researchers hope that the magnetic studies will help them understand to what extent bifluoride units and their hydrogen bonds influence the spin arrangement on neighboring magnetic centers.

In the past, this same group of investigators pioneered a new process for the synthesis of molecular superconductors that also rely on hydrogen bonding for their unique electronic properties. The researchers are now interested in making hybrid materials by inserting magnetic layers between the conducting sheets to form a simple spintronic device. To accomplish this, it is critical to understand how the conducting and magnetic layers communicate through their hydrogen bonds.

Spintronics, also known as spin electronics, is an emerging technology that looks to develop devices that exploit the quirky world of quantum physics, or physics at the incredibly small atomic level, particularly the up-or-down spin property of electrons. Whereas conventional electronics uses the charge of the electron, spintronic devices would use both the spin and charge, achieving vastly superior performance. Scientists across the globe are racing to develop the spintronics field. It could revolutionize the computing industry with chips that are more versatile and exponentially more powerful than today’s most cutting-edge technology.

Ultrasound Generates Intense Mechanoluminescence

Many people know that biting or breaking a Wint-O-Green LifeSaver in the dark produces a visible spark of green light. That light is called mechanoluminescence, also known as triboluminescence. This phenomenon was first discovered in 1605 by Sir Francis Bacon, who observed light emission when scraping a lump of sugar with a knife.

Typically, mechanoluminescence produces a dim light that is generated by simply grinding, cleaving, biting, or scratching a material. Now, Kenneth Suslick (ACS ’74) and colleagues at the University of Illinois at Urbana–Champaign have found a new way to generate mechanoluminescence, one that produces light up to 1000 times brighter than that produced by grinding.

The secret, the researchers found, is to use high-intensity ultrasound in liquid slurries of sugar and other organic crystals to create mechanoluminescence. The light results from a static electric discharge created when a crystal, such as sugar, is fractured.

Ultrasound in a liquid, just like any sound waves, causes expansion and compression of the liquid. If the ultrasound is powerful enough, this oscillation creates millions of bubbles, each with a diameter smaller than a shaft of hair. These bubbles grow and contract with each sound wave, and if conditions are just right, they can violently implode. These imploding bubbles form shock waves in the liquid that drive organic crystals, including sugar crystals, to zip around at roughly half the speed of sound.

When crystals moving at such high velocities collide with one another, they shatter into pieces. That shattering produces the mechanoluminescence as the fractured crystal surfaces pull apart and trigger an electric discharge. Far brighter light is generated by this route to mechanoluminescence simply because many more crystals shatter at any given moment than when we bite into a Wint-O-Green LifeSaver.

Edible Food Wrap Kills Deadly Bacteria

Researchers at the U.S. Department of Agriculture and the University of Lleida in Spain have developed an edible coating for fresh fruits and vegetables that kills deadly E. coli bacteria while also providing a flavor boost to food. Composed of apple puree and oregano oil, which acts as a natural antibacterial agent, the coating shows promise of becoming a long-lasting, potent alternative to conventional produce washes.

“All produce-cleaning methods help to some degree, but our new coatings and films may provide a more concentrated, longer-lasting method for killing bacteria,” says Tara McHugh (ACS ’91), a food chemist with the Agriculture Department’s Agricultural Research Service. And as an added benefit, the films are made of fruit or vegetable puree, making them good sources of vitamins, minerals, and antioxidants.

Researchers have known about the antimicrobial activity of plant-derived essential oils for some time, but McHugh says that her group is the first to incorporate them into a fruit- or vegetable-based edible food wrap for the purpose of improving food safety. Three years ago, she and her associates developed a similar edible food wrap, but without the antimicrobial properties.

In developing the coatings, McHugh and her associates tested oregano, cinnamon, and lemongrass oils in solutions of apple puree and dried films for their effectiveness against E. coli. Each compound was tested in a controlled series of dilutions, the scientists say.

Although all of the oils tested inhibited the growth of E. coli, oregano oil was the most effective, killing more than 50% of sample bacteria in 3 minutes at concentrations as small as 0.034%. The second most effective oil was lemongrass oil, followed by cinnamon oil. In contrast, the apple-puree film alone had no effect on E. coli survival.

What the apple antibacterial film brings to the table, though, is that it is composed of sticky sugars and lipids that allow the coating to adhere to fruits and vegetables for longer periods than conventional, water-based produce washes. That same stickiness also gives the suspended antimicrobial agents a more concentrated exposure to bacterial surfaces, increasing the film’s germ-killing potential.

The antibacterial coating could be used by produce manufacturers as a spray or dip for fresh fruits and vegetables. The resulting product will taste a bit like oregano, McHugh says, adding that this can be a desirable trait in salads.

Microfluidics Yield Rapid Gene Tests from Blood

In an accomplishment that represents a significant step toward an era of rapid, inexpensive, bedside testing for cancer, researchers at the University of Virginia have developed a microfluidic device that can process human blood samples and yield diagnostic results within an hour. The investigators, led by James Landers (ACS ’97), have used the device to develop 30-minute tests for bacterial infections and a 60-minute test for lymphoma.

Landers and his colleagues were able to link on a single glass slide the individual microfluidic components needed to remove DNA from blood, amplify the DNA using polymerase chain reaction (PCR), purify the amplified DNA using electrophoresis, and detect specific DNA sequences of diagnostic importance. Although Landers and other researchers had previously designed the components needed to conduct each step of this analysis, no one had managed to put them all in one easy-to-make device.

The key to the success of this device, the researchers noted, was solving a problem that had thwarted other such integration efforts, namely that the chemicals used to purify DNA from blood are incompatible with PCR. Landers’ team overcame this obstacle by taking advantage of the unique flow properties of fluids in microfluidic channels in order to divert these chemical away from the PCR chamber and into a waste chamber. They also made extensive use of polymer valves developed by Richard Mathies and his colleagues at the University of California, Berkeley, and credit the Mathies group for teaching them how to make and use these valves.

To keep costs low, the investigators made the microfluidic device itself as simple as possible. All injection ports, pumps, heaters, and optical detection components reside in a manifold that clamps around the glass microfluidic slide. Engineering work is now under way to develop a manifold suitable for use in clinical settings and eventual human clinical trials. The investigators, as well as researchers who did not participate in this study, predict that this device should work for any gene-based assay for which a PCR primer exists or can be developed.

Measuring Heat Flow from the Earth’s Molten Core into the Lower Mantle

For the first time, scientists have directly measured the amount of heat flowing from the molten metal of the earth’s core into a region at the base of the mantle. This heat-flow process helps drive both the movement of tectonic plates at the surface and the geodynamo in the core that generates the earth’s magnetic field.

The boundary between the core and the mantle lies half-way to the center of the earth, at a depth of 1740 miles (2900 kilometers). Seismologists are able to probe the structure of this region by studying its effects on seismic waves generated by earthquakes. Seismologists obtained the new temperature measurements by relating seismic observations to a recently discovered mineral transformation that occurs at the ultrahigh pressures and temperatures prevailing near the core–mantle boundary.

“This is the first time we’ve had a ‘thermometer’ that tells us the temperature half-way down to the center of the earth,” says Thorne Lay, a professor of earth and planetary sciences at the University of California, Santa Cruz. “If our interpretation is right, it gives us the temperature at two different depths right above each other, so we get not just the absolute temperature but the rate at which the temperature is changing with depth, as well as laterally,” Lay says. “This temperature gradient tells us the amount of heat flowing out of the core into the base of the mantle in that location.”

As heat flows from the outer core into the mantle, it drives important processes in both the mantle and the core. The mantle is a thick layer of silicate rock that surrounds a dense core, predominantly iron and nickel. The outer core is molten liquid and surrounds a solid inner core about the size of the moon. The cooling of the liquid outer core results in fluid motions in the molten metal that produce electric currents, which generate the earth's geomagnetic field.

Heating at the base of the mantle, meanwhile, drives upwellings of hot mantle material that may rise to volcanoes at the surface and contribute to the slow shifting of tectonic plates. These plates consist of the thin, rocky crust and the rigid top layer of the mantle. They float on the deeper mantle, which is solid yet plastic enough to flow very slowly, and their movements trigger earthquakes and gradually change the positions of continents.

“Heat flow is the holy grail, because it tells us how much energy powers the geodynamo, and it tells us how much the mantle is being heated from below. The approach we used is the most direct method so far for getting that information,” Lay says.

The researchers developed their inner-earth thermometer by using innovative methods for analyzing seismic signals that required 72,000 hours of supercomputer time. Their investigation also relied heavily on laboratory studies of mineral physics. Under the extreme pressures and temperatures deep in the earth, minerals are squeezed into crystal structures not seen on the surface, except in a few specialized mineral physics labs. For example, when scientists take the common mineral olivine and squeeze it—subjecting it to the ultrahigh pressures and temperatures associated with increasing depth in the earth—the mineral goes through phase transitions involving sudden reorganizations of its crystal structure.

These phase transitions change the mineral’s seismic properties—how fast it transmits certain seismic waves—enabling seismologists to detect where the phase transitions occur deep in the earth. The extent of the transition tells researchers the pressure, and from that they can get the temperature from laboratory calibrations, because the pressure at which the transition occurs depends on the temperature. “If we detect a sudden change in the seismic properties of the mantle, we can associate that with a phase transition in the minerals, and we can use the laboratory calibrations to tell us how hot it is,” Lay says.

From their analysis, the researchers believe that the total heat flow from the earth’s core is about 13 trillion watts. “The numbers you might read in a textbook are about one-third of that,” Lay says.

Such a high heat flow supports the idea that the upwelling of hot plumes of mantle material from near the core–mantle boundary makes a significant contribution to mantle convection, the slow turnover of mantle material that moves tectonic plates on the surface. It also suggests that the solid inner core may be relatively young.

“The core must have been pretty hot in the past for this much heat to be still coming out, and the inner core, which is slowly solidifying from the inside out as the core cools, may be only about a billion years old,” Lay says.