December 22, 2008

Volume 86, Number 51

pp. 11-15

Chemical Year In Review 2008

Steve Ritter, Nathan Becker, and Tchad Blair edited and produced C&EN's Chemical Year In Review

1

Surprise From S_N2 Snapshots

Adapted from Science

Unexpected Twist In the classic S_N2 mechanism (left series), Cl^– attacks CH₃I, and I^– leaves directly along the axis on which Cl^– entered. In the roundabout mechanism (right series), Cl^– bumps the methyl group, causing CH₃I to rotate. After one revolution, Cl^– displaces I^–.

By analyzing snapshots of single-molecule collisions, an international research team uncovered unanticipated details about the mechanism of the classic bimolecular nucleophilic substitution (S_N2) reaction (C&EN, Jan. 14, page 9; Science 2008, 319, 183). In addition to providing direct evidence for the traditional S_N2 mechanism in the gas phase, Roland Wester and colleagues at the University of Freiburg, in Germany, together with William L. Hase and colleagues at Texas Tech University detected an additional unexpected pathway. In this "roundabout mechanism" the nucleophile bumps into the substrate, spinning the substrate 360º before substitution and leaving-group displacement occur. To visualize these details, the Freiburg team crossed beams of reactants in a vacuum and detected the directional and speed distributions of the products. The data suggested at least two reaction mechanisms, one of which is the traditional S_N2 pathway. Atomic-level chemical dynamics simulations by the Texas Tech scientists were in accord with that conclusion, but they also discovered that some data were due to the roundabout mechanism. "Before performing the simulations we would never have thought the roundabout mechanism was in play," Hase said. These results "challenge some of our cherished models of elementary reaction mechanisms," said Benjamin J. Whitaker, a reaction dynamics expert at the University of Leeds, in England.

» Read "Surprise From S_N2 Snapshots" (C&EN, Jan. 14, page 9)
» View Animation: "Roundabout"
» View Animation: "In Line With Tradition"

2

Peeking At Catalytic Reactions

Science © 2008

Amplified The NMR signal of propane (shown) formed by hydrogenation of propene with p-H₂ is 300-fold stronger than the NMR signal of propene.

With a new nuclear magnetic resonance imaging technique, researchers were able to get an eye on catalytic hydrogenation reactions taking place inside microreactors (C&EN, Jan. 28, page 13; Science 2008, 319, 442). The scientists expect the method to be useful for studying and optimizing industrial catalysts and catalytic reactors. Alexander Pines, Louis-S. Bouchard, and coworkers at Lawrence Berkeley National Laboratory and the University of California, Berkeley, developed the method by taking advantage of the para form of hydrogen (p-H₂) to amplify the NMR signal of propane made by the hydrogenation of propene. On its own, p-H₂ has no observable NMR signal, but in a hydrogenation reaction the paired hydrogen atoms become magnetically inequivalent, resulting in an enhanced NMR signal. The researchers used the method to map propane formation and thereby pinpoint active regions in the microreactor catalyst bed.

3

Measuring Atomic Friction

IBM

Drag And Drop In this illustration, an AFM tip (red) measures the force it takes to move a cobalt atom (yellow) over a crystalline surface.

IBM

Push-Pull Arrows indicate the forces acting on an AFM tip as it moves a cobalt atom over a copper surface.

For the first time, scientists determined the forces needed to move a single atom across a surface. With this advance, it's now possible to quantify friction at the atomic level. Knowing how tightly an atom or a molecule "sticks" to a surface will be invaluable in nanoelectronics design and in bioengineering. Andreas J. Heinrich and Markus Ternes of IBM's Almaden Research Center, in San Jose, Calif.; physics professor Franz J. Giessibl of the University of Regensburg, in Germany; and colleagues used a modified atomic force microscope at ultrahigh vacuum and a temperature of only 5 K to measure both the lateral and vertical forces exerted on a cobalt atom and carbon monoxide molecule as the microscope tip dragged them across a platinum or copper surface (C&EN, Feb. 25, page 6; Science 2008, 319, 1066). Since the 1990s, many groups have succeeded in manipulating surface atoms, but measuring the forces associated with that movement is something "we all dreamed about," said Ludwig Bartels, a chemistry professor at the University of California, Riverside.

» Read "Measuring Atomic Friction" (C&EN, Feb. 25, page 6)
» View Video: "Atomic Force"

4

Molecular Target For DEET Discovered

Since World War II, people across the globe have liberally applied N,N-diethyl-m-toluamide, better known as DEET, to ward off mosquitoes and other insects that not only are annoying but can transmit diseases. But no one knew exactly how the most commonly used active ingredient in topical bug repellants worked until Leslie B. Vosshall and colleagues at Rockefeller University reported that DEET inhibits certain mosquito and fruit fly olfactory receptors (C&EN, March 17, page 42; Science 2008, 319, 1838). Previous work by other researchers had shown that DEET affects insects' ability to sniff out human odors, such as those caused by lactic acid. But Vosshall and colleagues were the first to pinpoint DEET's molecular targets: olfactory receptors that form a complex with a coreceptor called OR83b. To find these receptors, the researchers combined a genetic approach with an in vitro reconstitution of insect odorant receptors. Knowing how DEET affects receptors could lead to new insect repellents that, for example, could more safely be used on young children.

Courtesy of Carolyn Bertozzi and Coworkers

Shiny Fish Cell-surface glycans shine in this microscope image of the head of a three-day-old zebrafish embryo subjected to a technique for visualizing changes in cell-surface carbohydrates.

5

Imaging Technique Tracks Sugars In Live Animals

It is now possible to image carbohydrates as they are produced on cell surfaces of live animals, thanks to a research team at the University of California, Berkeley (C&EN, May 5, page 8; Science 2008, 320, 664). Cell glycans (oligosaccharides) are key markers and mediators of many physiological processes, but previously they couldn't be visualized in living organisms. Carolyn R. Bertozzi and coworkers fed azide-derivatized sugars to zebrafish, which incorporated the modified sugars into their glycans. The researchers then used difluorinated cyclooctyne reagents with attached fluorescent probes to mark the glycans so they could be visualized by optical imaging techniques. The approach makes it possible to observe patterns of glycan expression that previously would have been undetectable. The scientists demonstrated the method by using it to detect changes in glycan biosynthesis in specific locations in live zebrafish. The ability of the method "to determine how glycans are distributed spatially within a tissue and in time can help to reveal their functional roles and to identify cell-surface markers indicative of the physiological status of cells," commented glycan-imaging specialist Mary L. Kraft of the University of Illinois, Urbana-Champaign.

6

Two-For-One Catalyst

Itzik Yosef

CATALYST IN THE MIDDLE A rhodium phosphine cyclooctadiene complex that is trapped within a matrix of silver particles (silver spheres) forms a synergistic catalyst system (Rh is blue, Cl is green, P is purple, S is yellow, O is red, C is gray, and H is white). The nanoporous composite (below) exhibits a sheetlike morphology, as opposed to spherical particles observed for a catalyst adsorbed on the metal???s surface.

J. Am. Chem. Soc.

The catalyst-in-silver nanoporous composite (shown) exhibits a sheetlike morphology, as opposed to spherical particles observed for a catalyst adsorbed on the metal surface.

By entrapping a soluble rhodium complex inside a porous matrix of silver atoms, a team of Israeli chemists initiated a new approach to heterogeneous catalysis (C&EN, Sept. 1, page 9; J. Am. Chem. Soc. 2008, 130, 11880). Chemists often harness soluble homogeneous catalysts for surface-based heterogeneous reactions by fixing the catalyst on an organic polymer or an inorganic oxide such as silica—materials that are nonconducting. The catalyst-in-metal composite developed by Itzik Yosef, Raed Abu-Reziq, and David Avnir of Hebrew University of Jerusalem marks the first time a homogeneous catalyst has been "heterogenized" in a conducting material. Trapping the rhodium complex in a "sea of electrons" enhances its catalytic activity, presumably by altering its electron donor-acceptor properties and modifying substrate binding. To make the material, the researchers added zinc powder to a solution containing a rhodium phosphine cyclooctadiene catalyst and silver nitrate. The zinc reduces the silver cations, and as silver crystallites form, they aggregate and precipitate out of the solution, taking the catalyst with it. This catalyst entrapment process "is a watershed development in science," commented organometallic chemist Howard Alper of the University of Ottawa. Since the original report, Avnir's group has used the technique to entrap an acidic polymer in silver as an acid catalyst, entrap active enzymes in silver and in gold, and dope silver with different reagents to improve its catalytic performance.

7

Peptide-Producing Powerhouses

Adapted from Science

ANTIBIOTICS FACTORY The first published structure of an entire NRPS module is the termination module used to produce the antibiotic surfactin.

When bacteria want to build intricate peptides, they employ megacatalysts called nonribosomal peptide synthetase (NRPS) enzymes. Just one of these enormous assembly-line enzymes can possess as many as 40 catalytic sites, located in sequential modules that lengthen the chain one peptide bond at a time. Because many of the peptides produced through NRPS enzymes are potent antibiotics—think penicillin or vancomycin—researchers want to figure out how to harness the enzymes to produce existing antibiotics and engineer new ones. To that end, biochemist Mohamed A. Marahiel of the University of Marburg, in Germany, and colleagues published the first X-ray crystal structure of an entire NRPS module (C&EN, Oct. 6, page 48; Science 2008, 321, 659). Shortly thereafter, a team of chemists led by Gerhard Wagner and Christopher T. Walsh of Harvard Medical School published a nuclear magnetic resonance structure of components of a similar module (Nature 2008, 454, 903). The two structures represent the first views of how separate catalytic domains are organized within an NRPS enzyme, noted Janet L. Smith, a biochemist at the University of Michigan, Ann Arbor. The findings will "allow us to figure out how to engineer NRPS enzymes to do even more varied chemistry," she said.

8

Gibberellin's Role In Plant Puberty

View Enlarged Image Toshio Hakoshima

Boxed In Binding of gibberellin (gray space-filling structure) within its receptor (green) causes the receptor's N-terminus (purple) to close over the hormone like a lid. Closing the lid provides a platform for binding gene transcription blockers called DELLA (blue).

Making lemons and grapes plumper, persuading asparagus to send out more shoots, and waking up a wide variety of seeds from dormancy are all part of the plant hormone gibberellin's job description. But how this diterpenoid carboxylic acid gets down to business has long been a mystery. This year, Japanese scientists provided some key information by reporting the first X-ray crystal structures of gibberellin's receptor (C&EN, Dec. 1, page 9; Nature 2008, 456, 459). One structure reveals a deep pocket that accommodates the hormone, noted lead author Toshio Hakoshima, a crystallographer at the Nara Institute of Science & Technology. Gibberellin binding causes an unstructured section of the receptor's N-terminus to collapse into a helical bundle, which then closes over the gibberellin molecule like a lid. The top of the closed lid contains several hydrophobic residues, which then interact with a hydrophobic portion of DELLA, a protein that interferes with gene expression. The association with the gibberellin receptor causes DELLA to be chopped up, thereby allowing gene expression that stimulates germination, stem elongation, and flowering.

9

Beating An Alcohol Synthesis Problem

AMBIDEXTRIOUS ROUTE New synthesis yields enantiopure tertiary alcohols, with the selectivity depending on the choice of boron reagent.

Making chiral tertiary alcohols has always been a tricky endeavor. Varinder K. Aggarwal, a chemist at the University of Bristol, in England, and colleagues reported a novel strategy to selectively produce such enantiopure tertiary alcohols that relies simply on choosing the type of boron reagent to use (C&EN, Dec. 15, page 8; Nature 2008, 456, 778). Aggarwal's team started with relatively easy-to-make enantioenriched secondary alcohols and converted the hydroxyl group into a carbamate group. The researchers next used a base to nip a hydrogen atom from the carbamate to form an intermediate anion. Then, a boron-based reagent reacted with the anion to provide an alkyl group. The carbamate group was expelled, and hydrogen peroxide added to the pot reintroduced the alcohol functionality. The step involving the boron reagent came with "completely unexpected results," Aggarwal said. As it turns out, the nature of the reagent—that is, whether it is a boronate ester or a borane—dictates which enantiomer is produced, with striking selectivity. The work "is a superb piece of innovative reaction engineering," noted Princeton University's David MacMillan, who works on chiral synthesis. Karl B. Hansen, the scientific director of chemical process R&D for Amgen, called the strategy "striking" in a Nature commentary. "Because a compound's enantiomers often have different biological activities, this could be particularly useful for drug discovery and development," Hansen noted.

10

Superconductivity Back In The News

Electron Speedway Doping LaO (blue and gray) with F (green) injects electrons into the FeAs (red and orange) layers of a 43-K superconductor.

Haozhe Liu/Harbin Inst. of Technology

Under Pressure Subjecting rare-earth iron arsenides to high pressure shrinks the separation between F-doped rare-earth oxide layers and Fe-As layers and in some cases extends the temperature range over which the compounds superconduct (Nd is green, O or F is red, As is blue, and Fe is gold).

Superconductivity headlined science news in 2008 in a way not seen in more than 20 years. Hideo Hosono and coworkers at Tokyo Institute of Technology announced a new type of superconductor, a rare-earth iron arsenide, and within months researchers around the world discovered a family of chemically related compounds. Hosono's team reported the synthesis of LaOFeAs doped with fluoride ions and measured a critical superconductivity transition temperature, T_c, of 26 K in the material (C&EN, April 28, page 15; J. Am. Chem. Soc. 2008, 130, 3296).

Seeking to boost the Tc to make superconductivity applications practical, several research groups subsequently reported superconducting iron arsenide analogs (C&EN, Oct. 20, page 15). For example, scientists at the University of Science & Technology of China, in Hefei, boosted the T_c to 43 K with SmO_1–x F_xFeAs. Soon thereafter, physicists at the Chinese Academy of Sciences, in Beijing, achieved 52 K superconductivity in a praseodymium analog. They also found that the samarium analog's T_c reaches 55 K under pressure. And at Zhejiang University, in Hangzhou, China, scientists raised the iron arsenide family's T_c slightly higher, to 56 K, with their variation on the theme: Gd_0.8Th_0.2FeAsO. A variety of related materials containing Ce, Nd, Tb, and Dy were also reported this year.

The T_c for each of the new materials, however, remains far below the ultimate goal of room-temperature superconductivity.

» Read "'Hotter' Superconductors" C&EN, April 28, page 15)
» Read "Superconductivity Rekindles" (C&EN, Oct. 20, page 15)
» View Video: "Superconductivity"
» View Video: "How Superconducting Levitation Works"

11

Nobel Prize In Chemistry

UC San Diego

Tsien

Columbia University

Chalfie

MBL

Shimomura

The 2008 Nobel Prize in Chemistry honored Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien for the discovery and development of green fluorescent protein (GFP). This protein and mutated versions of it have become powerful tools for tagging and observing other proteins in cells (C&EN, Oct. 13, page 7).

Shimomura, 80, senior scientist emeritus at the Marine Biological Laboratory, in Woods Hole, Mass., was the first person to isolate GFP from the jellyfish Aequorea victoria.

Roger Tsien
View Enlarged Image

FLUORESCENT PROTEIN Conceptual rendering of a fusion between GFP and a peptide.

Roger Tsien
View Enlarged Image

CASCADE OF COLOR Engineered variations in GFP result in a rainbow of fluorescent proteins.

Chalfie, 61, a professor of biological sciences at Columbia University, pioneered the use of GFP as a fluorescent label inside living organisms. He genetically manipulated GFP to create fusion proteins in which GFP is linked to other proteins that can be expressed in various organisms.

Tsien, 56, a professor of pharmacology at the University of California, San Diego, showed how the GFP chromophore assumes its shape. He and his group have genetically engineered GFP mutants that absorb and emit light in other spectral regions, which allows the simultaneous labeling of multiple proteins inside cells.

12

Space Bounty From Mars, Mercury, And Venus

© 2008 Science/AAAS

Dynamic Planet This false color image of Mercury's Caloris Basin impact crater, taken by Messenger, reveals areas of high (orange) and low (blue) reflectivity, indicating different mineral compositions and geologic structures.

NASA/JPL-Caltech/U of Arizona

Hot Diggity Phoenix scooped trenches in the icy martian soil, discovering perchlorate and water-bearing minerals.

Mars dominated news from space this year, as the world tuned in to the life and times of the soil-probing Phoenix lander. But 2008 also saw new discoveries about Mercury and Venus.

Phoenix, a collaboration between NASA and the University of Arizona, made a flawless landing in May on a flat, icy patch near the martian north pole (C&EN, June 2, page 14). Battling sticky soil that thwarted attempts to deliver samples from a robotic scoop to ovens and wet chemistry beakers on board, scientists managed to learn that the pH of martian soil is a habitable 8 to 9 and that it contains water-bearing minerals and perchlorate ions (C&EN, Aug. 11, page 13).

As the martian winter set in, the chill and lack of sunlight took its toll on the craft, and it stopped communicating with Earth in early November. At C&EN press time, scientists were scheduled to present data from Phoenix' final experiments at the American Geophysical Union fall meeting in San Francisco.

Mercury also gave up some of its secrets (C&EN, July 28, page 65). Scientists reported that NASA's Mercury Messenger spacecraft spotted never-before-seen evidence of volcanic activity around the rim of a giant impact crater. They also confirmed that unlike Earth and Venus, Mercury is curiously devoid of iron.

Also, the European Space Agency's Venus Express spacecraft, which is orbiting that planet, detected infrared emissions from hydroxyl radicals (C&EN, May 26, page 7). Although HO∂ had not been seen before around a planet besides Earth, it has been thought to play a role in atmospheric chemistry and dynamics on both Venus and Mars. The radical had been difficult to detect before because it's rare and its spectroscopic bands overlap with those of other species.

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