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Chemists Find Molecules Switch Shapes Slowly

June 17, 2008

By Castelvecchi, Davide

Findings may challenge theory explaining vibrations Chemists can now watch the structures of molecules as they change shape, much like shooting multiple frames of a galloping horse. The new view reveals that when certain molecules switch between different conformations, they do so less often than expected – a finding that could require chemists to revise their theories and that could lead to a better understanding of processes such as how proteins fold.

Brooks Pate of the University of Virginia in Charlottesville brought the time-honored chemistry tool called rotational spectroscopy into the digital era. His team can now collect data about molecules 100 to 10,000 times faster than was previously possible, essentially combining multiple frames in one shot. “It used to be that it would take three to four months” to take a similar amount of data, Pate says. “Now you can do it in one day.”

“It’s a very sleek little design,” comments John Pearson of NASA’s Jet Propulsion Laboratory in Pasadena, Calif.

Using the new technique, Pate’s team looked at a small organic molecule in which a carbon atom sticks out like an arm, attached to another carbon atom. Vibrations of the molecule can make the arm randomly switch between two different stable positions. The researchers found that the molecules wiggle their carbon arms about 10 billion times a second -one-sixteenth as fast as the chemists had predicted based on prevailing theory. The team’s results appear in the May 16 Science.

The team repeated the experiment with about 10 other types of relatively small molecules, Pate says. All results disagreed with the prevailing theory of how vibrations move across a molecule and lead it to change shape or break up into pieces.

Terry Miller of Ohio State University in Columbus says that the calculation methods commonly used to get such theoretical predictions may need some amendment, although the basic tenets of the theory may in the end survive unscathed. Miller authored an accompanying commentary on the work in the same issue of Science.

“There’s clearly more going on with these molecules than we understand,” adds Pearson. A more precise theory would shed light on complex phenomena that involve molecules changing shape. For example, as a protein folds, it changes shape as bonded atoms pivot around one another.

The new method could also shed light on phenomena that involve molecules both changing shape and reacting chemically – such as, Pearson says, the firing of gunpowder.

The approach makes possible quick, accurate chemical analyses, such as of harmful chemicals used in a non-conventional attack, Pate says. The closer view of molecules could also help astrophysicists discover new molecules in the interstellar medium by matching these molecule’s radio-emission signatures with those seen in the lab.

The experiments were made possible by recent advances in digital electronics, Pate says. “You just could not imagine doing this 10 years ago.”

In rotational spectroscopy, a beam of molecules is exposed to microwave radiation. If the molecules are “polar” – meaning they have an uneven distribution of electrical charge – the microwaves’ electric fields will apply a torque to them, making them rotate slower or faster. As the molecules’ spinning rates change, the molecules give off radiation at frequencies characteristic of the molecules’ structure. In particular, a molecule that has an arm sticking out will tend to rotate at a slower pace (and to send out lower-frequency radiation) than one with a “retracted” arm. “It’s the ice-skater phenomenon,” Pate says.

In the past, researchers had to look at the molecules’ radiation one frequency at a time, essentially by turning a radio dial. “It was like tuning your receiver,” Pate says. Instead, Pate’s team used a digital device that picks up all frequencies from all molecules at once.

The team then looked at molecules as they change shape – a process during which the molecules go through many intermediate steps, emitting radiation at a particular frequency for each step.

A further refinement, Pate says, could enable researchers to track other types of chemical reactions as they happen, such as a molecule breaking up. For example, scientists could zap a molecule with a laser and time how quickly a bond’s length changes before it breaks.

Chemists can now watch as molecules such as cyclopropane carboxaldehyde (shown here) switch back and forth between two configurations.