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Posted: March 19, 2009

Seeing molecules move in real-time

(Nanowerk News) “Watching chemical reactions in real-time has long been a dream of chemists,” says Tahei Tahara of RIKEN’s Advanced Science Institute in Wako. “To reach a correct understanding of chemical reactions, this ‘watching’ is crucial.”
Tracking atoms in chemical reactions has previously seemed unrealistic, because the nuclei move so fast—movements can be complete within 1 picosecond (10-12 second). However, thanks to Tahara, scientists are awakening to a reality where an atom can be followed along a three-dimensional path.
In 2003, Tahara and his colleagues applied the technique known as impulsive stimulated Raman spectroscopy to measure short-lived, excited-state molecules for the first time (Time-resolved impulsive stimulated Raman scattering from excited-state polyatomic molecules in solution). Using this method, the researchers initiated a chemical reaction by exciting electrons. Then, they induced the entire molecule to vibrate using 10-femtosecond (10-14 second) lasers—which emit light faster than nuclei move. Finally, using a third laser pulse, they measured how these atoms vibrated as the reaction progressed.
Now Tahara and a team of international and Japanese scientists have directly observed how an organic molecule named stilbene rearranges its structure (Spectroscopic Tracking of Structural Evolution in Ultrafast Stilbene Photoisomerization). The initial isomer, called cis-stilbene, has two benzene rings positioned close together and connected by a carbon double bond. When excited by light, this molecule twists and rearranges to trans-stilbene, such that the benzene rings end up far apart.
Scientists have long believed that stilbene rearrangement is accomplished by the large motion of the benzene rings. Watching this reaction with Tahara’s spectroscopic method, however, revealed that the molecule changes geometry using a completely different mechanism.
“With excitation, the central carbon double bond is weakened,” explains Tahara. Then, hydrogen atoms attached to the carbon double bond moved in opposite directions, initiating a twisting motion that led to trans-stilbene. “That stilbene twisting is realized by hydrogen atom movement, [and] not by a large motion of benzene rings, was surprising to us,” says Tahara.
Schematic of a three-dimensional potential energy map of the twisting motion taken when cis-stilbene converts to trans-stilbene.
Schematic of a three-dimensional potential energy map of the twisting motion taken when cis-stilbene converts to trans-stilbene.
To visualize the three-dimensional molecular motion, the team combined experimental results with a high-level quantum-chemical calculation. The computation correlated the frequency changes observed in the experiment with particular molecular movements—and helped identify the exact twisting mechanism.
Tahara and his team’s advanced spectroscopy provides reliable checkpoints to gauge the accuracy of theoretical calculations—a combined approach that will be useful in visualizing other molecular systems.
Tahara says he doesn’t know how conceivable it is to control chemical reactions by light. “Nevertheless, I would like to try it on the basis of solid understanding of the potential energy of reactive molecules, which is obtainable by this type of study.”
Source: RIKEN