January 7, 2006
Chemists Calculate Structure of Puzzling ‘Scrambler’ Molecule
COLUMBUS, Ohio -- Chemists have calculated the structure of a very unusual molecule, one whose hyperactive atoms have earned it the nickname "the scrambler."
This highly caustic "protonated methane," or CH5+, is also called a "super acid," and it is a short-lived player in the chemical reactions that make petroleum products.
To identify chemicals on earth and in outer space, scientists record the spectrum of light absorbed by a molecule. Each molecule ever identified has its own unique spectrum, resembling lines in a bar code.
Since the 1960s, when petrochemical experiments suggested the existence of CH5+, scientists have been trying to record a complete spectrum of it, but the molecule won't sit still. Scientists who tried to image CH5+ have found that it's like a three-year-old child -- impossible to photograph, except in a blur.
"CH5+ has five hydrogen atoms scrambling around a carbon atom that sits at the center," McCoy explained. The hydrogen atoms are simultaneously rotating and vibrating.
Because the atoms are always on the move, scientists have difficulty interpreting the spectrum. Still, they have recorded several CH5+ spectra experimentally.
Study coauthors David Nesbitt, Chandra Savage, and Feng Dong of JILA, a joint research institute of the University of Colorado at Boulder and the National Institute of Standards and Technology, report the most recent and best resolved of these spectra to date in the Science paper. But in spite of this progress, researchers have not been able to match the lines in the CH5+ bar code to any specific motions of the molecule.
That's what McCoy and Professor Joel M. Bowman of Emory University did mathematically. For certain features on the spectrum, they calculated what the motions must be.
The result is most complete vibrational spectra ever calculated -- a theoretical picture of the molecule's structure.
The chemists' employed a unique strategy in their calculations.
"Although the hydrogen atoms are constantly scrambling, the overall range of types of structures can be characterized by three basic configurations," McCoy said. One configuration corresponds to a low energy state for the molecule, and the other two to higher energy states. McCoy, Bowman, Ohio State graduate student Lindsay M. Johnson and Emory postdoctoral researcher Xinchuan Huang calculated spectra for all three structures.
That in itself was standard procedure, she said -- but then they went on to examine the probability that the molecule would assume each of those three structures, and used that information to weight their calculations.
"It turns out that this was the crucial step," McCoy said.
She acknowledged that her team hasn't yet assembled a full picture of CH5+, since their calculations accounted for the vibration of the molecule but not its constant rotation. That will be their next step. If successful, they'll have a complete theoretical view of what the molecule's spectrum should look like.
"The ultimate goal of this work is to identify a kind of signature for CH5+," McCoy said. "Once we have it, we can compare it to what is observed from astronomical measurements to determine its abundance in different regions of space."
"From a more fundamental perspective, one thing that intrigues me is how we can characterize molecules like CH5+ that have no single well-defined structure and how this lack of a well-defined structure impacts its reactivity," she continued.
She and her coauthors have started calculating what would happen when the hydrogen atoms in CH5+ are replaced with deuterium, also known as "heavy hydrogen." They suspect that adding one or two heavy hydrogen atoms will stabilize the remaining hydrogen atoms and settle "the scrambler" down once and for all.
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