Tuesday, April 15, 2014

Roaming: a distinctly new dynamic mechanism for chemical reactions

Until recently, it was thought that the dynamics of breaking a chemical bond could occur via one of two mechanisms. The first is simply that one stretches a single bond until the relevant atoms are a long way apart. The second mechanism is via a transition state [a saddle point on a potential energy surface], where the geometry of the molecule is rearranged so that it is "half way" to the products of the chemical reaction. The energy of the transition state relative to the reactants determines the activation energy of the reaction. Transition state theory establishes this connection. Catalysts work by lowering the energy of the transition state. Enzymes work brilliantly because they are particularly good at lowering this energy barrier. An earlier post considered the controversial issue of whether it is necessary to go beyond transition state theory to explain some enzyme dynamics.

I have been struggling through an interesting Physics Today article Roaming reactions: the third way by Joel Bowman and Arthur Suits.

What is roaming?
It is a large amplitude trajectory on the potential energy surface that begins as a bond stretching.
It is best illustrated by watching videos such as this one which is an animation of a picture similar to that below.

What are the experimental signatures of roaming?
The key is to be able to resolve the distribution of the energy and angular momentum of the product molecules. It seems that if the reaction proceeds via a transition state that puts severe constraints on these distributions.

I was very happy that this week the UQ Chemistry seminar was given by Scott Kable who has pioneered recent experimental studies of roaming.
An interesting anecdote is that Scott's 2006 PNAS paper about roaming is actually based on data he took when he was a postdoc in 1990. He never published it because he did not understand it. I wonder how often this happens in science. Years ago, I wrote a short post arguing that experimentalists should not have to be able to explain their data in order to publish it.

Scott's work involves a nice experiment-theory collaboration with Meredith Jordan, who has calculated the relevant potential energy surfaces that are used in the dynamical calculations. Without the calculations it would be hard to definitively establish that roaming was an actual mechanism.

There has been an important un-anticipated consequence of this research. It may have solved a long mystery in atmospheric chemistry: the origin of organic acids in the troposphere. [See this Science paper]. This is a nice example of how basic "pure" research can lead to solutions to "applied" problems.

Roaming has now been clearly established in several gas phase reactions for small molecules.
An outstanding question is whether roaming can play a significant role in condensed phase reactions. It may be that molecular collisions will mess up the roaming trajectory. But, it may be just a matter of relative timescales. I look forward to seeing how all this develops.

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