Lee's team is exploring the uncatalyzed reaction by looking at what are known as isotope effects. An element's isotope has the same number of protons and electrons but a different number of neutrons. A reaction involving an atom and a reaction involving an isotope of that atom have the same chemical outcome. But, among other things, isotopes can impact the rate at which reactions occur. With this in mind, the team is calculating the energy required to effect the transformation into uracil and the rate at which that transformation takes place. They are computing these values for a variety of possible mechanisms.

They are also determining the energies and rates of the mechanisms when a variety of isotopes are substituted for particular atoms in orotic acid. By comparing the rates at which a reaction occurs when a given atom is present and when its isotope is present instead, the team can determine whether or not that atom is involved in the reaction's mechanism. Once they've compiled a catalog of isotope effects for a series of possible mechanisms, researchers can determine which mechanism is likely taking place.

"By looking at a variety of different hypothetical mechanisms, I can say, 'If it follows mechanism y, the isotope effect [for a particular element] is predicted to be x.' The experimentalist will then be able to measure the isotope effect [for a particular element in a particular reaction] and say 'I got x, so that means mechanism y,'" explains Lee.

Isotope effects also give researchers the opportunity to confirm the quality of assumptions inherent in theoretical work, says Dan Singleton, a chemistry professor at Texas A&M University. "Calculations can be wrong in themselves because of flaws in the method. And calculations can be wrong because of theoretical decisions in using the method. Not accounting for the surrounding solution. Or leaving out groups here, there, and everywhere to make the calculation simple enough to run. If your calculation corresponds to the experimental data, then you can presume that the method is good and that the simplifications are reasonable."

Lee and her team work with Singleton, whose work focuses on deriving isotope effects experimentally, to ensure that their theoretical computations match the real world. To date, they have completed calculations for three mechanisms and the effects of nitrogen and carbon isotopes on those mechanisms. Two of the mechanisms involve protonation, and one does not. The typical calculation takes between 20 minutes and six hours on eight Superdome processors, according to Linda Phillips, a PhD student in Lee's group.

Any sort of catalog for the orotic-acid-to-uracil reaction is far from complete. Early results, however, have shown that currently available nitrogen isotope effects cannot rule out the possibility of protonation, as some have claimed. Moreover, the results imply that further study of other nitrogen isotopes may allow researchers to distinguish among three of the most prominent hypothesized mechanisms, according to a 2001 Journal of the American Chemical Society paper by Lee and Phillips.

Just that sort of study, underway on Alliance supercomputers, may someday show us how ODCase does its amazing catalytic work.

This research is supported by the National Science Foundation, the Alfred P. Sloan Foundation, American Chemical Society Petroleum Research Fund, and the Research Corporation.