In search of an easy climb
To begin their computational modeling, Dibble's team chose several organic compounds emitted in large quantities to the atmosphere. The most important molecule the team has studied to date is isoprene, a volatile organic compound. Isoprene is emitted to the atmosphere almost entirely by vegetation, particularly deciduous trees like poplar and oak. Isoprene accounts for approximately 30 percent of organic compounds released. Because of isoprene's plentiful emission sources, knowledge of its possible chemical reactions is extremely important for an accurate understanding of ozone creation.

After choosing isoprene, Dibble's team identified the various ways isoprene molecules can react with other molecules and fall apart. Based on previous studies, they then identified the alkoxy radicals expected to result from the reactions.

To determine which reactions are most likely, the team used the HP Superdome cluster to three-dimensionally model the isoprene and the energy of the transition state for each reaction. To understand the transition state of a reaction, visualize the reaction process as a mountain range. One valley is the isoprene molecule. The mountain passes surrounding the isoprene are transition states. The passes lead to other valleys, which are the product molecules. The molecule is no Edmund Hillary and wants only the least daunting route. The isoprene will react by climbing the easiest pass, or completing the reaction with lowest energy barrier to the transition state.

Various experiments by other researchers confirm that isoprene usually reacts with a hydroxyl radical, and that subsequent reactions produce alkoxy radicals. Each alkoxy radical may then react with another nearby molecule or fall apart. One of the fragments may produce another alkoxy radical. The molecules often undergo long sequences of reactions, so the modeling process can be very complicated. For each individual reaction of each first- and second-generation of alkoxy radicals, Dibble's team must determine the energy barrier of the transition state (or the ruggedness of the mountain pass). Only then can they piece together the fate of the molecule in the atmosphere.