CLOUD

By Katherine A. Caponi, NCSA Science Writer -- Scientists know that organic compounds and nitrogen oxides interact with sunlight to produce ozone that pollutes the air we breath. Although a scientist may know that a particular type of ozone-producing compound is emitted, it can be very difficult to predict which specific reactions the molecules of the compound will undergo. A molecule's fate is constantly changing as it reacts with other nearby molecules or falls apart to make two new molecules. The determination of the amount of ozone production from any one molecule is largely a mystery. Computational modeling provides a method of discovering the most likely fates of atmospheric molecules. Models take into account emissions of organic compounds and nitrogen oxides, their transport, and their chemical reactions. Scientists can use the computational models to test regulations and requirements for minimizing ozone concentrations. If the models do not consider the correct chemical fates of the organic compounds, then the regulations may not be effective, or they may be more costly than necessary. Critical factors in atmospheric molecules' destinies are the reactions of alkoxy radicals, molecules that have an unpaired electron on an oxygen atom bound directly to a carbon atom. They are important because they are formed from nearly every organic compound in the atmosphere. At any given time, they might undergo any of five different reactions, which determine the amount of ozone produced. Identifying likely reactions Theodore Dibble, Melissa A. Ferenac, Wei Deng, and Andrew J. Davis of the State University of New York College of Environmental Science and Forestry are using an Alliance supercomputer to find out which reactions are most likely to occur by numerically simulating the range of reactions for alkoxy radicals. The team expects to challenge old assumptions about the mechanisms of atmospheric chemical reactions and the rates at which they occur. Dibble explains his enthusiasm about the potential of the team's computational models to turn fundamental science into practical applications, "What is so rewarding about this work is that we are able to do fundamental chemistry that is also very relevant to understanding the atmosphere and meets the needs of people using computers to model the behavior of pollutants in the atmosphere. The project continually produces results that are new and interesting both from an atmospheric chemistry point of view and a physical chemistry point of view." Dibble's team has used about 13,400 hours on the Alliance's Hewlett-Packard Superdome cluster at the University of Kentucky. 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. On to other molecules To date, the team has completed calculations for the reaction pathways of isoprene and two other parent molecules. Dibble states, "We are really near the beginning of this research, and there are so many steps in the reaction sequence just for isoprene. One of the things that hits home is that the experimentalists can see a wide range of reaction products with their techniques, even though they cannot quantify certain other compounds. They also know how much product they cannot account for, which inspires in them a certain caution in the interpretation of their own results. "With these computations, you ask one question at a time, 'How high is the barrier -- how fast is this reaction -- for this particular radical?' And get an answer. But you need to be careful to check all the reactions of all the intermediate radicals. Otherwise, you may miss an important reaction and reaction product without having a clue that anything is wrong!" Although Dibble's team is at an early stage of the modeling process, molecule-by-molecule they are building a valuable knowledge base for the reactions taking place in the atmosphere. The models will demonstrate which reactions dominate the fates of volatile atmospheric molecules and how they affect ozone production. Eventually, that information will help make ozone abatement strategies more efficient. -------------------- --Access story: http://access.ncsa.uiuc.edu/Stories/isoprene/