PTRJ, for Mac OS, was devised as a tool to help students develop an understanding of the relationship between reactions on the microscopic and macroscopic scales through the use of a reaction potential energy surface (PES). PTRJ includes five potential energy surfaces based upon the one developed by Porter and Karplus (1) for the H + H2 reaction. For each PES, the user can choose an initial state of the system and then calculate a classical reaction trajectory and find the final state of the system after the trajectory leaves the bounds of the surface. An animation of three atoms appears at the bottom of the screen as the path of the trajectory is plotted on the PES. This visualization in direct conjunction with the plot of the trajectory path allows students to quickly become expert at visualizing the motions of the atoms on the PES.
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| This screen from PTRJ shows the result of a trajectory. |
Because of its complex nature, a PES is difficult to discuss in a lecture setting. However, this same aspect facilitates experimentation in a discovery-style setting. PTRJ can be used as a guided laboratory exercise in which students observe the effects of initial conditions on the trajectory outcome. While they may not completely understand the mechanics behind the calculation of the trajectory, they are able to interpret the motions of the atoms on the PES in a way that introduces them to the concept of a reaction on a microscopic scale. Using leading questions, students are also able to begin to understand the relationship between microscopic and macroscopic reactions.
PTRJ's documentation includes an introduction to the concept of a reaction PES and reactions on the microscopic scale and provides students with the basic information they will need to understand what they see when they run a particular trajectory. However, students will require additional resources to fully understand the shape and topology of the three-dimensional PES. Many physical chemistry textbooks have a good three dimensional PES diagram, but even with this aid it is a good idea for the instructor to reinforce the physical topology of a reaction PES, perhaps using a three-dimensional model (2). A set of exercises for students to perform and the associated questions to answer are also included. The questions encourage students to develop the connection between microscopic and macroscopic reaction kinetics.
PTRJ conveniently fills a niche between the two programs Molecular Dynamics of the F + H2 Chemical Reaction (3) and Reaction Dynamics (4), published previously by JCE Software. Molecular Dynamics provides an excellent introduction to all features of a PES and can be used to complement PTRJ's introduction. Reaction Dynamics allows users to perform many different reaction trajectory calculations for a number of different systems. The many variables present in Reaction Dynamics may prevent a student from focusing on the nature of a single microscopic reaction on a PES. PTRJ focuses on one system with the pedagogical goal of understanding the relationship between the PES and the results of a particular trajectory. Once this connection has been made, Reaction Dynamics will provide students with a larger set of options with which to further explore microscopic reaction trajectories.
Acknowledgments
Stephen Prager, Paul Hladky, Daniel Firth, Jeff Benson, Bruce Prezzavento, Kenneth Leopold, and many others at the University of Minnesota made contributions to earlier versions of this program and provided helpful advice. Support for this project was received from both the University of Minnesota Chemistry Department and Rider University.
Literature Cited
- Porter, R. N.; Karplus, M. J. Phys. Chem. 1964, 40, 1105.
- Dye, J. L. J. Chem. Educ. 1957, 34, 215.
- Kutz, H. D.; Copeland, J. H.; Mathai, G. T. J. Chem. Educ. Software 1992, 4C2.
- Lacks, D. J. Chem. Educ. Software 1992, 4C2.
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