Chemical Reactions Modeled Using Classical Molecular Dynamics

We have created a two-dimensional molecular dynamics simulation to model the formation and dissociation of diatomic molecules using classical mechanics. This simulation is designed to be an educational tool used in lower-division physics or chemistry classes. The atoms interact via Lennard-Jones potential energies, while the chemical bonding is controlled by an additional short-range potential between active sites near the atoms' edges. Each active site is free to rotate around the atom, so bonding requires that atoms be in the proper orientations. As expected, most atoms form bonded pairs at sufficiently low temperatures. Somewhat counterintuitively, however, molecules in the gas phase tend to dissociate at temperatures well below the characteristic temperature determined by the bonding potential depth.