Introduction

This module illustrates qualitative concepts relating to chemical reaction equilibria. Problems in reaction equilibria are a staple of physical chemistry and thermodynamics courses, and their treatment via the formalism of the equilibrium constant is familiar to anyone with training in chemistry or chemical engineering. While the use of these tools is not difficult to learn, an intuitive understanding of the standard Gibbs energy, enthalpy, and entropy of reaction can be more elusive. Like everything in thermodynamics, they have their origin in molecular-level behaviors, and thus some understanding of them can be gained by observing molecules "react" while following Newtonian mechanics, and seeing how the emergent behavior can be analyzed using the formalism of chemical thermodynamics.

Chemical reaction processes in real systems can be explained only via recourse to quantum mechanics but---given the limits on time and computational resources available to a typical user of this module---we cannot afford rigorous treatment of quantum effects. Instead we use a simple classical mechanical model that carries some of the important qualitative features of real reacting systems. We perform molecular dynamics of a model having two atomic "elements" (labeled B and R), and we permit them to form three types of dimer, RR, RB, and BB. The dimers are held together by a strong but breakable attractive energy, and as the atoms follow their dynamics they dissociate and recombine to form fluctuating amounts of the five species (two atomic and three dimeric). Parameters of the atom-pair interactions can be adjusted to vary directly and independently the enthalpy and entropy of reaction. The dynamic equilibria arising from the easily-observed atomic motions yields equilibrium averages for the composition, and these results can be compared to the compositions expected according to the standard thermodyamic analysis based solely on the reaction enthalpy and entropy.