In the previous chapters, we have focused our discussion of reaction mechanisms on the critical points along the reaction path. These critical points-local energy minima (reactants, intermediates, and products) and transition states (TSs)-were discussed in terms of their geometries and energies. We discussed the nature of the mechanism in terms of the topology of the potential energy surface (PES), the structure of the TSs, and the presence or absence of intermediates. We think of reactants progressing over TSs on to intermediates, perhaps through multiple intermediates and ending at products. This path is called the reaction coordinate and corresponds to the intrinsic reaction coordinate (IRC) or the minimum energy path (MEP) (see Section 1.6 for discussion on these two paths).This standard mechanistic analysis has a long successful history. Organic chemistry textbooks are filled with PESs and discussions of the implication of single-step versus multiple-step mechanisms, concerted TSs, and so on. 1,2 Transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) theory provide tools for predicting rates based upon simple assumptions built upon the notion of reaction on the PES following the reaction coordinate. 3,4 An often-overlooked aspect of standard reaction mechanistic thought is that it really addresses only half of the picture. We talk about the positions of the atoms during the course of the reaction and the relative energies of points along the reaction path, but no mention is made of the time evolution of this process. In classical mechanics, description of a reactive system requires not just the particle positions but their momenta as well. The same is true for a quantum mechanical description, though one must keep in mind the limits imposed by the Heisenberg Uncertainty Principle. A complete description of a molecular reaction requires knowledge of both the position and the momentum of every atom for the entire time it takes for reactants to convert into products. This kind of description falls under the term molecular dynamics (MD).A few simple examples should suffice to demonstrate the critical role that MD plays in chemical reactions. Conservation of momentum must be enforced. Atoms and molecular fragments in motion must maintain their motion unless some barrier or force is applied to them. Consider the reaction of cis-2-butene with Computational Organic Chemistry, Second Edition. Steven M. Bachrach