Reaction dynamics topological aspects

Up to this point, we have emphasized the stereochemical properties of molecules as objects, without concern for processes which affect the molecular shape. The term dynamic stereochemistry applies to die topology of processes which effect a structural change. The cases that are most important in organic chemistry are chemical reactions, conformational changes, and noncovalent complex formation. In order to understand the stereochemical aspects of a dynamic process, it is essential not only that the stereochemical relationship between starting and product states be established, but also that the spatial features of proposed intermediates and transition states must account for the observed stereochemical transformations. 

There are two directions of study. One is with regard to the static aspect of reaction network structure (e.g., topology). The other is the number distribution of chemical species and their dynamics. Of course, one needs to combine the two aspects to fully understand the condition for recursive production of a cell. 

In the present article, we report a study concerning the reaction mechanism of a prototype reaction using both static and dynamic approaches to explore a DFT potential surface. The static approach is the standard IRC model, while the dynamic one is based on a Carr-Parrinello method performed with localized (Gaussian) orbitals, the so-called atom-centered density matrix propagation (ADMP) model.25 Our aim is to elucidate the differences, and the common aspects, between the two approaches in the analysis of bond breaking/formation. To this end, we have chosen topological quantities as probe molecular descriptors. 

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