The molecular structure hypothesis - that a molecule is a collection of atoms linked by a network of bonds - was forged in the crucible of nineteenth century experimental chemistry. It has continued to serve as the principal means of ordering and classifying the observations of chemistry. The difficulty with this hypothesis was that it was not related directly to quantum mechanics, the physics which governs the motions of the nuclei and electrons that make …showed first 75 words of 449 total…

…showed last 75 words of 449 total…together the functional groups of theory. These applications include the design and synthesis of new molecules and new materials with specific desirable properties. The theory of atoms in molecules enables one to take advantage of the single most important observation of chemistry, that of a functional group with a characteristic set of properties. This document outlines and illustrates the topological basis of the theory and its relation to the quantum mechanics of an open system.