The Intuitive Concept of Molecular Shape

Molecules are three-dimensional objects and they do occupy some space. When considering the space requirements of molecules, it is natural to associate with them a formal molecular body and a formal molecular surface [84-88]. In a simplistic model, this surface is a formal molecular boundary, a closed surface that separates the 3D space into two parts the molecular body enclosed by the surface that is supposed to represent the entire molecule, and the rest of the 3D space that falls on the outside of the surface, hence on the outside of the molecule. The above, intuitive concepts of molecular body and molecular surface are very useful for the interpretation of molecular size and shape properties within approximate models. 

Although in the process of quick recognition of major trends and dominant common features, a somewhat imprecise shape perception based on intuitive, subjective shape concepts are useful, the needs for clearly defined shape measures and for precise and accurately shape evaluation are evident if details of shape are important and if it is not well understood which shape characteristics are potentially responsible for a given molecular property (Mezey 1993). 

The molecular shape descriptors presented here are typically of a global nature. They offer ample evidence that shape as a volume or as a surface is an exciting and useful concept when applied to drug discovery. They provide a reliable scaffold for virtual screening and lead optimization by decoration with chemical intuition, but also have their unadorned use as in ligand fitting, prediction, or active site description. 

---