Shape Analysis of Functional Groups

1 Local Molecular Fragments in a Global Molecular Environment 

2 Local Shape Changes Induced by Molecular Environment 

The reactivities of functional groups are highly dependent on the molecular surroundings, and the effects of the global molecular environment on the local shape variations can be significant. 

In the following sections the actual electron density variations will be used for local shape analysis. 

We shall use the following notations A is the actual fragment for shape analysis, B is rest of the molecule, possibly composed from several fragments, Bj, 2 m-l- 

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The fundamental principle we shall follow in the local shape analysis of functional groups and local molecular moieties is a strict analogy with the shape analysis of complete molecules. Accordingly, instead of molecular isodensity contour (MIDCO) surfaces, the main tool of analysis will be the fragment isodensity contour (FIDCO) surfaces. Some of the ideas and concepts described in this section are illustrated in Figure 1. 

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