Molecular mechanics, conformation pigment

Figure 4, Minimum energy conformations of pigments C-I (a) and C-II (b) determined by MM2 molecular mechanics calculation. The B ring of the catechin moiety is folded under the malvidin C-ring and it is suggested that this protects the latter from attack by nucleophiles at the 2 or 4 positions.

Figure 3. Preferred conformation of pigment 15B determined by computer-assisted model building (MacroModel) and molecular mechanics (MM3) (31).

Pigments are comparatively large molecules. The relationship of the number of atoms versus the computation time for a crystal structure calculation is approximately linear. However, pigment molecules are fairly rigid and have limited conformational flexibility, which reduces computational expenses if only one or a few conformations must be considered. In many cases, even distinct low energy conformations may be obtained from molecular or quantum mechanical calculations. 

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