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Figure 5 | Algorithms for Molecular Biology

Figure 5

From: Atom mapping with constraint programming

Figure 5

Ambivalent reactions. (top) The Meisenheimer rearrangement [37] transforms nitroxides to hydroxylamines. It does not admit a simple alternating cycle as ITS when molecules are represented as graphs whose vertices are atoms. An extended representation, in which the additional electron at the oxygen is treated as a “pseudo-atom” can fix this issue. (bottom) Note that such even sized cycles with a virtual vertex for the moving charge (vertex label e) can be represented by smaller odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0). See Figure 2 for further details of such an ITS layout.

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