The proposed algorithm aims at finding an atom map minimizing the number of formed and broken bonds as a measure for the number of electrons that have to be redistributed. The bond information is stored in the molecular connectivity. Two atoms I and J are considered as bonded if their distance R IJ = |R I -R J | does not exceed the sum of their element-specific covalent radii R cov,I and R cov,J , taken from Ref. 38, by more than a threshold τ cov . The elements of the connectivity matrix of structure A are therefore given by