Step 2. Labeling of Atoms

Once a partitioning of the system has been established, one needs to label each of the atoms in the full system as QM, LI or MM atom type. For the example system, all atoms contained within the dotted polygon in Figure 5-3a are 'QM' atoms. All atoms that are marked with asterisks in Figure 5-3a are 'LI' atoms and finally the remaining atoms outside the dotted polygon are 'MM' atoms. The dummy atom that we need in order to define our reaction coordinate is designated a QM atom. This dummy atom will be made to lie midway between the two olefinic carbon atoms of the ethene moiety. It is important to realize that the linear transit constraint cannot involve any MM atoms. Two dummy atoms representing the center of the Cp rings of the ferrocenyl ligand will also be introduced. They we be part of the MM subsystem.