Step 1. Partitioning the System and the Model QM system.

First one must decide where to partition the system into QM and MM regions. For this example, we have decide to partition the system as illustrated in Figure 53b, whereby the QM region is contained in the dotted polygon. The corresponding QM model system, for which the electronic structure calculation will be performed, is depicted in Figure 5-3b. In the model QM system the link atoms have been replaced by capping hydrogen atoms. Notice that the QM/MM boundary cuts through the cyclopentadienyl ring of the ferrocenyl ligand. Based on experimental studies of this complex, it is assumed that the ferrocenyl ligand acts only as a spectator ligand and can be modeled effectively on a steric basis only. Using an olefinic group will approximate the sp2 hybridization of the Cp rings. Here, special care must be taken to preserver the structural features of the Cp ring. For example the C-C bond distance in the ferrocenyl ligand is approximately 1.45 Ang whereas it is about 1.34 Ang in an olefin. This will be elaborated on later. The replacement of the phenyl phosphine in the real system by hydrogen phosphine will have some consequences due to the different electronic properties of the substituents. It is known that the phenyl substitution on the phosphine is more electron withdrawing than the hydrogen substituent. The replacement of the phenyl phosphine with hydrogen phosphine will result in a contraction of the Pd-P bond in the QM model system and hence the Pd-P bond will be too short in our QM/MM model.