Step 1. Partitioning the System and the Model QM system

First one must decide where to partition the system into QM and MM regions. This is actually a very important step since the partitioning can be considered the 'original sin'. Much thought and testing should be put into deciding where to place the QM/MM boundary. In this example, we have chosen the partitioning depicted in Figure 5-1a in order to keep the example simple. In this figure the QM region enclosed in the dotted polygon, with two covalent bonds crossing the QM/MM boundary. One must also choose an appropriate QM model system for which the electronic structure calculation will be performed. To preserve the sp³ hybridization of the carbon center in the QM region, we must keep the carbon tetravalent. Thus, we will cap the two dangling bonds with dummy or capping hydrogen atoms. One can use any monovalent atom such as H or F, but H is probably best. The reason that monovalent atoms should be used for capping atoms is that one does not want capping atom to have any 'dangling' bonds. Capping or dummy groups can not be used. Figure 5-1b, depicts the QM model system with two capping hydrogen atoms. Thus, the electronic structure calculation will be performed on methane such that the capping hydrogen atoms lie along the bond vector of the link bond in the real system as shown in Figure 5-1b.

Figure 5-1 Cytocine QM/MM example model. a) Shows the whole system with the atoms enclosed in the dotted polygon making up the QM system. b) Shows the equivalent QM model system. The remainder of the cytocine molecule is shown ghosted to demonstrate the relationship between the model system and the full system. The QM model system consists of a closed shell methane molecule.