Biomedical Engineering Reference
In-Depth Information
24.1 Link Atoms
In the case of solution-phase studies, it is clear where we should draw a boundary between
the parts of a system that ought to be studied quantum mechanically, and those that can be
treated by the techniques of MM.
Biochemists have different problems in mind; they want to divide parts of a protein chain
into regions of interest that ought to be treated quantum mechanically, and the remainder
of the chain that can be treated according to the methods of MM.
Consider for example the protein shown in Figure 24.1. The bottom left-hand amino acid
is valine, which is linked to proline. Suppose for the sake of argument that we wanted to
treat this valine quantum mechanically, and the rest of the protein chain according to the
methods of MM. We would have to draw a QM/MM boundary somewhere between valine
and the rest of the protein. The
link atoms
define the boundary between the QM and the MM
regions. A great deal of care has to go into this choice of boundary. The boundary should
not give two species whose chemical properties are quite different from those implied by
the structural formulae on either side of this boundary.
Figure 24.1
A typical protein (1PCN, from the Protein Databank)
In order to achieve this aim, it is usual to 'cap' the exposed valency at the boundary by
adding an extra quantummechanical atom. There are several reasons for doing this, not the
least of which is that we do not want to be left with a radical for the quantum mechanical
part. The extra quantum mechanical atom does not see any atoms within the MM region
