Truncation of the QM Region

MM methods are defined atom by atom. Thus, having a carbon atom without all its bonds does not have a significant affect on other atoms in the system. In contrast, QM calculations use a wave function that can incorporate second atom effects. An atom with a nonfilled valence will behave differently than with the valence filled. Because of this, the researcher must consider the way in which the QM portion of the calculation is truncated. 

A few of the earliest methods did truncate the atom on the dividing line between regions. Leaving this unfilled valence is reasonable only for a few of the very approximate semiempirical methods that were used at that time. 

A number of methods fill the valence of the interface atoms with an extra orbital, sometimes centered on the connecting MM atom. This results in filling out the valence while requiring a minimum amount of additional CPU time. The concern, which is dilficult to address, is that this might still affect the chemical behavior of the interface atom or even induce a second atom affect. 

FIGURE 23.1 Example of a QM/MM region partitioning for a S l reaction, (a) Entire molecule is shown with a dotted line denoting the QM region. (A) Molecule actually used for the QM calculation. 

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Instead of atom-centered basis functions, plane waves are used in conjunction with Car-Parrinello molecular dynamics (76), and pseudopotentials are applied to avoid the explicit calculation of core electron effects. For combined QM/MM calculations, the pseudopotential of the boundary atom is specially optimized so that it minimizes errors in the electronic structure arising from truncation of the QM region. 

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