Pseudobond approach

Keywords Ab initio QM/MM method, Pseudobond approach, Enzyme catalysis, Reaction... 

Figure 12-1. Illustration of the difference between the pseudobond approach and the conventional link atom approach in the treatment of the QM/MM boundary problem...

In order to improve the accuracy and applicability of the pseudobond approach, very recently we have developed a new formulation to construct this seven-valence-electron boundary atom [29], The key difference is that the seven-valence-electron boundary atom has its own basis set instead of that of fluorine. Here a STO-2G... 

Zhang Y, Lee TS, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110 46-54... 

In the structurally coupled QM/MM implementation of Zhang et al. [55, 56], in which the QM/MM boundary was treated by use of the pseudobond approach [55, 57], the QM/MM minimization of the QM part is combined with FEP calculations. In this procedure the energy profile of the enzyme reaction is first determined by use of QM/MM energy minimizations. The structures and charges of the QM atoms are then used, in the same manner as in the QM/FE method, to determine the role of environment on the energy profile of the reaction. In this way the effects of a large number of MM conformations of protein and solvent environment can be included in the total energies. 

In addition to the hybridised orbital approach, Zhang et al 52 have proposed a pseudobond approach. The boundary atom of the MM region is replaced by a single free valence carbon atom, Cps. Each C, has 7 electrons, a nuclear charge of 7 and an effective core potential parameterised to mimic an sp2 hybridised orbital between it and the QM boundary atom, thereby forming a sort of... 

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