Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method

Abstract.

The application of combined quantum mechanical (QM) and molecular mechanical methods to large molecular systems requires an adequate treatment of the boundary between the two approaches. In this article, we extend the generalized hybrid orbital (GHO) method to the semiempirical parameterized model 3 (PM3) Hamiltonian combined with the CHARMM force field. The GHO method makes use of four hybrid orbitals, one of which is included in the QM region in self-consistent field optimization and three are treated as auxiliary orbitals that do not participate in the QM optimization, but they provide an effective electric field for interactions. An important feature of the GHO method is that the semiempirical parameters for the boundary atom are transferable, and these parameters have been developed for a carbon boundary atom consistent with the PM3 model. The combined GHO-PM3/CHARMM model has been tested on molecular geometry and proton affinity for a series of organic compounds.