Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods

The pseudobond approach offers a smooth connection at the quantum mechanical/molecular mechanical interface which passes through covalent bonds. It replaces the boundary atom of the environment part with a seven-valence-electron atom to form a pseudobond with the boundary atom of the active part Y. Zhang, T. S. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999)]. In its original formulation, the seven-valence-electron boundary atom has the basis set of fluorine and a parametrized effective core potential. Up to now, only the Cps(sp3)-C(sp3) pseudobond has been successfully developed; thus in the case of proteins, it can only be used to cut the protein side chains. Here we employ a different formulation to construct this seven-valence-electron boundary atom, which has its own basis set as well as the effective core potential. We have not only further improved Cps(sp3)-C(sp3) pseudobond, but also developed Cps(sp3)-C(sp2,carbonyl) and Cps(sp3)-N(sp3) pseudobonds for the cutting of protein backbones and nucleic acid bases. The basis set and effective core potential for the seven-valence-electron boundary atom are independent of the molecular mechanical force field. Although the parametrization is performed with density functional calculations using hybrid B3LYP exchange-correlation functional, it is found that the same set of parameters is also applicable to Hartree-Fock and MP2 methods, as well as DFT calculations with other exchange-correlation functionals. Tests on a series of molecules yield very good structural, electronic, and energetic results in comparison with the corresponding full ab initio quantum mechanical calculations.