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

Research output: Contribution to journalArticle

Abstract

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 C ps(sp 3)-C(sp 3) 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 C ps(sp 3)-C(sp 3) pseudobond, but also developed C ps(sp 3)-C(sp 2,carbonyl) and C ps(sp 3)-N(sp 3) 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.

Original languageEnglish (US)
Article number024114
JournalJournal of Chemical Physics
Volume122
Issue number2
DOIs
StatePublished - 2005

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Atoms
valence
atoms
Electrons
proteins
electrons
formulations
Proteins
Covalent bonds
Fluorine
covalent bonds
nucleic acids
Discrete Fourier transforms
functionals
Nucleic Acids
field theory (physics)
Density functional theory
fluorine
acids
Molecules

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. / Zhang, Yingkai.

In: Journal of Chemical Physics, Vol. 122, No. 2, 024114, 2005.

Research output: Contribution to journalArticle

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