Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms.

@article{Nam2007SpecificRP,
  title={Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms.},
  author={Kwangho Nam and Qiang Cui and Jiali Gao and Darrin M. York},
  journal={Journal of chemical theory and computation},
  year={2007},
  volume={3 2},
  pages={486-504}
}
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis ( http://theory.chem.umn.edu/Database/QCRNA ), including geometries and… CONTINUE READING