Transcript QM/MM calculations

Chemistry 6440 / 7440
QM / MM Calculations
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Cramer, C. J.; Essentials of Computational Chemistry; Wiley: Chichester, 2002, Chapter 13.
Froese, R. D. J.; Morokuma, K. Hybrid Methods, in Encyclopedia of Computational Chemistry; Wiley:
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1996; Vol. 7, pp 119-185.
Gao, J. Hybrid Methods, in Encyclopedia of Computational Chemistry; Wiley: Chichester, 1998; Vol. 2,
pp 1257-1263.
Merz, K. M.; Stanton, R. V. Quantum mechanicam / molecular mechanical (QM/MM) coupled potentials,
in Encyclopedia of Computational Chemistry; pp 2330-2343.
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1998; Vol. 1, pp 437-448.
Monard, G.; Merz, K. M. Combined quantum mechanical/molecular mechanical methodologies applied
to biomolecular systems. Acc. Chem. Res. 1999, 32, 904-911.
Mordasini, T. Z.; Thiel, W. Combined quantum mechanical and molecular mechanical approaches.
Chimia 1998, 52, 288-291.
Field, M. J.; Bash, P. A.; Karplus, M. A Combined Quantum-Mechanical and Molecular Mechanical
Potential for Molecular-Dynamics Simulations. J. Comput. Chem. 1990, 11, 700-733.
Singh, U. C.; Kollman, P. A. A Combined Abinitio Quantum-Mechanical and Molecular Mechanical
Method for Carrying out Simulations on Complex Molecular- Systems - Applications to the CH3Cl + ClExchange-Reaction and Gas-Phase Protonation of Polyethers. J. Comput. Chem. 1986, 7, 718-730.
Warshel, A.; Levitt, M. Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the
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QM/MM Methods
• The active site region is treated using high-level
molecular orbital theory, while the most distant parts of
the system are treated using low-cost molecular
mechanics.
QM/MM Methods
• Construct a Hamiltonian for the system
consisting of a QM region and an MM region
H  HQM  HMM  HQM / MM
• QM and MM regions interact mechanically and
electronically (electrostatics, polarization)
• If bonds cross boundary between QM and MM
region:
– Cap bonds of QM region with link atoms
– Use frozen or hybrid orbitals to terminate QM bonds
• Go to slides for
ONIOM Tutorial
Morokuma and Vreven
(ACS mtg 2000)