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Chemistry 6440 / 7440

Chemistry 6440 / 7440. QM / MM Calculations. Resources. 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: Chichester, 1998; Vol. 2, pp 1244-1257.

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Chemistry 6440 / 7440

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  1. Chemistry 6440 / 7440 QM / MM Calculations

  2. Resources • 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: Chichester, 1998; Vol. 2, pp 1244-1257. • Gao, J. Methods and Applications of Combined Quantum mechanical and Molecular Mechanical Potentials, in Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 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. • Tomasi, J.; Pomelli, C. S. Quantum mechanics / molecular mechanics (QM/MM), in Encyclopedia of Computational Chemistry; Vol. 4, pp 2343-2350. • Ruiz-López, M. F.; Rivail, J. L. Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity, in Encyclopedia of Computational Chemistry; Wiley: Chichester, 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 + Cl- Exchange-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 Reaction Site of Lysozyme. J. Mol. Biol. 1976, 103, 227-249.

  3. 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.

  4. QM/MM Methods • Construct a Hamiltonian for the system consisting of a QM region and an MM region • 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

  5. Go to slides for ONIOM Tutorial Morokuma and Vreven (ACS mtg 2000)

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