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Chem 1140; Molecular Modeling • Molecular Mechanics • Semiempirical QM Modeling • CaCHE

Chem 1140; Molecular Modeling • Molecular Mechanics • Semiempirical QM Modeling • CaCHE. A. Modeling Software. Overview: http://cmm.info.nih.gov/software.html

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Chem 1140; Molecular Modeling • Molecular Mechanics • Semiempirical QM Modeling • CaCHE

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  1. Chem 1140; Molecular Modeling • Molecular Mechanics • Semiempirical QM Modeling • CaCHE

  2. A. Modeling Software Overview: http://cmm.info.nih.gov/software.html - CaCHe: Structure building. Extended MM2(87) energy minimization, extended Hückel, MOPAC, ZINDO MO programs. Orbital electron density and electrostatic maps. Prediction of octanol/water partition coefficient and water solubility

  3. B. Introduction to Molecular Modeling • Objectives: • - Computer graphics visualization of molecules ("Dreiding models") • - Matching (overlays, docking) of molecules • - Use of empirical force-fields to determine molecular properties as well as interatomic distances. • - Correlate molecular properties with an electronic structure from ab initio quantum mechanics or semiempirical quantum mechanics. • - Gain information on dynamic molecular movements. • - Use computer-assisted design for molecular recognition in organic, bioorganic, and medicinal chemistry and material science.

  4. Computational Options

  5. C. Semiempirical Methods Molecular mechanics methods are based on classical concepts and require computer time roughly proportional to the square of the number of atoms. In contrast, semiempirical methods at the Hartree-Fock level use a combination of quantum chemical models and experimentally determined parameters to strive for accuracy and scale up as (4N)3. Finally, ab initio quantum mechanics proceeds as (10N)4 (for glucose: 1:1,500:6,000,000). There are important differences between classical molecular mechanics and quantum mechanical methods. MM methods are extremely fast and able to handle very large systems. Particularly for hydrocarbons, they are also as accurate as the best ab initio methods. But they are only parametrized for ground state systems and common bonding situations (functional groups). MM methods are unable to anticipate the making and breaking of most bonds, the electronic properties of molecules, and the chemistry of electronically excited states.

  6. Use molecular orbital methods to compute: - bond orders - dipole moments - ionization potentials - vibrational frequencies and IR, UV spectra - MO energies - partial charges - potential energy maps - reaction pathways - transition states - heats of formation - mapping bond breaking and bond formation The transition between semiempirical and ab initio quantum chemistry is not always obvious. Basis sets, for example, are empirical in nature, as are effective core potentials.

  7. Kondru, R. K.; Wipf, P.; Beratan, D. N., "Theory assisted determination of absolute stereochemistry for complex natural products via computation of molar rotation angles." J. Am. Chem. Soc.1998, 120, 2204-2205. Wipf, P.; Kerekes, A. D., "Structure reassignment of the fungal metabolite TAEMC161 as the phytotoxin viridiol." Journal of Natural Products2003, 66, 716-718.

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