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Molecular Modeling: Molecular Mechanics

Molecular Modeling: Molecular Mechanics. C372 Introduction to Cheminformatics II Kelsey Forsythe. Review. Energy components Guidelines for use Pros and Cons Geometry optimization. Today. Modeling inorganic systems Modeling macromolecules Ligand-receptor interactions

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Molecular Modeling: Molecular Mechanics

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  1. Molecular Modeling:Molecular Mechanics C372 Introduction to Cheminformatics II Kelsey Forsythe

  2. Review • Energy components • Guidelines for use • Pros and Cons • Geometry optimization

  3. Today • Modeling inorganic systems • Modeling macromolecules • Ligand-receptor interactions • Beyond Empirical Methods • Ab Initio • Semi-Empirical

  4. Comparison of Empirical Models • Copy of p.443 from Gundertofte article • See also Cramer Table 2.1

  5. Hypervalent Systems • SF6 • MMFF • r(SF) = 1.633A (EXPT = 1.564A) • SYBYL • r(SF) = 1.800A (EXPT = 1.564A)

  6. One Atom Heavy Hydrides • MMFF • r(NH3) = 1.019A (EXPT = 1.012A) • SYBYL • r(NH3) = 1.080A (EXPT = 1.012A) • Mean error (bond distances): • SYBYL - .262 • MMFF - .026 (Comparable to small basis Hartree-Fock) • Similar performance for multiple heavy atom hydrides Hehre, W. J., A Guide to Molecular Mechanics and Quantum Chemical Calculations

  7. Multiple Heavy Atom Systems • ~150 compounds • Benzene, difluromethane, tetrachlorosilane, ozone, magnesium fluoride • Mean error (bond distances): • SYBYL - .051 • MMFF - .034 • Ab initio (HF) - .028

  8. Transition Metal Molecules • MMFF and SYBYL NOT parameterized • MMX - some parameterization for inorganics • UFF - parameters for all elements • MOMEC • VALBOND

  9. Modeling macromolecules • Solvent-Solute (i.e. Non-Bonding) interactions very important • Ligand-Receptor interactions • Protein Folding • Dreiding • AMBER (protein structure) • OPLS • Chem-X • CHARMM (“ “) • YETI (ligand-protein) • CFF (proteins) • MMFF (hydrogen-bonding) • Tripos/SYBYL

  10. MMFF • Parameterized to Ab Initio • Non-Bonding Interactions • Hydrogen bonding • Water n-mers • Non-polar (vdW) • (H2)2 , (CH4)2

  11. Macromolecular Modeling • D-glucose - 11 different conformers • GROMOS, MM3 • 1.5-2.1 kcal/mol • CHARMM, MMFF • 0.9-1.5 kcal/mol • AMBER, Chem-X, OPLS • 0.6-0.8 kcal/mol Barrows, S. E. et al, 1998. J. Comput. Chem.19, 1111.

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