Unformatted text preview: 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 Ligandreceptor interactions Beyond Empirical Methods Ab Initio SemiEmpirical Comparison of Empirical Models Copy of p.443 from Gundertofte article See also Cramer Table 2.1 QuickTime and a TIFF (LZW) decompressor are needed to see this picture. Hypervalent Systems SF6 MMFF SYBYL r(SF) = 1.633A (EXPT = 1.564A) r(SF) = 1.800A (EXPT = 1.564A) One Atom Heavy Hydrides MMFF SYBYL r(NH3) = 1.019A (EXPT = 1.012A) r(NH3) = 1.080A (EXPT = 1.012A) Mean error (bond distances): Similar performance for multiple heavy atom Hehre, W. J., A Guide to Molecular Mechanics and hydrides Quantum Chemical Calculations SYBYL .262 MMFF .026 (Comparable to small basis Hartree Fock) Multiple Heavy Atom Systems ~150 compounds Mean error (bond distances): Benzene, difluromethane, tetrachlorosilane, ozone, magnesium fluoride SYBYL .051 MMFF .034 Ab initio (HF) .028 Transition Metal Molecules MMFF and SYBYL NOT parameterized MMX some parameterization for inorganics UFF parameters for all elements MOMEC VALBOND Modeling macromolecules SolventSolute (i.e. NonBonding) interactions very important LigandReceptor interactions Protein Folding Dreiding AMBER (protein structure) OPLS ChemX CHARMM (" ") YETI (ligandprotein) CFF (proteins) MMFF (hydrogenbonding) Tripos/SYBYL MMFF Parameterized to Ab Initio NonBonding Interactions Hydrogen bonding Nonpolar (vdW) Water nmers (H2)2 , (CH4)2 Macromolecular Modeling Dglucose 11 different conformers GROMOS, MM3 1.52.1 kcal/mol 0.91.5 kcal/mol 0.60.8 kcal/mol CHARMM, MMFF AMBER, ChemX, OPLS Barrows, S. E. et al, 1998. J. Comput. Chem. 19, 1111. ...
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This note was uploaded on 06/28/2011 for the course C 372 taught by Professor Yoonsuplee during the Spring '11 term at Korea Advanced Institute of Science and Technology.
- Spring '11