Molecular Modeling: Molecular Mechanics Review Today Comparison of Empirical Models Hypervalent Systems
Brinkley, Allen, Host has reference to this Academic Journal, PHwiki organized this Journal Molecular Modeling: Molecular Mechanics C372 Introduction to Chemin as long as matics II Kelsey Forsythe Review Energy components Guidelines as long as use Pros in addition to Cons Geometry optimization Today Modeling inorganic systems Modeling macromolecules Lig in addition to -receptor interactions Beyond Empirical Methods Ab Initio Semi-Empirical
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Comparison of Empirical Models Copy of p.443 from Gundertofte article See also Cramer Table 2.1 Hypervalent Systems SF6 MMFF r(SF) = 1.633A (EXPT = 1.564A) SYBYL r(SF) = 1.800A (EXPT = 1.564A) 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 per as long as mance as long as multiple heavy atom hydrides Hehre, W. J., A Guide to Molecular Mechanics in addition to Quantum Chemical Calculations
Multiple Heavy Atom Systems ~150 compounds Benzene, difluromethane, tetrachlorosilane, ozone, magnesium fluoride Mean error (bond distances): SYBYL – .051 MMFF – .034 Ab initio (HF) – .028 Transition Metal Molecules MMFF in addition to SYBYL NOT parameterized MMX – some parameterization as long as inorganics UFF – parameters as long as all elements MOMEC VALBOND Modeling macromolecules Solvent-Solute (i.e. Non-Bonding) interactions very important Lig in addition to -Receptor interactions Protein Folding Dreiding AMBER (protein structure) OPLS Chem-X CHARMM ( ) YETI (lig in addition to -protein) CFF (proteins) MMFF (hydrogen-bonding) Tripos/SYBYL
MMFF Parameterized to Ab Initio Non-Bonding Interactions Hydrogen bonding Water n-mers Non-polar (vdW) (H2)2 , (CH4)2 Macromolecular Modeling D-glucose – 11 different con as long as mers 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.
Brinkley, Allen Host
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