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Molecular Mechanics Tutorial (PDF 77P)
This note covers the following topics: steric energy, enthalpy of formation, comparing steric energies, energy minimization, molecular dynamics, distance geometry and d to d model conversion, free energy perturbation theory (FEP), continuum solvation electrostatics, normal mode analysis, partial atomic charges.
Author(s): Thomas W. Shattuck, Department of Chemistry, Colby College
77 Pages 
Molecular Modeling Lecture Notes
This lecture note explores a wide range of techniques and applications in molecular modeling and computational chemistry. Topics covered includes: ab Initio and Semi-Empirical Quantum Mechanics, Molecular Mechanics and Dynamics Simulation, Electrostatics, Coarse Graining Biomolecular Structure Prediction, Advanced Electrostatics for Force Fields, Molecular Dynamics Simulation, Monte Carlo Methods.
Author(s): Jay Ponder
NA Pages
Molecular Geometries and Covalent Bonding Theories
This note covers the following topics: Molecular Shapes, What Determines the Shape of a Molecule, Valence Shell Electron Pair, Repulsion Theory, Molecular Arrangments, Lone pairs and Bond Angle, Multiple Bonds and Bond Angles, Trigonal Bipyramidal arrangment, Polarity, Overlap and Bonding, Hybrid Orbitals, Valence Bond Theory, Single Bonds, Multiple Bonds, Delocalized Electrons, Orbitals in Molecules.
Author(s): Prof. Geiger, Michigan State University
54 Pages