Computational Chemistry

  1. Molecular Mechanics Methods
    1. Classical Mechanics Approach
      1. Newtonian Mechanics for Molecules
        1. Assumptions and Approximations
          1. Limitations of Classical Treatment
          2. Force Field Concept
            1. Mathematical Framework
              1. Functional Forms
                1. Parameterization Strategies
                  1. Transferability Issues
                  2. Bonded Interactions
                    1. Bond Stretching
                      1. Harmonic Potential
                        1. Morse Potential
                          1. Anharmonic Corrections
                          2. Angle Bending
                            1. Harmonic Angle Potential
                              1. Cosine Angle Potential
                                1. Urey-Bradley Terms
                                2. Torsional Angles
                                  1. Periodic Potentials
                                    1. Multiple Periodicity
                                      1. Barriers to Rotation
                                      2. Improper Torsions
                                        1. Out-of-Plane Bending
                                          1. Planarity Enforcement
                                            1. Chirality Maintenance
                                          2. Non-Bonded Interactions
                                            1. van der Waals Forces
                                              1. Lennard-Jones Potential
                                                1. Buckingham Potential
                                                  1. Repulsion Terms
                                                    1. Dispersion Terms
                                                    2. Electrostatic Interactions
                                                      1. Coulomb's Law
                                                        1. Point Charge Models
                                                          1. Multipole Expansions
                                                            1. Polarization Effects
                                                            2. Long-Range Interactions
                                                              1. Cutoff Methods
                                                                1. Switching Functions
                                                                  1. Ewald Summation
                                                                    1. Particle Mesh Ewald
                                                                  2. Force Field Families
                                                                    1. AMBER Force Fields
                                                                      1. Development History
                                                                        1. Parameter Sets
                                                                          1. Biomolecular Applications
                                                                          2. CHARMM Force Fields
                                                                            1. Protein Parameters
                                                                              1. Lipid Parameters
                                                                                1. Nucleic Acid Parameters
                                                                                2. GROMOS Force Fields
                                                                                  1. United Atom Approach
                                                                                    1. Solvent Models
                                                                                    2. OPLS Force Fields
                                                                                      1. All-Atom Parameters
                                                                                        1. Organic Molecules
                                                                                        2. MMFF Force Fields
                                                                                          1. Small Molecule Focus
                                                                                            1. Drug-Like Compounds
                                                                                          2. Applications and Limitations
                                                                                            1. Suitable System Types
                                                                                              1. Size Limitations
                                                                                                1. Accuracy Considerations
                                                                                                  1. Bond Breaking Limitations
                                                                                                    1. Quantum Effects

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                                                                                                  3. Potential Energy Surfaces

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                                                                                                  5. Quantum Mechanical Methods