Theoretical Chemistry

  1. Computational Chemistry Methods
    1. Potential Energy Surfaces
      1. Construction Methods
        1. Ab Initio Surfaces
          1. Semi-Empirical Surfaces
            1. Empirical Force Fields
            2. Topological Features
              1. Minima and Maxima
                1. Saddle Points
                  1. Valley-Ridge Inflection Points
                  2. Geometry Optimization
                    1. Steepest Descent Method
                      1. Newton-Raphson Method
                        1. Quasi-Newton Methods
                          1. Conjugate Gradient Method
                          2. Transition State Location
                            1. Synchronous Transit Methods
                              1. Eigenvector Following
                                1. Nudged Elastic Band Method
                                2. Reaction Path Analysis
                                  1. Intrinsic Reaction Coordinate
                                    1. Minimum Energy Path
                                      1. Steepest Descent Path
                                    2. Molecular Mechanics
                                      1. Force Field Components
                                        1. Bond Stretching Terms
                                          1. Angle Bending Terms
                                            1. Torsional Terms
                                              1. Out-of-Plane Bending
                                                1. Cross Terms
                                                2. Non-Bonded Interactions
                                                  1. van der Waals Interactions
                                                    1. Electrostatic Interactions
                                                      1. Hydrogen Bonding
                                                        1. Cutoff Methods
                                                        2. Common Force Fields
                                                          1. AMBER Force Field
                                                            1. CHARMM Force Field
                                                              1. OPLS Force Field
                                                                1. GROMOS Force Field
                                                                2. Parameterization
                                                                  1. Parameter Fitting
                                                                    1. Transferability
                                                                      1. Validation Methods
                                                                    2. Molecular Dynamics Simulations
                                                                      1. Integration Algorithms
                                                                        1. Verlet Algorithm
                                                                          1. Velocity Verlet Algorithm
                                                                            1. Leapfrog Algorithm
                                                                              1. Predictor-Corrector Methods
                                                                              2. Ensemble Control
                                                                                1. Microcanonical Ensemble
                                                                                  1. Canonical Ensemble
                                                                                    1. Isothermal-Isobaric Ensemble
                                                                                    2. Temperature Control
                                                                                      1. Velocity Scaling
                                                                                        1. Berendsen Thermostat
                                                                                          1. Nosé-Hoover Thermostat
                                                                                            1. Langevin Dynamics
                                                                                            2. Pressure Control
                                                                                              1. Berendsen Barostat
                                                                                                1. Parrinello-Rahman Method
                                                                                                  1. Martyna-Tobias-Klein Method
                                                                                                  2. Boundary Conditions
                                                                                                    1. Periodic Boundary Conditions
                                                                                                      1. Minimum Image Convention
                                                                                                        1. Ewald Summation
                                                                                                        2. Enhanced Sampling Methods
                                                                                                          1. Umbrella Sampling
                                                                                                            1. Replica Exchange
                                                                                                              1. Metadynamics
                                                                                                                1. Accelerated Dynamics
                                                                                                              2. Monte Carlo Methods
                                                                                                                1. Basic Monte Carlo Principles
                                                                                                                  1. Random Sampling
                                                                                                                    1. Importance Sampling
                                                                                                                      1. Markov Chains
                                                                                                                      2. Metropolis Algorithm
                                                                                                                        1. Acceptance Criteria
                                                                                                                          1. Detailed Balance
                                                                                                                            1. Move Types
                                                                                                                            2. Specialized MC Methods
                                                                                                                              1. Grand Canonical Monte Carlo
                                                                                                                                1. Gibbs Ensemble Monte Carlo
                                                                                                                                  1. Configurational Bias Monte Carlo
                                                                                                                                  2. Quantum Monte Carlo
                                                                                                                                    1. Variational Monte Carlo
                                                                                                                                      1. Diffusion Monte Carlo
                                                                                                                                        1. Path Integral Monte Carlo
                                                                                                                                      2. Free Energy Calculations
                                                                                                                                        1. Thermodynamic Integration
                                                                                                                                          1. Coupling Parameter
                                                                                                                                            1. Integration Methods
                                                                                                                                            2. Free Energy Perturbation
                                                                                                                                              1. Zwanzig Equation
                                                                                                                                                1. Overlap Problem
                                                                                                                                                  1. Soft-Core Potentials
                                                                                                                                                  2. Bennett Acceptance Ratio
                                                                                                                                                    1. Optimal Overlap
                                                                                                                                                      1. Error Analysis
                                                                                                                                                      2. Potential of Mean Force
                                                                                                                                                        1. Reaction Coordinates
                                                                                                                                                          1. Constraint Forces
                                                                                                                                                            1. Adaptive Biasing Force

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                                                                                                                                                        4. Statistical Mechanics and Thermodynamics

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                                                                                                                                                        6. Spectroscopy and Molecular Properties