Standard syllabus
Computational chemistry · Undergraduate · Chemistry
Topics
Foundations of computational chemistry
- Potential energy surfaces and stationary points
- Molecular mechanics: force fields and parameterization
- Energy minimization algorithms: steepest descent, conjugate gradient
- Conformational searching: systematic and stochastic methods
- Molecular dynamics: equations of motion and integrators
- Periodic boundary conditions and Ewald summation (intro)
- Thermodynamic ensembles: NVE, NVT, NPT
- Basis sets in quantum chemistry: STO, GTO, split-valence
- Hartree–Fock self-consistent field method
- Electron correlation: MP2, CI, CCSD (overview)
Quantum chemistry methods
- Variational principle and SCF convergence
- Kohn–Sham density functional theory (DFT)
- Common functionals: B3LYP, PBE, M06 (overview)
- Geometry optimization and frequency calculations
- Transition state search and IRC pathways
- Thermochemistry from computed energies: ZPE, enthalpy, entropy
- Solvation models: PCM, SMD, explicit solvent
- Basis set superposition error and counterpoise correction
- Spin contamination and unrestricted calculations
- Limitations and validation of computational methods
Molecular modeling applications
- Conformational analysis of organic molecules
- Protein–ligand docking (introduction)
- Homology modeling and structural bioinformatics (overview)
- QM/MM hybrid methods for large systems
- Reaction pathway analysis with DFT
- Spectroscopic property prediction: NMR, IR, UV-Vis
- Intermolecular interactions: hydrogen bonding, π-stacking
- Crystal structure prediction (overview)
- High-throughput virtual screening
- Visualization: molecular orbitals, electrostatic potentials, ESP maps
Simulation and statistical mechanics
- Monte Carlo methods: Metropolis algorithm
- Free energy calculations: FEP, TI (introduction)
- Coarse-grained models for biomolecules
- Replica exchange and enhanced sampling (overview)
- Radial distribution functions from MD trajectories
- Mean square displacement and diffusion coefficients
- Protein folding simulations (conceptual)
- Materials simulations: defects, surfaces, interfaces
- Machine learning potentials (overview)
- Reproducibility and benchmarking in computational chemistry
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$60.00 · 60 min · Undergraduate · Online ($60/hr)
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