5. Computational Chemistry

In these notes, I will introduce the theoretical foundations and practical tools used to model molecular systems. The course begins with quantum mechanical methods for computing molecular structure and energies, including the Schrödinger equation, variational approaches, Hartree–Fock theory, and basis sets. These ideas motivate the development of classical force fields and molecular mechanics models, followed by an introduction to statistical ensembles and their role in connecting microscopic behavior to macroscopic observables.

The second half of the notes focuses on molecular dynamics simulations in gas and condensed phases, with an emphasis on interpreting trajectories, evaluating sampling quality, and extracting structural and thermodynamic information. Weekly hands-on exercises using Linux, Python, Jupyter Notebooks, WebMO/Gaussian, Amber, and MDAnalysis provide students with practical experience running calculations, analyzing results, and automating workflows. The course ends with a short independent project applying these methods to a chemical or biochemical system.