Volume VI — Reactions and Free Energy

Chemistry is change, and change has a cost: the activation barrier a reaction must climb, and the free-energy landscape that decides which products form and how fast. These notebooks follow the course’s calculations of reacting systems, from the energy profile of a single bond-breaking step, through the nudged-elastic-band search for a transition state, to metadynamics reconstructing a free-energy surface from a biased trajectory. The energies are the course’s own committed density-functional and tight-binding results.

Source lectures

This volume develops Lecture 7 of Molecular and Materials Modelling (FS 2023) — density functionals and basis sets, on the ethanol dehydration — and Lecture 13 — transition states and free energy: the nudged elastic band and metadynamics. Each notebook repeats its specific lecture provenance in its overview; the full lecture map is in manifest.yml.

• 6.1 The Dehydration of Ethanol
• 6.2 The S\(_N\)2 Reaction by Nudged Elastic Band
• 6.3 Metadynamics: Nitric Acid on Graphene