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maintainers:andrewtarzia

Making models and finding minima and transition states

A PGR workshop by Andrew Tarzia (19/03/2026).

In this workshop, I ran through how to make simple and complex models, and then perform geometry optimisations of ground and transition states.

We reproduced parts of this paper: Bridging Theory and Experiment: A Teaching Project on l-Proline-Catalyzed Asymmetric Mannich Reactions

Usage

For the workshop, you can download the necessary code from this link

And getting this working on UoB devices can follow this setup: SETUP.md

Installation

All software is installed through the University of Birmingham IT-managed AppsAnywhere. The purpose here was free software (for academic/teaching usage, see ORCA) and low-cost methods (e.g., GFN2-xTB).

All code is run through the marimo notebooks with a presentation, part 1 and part 2.

In a new mamba environment:

pip install marimo
pip install stk stko bbprepared py3Dmol

marimo edit PGR_workshop_v1.py

Acknowledgements

This work is now developed as part of the Tarzia Research Group at the University of Birmingham.