autode

Autode is an open-source Python toolkit designed to automate the discovery of chemical reactions and their mechanisms. It provides a framework for automated exploration of reaction space, including conformer generation, geometry optimization, reaction proposal, and transition-state search, with the goal of reducing manual intervention in computational mechanistic studies.

Key features include automatic generation of reaction candidates by combining reactive centers in provided species, graph-based representations of molecules and reactions, and integration with quantum chemistry programs. Autode supports fast pre-optimization with semi-empirical methods and subsequent refinement with higher-level quantum chemistry calculations. It can work with solvent models where supported and handles both gas-phase and condensed-phase systems.

Workflow typically starts from one or more reactants (and optional catalysts or solvents). Autode builds 3D structures, samples low-energy conformers, and enumerates plausible reaction paths. It attempts to locate transition states using automated guess generation and TS-search algorithms, then refines them with downstream quantum chemistry calculations. When possible, it computes intrinsic reaction coordinates and reports barriers, reaction energies, and thermochemical data.

Implementation notes: autode is written in Python and makes use of cheminformatics tools for representation and manipulation. It interfaces with external quantum codes (such as ORCA, Gaussian, or other packages) and uses standard file formats for interoperability. The project emphasizes reproducibility and configurable workflows via configuration files or programmatic APIs.

Autode is used mainly in academic and industrial research to automate reaction mechanism discovery, pathway exploration, and catalysis studies. Users should be aware of computational cost and method limitations, as results depend on the chosen level of theory and initial guesses.

See also: computational chemistry, reaction discovery, transition state search, conformer generation.