Molecular Representations

Comprehensive overview of SMILES notation for chemical structures, covering syntax for atoms, bonds, branches, rings, and stereochemistry, plus its key limitations for machine learning.

A foundational 1931 paper that derives exact recursive formulas for counting alkane structural isomers, correcting historical errors and establishing the first systematic enumeration up to C₄₀.

Can mathematical signatures capture molecular shape? We test whether Coulomb matrix eigenvalues can distinguish alkane constitutional isomers, from unsupervised clustering failures to supervised learning successes.

A practical introduction to Coulomb matrices: how they transform molecular 3D structures into ML features, complete with Python examples and honest assessment of their limitations.