MolBar: A Molecular Identifier for Inorganic and Organic Molecules with Full Support of Stereoisomerism

Nils van Staalduinen, Christoph Bannwarth

When a new molecular structure is to be registered to a chemical structure database, a duplicate check is essential to ensure the integrity of the database. Existing identifiers like SMILES and InChI have limitations when it comes to inorganic compounds or those with non-central stereochemistry. To address this limitation, we introduce a novel chemical identifier called the Molecular Barcode (MolBar), which can uniquely identify a molecule based on its Cartesian coordinates. In this approach, fragments are conceptualized using a specialized force field and characterized by physically inspired matrices derived solely from atomic positions. The resulting permutation-invariant representation is constructed from the eigenvalue spectra, providing comprehensive information on both bonding and stereochemistry. Hence, MolBar encompasses a wider spectrum of chiral types, including axial and planar chirality, offering a unified description applicable to both organic and inorganic chemistry alike. The robustness of MolBar is demonstrated through duplication and permutation invariance tests on the Molecule3D dataset of 3.9 million molecules. A Python implementation is available as open source and is also listed on PyPI for broader accessibility. The intended use is for duplicate removal in molecular database as well as unique molecule identification in chemical space exploration.

Figure 1. Workflow to generate the unique MolBar identifier from Cartesian coordinates as input. The final identifier is a concatenation of rounded eigenvalue spectra of different matrices describing the topology, as well as relative and absolute configuration.

1. N. van Staalduinen, C. Bannwarth, ChemRxiv 2024, DOI 10.26434/chemrxiv-2024-k40v5.
2. https://git.rwth-aachen.de/bannwarthlab/molbar (last accessed 03.04.2024).