Orthonym: verified IUPAC names for chemical structures in the wild
Abstract
Chemical structures can be named systematically, and the 2013 IUPAC recommendations define one preferred name for each. For most of history, only a specially trained chemist or dedicated closed software tools could generate a correct, systematic molecule name from a chemical structure. Published neural structure-to-name translators can produce a fluent name for the wrong molecule. Here we present Orthonym: a generator of verified IUPAC names for chemical structures. This open, deterministic, rule-based generator emits a name only after verifying that it correctly describes the input structure. OPSIN reads back each candidate name, and the InChIKey of the parsed structure must equal that of the input; otherwise, the engine declines to name. On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly and emitted no name for the wrong molecule. Orthonym is available under the MIT licence as a Python package and a web application.
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BibTeX
@misc{rajan2026orthonym,
title = {{Orthonym: verified IUPAC names for chemical structures in the wild}},
author = {Kohulan Rajan and Achim Zielesny and Christoph Steinbeck},
howpublished = {ChemRxiv},
year = {2026},
month = oct,
doi = {10.26434/chemrxiv.15009769/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009769/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Orthonym: verified IUPAC names for chemical structures in the wild
AU - Kohulan Rajan
AU - Achim Zielesny
AU - Christoph Steinbeck
PY - 2026
DA - 2026/10/02
PB - ChemRxiv
DO - 10.26434/chemrxiv.15009769/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009769/v1
AB - Chemical structures can be named systematically, and the 2013 IUPAC recommendations define one preferred name for each. For most of history, only a specially trained chemist or dedicated closed software tools could generate a correct, systematic molecule name from a chemical structure. Published neural structure-to-name translators can produce a fluent name for the wrong molecule. Here we present Orthonym: a generator of verified IUPAC names for chemical structures. This open, deterministic, rule-based generator emits a name only after verifying that it correctly describes the input structure. OPSIN reads back each candidate name, and the InChIKey of the parsed structure must equal that of the input; otherwise, the engine declines to name. On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly and emitted no name for the wrong molecule. Orthonym is available under the MIT licence as a Python package and a web application.
ER -