Same molecule, Different Knowledge: Cross-Identifier Binding Failures in LLMs For chemistry

Abstract

Chemical AI workflows routinely represent the same molecule through multiple co-referring identifiers, including trivial names, IUPAC names, and SMILES, implicitly assuming that these representations provide interchangeable access to an LLM's knowledge. To test this assumption, we first introduce a controlled benchmark and show that it does not hold. Across foundation models spanning 7B to 72B parameters, even chemistry-specialized models, co-referring molecular identifiers consistently expose different subsets of the model's knowledge. We then conduct a series of controlled behavioral, representational, and causal analyses to characterize this failure. We show that even when a model can identify a molecule from its SMILES and retrieve a fact through the corresponding name, the same fact can remain inaccessible directly from SMILES. We term this phenomenon \emph{cross-identifier binding failure}. Further analysis of internal representations, conflicting identifiers, and parameter editing shows that neither improved chemical representation competence nor modification of individual facts is sufficient to establish reliable access across identifiers. Together, these results indicate that the core failure lies in the binding between an identifier and knowledge already present in the model. Motivated by this diagnosis, we introduce Binding Self-Distillation, a simple mitigation that uses lexical identity during training to transfer the model's existing knowledge access to the structural route. This enables factual retrieval directly from SMILES at inference time, without requiring a name lookup or training the underlying model from scratch.