Structurally based identifiers such as SMILES, molfile and InChI have been shown to be exceptionally useful in modern chemical information and cheminformatics research by enabling the digitalization of small molecules. However, since most existing identifiers are designed under the premise that each chemical species corresponds to one well-defined chemical structure, their applicability to polymers, which are intrinsically stochastic molecules that are usually ensembles of molecules with a distribution of chemical structures, are markedly limited.<br/><br/>To provide support over polymers, a new line notation, BigSMILES, that is built on top of the popular line notation SMILES, is proposed. In BigSMILES, ensembles of polymeric fragments are represented by “stochastic objects” that encodes the chemical structures by specifying the structures of the constituent repeating units and the permissible set of connectivity patterns between the repeating untis. This allows efficient and compact representation of the ensemble of possible molecular structures for a polymer based on its fundamental polymerization chemistry. Through a few simple extensions to the SMILES syntax, the new BigSMILES system can easily encode a variety of polymer chemistries, including but not limited to linear polymers formed from chain and step polymerization, including random or block copolymers, branched polymers, polymer networks and ring polymers.<br/><br/>Aside from the line notation, an accompanying standard data format is also developed to store any additional quantifications on the distribution of the ensemble prescribed by the line notation. This information could be used to reconstruct the ensemble and infer properties necessary for informatics studies. With the two components, the BigSMILES digitalization scheme offers a multi-purpose system that can serve as both compact identifiers and comprehensive standard polymer data sharing scheme that could be useful to both the polymer and the cheminformatics communities.

BigSMILES: Digitalization scheme for macromolecules

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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