Extending BigSMILES to Include Topological Bonds

Machine-readable line notations such as SMILES are rapidly gaining popularity as a means of storing, searching, and analyzing chemical information. Within the SMILES framework, BigSMILES was developed to represent the stochastic connectivity characteristics of polymers. More recently, noncovalent BigSMILES extended the notation to encode noncovalent interactions, recognizing the stochastic nature of these bonds. Inspired by this framework, Topological BigSMILES is introduced to provide a further extension to represent topological interactions in macromolecules. This notation appends optional topological bond descriptors and associated indices, enabling the annotation of complex molecular architectures. In particular, the notation presented herein can encode the topological interactions found in knotted macrocycles and polymers, polycatenanes, and polyrotaxanes. The progression from BigSMILES to Topological BigSMILES highlights the potential for this framework to be used in representing broader classes of soft materials systems.