Prediction of peptide IMS cross sections from extended molecular connectivity

It is shown that extended molecular connectivity encoded by the Kier–Hall second order valence connectivity index (2χv) provides an excellent single-parameter correlation with ion mobility spectroscopy (IMS) cross-sections of tripeptides. This second order index is particularly relevant to peptides, because it is calculated over all triatomic chains and thus encodes critical peptide fragments such as Ni–Cα–Ci, Cα–Ci–O, and Cα–Ci–Ni+1. Empirical intrinsic size parameters, reported by previous authors, are now rationalized in terms of extended molecular connectivity.

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► Molecular connectivity significantly controls peptide IMS cross-section.
► Topological indices based on extended connectivity provide excellent one-parameter correlations with IMS cross-section of tripeptides.
► Second order valence connectivity index 2χv is particularly relevant because it encodes tri-atomic peptide fragments.