Ion mobility coupled with mass spectrometry (IM-MS) is a method that allows measuring the collisional cross-sections (CCS) of mass-to-charge resolved ions in the gas phase. As the CCS depends on the size and shape of the ion, the secondary structure of the charged molecule is imprinted in the CCS. By computing the electronic structure and comparing the computed and experimental CCS, we can determine possible structures of gas phase molecules and deduced their secondary structure. Such tool could play a major role in the characterization of artificial molecular machines in gas phase. Towards this aim, we investigated the oligorotaxane composed of a flexible PEO chain functionalized with 1,5-dioxynaphthalene and in which three blueBOXes (tetracationic cyclobis(paraquat-p -phenylene)) are threaded. As each blueBOX has a charge of +4, the total charge is counterbalanced by 12 PF6- counter ions. The vaporization and ionization of the oligorotaxane in the spectrometer generates a broad range of charged oligoratoxanes with a charge varying from +4 to +12, corresponding to molecules with respectively 8 to 0 PF6-. The CCS strongly increases with the oligorotaxane charge state, indicating a stepwise co-conformational transition. We focus here on the theory side and show that the change of CCS is due to a rearrangement of the secondary structure of the oligorotaxane from a compact ball like structure to an elongated linear structure passing through a helical structure. The PF6- counter ions play a key role in the structure as they lie between the blueBOXes, limiting the repulsion between them. The repulsion between the blueBOXes increases when the charge increases (decrease of the number of PF6-), which leads to a change of the secondary structure from compact to linear. The good agreement between the computed and experimental CCS confirms the computed structures. In addition, we also investigated the folding and unfolding mechanism of the oligorotaxane with Born-Oppenheimer molecular dynamics simulations carried-out at the PM6 level.

Characterization of the secondary structure of gas phase artificial molecular machines with ion-mobility mass spectrometry and molecular modeling

256th National Meeting (2018)

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