Kinetics of Collision-Induced Back-Isomerization of Photoisomer Ions

Abstract Understanding and quantifying activation parameters associated with the gas-phase isomerization kinetics of stereoisomeric ions, such as Z- and E-azobenzene ions, remains a key challenge in modern mass spectrometry. Here, we explore collisional activation as a fast and efficient method to probe isomerization kinetics on QToF instruments equipped with traveling wave-ion mobility spectrometry (TWIMS), such as the Waters Synapt platform. Using sequence-defined peptoids bearing an azobenzene chromophore, we investigate the collision-induced isomerization (CII) of Z-isomer ions into stable E-isomer ions within the Trap Cell–IMS configuration. The extent of Z → E conversion is monitored as a function of the activation voltage (Trap CV), allowing the extraction of kinetic constants based on the known residence time of ions in the Trap Cell. By integrating previously determined gas-phase activation parameters (ΔH‡ and ΔS‡) into a modified Eyring framework, we derived effective temperatures (Teff) that characterize the internal energy distribution of activated ions. The dependence of Teff on Trap CV yields two critical parameters: α, describing the kinetic-to-internal energy conversion efficiency, and T0, the pre-activation ion population temperature. The measured α values are of the same order as those previously derived for protein ions. However, T0 values are found to be system-dependent, which is detrimental for establishing a universal temperature calibration. Ongoing work focuses on expanding the switchable molecule library to map α and T0 across diverse molecular architectures and decipher at the molecular level the origin of these two parameters.