Protoisomerization of Indigo and Isoindigo Dyes Confirmed by Gas-Phase Infrared Ion Spectroscopy

[Image: see text] Gas-phase infrared multiple-photon dissociation (IRMPD) spectra are recorded for the protonated dye molecules indigo and isoindigo by using a quadrupole ion trap (QIT) mass spectrometer coupled to the free electron laser for infrared experiments (FELIX). From their fingerprint IR spectra (600—1800 cm(–1)) and comparison with quantum-chemical calculations at the density functional level of theory (B3LYP/6-31++G(d,p)), we derive their structures. We focus particularly on the question of whether trans-to-cis isomerization occurs upon protonation and transfer to the gas phase. The trans-configuration is energetically favored in the neutral forms of the dyes in solution and in the gas phase. Instead, the cis-isomer is lower in energy for the protonated forms of both species, but indigo is also notorious for not undergoing double-bond trans-to-cis isomerization, in contrast to many other conjugated systems. The IR spectra suggest that protoisomerization from trans to cis indeed occurs for both dyes. To estimate the extent of isomerization, on-resonance kinetics are measured on diagnostic and common vibrational frequencies to determine the ratio of cis-to-trans isomers. We find ratios of 65–70% cis and 30–35% trans for indigo versus 75–80% cis and 20–25% trans for isoindigo. Transition-state calculations for the isomerization reactions have been carried out, which indeed suggest a lower barrier for protonated isoindigo, qualitatively explaining the more efficient isomerization.