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

Abstract

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.

Profiling the Philippine Blue: Liquid chromatography/mass spectrometry‐based metabolomics study on Philippine Indigofera

“…Proposed fragmentation mechanism for protonated leucoindigo ( 1 ). For the series of reactions: (a) H + transfer, (b) inductive cleavage, (c) keto‐enol tautomerization, (d) bond rotation, 32 (e) nucleophilic attack leading to cyclization, (f) heterocyclic ring fission, and (g) loss of H 2 by remote H‐rearrangement…”

“…Based on previous work, the cis isomer (65–70%) is the dominant form of indigotin because of the stabilizing effect of hydrogen bonding. This is also assumed to be the same for indirubin 32 . The protonated cis isomer, therefore, is considered as the starting point in the fragmentation of m/z 263.08 to m/z 219.09 (Figure 7A).…”

Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches

“…The IRMPD spectra for [AsnSer+H-NH 3 ] + described above suggest that there are two distinct product ion structures in the m / z 203 population. Figure shows the result of a population analysis that allows an estimate of the approximate relative abundance of the two structures. − To achieve this, the IR laser was tuned to a frequency where one of the isomers absorbs but the other is transparent. As the irradiation was performed with an increasing number of IR pulses, complete dissociation of the absorbing isomer can be achieved while leaving the other isomer intact.…”

Predicting the substituent effects in the optical and electrochemical properties of N,N′-substituted isoindigos

“…At the same time, aromatic substituents at the nitrogen are rare and only found in a few bio-active iso-Is [3,5]. iso-I is very stable towards photobleaching [20], a property attributable to the ultrafast intramolecular singlet fission that the molecule undergoes after excitation [21]. This sub-ns event leads to efficient triplet pair separation in thiophene-functionalised derivatives, while in solution it affords radiationless deactivation of the excited state, recovering the starting material at the ground state.…”