Chemical characterization of complex mixtures of large saturated hydrocarbons is critically important for numerous fields, including petroleomics and renewable transportation fuels, but difficult to achieve. Atmospheric pressure chemical ionization (APCI) mass spectrometry has shown some promise in the analysis of saturated hydrocarbons. However, APCI causes extensive fragmentation to these compounds, which impedes its effectiveness. To prevent this fragmentation, its causes were examined via gas-phase ion−molecule reactions in vacuum in a linear quadrupole ion trap mass spectrometer. The results demonstrate that the mechanism proposed previously for ionization of saturated hydrocarbons upon APCI, hydride abstraction by carbocation reagent ions, is not correct. Instead, the fragmentation is caused by ionization of saturated hydrocarbons via exothermic proton-transfer reactions involving highly acidic, protonated atmospheric molecules, such as nitrogen and water. Accordingly, the extent of fragmentation was found to correlate with the proton affinities of the atmospheric molecules studied. Remarkably, controlled experiments involving isolated atmospheric ions and neat saturated hydrocarbons in vacuum yielded almost identical mass spectra as APCI involving atmospheric pressure conditions, the presence of many different chemicals, and an electrical discharge. In order to prevent or reduce the extent of fragmentation of saturated hydrocarbons upon APCI, and therefore enable accurate mass spectrometric characterization of complex mixtures of saturated hydrocarbons, the ion source should be purged of air to remove nitrogen and water and fill it with an inert gas with a substantially lower proton affinity.

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Unlabeled and deuterium-labeled dimeric lignin model compounds with β-O-4 linkages were evaporated and ionized using negative ion mode electrospray ionization, transferred into a linear quadrupole ion trap, isolated, and subjected to collision-activated dissociation (CAD; MS2 experiments). The elemental compositions of the fragment ions were determined by using a high-resolution Orbitrap mass analyzer, and their structures were examined using further CAD experiments (MS n experiments wherein n = 2–5). Data analysis was facilitated by determining the fragmentation pathways for several deprotonated model compounds. The structures of the key fragment ions of several pathways were determined by comparison of the CAD mass spectra measured for undeuterated and deuterated analogues and for deprotonated authentic compounds. Some of the proposed reaction mechanisms were tested by examining additional deprotonated synthetic model compounds. Quantum chemical calculations were used to delineate the most likely reaction pathways and reaction mechanisms. This work provides basic information needed for the design of tandem mass spectrometry-based CAD sequencing strategies for mixtures of lignin degradation products.

The proton affinity (PA) of a neutral molecule is defined as the negative of the enthalpy change for the gas-phase reaction between a proton and the neutral molecule to produce the (charged) conjugate acid of the molecule. PA is a fundamental property that is related to the structure of a molecule and affects its reactivity. Very few PA values are available for basic organic monoradicals and none for biradicals. Here, the PA values for several σ-type carbon-centered pyridine-based monoradicals and biradicals have been experimentally determined by monitoring proton transfer from the protonated mono- and biradicals to reference bases with known proton affinities as a function of time in Fourier-transform ion cyclotron resonance (FT-ICR) and linear quadrupole ion trap (LQIT) mass spectrometers. A procedure was developed for both instruments that permits differentiation between exo- and endothermic proton transfer reactions. The PA values of all the (bi)­radicals studied were found to be lower than that of pyridine. This is rationalized based on the electron-withdrawing nature of the radical site(s). Thus, the PA values decrease in the order: pyridine > monoradicals > biradicals. The PA values of the monoradicals were also found to increase (making the protonated radicals less acidic) as the distance between the basic nitrogen atom and the radical site increases. Similar behavior was found for the biradicals, with one exception: 3,5-didehydropyridine has a larger PA (215.3 ± 3.3 kcal mol–1) than 3,4-didehydropyridine (PA = 213.4 ± 3.3 kcal mol–1) even though the latter biradical has one radical site farther away from the basic nitrogen atom. Quantum chemical calculations of the PAs of the (bi)­radicals are in reasonably good agreement with the experimentally determined values. At the DFT (B3LYP), CCSD­(T), and CASPT2 levels of theory, the mean unsigned errors are 2.3, 1.7, and 2.1 kcal mol–1.