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A method is presented for the rapid identification of tertiary aliphatic and aromatic N-oxide functionalities in protonated analytes via ion-molecule reactions with dimethylamine (DMA) in a linear quadrupole ion trap mass spectrometer (LQIT). DMA was leaked into the trapping region of the mass spectrometer and allowed to react with protonated analytes (ionized by electrospray ionization) for 500 ms, after which all ions were detected. Protonated analytes with the tertiary N-oxide functionality react with DMA to yield exclusively product ions with m/z-values that are 45 units greater than that of the protonated analyte, corresponding to a stable DMA adduct. Collision-activated dissociation of the adduct ions suggests that formation of a hydrogen bond between DMA and the protonated analytes is responsible for the formation of the stable adduct. Hydrogen bond energies were calculated for several adducts at the B3LYP/6-31++G(d,p) level of theory (including correction for basis-set superposition error) to define the potential energy wells for the formation of [M+H+DMA]+ adduct ions. The relative enthalpies calculated for the [M+H+DMA]+ adduct ions were found to be lower than those of the products resulting from proton transfer from protonated tertiary N-oxides and one aromatic ketone, ketoprofen, to DMA. On the other hand, a protonated primary N-oxide, nitrosobenzene, exclusively reacts via proton transfer with DMA, which was calculated to be more exothermic than formation of an adduct ion. Collisional cooling was found to be crucial to the formation of an adduct ion for analytes with proton affinities lower than that of DMA. Ion-molecule reactions of protonated 4-nitro-2-picoline N-oxide (PA = 206 kcal mol−1) with DMA (PA = 222 kcal mol−1) in an FT-ICR at ultra-high vacuum with no buffer gas resulted solely in proton transfer to DMA. Finally, examination of the reactions of DMA with protonated clozapine and clozapine-4′-N-oxide demonstrated that DMA can be used to identify the N-oxide functionality in the presence of other basic functionalities. Compared to other reagents reported for the identification of tertiary N-oxide functionalities via ion-molecule reactions in a mass spectrometer, DMA is the only one volatile enough to be used in a multi-ported pulsed valve system designed for rapid introduction of several reagents, each diagnostic for a different functionality, for characterization of analytes as they elute from an HPLC.

A chemical ionization reagent ion, ClMn2+, has been identified for the analysis of mixtures of organic compounds since it allows ionization of both polar and nonpolar analytes so that only one product ion, ClMn+ adduct of the analyte, is generated without fragmentation. The reagent ion is formed upon ionization of ClMn(CO)5 via corona discharge in an atmospheric pressure chemical ionization source of a linear quadrupole ion trap mass spectrometer. Volatile analytes were introduced into the ion trap via a reagent mixing manifold. Nonvolatile analytes were deposited on a titanium foil and desorbed using laser-induced acoustic desorption (LIAD). Formation of a ClMn+ adduct with no accompanying fragmentation was observed for all analytes, including branched saturated hydrocarbons. Calculations indicate that ClMn+ binds to saturated hydrocarbons via an agostic interaction involving the manganese center and a C H bond of the analyte. The reagent ion Mn+ was also investigated. This ion forms a stable adduct with most analytes studied. It binds fairly strongly to saturated hydrocarbons via two agostic interactions with two C H bonds instead of insertion into a C H bond. However, it was found to cause fragmentation for alcohols. ClMn(H2O)+ has been previously shown to ionize most compounds by ClMn+ adduct formation but also to yield molecular ions for amines due to their low ionization energies ( C bond cleavages for highly branched alkanes upon ionization. This was not observed for the reagent ions studied here. ClMn2+ ion is a more universal ionization reagent than Mn+ and the previously reported reagent ions due to its ability to ionize analytes with low ionization energies without electron transfer and due to the complete lack of fragmentation for all analytes. Furthermore, based on the examination of six very different analytes, it has no significant bias toward specific types of analytes.

Despite extensive studies of the asphaltene fraction of petroleum, the molecular structures of asphaltenes remain a highly debated topic. Tandem mass spectrometry is the only technique that allows the examination of the structures of individual asphaltene molecules due to the extreme complexity of asphaltenes. Recently, atmospheric pressure chemical ionization (APCI) using CS2 as the reagent was demonstrated to produce abundant and stable molecular ions for polyaromatic hydrocarbons with long alkyl chains. Hence, coupling APCI/CS2 with tandem mass spectrometry appears to be a promising method for the examination of the structures of molecules in asphaltenes. However, the fragmentation pathways of the molecular ions of large alkyl aromatic compounds are not well understood. In order to address this issue, a detailed examination of the collision-activated dissociation reactions of the molecular ions and several of their fragment ions (MSn experiments) was carried out for several model compounds of asphaltenes. The results show that information on various structural aspects of asphaltenes can be obtained from these experiments, such as alkyl chain lengths and sizes of aromatic cores. Based on these results, MS2 experiments may provide enough information to determine approximate core sizes for molecules with archipelago structures. However, the number of ion isolation and collision-activated dissociation (CAD) experiments needed to elucidate maximum structural information for molecules with island structures depends on the number of carbon chains on the aromatic core.

In the search for alternatives to fossil fuel and the valuable chemicals now derived from crude oil, lignocellulosic biomass has attracted wide interest. Degradation of the cellulose and lignin components of the biomass results in complex mixtures. Hence, the ability to identify the products of processed cellulose and lignin is important. Unfortunately, mass spectrometric analysis of processed lignin (and the lignome in general) is hindered by poor ion generation and/or extensive fragmentation upon ionization. After examination of several different ionization approaches, we demonstrate here that ionization of model compounds of lignin degradation products and lignome by using positive ion mode electrospray ionization (ESI) doped with sodium chloride results in the formation of abundant adduct ions, [M + Na]+, with no accompanying fragmentation. Hence, this approach allows for the determination of the molecular weights of lignin degradation products (and lignome) directly in mixtures. However, no structural information can be obtained by examining collision-activated dissociation of the sodiated molecules. Hence, a different ionization method was identified. Doping negative ion mode ESI with hydroxide ions (from NaOH) yields only one type of an ion per analyte, the deprotonated analyte, without fragmentation. Valuable structural information can be obtained for these anions by subjecting them to multiple consecutive ion isolation and collision-activated dissociation (CAD) steps (up to MS7). This methodology significantly improves the information that can be obtained by mass spectrometric analysis for lignin degradation products and lignome.