Search

Gas-phase ion/molecule reactions have been used extensively for the structural elucidation of organic compounds in tandem mass spectrometry. Reagents for ion/molecule reactions can be introduced into a mass spectrometer via a continuous flow apparatus or through a pulsed inlet system. However, most of these approaches enable the use of only a single reagent at a time. In this work, a multichannel pulsed-valve inlet system was developed for the rapid consecutive introduction of up to nine different reagents or reagent systems into a linear quadrupole ion trap mass spectrometer for diagnostic gas-phase ion/molecule reactions. Automated triggering of the pulsed valves enabled these experiments to be performed on the high-performance liquid chromatography (HPLC) time scale. This enables high-throughput screening of several functionalities in analytes as they elute from an HPLC column.

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.

Seven synthesized G-lignin oligomer model compounds (ranging in size from dimers to an octamer) with 5-5 and/or β-O-4 linkages, and three synthesized S-lignin model compounds (a dimer, trimer, and tetramer) with β-O-4 linkages, were evaporated and deprotonated using negative-ion mode ESI in a linear quadrupole ion trap/Fourier transform ion cyclotron resonance mass spectrometer. The collision-activated dissociation (CAD) fragmentation patterns (obtained in MS2 and MS3 experiments, respectively) for the negative ions were studied to develop a procedure for sequencing unknown lignin oligomers. On the basis of the observed fragmentation patterns, the measured elemental compositions of the most abundant fragment ions, and quantum chemical calculations, the most important reaction pathways and likely mechanisms were delineated. Many of these reactions occur via charge-remote fragmentation mechanisms. Deprotonated compounds with only β-O-4 linkages, or both 5-5 and β-O-4 linkages, showed major 1,2-eliminations ...

Isomeric O- and N-glucuronides are common drug metabolites produced in phase II of drug metabolism. Distinguishing these isomers by using common analytical techniques has proven challenging. A tandem mass spectrometric method based on gas-phase ion/molecule reactions of deprotonated glucuronide drug metabolites with trichlorosilane (HSiCl3) in a linear quadrupole ion trap mass spectrometer is reported here to readily enable differentiation of the O- and N-isomers. The major product ion observed upon reactions of HSiCl3 with deprotonated N-glucuronides is a diagnostic HSiCl(3) adduct that has lost two HCl molecules ([M − H + HSiCl3 − 2HCl]-). This product ion was not observed for deprotonated O-glucuronides. Reaction mechanisms were explored with quantum chemical calculations at the M06-2X/6-311++G(d,p) level of theory.

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.

Current biomass utilization processes do not make use of lignin beyond its heat value. Here we report on a bimetallic Zn/Pd/C catalyst that converts lignin in intact lignocellulosic biomass directly into two methoxyphenol products, leaving behind the carbohydrates as a solid residue. Genetically modified poplar enhanced in syringyl (S) monomer content yields only a single product, dihydroeugenol. Lignin-derived methoxyphenols can be deoxygenated further to propylcyclohexane. The leftover carbohydrate residue is hydrolyzed by cellulases to give glucose in 95% yield, which is comparable to lignin-free cellulose (solka floc). New conversion pathways to useful fuels and chemicals are proposed based on the efficient conversion of lignin into intact hydrocarbons.

The absolute configurations of the separated enantiomers of fluralaner, a racemic animal health product used to prevent fleas and ticks, have been assigned using vibrational circular dichroism (VCD). The crystallographic structure of the active enantiomer (+)-fluralaner has previously been shown to have the (S) configuration using small molecule crystallography. We sought a faster analytical method to determine the absolute configuration of the separated enantiomers. When comparing the measured IR (infrared) and VCD spectra, it is apparent that the amide carbonyl groups appear in the IR but are nearly absent in the VCD. Computational work to calculate the VCD and IR using in vacuo models, implicit solvation, and explicitly solvated complexes has implicated conformational averaging of the carbonyl VCD intensities.

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.

Lignin is an aromatic biopolymer that may yield valuable chemicals currently obtained solely from petroleum. However, extraction of lignin by using traditional methods, such as organosolv extraction, produces very complex mixtures. Molecular level characterization of the major components is essential to be able to rationally tailor methodology for the conversion of these mixtures to transportation fuel and valuable chemicals. In this study, high performance liquid chromatography/high resolution tandem mass spectrometry (HPLC/MSn) was used to obtain molecular weight, elemental composition and structural information for the major components in an organosolv lignin sample. HPLC/MSn coupled with hydroxide-doped electrospray ionization was used to identify the structures of the major components by using a Thermo Scientific linear quadrupole ion trap-Fourier transform ion cyclotron resonance hybrid mass spectrometer (LQIT/FT-ICR). The results reported here demonstrate that the major products of organosolv extraction are low molecular weight compounds, including monomeric and dimeric lignin units, with various functionalities.

The development of chemical methods for the direct catalytic conversion of biomass to high value organic molecules is an area of increasing interest. The plant matter component known as lignin is a polymer consisting of aromatic rings that could provide a means of obtaining aromatic materials currently derived solely from petroleum. This report describes a bimetallic Pd/C and Zn catalytic system that can perform selective hydrodeoxygenation (HDO) of monomeric lignin surrogates as well as successfully cleave the β-O-4 linkages found in dimeric lignin model complexes and synthetic lignin polymers with near quantitative conversions and yields between 80–90%. The reaction with lignin polymer was highly selective affording methoxy substituted propylphenol as the major product. These reactions were performed in a Parr reactor operating at relatively mild temperature (150 °C) and pressure (20 bar H2) using methanol as a solvent. Reaction products were characterized using high-pressure liquid chromatography coupled to a linear quadrupole ion trap mass spectrometer equipped with an electrospray ionization source using negative ion mode. Hydroxide ions were doped into the analyte solutions to encourage negative ion formation. This method ionizes all the mixture components to yield a single ion/analyte with no fragmentation. The catalyst is fully recyclable without the need for additional zinc. X-ray absorption spectroscopy (EXAFS) is consistent with Pd nanoparticles (4–5 nm) and no evidence of Pd–Zn alloy formation. A mechanistic hypothesis on the synergy between Pd and Zn is presented.

Laser-induced acoustic desorption (LIAD) allows for desorption of neutral nonvolatile compounds independent of their volatility or thermal stability. Many different ionization methods have been coupled with LIAD. Hence, this setup provides a better control over the types of ions formed than other mass spectrometry evaporation/ionization methods commonly used to characterize biomolecules, such as ESI or MALDI. In this study, the utility of LIAD coupled with electron ionization (EI) was tested for the analysis of common amino acids with no derivatization. The results compared favorably with previously reported EI mass spectra obtained using thermal desorption/EI. Further, LIAD/EI mass spectra collected for hydrochloride salts of two amino acids were found to be similar to those measured for the neutral amino acids with the exception of the appearance of an HCl+● ion. However, the hydrochloride salt of arginine showed a distinctly different LIAD/EI mass spectrum than the previously published literature EI mass spectrum, likely due to its highly basic side chain that makes a specific zwitterionic form particularly favorable. Finally, EI mass spectra were measured for seven small peptides, including di-, tri-, and tetrapeptides. These mass spectra show a variety of ion types. However, an type ions are prevalent. Also, electron-induced dissociation (EID) of protonated peptides has been reported to form primarily an type ions. In addition, the loss of small neutral molecules and side-chain cleavages were observed that are reminiscent of other high-energy fragmentation methods, such as EID. Finally, the isomeric dipeptides LG and IG were found to produce drastically different EI mass spectra, thus allowing differentiation of the leucine and isoleucine amino acids in these dipeptides.

The collision-activated fragmentation pathways and reaction mechanisms of 34 deprotonated model compounds representative of lignin degradation products were explored experimentally and computationally. The compounds were evaporated and ionized by using negative-ion mode electrospray ionization doped with NaOH to produce abundant deprotonated molecules. The ions were isolated and subjected to collision-activated dissociation (CAD). Their fragment ions were then isolated and also subjected to CAD. This was repeated until no further fragmentation was observed (up to MS6 ). This approach enabled the identification of characteristic reaction pathways and delineation of reasonable fragmentation mechanisms for deprotonated molecules containing various functional groups. The varying fragmentation patterns observed for different types of compounds allow for the identification of the functionalities in these compounds. This information was utilized to identify the presence of specific functionalities and their combinations in molecules in an organosolv lignin sample.

Conversion of lignin into smaller molecules provides a promising alternate and sustainable source for the valuable chemicals currently derived from crude oil. Better understanding of the chemical composition of the resulting product mixtures is essential for the optimization of such conversion processes. However, these mixtures are complex and contain isomeric molecules with a wide variety of functionalities, which makes their characterization challenging. Tandem mass spectrometry based on ion-molecule reactions has proven to be a powerful tool in functional group identification and isomer differentiation for previously unknown compounds. This study demonstrates that the identification of the phenol functionality, the most commonly observed functionality in lignin degradation products, can be achieved via ion-molecule reactions between diethylmethoxyborane (DEMB) and the deprotonated analyte in the absence of strongly electron-withdrawing substituents in the ortho- and para-positions. Either a stable DEMB adduct or an adduct that has lost a methanol molecule (DEMB adduct-MeOH) is formed for these ions. Deprotonated phenols with an adjacent phenol or hydroxymethyl functionality or a conjugated carboxylic acid functionality can be identified based on the formation of DEMB adduct-MeOH. Deprotonated compounds not containing the phenol functionality and phenols containing an electron-withdrawing ortho- or para-substituent were found to be unreactive toward diethylmethoxyborane. Hence, certain deprotonated isomeric compounds with phenol and carboxylic acid, aldehyde, carboxylic acid ester, or nitro functionalities can be differentiated via these reactions. The above mass spectrometry method was successfully coupled with high-performance liquid chromatography for the analysis of a complex biomass degradation mixture. Graphical Abstract ᅟ.

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.

Ion-molecule reactions provide a powerful tool for structural elucidation of ionized pharmaceutical analytes in tandem mass spectrometry. However, all previous interfaces for the introduction of reagents for ion-molecule reactions have utilized a single reagent approach. In this study, a multiported pulsed valve system was designed and characterized for rapid introduction of three neutral reagents into a linear quadrupole ion trap. Additionally, automatic triggering was used to allow for the introduction of the reagents on a chromatographic time scale. This system enables automatic, high throughput screening of complex mixtures by using at least three different ion-molecule reactions. Further, rapid testing of new neutral reagents is also possible.

A novel differentially pumped dual linear quadrupole ion trap (DLQIT) mass spectrometer was designed and built to facilitate tandem MS experiments free from interfering reactions. The instrument consists of two differentially pumped Thermo Scientific linear quadrupole ion trap (LQIT) systems that have been connected via an ion transfer octupole encased in a machined manifold. Tandem MS experiments can be performed in the front trap and then the resulting product ions can be transferred via axial ejection into the back trap for further, independent tandem MS experiments in a differentially pumped area. This approach allows the examination of consecutive collision-activated dissociation (CAD) and ion-molecule reactions without unwanted side reactions that often occur when CAD and ion-molecule reactions are examined in the same space. Hence, it greatly facilitates investigations of ion structures. In addition, the overall lower pressure of the DLQIT, as compared to commercial LQIT instruments, results in a reduction of unwanted side reactions with atmospheric contaminants, such as water and oxygen, in CAD and ion-molecule experiments.

In the search for a replacement for fossil fuel and the valuable chemicals currently obtained from crude oil, lignocellulosic biomass has become a promising candidate as an alternative biorenewable source for crude oil. Hence, many research efforts focus on the extraction, degradation, and catalytic transformation of lignin, hemicellulose, and cellulose. Unfortunately, these processes result in the production of very complex mixtures. Further, while methods have been developed for the analysis of mixtures of oligosaccharides, this is not true for the complex mixtures generated upon degradation of lignin. For example, high-performance liquid chromatography/multiple stage tandem mass spectrometry (HPLC/MS(n)), a tool proven to be invaluable in the analysis of complex mixtures derived from many other biopolymers, such as proteins and DNA, has not been implemented for lignin degradation products. In this study, we have developed an HPLC separation method for lignin degradation products that is amenable to negative-ion-mode electrospray ionization (ESI doped with NaOH), the best method identified thus far for ionization of lignin-related model compounds without fragmentation. The separated and ionized compounds are then analyzed by MS(3) experiments to obtain detailed structural information while simultaneously performing high-resolution measurements to determine their elemental compositions in the two parts of a commercial linear quadrupole ion trap/Fourier-transform ion cyclotron resonance mass spectrometer. A lignin degradation product mixture was analyzed using this method, and molecular structures were proposed for some components. This methodology significantly improves the ability to analyze complex product mixtures that result from degraded lignin.