Mass spectrometric studies of organic ion/molecule reactions

Effects of Oxygenation on the Reactions of the Iodiranium Ion c-C2H4I+ with Unsaturated Compounds in the Gas Phase

The potential for ion-molecule reactions to identify alkene functional groups in substrates with increasing oxygenation is explored by using linear ion-trap mass spectrometry. Electrophilic attack by the iodiranium ion, c-C2H4I+ (m/z 155), proceeds at the collision rate with terminal alkenes RCH═CH2 (R = n-Pr), allyl ethers (R = MeOCH2), and nonconjugated methyl esters (R = MeO2CCH2), favoring transfer of the iodenium cation to the point of unsaturation by π-ligand exchange. Density functional theory (DFT) calculations at M06-2X-D3/def2-TZVP revealed a single energy well for π-ligand exchange, allowing for a barrierless and hence kinetically favorable reaction pathway. In contrast, ring-opening of the iodiranium ion with subsequent elimination of HI proceeds via a relatively high barrier and is only a minor product channel despite being thermodynamically preferable. Conjugation of the carbon-carbon double bond to an ester group in methyl acrylate had a significant impact on the reaction partitioning with exclusive attack by the carbonyl oxygen to give an allylic stabilized oxonium ion. However, substitution at the point of unsaturation with an inductively donating methyl group enabled the formation of a π-ligand exchange product, which underwent secondary reactions with the neutral. Comparison of the ion-molecule reactions of methyl crotonate, methyl methacrylate, and methyl 3-butenoate with c-C2H4I+ show this shift in reaction partitioning between ring-opening by the ester carbonyl oxygen and π-ligand exchange is related to the nucleophilicity of the carbon-carbon double bond. The branching ratios of these product channels reveal significant differences between these three structural isomers encompassing conjugated and nonconjugated unsaturated esters.

Mechanistic insights into nonlinear effects in copper-catalyzed asymmetric esterification

Nonlinear effects (NLEs) serve as a widespread tool in the study of asymmetric catalytic reactions. However, due to the diversity in ligand-metal coordination modes, the information obtained solely from the linear relationship between the ee values of ligands and products in complex systems is often indirect. Here, we report a precise method that directly connects the relationship between the ee values of metal complexes and products, with the purpose of determining the active species that occur in complex systems. Through an in-depth analysis of the mechanism of our previous copper-catalyzed asymmetric esterification reactions, we find an intrinsic linear relationship between the ee values of the key active metal complex (LLCuI) and products within this traditionally non-linear system. This method holds promise as a powerful tool for the exploration of asymmetric catalysis mechanisms, heralding new avenues in the understanding and application of catalytic processes.

Electrostatically tuning radical addition and atom abstraction reactions with distonic radical ions

Although electrostatic catalysis can enhance the kinetics and selectivity of reactions to produce greener synthetic processes, the highly directional nature of electrostatic interactions has limited widespread application. In this study, the influence of oriented electric fields (OEF) on radical addition and atom abstraction reactions are systematically explored with ion-trap mass spectrometry using structurally diverse distonic radical ions that maintain spatially separated charge and radical moieties. When installed on rigid molecular scaffolds, charged functional groups lock the magnitude and orientation of the internal electric field with respect to the radical site, creating an OEF which tunes the reactivity across the set of gas-phase carbon-centred radical reactions. In the first case, OEFs predictably accelerate and decelerate the rate of molecular oxygen addition to substituted phenyl, adamantyl, and cubyl radicals, depending on the polarity of the charged functional group and dipole orientation. In the second case, OEFs modulate competition between chlorine and hydrogen atom abstraction from chloroform based on interactions between charge polarity, dipole orientation, and radical polarizability. Importantly, this means the same charge polarity can induce different changes to reaction selectivity. Quantum chemical calculations of these reactions with DSD-PBEP86-D3(BJ)/aug-cc-pVTZ show correlations between the barrier heights and the experimentally determined reaction kinetics. Field effects are consistent between phenyl and cubyl scaffolds, pointing to through-space rather than through-bond field effects, congruent with computations showing that the same effects can be mimicked by point charges. These results experimentally demonstrate how internal OEFs generated by carefully placed charged functional groups can systematically control radical reactions.

Tandem Mass Spectrometry of Perfluorocarboxylate Anions: Fragmentation Induced by Reactive Species Formed From Microwave Excited Hydrogen and Water Plasmas

RATIONALE

Polyfluoroalkyl substances (PFAS) like perfluorooctanoic acid have persistent environmental and physiological effects. This study investigates the degradation of CnF2n+1CO2 - (n = 1-7) with neutral radical fragmentation under oxygen attachment dissociation (OAD). Unique fragments absent from collision-induced dissociation (CID) are observed. Further, potential mechanisms are uncovered by density functional theory (DFT) calculations.

METHODS

From a standard mixture of PFAS, straight-chain perfluorinated carboxylic acids with carbon chain lengths of one to eight were separated via liquid chromatography and transferred to the gas phase via negative-mode electrospray ionisation. Each CnF2n+1CO2 - of interest was mass selected and fragmented via both CID and OAD in a quadrupole time-of-flight mass spectrometer. DFT optimisations of structures were performed at M06/6-31+g(d), and single point energy calculations were performed at M06-2X/aug-cc-pVTZ for C3F7CO2 -.

RESULTS

Decarboxylation was observed from both CID and OAD, but fluorine abstraction and hydroxyl addition only occurred with OAD. The DFT calculations suggest that C3F6 -• (m/z 150) is most likely formed from by H• attack onto a β- C-F bond, then loss of HF, finally decarboxylation. Further, C3F5O- (m/z 147) likely arises from C3F6 -• recombining with OH• to produce energised C3F6OH- ions, followed by α- or β- elimination of HF to give enolate and/or epoxide-type products.

CONCLUSIONS

OAD of C3F7CO2 - yields unique product ions C3F6 -• (m/z 150) and C3F5O- (m/z 147) absent from collision-induced dissociation. DFT calculations suggest an intricate pathway of H• attack onto a β C-F bond, then loss of HF, decarboxylation, recombination with OH•, and finally α- or β- elimination of HF to give the products.

Demethylation C-C coupling reaction facilitated by the repulsive Coulomb force between two cations

Carbon chain elongation (CCE) is normally carried out using either chemical catalysts or bioenzymes. Herein we demonstrate a catalyst-free approach to promote demethylation C-C coupling reactions for advanced CCE constructed with functional groups under ambient conditions. Accelerated by the electric field, two organic cations containing a methyl group (e.g., ketones, acids, and aldehydes) approach each other with such proximity that the energy of the repulsive Coulomb interaction between these two cations exceeds the bond energy of the methyl group. This results in the elimination of a methyl cation and the coupling of the residual carbonyl carbon groups. As confirmed by high-resolution mass spectrometry and isotope-labeling experiments, the C-C coupling reactions (yields up to 76.5%) were commonly observed in the gas phase or liquid phase, for which the mechanism was further studied using molecular dynamics simulations and stationary-point calculations, revealing deep insights and perspectives of chemistry.

Investigation of unexpected silane ions caused by gas-phase reactions in Orbitrap gas chromatography-mass spectrometry

RATIONALE

The mass spectra of compounds containing dimethyl (phenyl)silyl group (-SiMe2Ph) sometimes exhibit unusual ion peaks when measured using Orbitrap gas chromatography-mass spectrometry (GC-MS). This would complicate the mass spectra and may limit the matching of spectral data with preexisting resources for compound annotation. These peaks were identified as products from reactions with residual water.

METHODS

A series of dimethyl (phenyl)silyl compounds were dissolved in methanol and investigated using Orbitrap GC-MS. Certain ions reacted with residual water in the C-trap. The reaction was confirmed using accurate mass and elemental composition analysis via MS studies, and the active center of the reaction was determined using density functional theory (DFT) calculations.

RESULTS

Two types of gas-phase reactions between gaseous water and cations from a series of silanes were identified. DFT calculations indicate that silicon (Si) acts as the active center for these gas-phase water reactions. Compounds with multiple Si atoms generate a larger number of additional ions, which would complicate the mass spectra. The mass spectra of vinylsilanes and alkylsilanes with -SiMe2Ph indicate that the conjugated group linked to -SiMe2Ph can affect the water adduction process.

CONCLUSIONS

Silane ions could react with residual water in the C-trap of an Orbitrap mass spectrometer. The mass spectra of these compounds may exhibit unexplained peaks arising from gas-phase reactions. Although these reactions may decrease spectral matching scores for compound annotation, they offer opportunities for systematic investigations into the mechanistic and kinetic aspects of high-energy ion reactivity.

Ion-molecule reactions of mass-selected ions

Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.

Competition between Elimination and Substitution for Ambident Nucleophiles CN- and Iodoethane Reactions in Gaseous and Aqueous Medium

Nucleophilic substitution (SN2) and elimination (E2) reactions between ambident nucleophiles have long been considered as typical reactions in organic chemistry, and exploring the competition between the two reactions is of great importance in chemical synthesis. As a nucleophile, CN- can use its C and N atoms as the reactive centers to undergo E2 and SN2 reactions, but related research is currently limited. This study uses the CCSD(T)/pp/t//MP2/ECP/d electronic structure method to perform detailed investigations on the potential energy profiles for SN2 and E2 reactions between CN- and CH3CH2I in gaseous and aqueous media. The potential energy profiles reveal that the energy barriers for SN2 and E2 reactions with the C atom as the reactive center are consistently lower than those with the N atom, indicating that the C atom has a stronger nucleophilic ability and stronger basicity. Furthermore, the potential energy profiles in both gas and aqueous environments show that the barriers of SN2 reactions are lower than those for E2 reactions with both C and N as the attacking atom. By using the frontier molecular orbital and activation strain models to explain the interesting phenomenon, the transition from the gas phase to solution was investigated, specifically in the gas-microsolvation-water transition. The results show that water molecules reduce the nucleophilicity and basicity of CN-, while strain energy (ΔEstrain) causes a greater increase in the energy barrier for E2 reactions. This study provides new insights and perspectives on the understanding of CN- as a nucleophile in SN2 reactions and serves as theoretical guidance for organic synthesis.

SN 2 versus E2 Competition of Cyclic Ethers

We have quantum chemically studied the influence of ring strain on the competition between the two mechanistically different SN 2 and E2 pathways using a series of archetypal ethers as substrate in combination with a diverse set of Lewis bases (F- , Cl- , Br- , HO- , H3 CO- , HS- , H3 CS- ), using relativistic density functional theory at ZORA-OLYP/QZ4P. The ring strain in the substrate is systematically increased on going from a model acyclic ether to a 6- to 5- to 4- to 3-membered ether ring. We have found that the activation energy of the SN 2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the SN 2 reactivity increases. In contrast, the activation energy of the E2 pathway generally rises along this same series, that is, from large to small cyclic ethers. The opposing reactivity trends induce a mechanistic switch in the preferred reaction pathway for strong Lewis bases from E2, for large cyclic substrates, to SN 2, for small cyclic substrates. Weak Lewis bases are unable to overcome the higher intrinsic distortivity of the E2 pathway and, therefore, always favor the less distortive SN 2 reaction.

C versus O Protonation in Zincate Anions: A Simple Gas-Phase Model for the Surprising Kinetic Stability of Organometallics

For better understanding the intrinsic reactivity of organozinc reagents, we have examined the protolysis of the isolated zincate ions Et₃ Zn^- , Et₂ Zn(OH)^- , and Et₂ Zn(OH)₂ Li^- by 2,2,2-trifluoroethanol in the gas phase. The protonation of the hydroxy groups and the release of water proceed much more efficiently than the protonation of the ethyl groups and the liberation of ethane. Quantum-chemical computations and statistical-rate theory calculations fully reproduce the experimental findings and attribute the lower reactivity of the more basic ethyl moiety to higher intrinsic barriers, which override the thermodynamic preference for its protonation. Thus, our minimalistic gas-phase model provides evidence for the intrinsically low reactivity of organozinc reagents toward proton donors and helps to explain their remarkable kinetic stability against moisture and even protic media.

Hydroxyl transfer versus cyclization reaction in the gas phase: Sequential loss of NH3 and CH2CO from protonated phenylalanine derivatives

Collisional activation of protonated phenylalanine derivatives deamination products leads to hydroxyl skeletal rearrangement versus cyclization reaction, and to form hydroxylbenzyl cation via elimination of CH₂CO. To better clarify this unusual fragmentation reaction, accurate mass measurements experiments, native isotope experiments, multiple-stage mass spectrometry experiments, different substituents experiments, and density functional theory (DFT) calculations were carried out to investigate the dissociation mechanistic pathways of protonated phenylalanine derivatives deamination products. In route 1, a three-membered ring-opening reaction and a 1,3-hydroxyl transfer (from the carbonyl carbon atom to the interposition carbon atom of carbonyl) occurs to form 3-hydroxy-1-oxo-3-phenylpropan-1-ylium, followed by dissociation to lose CH₂CO to give hydroxy (phenyl)methylium. In route 2, a successive cyclization rearrangement reaction and proton transfer occur to form a 2-hydroxylphenylpropionyl cation or protonated 2-hydroxy-4H-benzopyran, followed by dissociation to lose CH₂CO or CH≡COH to give 2-hydroxylbenzyl cation. In route 3, a successive hydroxyl transfer (from the carbonyl carbon atom to the ortho carbon atom on benzene) and two stepwise proton transfer (1,2-proton transfer to the ipso-carbon atom of the phenyl ring followed by 1,3-proton transfer to the ortho carbon atom of carbonyl) occurs to form a 2-hydroxylphenylpropionyl cation, which subsequently dissociates to form 2-hydroxylbenzyl cation by elimination of CH₂CO. DFT calculations suggested that route 1 was more favorable than route 2 and route 3 from a thermodynamic point of view.

A Portable Reagent Inlet System Designed to Diminish the Impact of Air and Water to Ion-Molecule Reactions Studied in a Linear Quadrupole Ion Trap

A portable reagent inlet system for a linear quadrupole ion trap (LQIT) mass spectrometer was designed to diminish the impact of air and water on gas-phase ion-molecule reactions. Compared to the traditional reagent mixing manifolds that has been extensively used for decades, the portable system is much simpler and has fewer junctions and a smaller inner space. These changes reduce the amount of air and water introduced into the mass spectrometer with the reagent. Furthermore, unlike the traditional manifolds, the portable system can be easily attached to or detached from the LQIT mass spectrometer. Finally, the price of the portable system is only 1/10 of that of a traditional manifold as estimated in 2022. Therefore, the portable system has several advantages over the traditional reagent mixing manifolds.

Kinetic Study of the Maillard Reaction in Thin Film Generated by Microdroplets Deposition

The Maillard reaction kinetics in the confined volume of the thin film produced by ESI microdroplet deposition was studied by mass spectrometry. The almost exclusive formation of the Amadori product from the reaction of D-xylose and D-glucose toward L-glycine and L-lysine was demonstrated. The thin film Maillard reaction occurred at a mild synthetic condition under which the same process in solution was not observed. The comparison of the thin film kinetics with that of the reaction performed in solution showed strong thin film rate acceleration factors.

Mass spectrometry in organic and bio-organic catalysis: Using thermochemical properties to lend insight into mechanism

In this review, we discuss gas phase experimentation centered on the measurement of acidity and proton affinity of substrates that are useful for understanding catalytic mechanisms. The review is divided into two parts. The first covers examples of organocatalysis, while the second focuses on biological catalysis. The utility of gas phase acidity and basicity values for lending insight into mechanisms of catalysis is highlighted.

Does Steric Hindrance Actually Govern the Competition between Bimolecular Substitution and Elimination Reactions?

Bimolecular nucleophilic substitution (SN2) and elimination (E2) reactions are prototypical examples of competing reaction mechanisms, with fundamental implications in modern chemical synthesis. Steric hindrance (SH) is often considered to be one of the dominant factors determining the most favorable reaction out of the SN2 and E2 pathways. However, the picture provided by classical chemical intuition is inevitably grounded on poorly defined bases. In this work, we try to shed light on the aforementioned problem through the analysis and comparison of the evolution of the steric energy (EST), settled within the IQA scheme and experienced along both reaction mechanisms. For such a purpose, the substitution and elimination reactions of a collection of alkyl bromides (R-Br) with the hydroxide anion (OH-) were studied in the gas phase at the M06-2X/aug-cc-pVDZ level of theory. The results show that, generally, EST recovers the appealing trends already anticipated by chemical intuition and organic chemistry, supporting the role that SH is classically claimed to play in the competition between SN2 and E2 reactions.

Modelling Reaction Kinetics of Distonic Radical Ions: A Systematic Investigation of Phenyl-type Radical Addition to Unsaturated Hydrocarbons

Gas phase ion−molecule reactions are central to chemical processes across many environments. A feature of many of these reactions is an inverse relationship between temperature and reaction rate arising from...

Intracluster Sulphur Dioxide Oxidation by Sodium Chlorite Anions: A Mass Spectrometric Study

The reactivity of [NaL·ClO₂]⁻ cluster anions (L = ClO_x⁻; x = 0–3) with sulphur dioxide has been investigated in the gas phase by ion–molecule reaction experiments (IMR) performed in an in-house modified Ion Trap mass spectrometer (IT-MS). The kinetic analysis revealed that SO₂ is efficiently oxidised by oxygen-atom (OAT), oxygen-ion (OIT) and double oxygen transfer (DOT) reactions. The main difference from the previously investigated free reactive ClO₂⁻ is the occurrence of intracluster OIT and DOT processes, which are mediated by the different ligands of the chlorite anion. This gas-phase study highlights the importance of studying the intrinsic properties of simple reacting species, with the aim of elucidating the elementary steps of complex processes occurring in solution, such as the oxidation of sulphur dioxide.

Anion-Anion Chemistry with Mass-Selected Molecular Fragments on Surfaces

While reactions between ions and neutral molecules in the gas phase have been studied extensively, reactions between molecular ions of same polarity remain relatively unexplored. Herein we show that reactions between fragment ions generated in the gas phase and molecular ions of the same polarity are possible by soft-landing of both reagents on surfaces. The reactive [B₁₂ I₁₁ ]^1- anion was deposited on a surface layer built up by landing the generally unreactive [B₁₂ I₁₂ ]^2- . Ex-situ analysis of the generated material shows that [B₂₄ I₂₃ ]^3- was formed. A computational study shows that the product is metastable in the gas phase, but a charge-balanced environment of a grounded surface may stabilize the triply charged product, as suggested by model calculations. This opens new opportunities for the generation of highly charged clusters using unconventional building blocks from the gas phase.

σ-Hole activation and structural changes upon perfluorination of aryl halides: direct evidence from gas phase rotational spectroscopy

Enhancement of the σ-hole on the halogen atom of aryl halides due to perfluorination of the ring is demonstrated by use of the Extended Townes-Dailey (ETD) model coupled to a Natural Atomic Orbital Bond analysis on two perfluorinated aryl halides (C₆F₅Cl and C₆F₅Br) and their hydrogenated counterparts. The ETD analysis, which quantifies the halogen p-orbitals populations, relies on the nuclear quadrupole coupling constants which in this work are accurately determined experimentally from the rotational spectra. The rotational spectra investigated by Fourier-transform microwave spectroscopy performed in supersonic expansion are reported for the parent species of C₆F₅Cl and C₆F₅Br and their ¹³C, ³⁷Cl or ⁸¹Br substituted isotopologues observed in natural abundance. The experimentally determined rotational constants combined with theoretical data at the MP2/aug-cc-pVTZ level provide precise structural information from which an elongation of the ring along its symmetry axis due to perfluorination is proved.

Determination of the compound class and functional groups in protonated analytes via diagnostic gas-phase ion-molecule reactions

Diagnostic gas-phase ion-molecule reactions serve as a powerful alternative to collision-activated dissociation for the structural elucidation of analytes when using tandem mass spectrometry. The use of such ion-molecule reactions has been demonstrated to provide a robust tool for the identification of specific functional groups in unknown ionized analytes, differentiation of isomeric ions, and classification of unknown ions into different compound classes. During the past several years, considerable efforts have been dedicated to exploring various reagents and reagent inlet systems for functional-group selective ion-molecule reactions with protonated analytes. This review provides a comprehensive coverage of literature since 2006 on general and predictable functional-group selective ion-molecule reactions of protonated analytes, including simple monofunctional and complex polyfunctional analytes, whose mechanisms have been explored computationally. Detection limits for experiments involving high-performance liquid chromatography coupled with tandem mass spectrometry based on ion-molecule reactions and the application of machine learning to predict diagnostic ion-molecule reactions are also discussed.

Chemical reactivity from an activation strain perspective

Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.

Advances in transition metal-free deborylative transformations of gem-diborylalkanes

Carbanions serve as key intermediates in a variety of chemical transformations. Particularly, α-borylcarbanions have received considerable attention in recent years because of their peculiar properties, including the ability of boron atom resonance to stabilise the adjacent negatively charged carbon atom. This feature article summarises recent progress in the synthetic utilisation of α-borylcarbanions, including carbon-carbon bond formation with alkyl halides, alkenes, N-heteroarenes, and carbonyls. Carbon-boron bond formation in organohalides mediated by α-borylcarbanions is also summarised.

Perspective on Emerging Mass Spectrometry Technologies for Comprehensive Lipid Structural Elucidation

Lipids and metabolites are of interest in many clinical and research settings because it is the metabolome that is increasingly recognized as a more dynamic and sensitive molecular measure of phenotype. The enormous diversity of lipid structures and the importance of biological structure-function relationships in a wide variety of applications makes accurate identification a challenging yet crucial area of research in the lipid community. Indeed, subtle differences in the chemical structures of lipids can have important implications in cellular metabolism and many disease pathologies. The speed, sensitivity, and molecular specificity afforded by modern mass spectrometry has led to its widespread adoption in the field of lipidomics on many different instrument platforms and experimental workflows. However, unambiguous and complete structural identification of lipids by mass spectrometry remains challenging. Increasingly sophisticated tandem mass spectrometry (MS/MS) approaches are now being developed and seamlessly integrated into lipidomics workflows to meet this challenge. These approaches generally either (i) alter the type of ion that is interrogated or (ii) alter the dissociation method in order to improve the structural information obtained from the MS/MS experiment. In this Perspective, we highlight recent advances in both ion type alteration and ion dissociation methods for lipid identification by mass spectrometry. This discussion is aimed to engage investigators involved in fundamental ion chemistry and technology developments as well as practitioners of lipidomics and its many applications. The rapid rate of technology development in recent years has accelerated and strengthened the ties between these two research communities. We identify the common characteristics and practical figures of merit of these emerging approaches and discuss ways these may catalyze future directions of lipid structural elucidation research.

Intramolecular benzyl cation transfer in the gas-phase fragmentation of protonated benzyl phenyl sulfones

In this study, the gas-phase fragmentations of protonated benzyl phenyl sulfones were investigated by electrospray ionization tandem mass spectrometry (ESI-MSⁿ ). Upon collisional activation, several characteristic fragment ions were observed, and the similar results occurred with different substituted benzyl phenyl sulfones. A mechanism involving an intramolecular benzyl cation transfer and the formation of intermediate ion was proposed and further identified by density functional theory (DFT) calculations. In addition, a reference compound, benzenesulfinic acid benzyl ester, has been synthesized, and its protonated ion has the same gas-phase behavior as compared to the protonated benzyl phenyl sulfone. This work provides access to some insight into the intramolecular benzyl-transfer reactions of benzyl phenyl sulfones in the gas phase and orients the characteristic peaks in collision-induced dissociation spectrometry (CID-MS).

The role of intermolecular forces in ionic reactions: the solvent effect, ion-pairing, aggregates and structured environment

The environment enclosing an ionic species has a critical effect on its reactivity. In a more general sense, medium effects are not limited to the solvent, but involve the counter ion effect (ion pairing), formation of larger aggregates and structured environment as provided by the host in the case of host-guest complexes. In this review, a general view of the medium effect on anion-molecule reactions is presented. Nucleophilic substitution reactions of aliphatic (SN2) and aromatic (SNAr) systems, as well as elimination reactions (E2), are the focus of the discussion. In particular, nucleophilic fluorination with KF, CsF and tetraalkylammonium fluoride was used as the main model, because of the importance of this kind of reaction and the recent advances in the study of these systems. The solvent effect, ion pairing, formation of aggregates and formation of complexes with crown ethers, cryptands and calixarenes are discussed. For a deeper insight into the medium effect, many results of reliable theoretical calculations in close agreement with experiments were chosen as examples.

Reactivity Trends in the Gas-Phase Addition of Acetylene to the N-Protonated Aryl Radical Cations of Pyridine, Aniline, and Benzonitrile

A key step in gas-phase polycyclic aromatic hydrocarbon (PAH) formation involves the addition of acetylene (or other alkyne) to σ-type aromatic radicals, with successive additions yielding more complex PAHs. A similar process can happen for N-containing aromatics. In cold diffuse environments, such as the interstellar medium, rates of radical addition may be enhanced when the σ-type radical is charged. This paper investigates the gas-phase ion-molecule reactions of acetylene with nine aromatic distonic σ-type radical cations derived from pyridinium (Pyr), anilinium (Anl), and benzonitrilium (Bzn) ions. Three isomers are studied in each case (radical sites at the ortho, meta, and para positions). Using a room temperature ion trap, second-order rate coefficients, product branching ratios, and reaction efficiencies are measured. The rate coefficients increase from para to ortho positions. The second-order rate coefficients can be sorted into three groups: low, between 1 and 3 × 10^-12 cm³ molecule^-1 s^-1 (3Anl and 4Anl); intermediate, between 5 and 15 × 10^-12 cm³ molecule^-1 s^-1 (2Bzn, 3Bzn, and 4Bzn); and high, between 8 and 31 × 10^-11 cm³ molecule^-1 s^-1 (2Anl, 2Pyr, 3Pyr, and 4Pyr); and 2Anl is the only radical cation with a rate coefficient distinctly different from its isomers. Quantum chemical calculations, using M06-2X-D3(0)/6-31++G(2df,p) geometries and DSD-PBEP86-NL/aug-cc-pVQZ energies, are deployed to rationalize reactivity trends based on the stability of prereactive complexes. The G3X-K method guides the assignment of product ions following adduct formation. The rate coefficient trend can be rationalized by a simple model based on the prereactive complex forward barrier height.

A Unified Framework for Understanding Nucleophilicity and Protophilicity in the SN 2/E2 Competition

The concepts of nucleophilicity and protophilicity are fundamental and ubiquitous in chemistry. A case in point is bimolecular nucleophilic substitution (SN 2) and base-induced elimination (E2). A Lewis base acting as a strong nucleophile is needed for SN 2 reactions, whereas a Lewis base acting as a strong protophile (i.e., base) is required for E2 reactions. A complicating factor is, however, the fact that a good nucleophile is often a strong protophile. Nevertheless, a sound, physical model that explains, in a transparent manner, when an electron-rich Lewis base acts as a protophile or a nucleophile, which is not just phenomenological, is currently lacking in the literature. To address this fundamental question, the potential energy surfaces of the SN 2 and E2 reactions of X- +C2 H5 Y model systems with X, Y = F, Cl, Br, I, and At, are explored by using relativistic density functional theory at ZORA-OLYP/TZ2P. These explorations have yielded a consistent overview of reactivity trends over a wide range in reactivity and pathways. Activation strain analyses of these reactions reveal the factors that determine the shape of the potential energy surfaces and hence govern the propensity of the Lewis base to act as a nucleophile or protophile. The concepts of "characteristic distortivity" and "transition state acidity" of a reaction are introduced, which have the potential to enable chemists to better understand and design reactions for synthesis.

Accelerated Reaction Kinetics in Microdroplets: Overview and Recent Developments

Various organic reactions, including important synthetic reactions involving C-C, C-N, and C-O bond formation as well as reactions of biomolecules, are accelerated when the reagents are present in sprayed or levitated microdroplets or in thin films. The reaction rates increase by orders of magnitude with decreasing droplet size or film thickness. The effect is associated with reactions at the solution-air interface. A key factor is partial solvation of the reagents at the interface, which reduces the critical energy for reaction. This phenomenon is of intrinsic interest and potentially of practical value as a simple, rapid method of performing small-scale synthesis.

Graph-based machine learning interprets and predicts diagnostic isomer-selective ion-molecule reactions in tandem mass spectrometry

Diagnostic ion-molecule reactions employed in tandem mass spectrometry experiments can frequently be used to differentiate between isomeric compounds unlike the popular collision-activated dissociation methodology. Selected neutral reagents, such as 2-methoxypropene (MOP), are introduced into an ion trap mass spectrometer where they react with protonated analytes to yield product ions that are diagnostic for the functional groups present in the analytes. However, the understanding and interpretation of the mass spectra obtained can be challenging and time-consuming. Here, we introduce the first bootstrapped decision tree model trained on 36 known ion-molecule reactions with MOP. It uses the graph-based connectivity of analytes' functional groups as input to predict whether the protonated analyte will undergo a diagnostic reaction with MOP. A Cohen kappa statistic of 0.70 was achieved with a blind test set, suggesting substantial inter-model reliability on limited training data. Prospective diagnostic product predictions were experimentally tested for 13 previously unpublished analytes. We introduce chemical reactivity flowcharts to facilitate chemical interpretation of the decisions made by the machine learning method that will be useful to understand and interpret the mass spectra for chemical reactivity.

Relationship Investigation between C(sp2)-X and C(sp3)-X Bond Energies Based on Substituted Benzene and Methane

The C-X bonds of organic compounds between group X and a saturated or unsaturated carbon atom differ in bond energy. To identify the causes of variation is of great significance in terms of bond nature understanding and bond energy estimation. In this paper, the electronegativity χ[X] of group X was calculated by the "valence electron equalized electronegativity" method. Then, χ[X] and the electronic effect constant of the substituent were taken as variables to establish equations for quantitative correlation between C(sp³)-X and C(sp²)-X for the calculation of C-X bond energies. The aim is make comparison between substituted methane, Me-X, and substituted benzene, Ph-X, as well as that between Me-X and substituted ethylene, C₂H₃-X. We conducted calculation over 40 compounds that contain different X groups, and the results reveal that the C(sp³)-X and C(sp²)-X bond energies are under the influence of a number of factors. In addition to the covalent properties of C and X atoms and χ[X], the bond energies of C(sp²)-X (i.e., D[C(sp²)-X]) are under the influence of the field/inductive effect (σ_F[X]) and conjugated effect (σ_R[X]) of group X, with the former causing a decrease while the latter an increase of D[C(sp²)-X]. Using the acquired quantitative correlation equations and on the basis of a relatively rich set of measured D[Me-X] data, we estimated D[Ph-X] of Ph-X and D[C₂H₃-X] of C₂H₃-X, and the estimation accuracy is within experimental uncertainty. Employing the above method, the D[C(sp²)-X] of 33 substituted benzenes, 53 substituted ethenes, and 82 α-substituted naphthalenes was estimated with satisfactory outcomes.

Integration of a Multichannel Pulsed-Valve Inlet System to a Linear Quadrupole Ion Trap Mass Spectrometer for the Rapid Consecutive Introduction of Nine Reagents for Diagnostic Ion/Molecule Reactions

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.

Kinetic hydricity of silane hydrides in the gas phase

Herein, gas phase studies of the kinetic hydricity of a series of silane hydrides are described. An understanding of hydricity is important as hydride reactions figure largely in many processes, including organic synthesis, photoelectrocatalysis, and hydrogen activation. We find that hydricity trends in the gas phase differ from those in solution, revealing the effect of solvent. Calculations and further experiments, including H/D studies, were used to delve into the reactivity and structure of the reactants. These studies also represent a first step toward systematically understanding nucleophilicity and electrophilicity in the absence of solvent.

Reactions of Thiiranium and Sulfonium Ions with Alkenes in the Gas Phase

Ion-molecule reactions between thiiranium ion 11 (m/z 213) and cyclohexene and cis-cyclooctene resulted in the formation of addition products 17a and 17b (m/z 295 and m/z 323, respectively) via an electrophilic addition pathway. Associative π-ligand exchange involving direct transfer of the PhS⁺ moiety, which has been observed for analogous seleniranium ions in the gas phase, did not occur despite previous solution experiments suggesting it as a valid pathway. DFT calculations at the M06-2X/def2-TZVP level of theory showed high barriers for the exchange reaction, while the addition pathway was more plausible. Further support for this pathway was provided with Hammett plots showing the rate of reaction to increase as the benzylic position of thiiranium ion derivatives became more electrophilic (ρ = +1.69; R² = 0.974). The more reactive isomeric sulfonium ion 22 was discounted as being responsible for the observed reactivity with infrared spectroscopy and DFT calculations suggesting little possibility for isomerization. To further explore the differences in reactivity, thiiranium ion 25 and sulfonium ion 27 were formed independently, with the latter ion reacting over 260 times faster toward cis-cyclooctene than the thiiranium ion rationalized by calculations suggesting a barrierless pathway for sulfonium ion 27 to react with the cycloalkene.

Selective Gas-Phase Mass Tagging via Ion/Molecule Reactions Combined with Single Analyzer Neutral Loss Scans to Probe Pharmaceutical Mixtures

We have demonstrated the use of a simple single ion trap mass spectrometer to identify classes of compounds as well as individual components in complex mixtures. First, a neutral reagent was used to mass tag oxygen-containing analytes using a gas-phase ion/molecule reaction. Then, a neutral loss scan was used to indicate the carboxylic acids. The lack of unit mass selectivity in the neutral loss scan required subsequent product ion scans to confirm the presence and identity of the individual carboxylic acids. The neutral loss scan technique reduced the number of data-dependent MS/MS scans required to confirm identification of signals as protonated carboxylic acids. The method was demonstrated on neat mixtures of standard carboxylic acids as well as on solutions of relevant pharmaceutical tablets and may be generalizable to other ion/molecule reactions.

Gas-Phase Chemistry in the GC Orbitrap Mass Spectrometer

Gas-phase reactions of temporally stored ions play a significant role in trapped ion mass spectrometry. Especially highly labile ion species generated through electron ionization (EI) are prone to undergo gas-phase reactions after relaxation to a low vibrational state. Here, we show that in the C-Trap of the Q Exactive GC Orbitrap mass spectrometer, gaseous water reacts with radical cations of various compound classes. High-resolution accurate mass spectrometry of the resulting ions provides a key to the mechanistic understanding of the chemistry of high energetic species generated during EI. We systematically addressed water adduct formation by use of H₂O and D₂¹⁸O in the C-Trap. Mass spectra of halogen cyanides XCN (X=Cl, Br, I) showed the formation of HXCN⁺ species, indicating hydrogen atomic transfer reactions. Relative ratios of HXCN⁺/XCN^+• increased as the electronegativity of the halide increased. The common internal calibrant perfluorotributylamine forms oxygenated products from water reactive fragment ions. These can be explained by the addition of water to an initial cation followed by elimination of two HF molecules. This addition/elimination chemistry can also explain [M+2]⁺ and [M+3]⁺ ions that commonly occur in mass spectra of silylated analytes. High-resolution accurate mass spectra of trimethylsilyl (TMS) derivatives revealed these as [M-CH₃^•+H₂O]⁺ and [M-CH₄+H₂O]^•+, respectively. This study explains common fragment ions in ion trap mass spectrometry. It also opens up perspectives for the systematic mechanistic and kinetic investigation of high-energy ion reactivity. Graphical Abstract.

Fortuitous Ion-Molecule Reaction Enables Enumeration of Metal-Hydrogen Bonds Present in Gaseous Ions

Upon mass selection and ion activation under mass spectrometric conditions, gaseous formate adducts of many metal formates undergo decarboxylation and form product ions that bear metal-hydrogen bonds. Fortuitously, we noted that negative-ion spectra of several such formate adducts showed many peaks that could not be rationalized by the conventional fragmentation pathways attributed to the precursor ion. Subsequent experimentation proved that these enigmatic peaks are due to an ion-molecule reaction that takes place between traces of adventitious water vapor in the collision gas and the in situ formed product anions bearing metal-hydrogen bonds, generated by the fragmentation of the formate adducts. Results show that metal-hydrogen bonds of the group 2 elements are particularly susceptible to this reaction. For example, in the product-ion spectrum of [Sr(η²-O₂CH)₃]^-, the peak at m/z 91 for SrH₃ ^- was accompanied by three peaks at higher m/z ratios. These peaks, at m/z 107, 123, and 139, represented SrH₂(OH)₁ ^-, SrH₁(OH)₂ ^-, and Sr(OH)₃ ^-, respectively. These satellite peaks, which were separated by 16 m/z units, were attributed to adducts formed due to the high affinity of gas-phase anions bearing metal-hydrogen bonds to water. Although undesired, these peaks are diagnostically useful to determine the number of metal-hydrogen bonds present in a precursor ion. Even though the peaks were less pronounced, analogous reactions were noted from the adducts of the group 1 elements as well. Moreover, Gibbs free energy values computed for the interaction of [H-Mg(η²-O₂CH)₂]^- with water to form [HO-Mg(η²-OCOH)₂]^- and H₂ indicated that this is an exergonic reaction.

Mechanistic understanding of catalysis by combining mass spectrometry and computation

The combination of mass spectrometry and computational chemistry has been proven to be powerful for exploring reaction mechanisms. The former provides information of reaction intermediates, while the latter gives detailed reaction energy profiles.

Photoelectron spectroscopy and thermochemistry of o-, m-, and p-methylenephenoxide anions

The anionic products following (H + H+) abstraction from o-, m-, and p-methylphenol (cresol) are investigated using flowing afterglow-selected ion flow tube (FA-SIFT) mass spectrometry and anion photoelectron spectroscopy (PES). The PES of the multiple anion isomers formed in this reaction are reported, including those for the most abundant isomers, o-, m- and p-methylenephenoxide distonic radical anions. The electron affinity (EA) of the ground triplet electronic state of neutral m-methylenephenoxyl diradical was measured to be 2.227 ± 0.008 eV. However, the ground singlet electronic states of o- and p-methylenephenoxyl were found to be significantly stabilized by their resonance forms as a substituted cyclohexadienone, resulting in measured EAs of 1.217 ± 0.012 and 1.096 ± 0.007 eV, respectively. Upon electron photodetachment, the resulting neutral molecules were shown to have Franck-Condon active ring distortion vibrational modes with measured frequencies of 570 ± 180 and 450 ± 80 cm-1 for the ortho and para isomers, respectively. Photodetachment to excited electronic states was also investigated for all isomers, where similar vibrational modes were found to be Franck-Condon active, and singlet-triplet splittings are reported. The thermochemistry of these molecules was investigated using FA-SIFT combined with the acid bracketing technique to yield values of 341.4 ± 4.3, 349.1 ± 3.0, and 341.4 ± 4.3 kcal mol-1 for the o-, m-, and p-methylenephenol radicals, respectively. Construction of a thermodynamic cycle allowed for an experimental determination of the bond dissociation energy of the O-H bond of m-methylenephenol radical to be 86 ± 4 kcal mol-1, while this bond is significantly weaker for the ortho and para isomers at 55 ± 5 and 52 ± 5 kcal mol-1, respectively. Additional EAs and vibrational frequencies are reported for several methylphenyloxyl diradical isomers, the negative ions of which are also formed by the reaction of cresol with O-.

Experimental and Theoretical Studies on Gas-Phase Fragmentation Reactions of Protonated Methyl Benzoate: Concomitant Neutral Eliminations of Benzene, Carbon Dioxide, and Methanol

Protonated methyl benzoate, upon activation, fragments by three distinct pathways. The m/z 137 ion for the protonated species generated by helium-plasma ionization (HePI) was mass-selected and subjected to collisional activation. In one fragmentation pathway, the protonated molecule generated a product ion of m/z 59 by eliminating a molecule of benzene (Pathway I). The m/z 59 ion (generally recognized as the methoxycarbonyl cation) produced in this way, then formed a methyl carbenium ion in situ by decarboxylation, which in turn evoked an electrophilic aromatic addition reaction on the benzene ring by a termolecular process to generate the toluenium cation (Pathway II). Moreover, protonated methyl benzoate undergoes also a methanol loss (Pathway III). However, it is not a simple removal of a methanol molecule after a protonation on the methoxy group. The incipient proton migrates to the ring and randomizes to a certain degree before a subsequent transfer of one of the ring protons to the alkoxy group for the concomitant methanol elimination. The spectrum recorded from deuteronated methyl benzoate showed two peaks at m/z 105 and 106 for the benzoyl cation at a ratio of 2:1, confirming the charge-imparting proton is mobile. However, the proton transfer from the benzenium intermediate to the methoxy group for the methanol loss occurs before achieving a complete state of scrambling. Graphical Abstract ᅟ.

Differentiating Isomeric Deprotonated Glucuronide Drug Metabolites via Ion/Molecule Reactions in Tandem Mass Spectrometry

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 HSiCl₃ 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.

The importance of N-heterocyclic carbene basicity in organocatalysis

This review highlights the importance of N-heterocyclic carbene (NHC) basicity for transformations in which NHCs are used as catalysts.

Conservation of direct dynamics in sterically hindered SN2/E2 reactions

Nucleophilic substitution (S_N2) and base-induced elimination (E2), two indispensable reactions in organic synthesis, are commonly assumed to proceed under stereospecific conditions. Understanding the way in which the reactants pre-orient in these reactions, that is its stereodynamics, is essential in order to achieve a detailed atomistic picture and control over such processes. Using crossed beam velocity map imaging, we study the effect of steric hindrance in reactions of Cl^- and CN^- with increasingly methylated alkyl iodides by monitoring the product ion energy and scattering angle. For both attacking anions the rebound mechanism, indicative of a direct S_N2 pathway, is found to contribute to the reaction at high relative collision energies despite being increasingly hindered. An additional forward scattering mechanism, ascribed to a direct E2 reaction, also contributes at these energies. Inspection of the product energy distributions confirms the direct and fast character of both mechanisms as opposed to an indirect reaction mechanism which leads to statistical energy redistribution in the reaction complex. This work demonstrates that nonstatistical dynamics and energetics govern S_N2 and E2 pathways even in sterically hindered exchange reaction systems.

Loss of benzaldehyde in the fragmentation of protonated benzoylamines: Benzoyl cation as a hydride acceptor in the gas phase

In electrospray ionization tandem mass spectrometry of protonated 1-benzoylamines (1-benzoylpiperadine, 1-benzoylmorpholine, and 1-benzoyl-4-methylpiperazine), the dominant fragmentation pathway was amide bond cleavage to form benzoyl cation and neutral amine. Meanwhile, in their fragmentations, an interesting loss of benzaldehyde (106 Da) was observed and identified to derive from hydride transfer reaction between the benzoyl cation and amine. A stepwise mechanism for loss of 106 Da (benzene and CO) could be excluded with the aid of deuterium labeling experiment. Theoretical calculations indicated that hydride transfers from amines (piperadine, morpholine, and 1-methylpiperazine) to benzoyl cation were thermodynamically permitted, and 1-methylpiperazine was the best hydride donor among the 3 amines. The mass spectrometric experimental results were consistent with the computational results. The relative abundance of the iminium cation (relative to the benzoyl cation) in the fragmentation of protonated 1-benzoyl-4-methylpiperazine was higher than that in the fragmentation of the other 2 protonated 1-benzoylamines. By comparing the fragmentations of protonated 1-benzyl-4-methylpiperazine and protonated 1-benzoyl-4-methylpiperazine and the energetics of their hydride transfer reactions, this study revealed that benzoyl cation was a hydride acceptor in the gas phase, but which was weaker than benzyl cation.

Identification of Carboxylate, Phosphate, and Phenoxide Functionalities in Deprotonated Molecules Related to Drug Metabolites via Ion-Molecule Reactions with water and Diethylhydroxyborane

Tandem mass spectrometry based on ion-molecule reactions has emerged as a powerful tool for structural elucidation of ionized analytes. However, most currently used reagents were designed to react with protonated analytes, making them suboptimal for acidic analytes that are preferentially detected in negative ion mode. In this work we demonstrate that the phenoxide, carboxylate, and phosphate functionalities can be identified in deprotonated molecules by use of a combination of two reagents, diethylmethoxyborane (DEMB) and water. A novel reagent introduction setup that allowed DEMB and water to be separately introduced into the ion trap region of the mass spectrometer was developed to facilitate fundamental studies of this reaction. A new reagent, diethylhydroxyborane (DEHB), was generated inside the ion trap by hydrolysis of DEMB on introduction of water. Most carboxylates and phenoxides formed a DEHB adduct, followed by addition of one water molecule and subsequent ethane elimination (DEHB adduct +H₂O - CH₃CH₃) as the major product ion. Phenoxides with a hydroxy group adjacent to the deprotonation site and phosphates formed a DEHB adduct, followed by ethane elimination (DEHB adduct - CH₃CH₃). Deprotonated molecules with strong intramolecular hydrogen bonds or without the aforementioned functionalities, including sulfates, were unreactive toward DEHB/H₂O. Reaction mechanisms were explored via isotope labeling experiments and quantum chemical calculations. The mass spectrometry method allowed the differentiation of phenoxide-, carboxylate-, phosphate-, and sulfate-containing analytes. Finally, it was successfully coupled with high-performance liquid chromatography for the analysis of a mixture containing hymecromone, a biliary spasm drug, and its three possible metabolites. Graphical Abstract ᅟ.

Flame Atmospheric Pressure Chemical Ionization Coupled with Negative Electrospray Ionization Mass Spectrometry for Ion Molecule Reactions

Flame atmospheric pressure chemical ionization (FAPCI) combined with negative electrospray ionization (ESI) mass spectrometry was developed to detect the ion/molecule reactions (IMRs) products between nitric acid (HNO₃) and negatively charged amino acid, angiotensin I (AI) and angiotensin II (AII), and insulin ions. Nitrate and HNO₃-nitrate ions were detected in the oxyacetylene flame, suggesting that a large quantity of nitric acid (HNO₃) was produced in the flame. The HNO₃ and negatively charged analyte ions produced by a negative ESI source were delivered into each arm of a Y-shaped stainless steel tube where they merged and reacted. The products were subsequently characterized with an ion trap mass analyzer attached to the exit of the Y-tube. HNO₃ showed the strongest affinity to histidine and formed (M_histidine-H+HNO₃)^- complex ions, whereas some amino acids did not react with HNO₃ at all. Reactions between HNO₃ and histidine residues in AI and AII resulted in the formation of dominant [M_AI-H+(HNO₃)]^- and [M_AII-H+(HNO₃)]^- ions. Results from analyses of AAs and insulin indicated that HNO₃ could not only react with basic amino acid residues, but also with disulfide bonds to form [M-3H+(HNO₃)_n]^3- complex ions. This approach is useful for obtaining information about the number of basic amino acid residues and disulfide bonds in peptides and proteins. Graphical Abstract ᅟ.

Competitive benzyl cation transfer and proton transfer: collision-induced mass spectrometric fragmentation of protonated N,N-dibenzylaniline

Collision-induced dissociation of protonated N,N-dibenzylaniline was investigated by electrospray tandem mass spectrometry. Various fragmentation pathways were dominated by benzyl cation and proton transfer. Benzyl cation transfers from the initial site (nitrogen) to benzylic phenyl or aniline phenyl ring. The benzyl cations transfer to the two different sites, and both result in the benzene loss combined with 1,3-H shift. In addition, after the benzyl cation transfers to the benzylic phenyl ring, 1,2-H shift and 1,4-H shift proceed competitively to trigger the diphenylmethane loss and aniline loss, respectively. Deuterium labeling experiments, substituent labeling experiments and density functional theory calculations were performed to support the proposed benzyl cation and proton transfer mechanism. Overall, this study enriches the knowledge of fragmentation mechanisms of protonated N-benzyl compounds. Copyright © 2017 John Wiley & Sons, Ltd.