Intramolecular proton transfers in stereoisomeric gas-phase ions and the kinetic nature of the protonation process upon chemical ionization

Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules

Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.

Protomer Formation Can Aid the Structural Identification of Caffeine Metabolites

The structural annotation of isomeric metabolites remains a key challenge in untargeted electrospray ionization/high-resolution mass spectrometry (ESI/HRMS) metabolomic analysis. Many metabolites are polyfunctional compounds that may form protomers in electrospray ionization sources and therefore yield multiple peaks in ion mobility spectra. Protomer formation is strongly structure-specific. Here, we explore the possibility of using protomer formation for structural elucidation in metabolomics on the example of caffeine, its eight metabolites, and structurally related compounds. It is observed that two-thirds of the studied compounds formed high- and low-mobility species in high-resolution ion mobility. Structures in which proton hopping was hindered by a methyl group at the purine ring nitrogen (position 3) yielded structure-indicative fragments with collision-induced dissociation (CID) for high- and low-mobility ions. For compounds where such a methyl group was not present, a gas-phase equilibrium could be observed for tautomeric species with two-dimensional ion mobility. We show that the protomer formation and the gas-phase properties of the protomers can be related to the structure of caffeine metabolites and facilitate the identification of the structural isomers.

Overestimation of 3α- over 3β-25-Hydroxyvitamin D3 Levels in Serum: A Mechanistic Rationale for the Different Mass Spectral Properties of the Vitamin D Epimers

The metabolism of vitamin D₃ includes a parallel C-3 epimerization pathway-in addition to the standard metabolic processes for vitamin D₃-reversing the stereochemical configuration of the -OH group at carbon-3 (β→α). While the biological function of the 3α epimer has not been elucidated yet, the additional species cannot be neglected in the analytical determination of vitamin D₃, as it has the potential to introduce analytical errors if not properly accounted for. Recently, some inconsistent mass spectral behavior was seen for the 25-hydroxyvitamin D₃ (25(OH)D₃) epimers during quantification using electrospray LC-MS/MS. The present work extends that of Flynn et al. ( Ann. Clin. Biochem. 2014, 51, 352-559) and van den Ouweland et al. ( J. Chromatogr. B 2014, 967, 195-202), who reported larger electrospray ionization response factors for the 3α epimer of 25(OH)D₃ in human serum samples as compared to the regular 3β variant. The present work was concerned with the mechanistic reasons for these differences. We used a combination of electrospray ionization, atmospheric pressure chemical ionization, and density functional theory calculations to uncover structural dissimilarities between the epimers. A plausible mechanism is described based on intramolecular hydrogen bonding in the gas phase, which creates a small difference of proton affinities between the epimers. More importantly, this mechanism allows the explanation of the different ionization efficiencies of the epimers based on kinetic control of the ionization process, where ionization initially takes place at the hydroxyl group with subsequent proton transfer to a basic carbon atom. The barrier for this transfer differs between the epimers and is in direct competition with H₂O elimination from the protonated hydroxyl group. The "hidden" site of high gas phase basicity was revealed through computational calculations and appears to be inaccessible via direct protonation.

Stereochemistry-dependent structure of hydrogen-bonded protonated dimers: the case of 1-amino-2-indanol

Stereochemistry effects on the structure of molecular aggregates are studied in the prototypical 1-amino-2-indanol. Conformer-selective IR-UV double resonance spectroscopy reveals how stereochemistry shapes its dimers.

The protonation site of para-dimethylaminobenzoic acid using atmospheric pressure ionization methods

The protonation site of para-dimethylaminobenzoic acid (p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

Kinetic and thermodynamic control of protonation in atmospheric pressure chemical ionization

For p-(dimethylamino)chalcone (p-DMAC), the N atom is the most basic site in the liquid phase, whereas the O atom possesses the highest proton affinity in the gas phase. A novel and interesting observation is reported that the N- and O-protonated p-DMAC can be competitively produced in atmospheric pressure chemical ionization (APCI) with the change of solvents and ionization conditions. In neat methanol or acetonitrile, the protonation is always under thermodynamic control to form the O-protonated ion. When methanol/water or acetonitrile/water was used as the solvent, the protonation is kinetically controlled to form the N-protonated ion under conditions of relatively high infusion rate and high concentration of water in the mixed solvent. The regioselectivity of protonation of p-DMAC in APCI is probably attributed to the bulky solvent cluster reagent ions (S(n)H(+)) and the analyte having different preferred protonation sites in the liquid phase and gas phase.

Kinetic control of protonation in electrospray ionization

The site of protonation in a molecule can greatly affect the fragments observed in product ion MS/MS spectra. In electrospray positive ionization mass spectra, protonation usually occurs predominantly on the most basic site on the molecule to produce the thermodynamically favored protonated species. However, the literature is unclear whether liquid phase or gas phase thermodynamics has the greater influence. This paper describes the protonation and fragmentation behavior of crizotinib and two of its impurities. Crizotinib has two possible protonation sites, a pyridine nitrogen and a secondary amine, piperidine nitrogen; the former is the favored site in the gas phase and the latter the more favored site in the liquid phase. The impurities contain alkyl substitution on the piperidine nitrogen, producing tertiary amine species. Literature precedence suggests that in the liquid phase, the piperidine nitrogen is still the most basic site but, in the gas phase, the pyridine nitrogen and the piperidine nitrogen have very similar basicities. Fragmentation data for the three molecules suggest that the secondary and tertiary amines protonate preferentially and almost exclusively on different sites. We propose that the secondary amine protonates on the piperidine nitrogen (influenced by solution thermodynamics) and the two tertiary amine structures protonate on the pyridine nitrogen because of steric hindrance at the most basic site of the molecule, allowing kinetic control of the protonation process.

Dissociative Protonation Sites: Reactive Centers in Protonated Molecules Leading to Fragmentation in Mass Spectrometry

It is often found in mass spectrometry that when a molecule is protonated at the thermodynamically most favorable site, no fragmentation occurs, but a major reaction is observed when the proton migrates to a different position. For benzophenones, acetophenones, and dibenzyl ether, which are all preferentially protonated at the oxygen, deacylation or dealkylation was observed in the collision-induced dissociation of the protonated molecules. For para-monosubstituted benzophenones, electron-withdrawing substituents favor the formation of RC6H4CO+ (R = substituent), whereas electron-releasing groups favor the competing reaction leading to C6H5CO+. The ln[(RC6H4CO+)/(C6H5CO+)] values are well-correlated with the sigmap+ substituent constants. In the fragmentation of protonated acetophenones, deacetylation proceeds to give an intermediate proton-bound dimeric complex of ketene and benzene. The distribution of the product ions was found to depend on the proton affinities of ketene and substituted benzenes, and the kinetic method was applied in identifying the reaction intermediate. Protonated dibenzyl ether loses formaldehyde upon dealkylation, via an ion-neutral complex of the benzyloxymethyl cation and neutral benzene. These gas-phase retro-Friedel-Crafts reactions occurred as a result of the attack of the proton at the carbon atom to which the carbonyl or the methylene group is attached on the aromatic ring, which is described as the dissociative protonation site.

Hydrogen-shift isomerism: mass spectrometry of isomeric benzenesulfonate and 2-, 3- and 4-dehydrobenzenesulfonic acid anions in the gas phase

The isomeric 3- and 4-dehydrobenzenesulfonic acid anions b and c were prepared by collision induced dissociation (CID) of the [M - H](-) ions of isomeric sulfobenzoic acids obtained by negative electrospray ionization (ESI). The CID spectra (MS(3)) of anions b and c are different from each other, and both are different from that of the isomeric benzenesulfonate anion a, obtained from benzenesulfonic acid. The stability of ions b and c shows that 1,2-proton transfer does not take place in this system under the conditions of the CID experiment. Density functional (DFT) calculations at B3LYP/6-31+G(2d,p) level of theory show that benzenesulfonate anion a is the most stable isomer, and the energies of isomers b and c are higher by more than 65 kcal mol(-1). The calculated energies of the transition states involved in the 1,2-hydrogen migration leading to the interconversion of the isomeric anions are very high (>120 kcal mol(-1)relative to ion a, barrier energies >55 kcal mol(-1)), much higher than those of transition structures leading to fragmentation. This situation does not allow isomerization of ions b and c to a, under the conditions of the CID experiments. The isomeric 2-dehydrobenzenesulfonic acid anion isomerizes to the benzenesulfonate anion a by a facile proton transfer from the SO(3)H group to the adjacent position 2. The results of this work indicate that the gas phase deprotonation of meta- and para-sulfobenzoic acids is a kinetically controlled process.

Solvation in Electrospray Mass Spectrometry: Effects on the Reaction Kinetics of Fragmentation Mediated by Ion-Neutral Complexes

In electrospray ionization (ESI) on a triple quadrupole mass spectrometer, benzydamine, a molecule with an N,N-dimethylaminopropoxyl side chain, showed a fragmentation pattern in Q1 scans that is dramatically different from the mass-selected collision-induced dissociation (CID) of its MH(+) ion. The N,N-dimethylimmonium ion, which dominates in Q1 scans at higher energies, is only a minor product in all CID spectra. By using a smaller model molecule, N,N,N',N'-tetramethyl-1,3-propanediamine, with the kinetic energy release measured for the corresponding reaction, we have demonstrated that an ion-neutral complex composed of the N,N-dimethylazetidine cation and a neutral counterpart is involved. When the ion-neutral complex intermediate evolves toward elimination to form the immonium ion, the transition state is stabilized by the neutral species. Solvation of the ion-neutral complex, which obstructs the separation of the two partners by the resulting tighter enclosure, facilitates the elimination by enhancing the stabilization of the transition state. Therefore, the prevalence of the immonium ion in Q1 scans was a result of solvation in the ESI source. In CID reactions, where the decomposing ions are mass-selected and thus solvation does not exist, the immonium ion was a minor product, and the separation of the ion-neutral complex became dominant.

Substituent effect and multisite protonation in the fragmentation of alkyl benzoates

The dissociation of protonated alkyl benzoates (para H, CN, OMe and NO(2)) into protonated benzoic acids and alkyl cations was studied in the gas phase. It was found that the product ratio depends on the substituent at the para position of the phenyl ring. The substituent effect is probably the result of the formation of an ion-neutral complex intermediate that decomposes to an ion and a neutral, according to the relative proton affinities of the two moieties. The experimental results and theoretical calculations indicate that the favored protonation site in these compounds is the ester's carbonyl and that proton transfer from the phenyl ring to the ester group is very likely to occur under chemical ionization conditions. It is most probable that the carbonyl protonated form is a common intermediate in the fragmentation process, regardless of the protonation site.

Structurally diagnostic ion-molecule reactions: acylium ions with alpha-, beta- and gamma-hydroxy ketones

Gas-phase reactions of four acylium ions and a thioacylium ion with three isomeric alpha-, beta- and gamma-hydroxy ketones are performed by pentaquadrupole mass spectrometric experiments. Novel structurally diagnostic reactions are observed, and found to correlate directly with interfunctional group separation. All five ions tested (CH(3)CO(+), CH(2)(double bond)CHCO(+), PhCO(+), (CH(3))(2)NCO(+) and (CH(3))(2)NCS(+)) react with the gamma-hydroxy ketone (5-hydroxy-2-pentanone) to form nearly exclusively a cyclic oxonium ion of m/z 85 that formally arises from hydroxy anion abstraction. With the beta-hydroxy ketone (4-hydroxy-2-pentanone), CH(2)(double bond)CHCO(+), PhCO(+) and (CH(3))(2)NCO(+) form adducts that undergo fast cyclization via intramolecular water displacement, yielding resonance-stabilized cyclic dioxinylium ions. With the alpha-hydroxy ketone (3-hydroxy-3-methyl-2-butanone), PhCO(+), (CH(3))(2)NCO(+) and (CH(3))(2)NCS(+) form stable adducts. Evidence that these adducts display cyclic structures is provided by the triple-stage mass spectra of the (CH(3))(2)NCS(+) adduct; it dissociates to (CH(3))(2)NCO(+) via a characteristic reaction-dissociation pathway that promotes sulfur-by-oxygen replacement. If cyclizations are assumed to occur with intramolecular anchimeric assistance, relationships between structure and reactivity are easily recognized.

Ketalization of gaseous acylium ions

A novel reaction of gaseous acylium ions: ketalization with diols and analogs, has been systematically studied via pentaquadrupole MS2 and MS3 experiments and ab initio calculations. A variety of alpha,beta-diols and their amino, thiol, ether, and thioether analogs have been tested for reactivity, mechanism evaluation, site selectivity, and for the effects of alpha- and beta-interfunctional separation. As for condensed-phase ketalization of neutral carbonyl compounds followed by hydrolysis, gaseous acylium ions are chemically deactivated in the form of cyclic ionic ketals by ketalization, and are efficiently released via on-line collision-induced dissociation. Ketalization of acylium ions is shown to identify and structurally characterize alpha,beta-diols and their analogs, and to distinguish regioisomers. Diastereomers can also be distinguished, as illustrated for cis and trans 1,2-diaminocyclohexane. The MS2 and MS3 data together with 18O-labeling and ab initio calculations establish for acylium ion ketalization a mechanism of anchimeric assistance with participation of the neighboring acyl group.

Fragmentation study of simvastatin and lovastatin using electrospray ionization tandem mass spectrometry

The fragmentation mechanism of simvastatin and lovastatin was investigated using both triple quadrupole and ion trap mass spectrometers. The elimination of the ester side-chain followed by dehydration and dissociation of the lactone moiety were observed as the main fragmentation pathways for both compounds. Another major fragmentation process was a C==C double-bond facilitated rearrangement. Our tandem mass spectrometric (MS/MS) data suggested that the beta-hydroxy group was involved in the fragmentation by interacting with the carboxyl group generated from the ring opening of the lactone. As a result, a facile neutral loss of 60 Da (CH(3)COOH or a combination of CH(2)==C==O and H(2)O) was detected. MS/MS studies of the structural analogs also provided evidence that the dehydration of the beta-hydroxy lactone generated preferentially the beta,gamma-unsaturated lactones.

New results on the mass spectra of cinchona alkaloids

The electrospray ionization (ESI) mass spectra of 16 cinchona alkaloid compounds were studied for the first time. The electron ionization (EI) spectra of 22 cinchona alkaloids were also recorded, 14 of which had not been examined previously. In the case of EI the characteristic direction of the fragmentation is the scission of the C8-C9 bond. Under EI the cleavage of the C4'-C9 bond occurs only in the case of hydrogenated cinchona alkaloids, whereas the C9-O bond cleavage can be observed in the case of ester and ether derivatives. At a low capillary exit voltage (CapEx) in the ESI measurements there is no fragmentation, and only the [M + H](+) and in some cases the double protonated [M + 2H](2+) ions can be detected. On increasing the CapEx the characteristic primary direction is the cleavage of the C9-O bond, which was observed in the case of epialkaloids and esterified or etherified cinchona derivatives, respectively. Copyright 2000 John Wiley & Sons, Ltd.