Mass spectrometry-based gas phase intramolecular benzyl migration in sparsentan, a novel endothelin and angiotensin II receptor antagonist

We report a collision-induced dissociation (CID) based gas phase rearrangement study using quadrupole time-of-flight mass spectrometry coupled with liquid chromatography on a novel endothelin and angiotensin II receptor antagonist, sparsentan. We performed tandem mass spectrometry to identify precursor and fragment ion relationships and assigned structures for major fragment ions. We propose a benzyl migration mechanism based on bond length measurements in density functional theory (B3LYP/6-31+G*) optimized geometries of protonated sparsentan and its m/z 547 fragment. Protonated sparsentan undergoes loss of ethanol, which yields a resonance-stabilized benzylic cation with m/z 547, which further fragments into m/z 353 via benzyl migration, where the benzylic cation migrates to one of the nucleophilic nitrogen atoms followed by proton transfer from the sulfonamide nitrogen to a carbonyl oxygen, resulting in a neutral loss of mass 194. Further fragmentation of m/z 353 results in m/z 258, which undergoes radical and neutral loss to yield m/z 193 and 194, respectively. The proposed mechanism of generation of m/z 353 was confirmed by CID of deuterated sparsentan. Considering the importance of gas phase rearrangements of organic molecules in structural identifications as well as the novelty of the molecule, these findings will be helpful for future studies to predict gas phase benzyl migration in sparsentan analogs and for degradation product and metabolite identification of sparsentan and its analogs using LC-MS.

Hydrogen transfer-induced S-C rearrangement in the molecular ion of thioanisole derivatives with site-specificity

In this study, the gas-phase fragmentations of molecular ions of thioanisole derivatives were investigated using electron ionization mass spectrometry (EI-MS). In the EI-MS spectrum, a characteristic fragment ion [M - SH]⁺ was observed. The same result with the molecular ion of 3-aminothioanisole was enhanced, while the same phenomenon was not obvious in the EI-MS spectra of 2- or 4-aminothioanisole. To explain the fragmentation, we proposed a mechanism that involved the hydrogen transfer-induced S-C rearrangement with 3 pathways. Substituent effect results, deuterium-labelled experiments and density functional theory (DFT) calculations also confirmed the proposed mechanism.

Fragmentation of Polyfunctional Compounds Recorded Using Automated High-Throughput Desorption Electrospray Ionization

Using desorption electrospray ionization (DESI) as part of an automated high-throughput system, tandem mass spectra of the compounds in a pharmaceutical library were recorded in the positive mode under standardized conditions. Quality control filtering yielded an MS/MS library of 16 662 spectra. Fragmentation of subsets of the compounds in the library chosen to contain a single instance of a particular functional group (amide, piperazine, sulfonamide) was predicted by experts, and the results were compared with the experimental data. Expert performance was good to excellent for all the cases evaluated. Substituents on the functional groups were found to exert important secondary control over the fragmentation, with the main effect observed being product ion stabilization by aromatic substitution, which was consistent across the different groups evaluated. These substituent effects are generally explicable in terms of standard physical organic chemistry considerations of product ion stability as controlling fragmentation. A somewhat unexpected feature was the incidence of homolytic cleavages, driven by the stability of substituted amine radical cations. The findings of this study are intended to lay the groundwork for machine learning approaches to performing MS/MS spectrum → structure and structure → MS/MS spectrum operations on the same experimental data set. The effort involved and the success achieved in computer-aided interpretation, now underway, will be compared with the expert performance as described here.

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).

Comparing the fragmentation reactions of protonated cyclic indolyl α-amino esters in quadrupole/orbitrap and quadrupole time-of-flight mass spectrometers

RATIONALE

The comparative study of higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) mechanisms for protonated cyclic indolyl α-amino esters in quadrupole/orbitrap (Q/Orbitrap) and quadrupole time-of-flight (QTOF) mass spectrometers, respectively, is helpful to study the structures and properties of biologically active indole derivatives using tandem mass spectrometry (MS/MS) technology.

METHODS

HCD and CID experiments were carried out using electrospray ionization Q/Orbitrap MS and QTOFMS in positive ion mode, respectively. Only the labile hydrogens were exchanged with deuterium in hydrogen/deuterium exchange (HDX) experiments and only the aromatic indole C-H hydrogens were substituted with deuterium in regiospecific hydrogen-deuterium labeling experiments. Theoretical calculations were carried out using the density functional theory (DFT) method at the B3LYP level with the 6-311G(d,p) basis set in the Gaussian 03 package of programs.

RESULTS

In Q/Orbitrap MS/MS, when the added proton on the N⁸ position of protonated cyclic indolyl α-amino esters migrated in a stepwise fashion to the C³ position via two sequential 1,4-H shifts, an ion-neutral complex INC₁ of [protonated cyclic N-sulfonyl ketimino esters/indoles] was formed by a charge-directed heterolytic cleavage of the C³ -C¹⁰ bond, while an ion-neutral complex INC₃ of [cyclic N-sulfonyl ketimino esters/protonated indoles] was formed when another labile hydrogen on the N⁸ position successively migrated to the C⁴ position. Direct decomposition of INC₁ and INC₃ resulted in protonated cyclic N-sulfonyl ketimino esters and protonated indoles, respectively, while proton transfer led to protonated indoles and protonated cyclic N-sulfonyl ketimino esters. The HDX reaction with residual water in the HCD cell was also observed. In QTOF-MS/MS, protonated cyclic N-sulfonyl ketimino esters and protonated indoles resulted from direct decomposition of INC₁ and INC₃ , respectively, rather than proton transfer.

CONCLUSIONS

Due to the specific construction of the Q/Orbitrap and QTOF mass spectrometers, different fragmentation mechanisms medicated by ion-neutral complexes of protonated cyclic indolyl α-amino esters were proposed. This study is desirable for qualitative and quantitive investigation of indole derivatives using MS/MS technology.

Benzyl anion transfer in the fragmentation of N-(phenylsulfonyl)-benzeneacetamides: a gas-phase intramolecular S(N)Ar reaction

In this study, we report a gas-phase benzyl anion transfer via intramolecular aromatic nucleophilic substitution (SNAr) during the course of tandem mass spectrometry of deprotonated N-(phenylsulfonyl)-benzeneacetamide. Upon collisional activation, the formation of the initial ion/neutral complex ([C6H5CH2(-)/C6H5SO2NCO]), which was generated by heterolytic cleavage of the CH2-CO bond, is proposed as the key step. Subsequently, the anionic counterpart, benzyl anion, is transferred to conduct the intra-complex SNAr reaction. After losing neutral HNCO, the intermediate gives rise to product ion B at m/z 231, whose structure is confirmed by comparing the multistage spectra with those of deprotonated 2-benzylbenzenesulfinic acid and (benzylsulfonyl)benzene. In addition, intra-complex proton transfer is also observed within the complex [C6H5CH2(-)/C6H5SO2NCO] to generate product ion C at m/z 182. The INC-mediated mechanism was corroborated by theoretical calculations, isotope experiments, breakdown curve, substituent experiments, etc. This work may provide further understanding of the physicochemical properties of the gaseous benzyl anion.

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.

Intramolecular electrophilic aromatic substitution in gas-phase fragmentation of protonated N-benzylbenzaldimines

In this study, the gas-phase fragmentations of protonated N-benzylbenzaldimines were investigated by electrospray ionization tandem mass spectrometry (ESI-MS(n)). Upon collisional activation, several characteristic fragment ions are produced and their fragmentation mechanisms are rationalized by electrophilic aromatic substitution accompanied by benzyl cation transfer. (1) For N-(p-methoxybenzylidene)-1-phenylmethanimine, concomitant with a loss of HCN, a product ion at m/z 121 was observed. It is proposed to be generated from electrophilic substitution at the ipso-position by transferring benzyl cation rather than cleavage of the C-N double bond. (2) For N-(m-methoxybenzylidene)-1-phenylmethanimine, a product ion at m/z 209 was obtained, corresponding to the elimination of NH(3) carrying two hydrogens from the two aromatic rings respectively. This process can be rationalized by two sequential electrophilic substitutions and cyclodeamination reaction based on the benzyl cation transfer. Deuterium-labeled experiments, density functional theory (DFT) calculation and substituent effect results also corroborate the proposed mechanism.

The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol

Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS) during loop opening.

Gas-phase fragmentation of the protonated benzyl ester of proline: intramolecular electrophilic substitution versus hydride transfer

In this study, the gas phase chemistry of the protonated benzyl esters of proline has been investigated by electrospray ionization mass spectrometry and theoretical calculation. Upon collisional activation, the protonated molecules undergo fragmentation reactions via three primary channels: (1) direct decomposition to the benzyl cation (m/z 91), (2) formation of an ion-neutral complex of [benzyl cation + proline](+), followed by a hydride transfer to generate the protonated 4,5-dihydro-3H-pyrrole-2-carboxylic acid (m/z 114), and (3) electrophilic attack at the amino by the transferring benzyl cation, and the subsequent migration of the activated amino proton leading to the simultaneous loss of (H2O + CO). Interestingly, no hydrogen/deuterium exchange for the fragment ion m/z 114 occurs in the d-labeling experiments, indicating that the transferring hydride in path-b comes from the methenyl hydrogen rather than the amino hydrogen. For para-substituted benzyl esters, the presence of electron-donating substituents significantly promotes the direct decomposition (path-a), whereas the presence of electron-withdrawing ones distinctively inhibits that channel. For the competing channels of path-b and path-c, the presence of electron-donating substituents favors path-b rather than path-c, whereas the presence of electron-withdrawing ones favors path-c rather than path-b.

Elimination of benzene from protonated N-benzylindoline: benzyl cation/proton transfer or direct proton transfer?

Collision-induced dissociation (CID) of protonated N-benzylindoline and its derivatives was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Elimination of benzene was observed besides hydride transfer and electron transfer reactions. D-labeling experiments and accurate mass determinations of the product ions confirm that the external proton is retained in the fragment ion, and the elimination reaction was proposed to be initiated by benzyl cation transfer rather than proton transfer. Benzyl cation transfer from the nitrogen atom to one of the sp(2)-hybridized carbon atoms in the indoline core is the key step, and subsequent proton transfer reaction leads to the elimination of benzene. Density functional theory (DFT)-based calculations were performed and the computational results also support the benzyl cation/proton transfer mechanism. Figure ᅟ

SmI2-mediated intermolecular coupling of γ-lactam N-α-radicals with activated alkenes: asymmetric synthesis of 11-hydroxylated analogues of the lead compounds CP-734432 and PF-04475270

We report, for the first time, the synthesis of 8-aza-analogues of PGE2. The SmI2-mediated cross coupling reactions of γ-lactam-hemiaminal 9, lactam 2-pyridyl sulfide 17, and lactam 2-pyridyl sulfone 18 with activated alkenes/alkyne were first developed, giving the corresponding γ-lactams in 49-78%, 45-75%, and 75-90%, respectively. The reactions of lactam 2-pyridyl sulfide and 2-pyridyl sulfone proceeded with ≥12:1 trans-diastereoselectivities. This represents the first intermolecular coupling reaction of the γ-lactam N-α-alkyl radicals of types B, B1, and B2 with activated alkenes. Two radical-based mechanisms were suggested. The asymmetric synthesis of the 11-hydroxylated analogue of the highly selective EP4 receptor agonist PF-04475270 (30), the 11-hydroxylated analogue of ocular hypotensive CP-734432 (31), compounds 35 and 36 have been achieved on the basis of this method.

Gas phase retro-Michael reaction resulting from dissociative protonation: fragmentation of protonated warfarin in mass spectrometry

A mass spectrometric study of protonated warfarin and its derivatives (compounds 1 to 5) has been performed. Losses of a substituted benzylideneacetone and a 4-hydroxycoumarin have been observed as a result of retro-Michael reaction. The added proton is initially localized between the two carbonyl oxygens through hydrogen bonding in the most thermodynamically favorable tautomer. Upon collisional activation, the added proton migrates to the C-3 of 4-hydroxycoumarin, which is called the dissociative protonation site, leading to the formation of the intermediate ion-neutral complex (INC). Within the INC, further proton transfer gives rise to a proton-bound complex. The cleavage of one hydrogen bond of the proton-bound complex produces the protonated 4-hydroxycoumarin, while the separation of the other hydrogen bond gives rise to the protonated benzylideneacetone. Theoretical calculations indicate that the 1, 5-proton transfer pathway is most thermodynamically favorable and support the existence of the INC. Both substituent effect and the kinetic method were utilized for explaining the relative abundances of protonated 4-hydroxycoumarin and protonated benzylideneacetone derivative. For monosubstituted warfarins, the electron-donating substituents favor the generation of protonated substituted benzylideneacetone, whereas the electron-withdrawing groups favor the formation of protonated 4-hydroxycoumarin.

Gas phase chemistry of Li+ with amides: the observation of LiOH loss in mass spectrometry

Collision-induced dissociation (CID) of Li(+) adducts of three sets of compounds that contains an amide bond, including 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide, its derivatives and simpler structures was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Observed fragment ions include those that reflect loss of LiOH. Other product ions result from the Smiles rearrangement and direct C-S bond cleavage. MS/MS of H/D exchange products demonstrated occurrence of a 1,3-H shift from the amide nitrogen atom to the phenyl ring of these compounds. The LiOH loss from Li(+) adducts of amides was further examined by CID of [M + Li](+) ions of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H(2)O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.

Gas-phase chemistry of benzyl cations in dissociation of N-benzylammonium and N-benzyliminium ions studied by mass spectrometry

In this study, the fragmentation reactions of various N-benzylammonium and N-benzyliminium ions were investigated by electrospray ionization mass spectrometry. In general, the dissociation of N-benzylated cations generates benzyl cations easily. Formation of ion/neutral complex intermediates consisting of the benzyl cations and the neutral fragments was observed. The intra-complex reactions included electrophilic aromatic substitution, hydride transfer, electron transfer, proton transfer, and nucleophilic aromatic substitution. These five types of reactions almost covered all the potential reactivities of benzyl cations in chemical reactions. Benzyl cations are well-known as Lewis acid and electrophile in reactions, but the present study showed that the gas-phase reactivities of some suitably ring-substituted benzyl cations were far richer. The 4-methylbenzyl cation was found to react as a Brønsted acid, benzyl cations bearing a strong electron-withdrawing group were found to react as electron acceptors, and para-halogen-substituted benzyl cations could react as substrates for nucleophilic attack at the phenyl ring. The reactions of benzyl cations were also related to the neutral counterparts. For example, in electron transfer reaction, the neutral counterpart should have low ionization energy and in nucleophilic aromatic substitution reaction, the neutral counterpart should be piperazine or analogues. This study provided a panoramic view of the reactions of benzyl cations with neutral N-containing species in the gas phase.