Dissociative Protonation Research Articles

The ion-neutral complex-mediated fragmentation reaction in electrospray ionization tandem mass spectrometric analysis of N-phenyl-3-(phenylthio)propanamides.

Amides are the fundamental units of both peptides and proteins, and also important functional groups of medical chemicals. Investigation of the fragmentation mechanism of amides in the gas phase is scientifically important for structural analysis. However, understanding of this problem is still elusive. Protonated N-phenyl-3-(phenylthio)propanamide and its derivatives were investigated using positive ion tandem mass spectrometry (ESI-MS/MS) with an LCQ mass spectrometer. Accurate mass analysis was conducted with a micrOTOF-QII mass spectrometer. Density functional theory (DFT) calculations using the Gaussian 03 program and deuterium-labelling (D-labelling) experiments were performed to verify the proposed fragmentation mechanism. Interpretation of the fragment ions in the collision-induced dissociation mass spectra showed that the ionizing proton in the protonated ion transferred from the most thermodynamically favorable carbonyl oxygen to the dissociative protonation site at amide nitrogen or sulfur atom upon collisional activation. The dissociation of the amide or the C-S bond was induced by such proton transfer. An ion-neutral complex (INC) was generated via the dissociation of the amide bond. In the INC, it was observed that the carbocation of the ionic part attacked the ortho phenyl carbon atom adjacent to the sulfur atom, and proton transfer from the carbon atom to the nitrogen atom led to the formation of protonated aniline. The fragmentation mechanism of protonated N-phenyl-3-(phenylthio)propanamide and its derivatives was proposed and elucidated. All the compounds studied showed similar fragmentation pathways, and the competitive formation of two ions, RC9 H9 OS+ and C6 H8 N+ , was observed. The generation of protonated aniline is mediated by INC in ESI-MS/MS.

Dissociative protonation and long-range proton migration: The chemistry of singly- and doubly-protonated tigecycline

Tigecycline is an antibacterial drug in the tetracycline class. In electrospray mass spectrometry both singly-protonated (MH+) and doubly-protonated molecules (MH22+) are formed in abundance. The major fragmentation reactions of the molecular ions in both charge states take place around the amido group at the C2-position on the A-ring and the t-butylamino group of the side chain at the C9-position on the D-ring. Deuterium labeling reveals that losses of ammonia from C2 and isobutene from C9 from both MH+ and MH22+ take place in a consecutive fashion, and elimination of the constitutive t-butylamine as a distinct neutral species does not occur as suggested intuitively. In addition, it is found that the elimination of isobutene from MH22+ is more than 10-fold as much as that from MH+ relative to the ammonia loss. This suggests that in the “double engine” molecular ion (MH22+), the first protonation occurs on the N,N-dimethylamino substituent on the A-ring, responsible for the loss of ammonia from the adjacent C2-amido group, and the second protonation occurs on the t-butylamino moiety on the D-ring to initiate the removal of isobutene. Since these two reactions are also observed with the “single engine” molecular ion (MH+), it is clear that upon the first neutral loss (either ammonia or isobutene), a proton is required to travel across the tetracycline core to trigger the second neutral loss. Multistage mass spectrometry confirms that the structure of the final product ion is the same regardless of the order in which the two neutral species are eliminated, supporting the requirement for a long-range proton migration.

An experimental and theoretical study on fragmentation of protonated N‐(2‐pyridinylmethyl)indole in electrospray ionization mass spectrometry

The dissociation reactions of protonated molecules are the base of structural analysis in electrospray ionization tandem mass spectrometry (ESI-MS(n)). However, general rules for elucidating the numerous fragmentation reactions in ESI-MS(n) are still rather lacking. Therefore, it is very important at all times to carry out mechanistic investigations for fragmentation reactions in the gas phase. The fragmentation reactions of protonated N-(2-pyridinylmethyl)indoles were studied by both of ESI ion trap tandem mass spectrometry and ESI Fourier transform ion cyclotron resonance tandem mass spectrometry in positive-ion mode. In ESI-MS/MS, the ionizing proton is first bound to the most thermodynamically favored site, the pyridine nitrogen; then it transfers to the dissociative protonation sites and triggers the fragmentation. In the fragmentation of the target compounds, some interesting reactions, such as rearrangement, proton transfer and electron transfer reactions, take place via ion/neutral complexes. The proposed mechanisms are supported by both theoretical calculations and isotopic labeling experiments. This study is a case for better understanding the dissociative protonation sites and enriching the knowledge about the role of ion/neutral complexes in ESI-MS. It also provides useful information for the structural analysis of organic compounds, especially drug analysis in pharmaceutical chemistry.

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.

Dissociative protonation and fragmentation: Retro-Friedel–Crafts reactions of heterocyclic drug and metabolite molecules in mass spectrometry

Identification of drug metabolites by mass spectrometry plays an indispensable role in drug discovery and development. As important pharmacophores, the heterocyclic cores are complicated in protonation especially when substituted with various functional groups. Tolmetin, naratriptan and lansoprazole selected in this study are derivatives of pyrrole, indole and benzimidazole, respectively. In the electrospray mass spectrometry of these heterocyclic drugs and their metabolites, fragmentations through deacylation, dealkylation, desulfoxidation or desulfonation are the prominent dissociation reactions of the protonated molecules. The thermodynamically most favorable sites of protonation for these molecules are determined based on proton affinities of pertinent substructures; however, it has been demonstrated that the major fragmentation is not induced by protonation at these sites. Instead, it is required that the proton be transferred to the carbon positions on the heterocyclic cores to which the acyl, alkyl, sulfoxide or sulfone group is attached. These positions are described as the dissociative protonation sites. It is shown again that the proton affinity at the dissociative site is lower than that at many other positions in the molecules, and proton transfer is required to trigger the fragmentation.

Intriguing roles of reactive intermediates in dissociation chemistry of N-phenylcinnamides

In mass spectrometry of protonated N-phenylcinnamides, the carbonyl oxygen is the thermodynamically most favorable protonation site and the added proton is initially localized on it. Upon collisional activation, the proton transfers from the carbonyl oxygen to the dissociative protonation site at the amide nitrogen atom or the α-carbon atom, leading to the formation of important reactive intermediates. When the amide nitrogen atom is protonated, the amide bond is facile to rupture to form ion/neutral complex 1, [RC(6)H(4)CH=CHCO(+)/aniline]. Besides the dissociation of the complex, proton transfer reaction from the α-carbon atom to the nitrogen atom within the complex takes place, leading to the formation of protonated aniline. The presence of electron-withdrawing groups favored the proton transfer reaction, whereas electron-donating groups strongly favored the dissociation (aniline loss). When the proton transfers from the carbonyl oxygen to the α-carbon atom, the cleavage of the C(α)-CONHPh bond results in another ion/neutral complex 2, [PhNHCO(+)/RC(6)H(4)CH=CH(2)]. However, in this case, electron-donating groups expedited the proton transfer reaction from the charged to the neutral partner to eliminate phenyl isocyanate. Besides the cleavage of the C(α)-CONHPh bond, intramolecular nucleophilic substitution (a nucleophilic attack of the nitrogen atom at the β-carbon) and stepwise proton transfer reactions (two 1,2-H shifts) also take place when the α-carbon atom is protonated, resulting in the loss of ketene and RC(6)H(5), respectively. In addition, the H/D exchanges between the external deuterium and the amide hydrogen, vinyl hydrogens and the hydrogens of the phenyl rings were discovered by D-labeling experiments. Density functional theory-based (DFT) calculations were performed to shed light on the mechanisms for these reactions.

On stability and protonation of multielectron systems: The concept of proton affinity. II. Dissociative proton attachment and protonation—Deprotonation mapping

AbstractA few touches on the thematic palette “molecular protonation” directly linked to the concept of molecular stability have been accomplished. They are of different nature, of different origin, and taken from “different angles” of lighting; however, together, they definitely provide a sufficiently complete picture “The protonation interaction, as being strong enough, may break the stability of molecules subject to protonation.” © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

An experimental and computational investigation on the fragmentation behavior of enaminones in electrospray ionization mass spectrometry

The dissociation pathways of protonated enaminones with different substituents were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in positive ion mode. In mass spectrometry of the enaminones, ArCOCHCHN(CH(3) )(2) , the proton transfers from the thermodynamically favored site at the carbonyl oxygen to the dissociative protonation site at ipso-position of the phenyl ring or the double bond carbon atom adjacent to the carbonyl leading to the loss of a benzene or elimination of C(4) H(9) N, respectively. And the hydrogendeuterium (H/D) exchange between the added proton and the proton of the phenyl ring via a 1,4-H shift followed by hydrogen ring-walk was witnessed by the D-labeling experiments. The elemental compositions of all the ions were confirmed by ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS). The enaminones studied here were para-monosubstituted on the phenyl ring and the electron-donating groups were in favor of losing the benzene, whereas the electron-attracting groups strongly favored the competing proton transfer reaction leading to the loss of C(4) H(9) N to form a benzoyl cation, Ar-CO(+) . The abundance ratios of the two competitive product ions were relatively well-correlated with the σ(p) (+) substituent constants. The mechanisms of these reactions were further investigated by density functional theory (DFT) calculations.

Ion-Neutral Complexes Resulting from Dissociative Protonation: Fragmentation of α-Furanylmethyl Benzyl Ethers and 4- N,N-dimethylbenzyl Benzyl Ethers

The loss of CH(2)O during mass spectrometry in two series of alpha-aromaticmethyl benzyl ether compounds, namely, alpha-furanylmethyl p-substituted-benzyl ethers and 4-N,N-dimethylbenzyl p-substituted-benzyl ethers, is particularly interesting. The fragmentation mechanism is proposed to involve an ion-neutral complex-mediated pathway. Specifically, before the formation of an ion-neutral intermediate, the proton is transferred from the thermodynamically favored site at either the ether oxygen atom or the nitrogen atom to the dissociative protonation site at C(alpha) position in either the furyl group or the 4-N,N-dimethylphenyl group. This transfer has been clarified via computational studies and isotopically labeled experiments. In addition, the decomposition of the intermediate may be affected by the substituent groups on the phenyl ring. This conclusion is indicated by the reasonably good correlation between ln[([M + H - CH(2)O](+))/([M + H - CH(2)O - C(6)H(5)R](+))] and the substituent constants.

Intramolecular transacylation: fragmentation of protonated molecules via ion‐neutral complexes in mass spectrometry

An intramolecular transacylation reaction was observed in the mass spectrometry of molecules containing both benzoyl and carboxymethyl groups on an aromatic heterocyclic core. The reaction is triggered by a dissociative protonation on the heterocyclic ring at the atom (carbon or nitrogen) that bonds to the benzoyl group, leading to an intermediate ion-neutral complex. The incipient benzoyl cation in the complex migrates to attack the carboxyl group of the neutral partner at the carbonyl or hydroxyl oxygen under thermodynamic or kinetic control, respectively. Elimination of benzoic acid followed by loss of carbon monoxide takes place as a result of the transacylation.

Dissociative Protonation and Proton Transfers: Fragmentation of α, β-Unsaturated Aromatic Ketones in Mass Spectrometry

In mass spectrometry of the alpha,beta-unsaturated aromatic ketones, Ph-CO-CH=CH-Ph', losses of a benzene from the two ends and elimination of a styrene are the three major fragmentation reactions of the protonated molecules. When the ketones are substituted on the right phenyl ring, the electron-donating groups are in favor of losing a styrene to form the benzoyl cation, PhCO(+), whereas the electron-withdrawing groups strongly favor loss of benzene of the left side to form a cinnamoyl cation, Ph'CH=CHCO(+). When the ketones are substituted on the left phenyl ring, the substituent effects on the reactions are reversed. In both cases, the ratios of the two competitive product ions are well-correlated with the sigma p(+) substituent constants. Theoretical calculations indicate that the carbonyl oxygen is the most favorable site for protonation, and the olefinic carbon adjacent to the carbonyl is also favorable especially when a strong electron-releasing group is present on the right phenyl ring. The energy barrier to the interconversion between the ions formed from protonation at these two sites regulates the overall reactions. Transfer of a proton from the carbonyl oxygen to the ipso position on either phenyl ring, which is dissociative, triggers loss of benzene.

Ammonia Elimination from Protonated Nucleobases and Related Synthetic Substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.

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.

Revisiting the Mechanism of the Unimolecular Fragmentation of Protonated Fluorobenzene

The composite kinetic energy release (KER) associated with the decomposition of metastable, protonated fluorobenzene is examined in detail by means of mass spectrometry and analyzed theoretically using a combination of RRKM theory and the statistical adiabatic channel model (SACM). A model for the KER is presented, and contributions of rotational, vibrational, and zero-point energies are calculated. The predictions are in reasonable agreement with the experimentally measured data for two of three components of the KER. With respect to the third, the results lead to a reconsideration of earlier mechanistic models and indicate that ring-opening may occur during the unimolecular decomposition of protonated fluorobenzene. This hypothesis is supported by the ion/molecule reactions of C6H5+ cations formed by dissociative protonation of fluorobenzene with strong Brønsted acids.

Proton Transfer in Dissociative Protonation Processes

Proton transfer in dissociative protonation processes involving fluoroadamantane and other smaller model compounds with different reference bases has been studied, through the use of B3LYP density ...

A high pressure mass spectrometric study of the formation and chemistry of the pentafluorosulphur cation (SF +5)

The pentafluorosulphur cation (SF + 5) is formed by the dissociative protonation of sulphur hexafluoride by CH + 5. This place an upper limit of 9.83 ± 0.18 eV on the appearance energy (AE) of SF + 5 from SF 6. SF + 5 forms adducts with many bases. The water and methanol adducts lose 2HF and HF + CH 3F respectively to give the very stable ion SF 3O +. The adducts of acetone and ethanol transfer a proton to the neutral molecule. Benzene and toluene are the only aromatic hydrocarbons to form significant yields of adducts; these lose one molecule of HF at long reaction times. SF + 5 reacts with the higher aromatic hydrocarbons mainly by electron transfer. Nitriles form very stable adducts. In all the adducts the binding between sulphur and the basic site of the molecule appears to be particularly strong although the actual binding energies could not be quantified by equilibrium SF + 5 transfer measurements. Only the nitrile adducts showed some evidence that SF + 5 transfer might occur between different bases.