Derivatization of protonated peptides via gas phase ion—molecule reactions with acetone

The protonated [M + H]+ ions of glycine, simple glycine containing peptides, and other simple di- and tripeptides react with acetone in the gas phase to yield [M + H + (CH3)2CO]+ adduct ion, some of which fragment via water loss to give [M + H + (CH3)2CO - H2O]+ Schiff's base adducts. Formation of the [M + H + (CH3)2CO]+ adduct ions is dependent on the difference in proton affinities between the peptide M and acetone, while formation of the [M + H + (CH3)2CO - H2O]+ Schiff's base adducts is dependent on the ability of the peptide to act as an intramolecular proton "shuttle." The structure and mechanisms for the formation of these Schiff's base adducts have been examined via the use of collision-induced dissociation tandem mass spectrometry (CID MS/MS), isotopic labeling [using (CD3)2CO] and by comparison with the reactions of Schiff's base adducts formed in solution. CID MS/MS of these adducts yield primarily N-terminally directed a- and b-type "sequence" ions. Potential structures of the b1 ion, not usually observed in the product ion spectra of protonated peptide ions, were examined using ab initio calculations. A cyclic 5 membered pyrrolinone, formed by a neighboring group participation reaction from an enamine precursor, was predicted to be the primary product.     

Can transacylation reactions occur via S(N)2 pathways in the gas phase? Insights via ion-molecule reactions of N-acylpyridinium ions and ab initio calculations

[reaction: see text]The gas-phase identity exchange reactions of N-acylpyridinium ions with pyridine have been examined experimentally in an ion trap mass spectrometer through the use of isotope labeling experiments. The nature of the acyl group plays a crucial role, with the bimolecular rates following the order acetyl > benzoyl > N,N-dimethylaminocarbamyl. The experimental results correlate with ab initio calculations on the simple model system RC(O)NH3+ + NH3, which also demonstrates that these are "SN2 like" processes.     

N-Cα bond cleavage of the peptide backbone via hydrogen abstraction

The specific cleavage of N-C_α bonds on the peptide backbone to form the so-called ‘c’ and ‘z + 2’ products, which can be used for the rapid determination of protein amino-acid sequences, has been examined to clarify the mechanism(s) that occur during hydrogen abstraction induced by bombardment with 337-nm laser photons in matrix-assisted laser desorption/ionization (MALDI) method. Intramolecular hydrogen abstraction, which results from the hydrogen(s) on the C_α or C_β carbon, did not occur with a deuterium-labeled dodecapeptide. To confirm a proposition that intermolecular hydrogen abstraction occurs between the peptide and the MALDI matrix, a deuterium dodecapeptide embedded in a deuterium 2,5-dihydroxybenzoic acid matrix at a molar ratio of 1:7000 was analyzed. The resulting deuterium c product ions suggested that c ions form via intermolecular hydrogen abstraction, although the results obtained did not deny any other possibilities such as intramolecular transfer of labile hydrogen. A mechanism for the N-C_α bond cleavage has been proposed that the formation of hypervalent radical species and subsequent prompt bond cleavages occur. The proposed mechanism successfully rationalizes the formation of both the z + 2 and the c product ions.     

C–H bond activation versus ring cleavage in the gas phase ion-molecule reactions of Nb+ and Ta+ with toluene and picoline

The reactions of Nb⁺ and Ta⁺ with toluene and picoline and their deuterium-labelled analogues were studied in a Fourier transform ion cyclotron resonance mass spectrometer. Methyl substitution completely changes the reactivities relative to benzene and pyridine. Both metals react to dehydrogenate toluene exclusively. In contrast to benzene, no ring cleavage is observed in the Ta⁺/toluene reaction. A simple explanation for this difference in reactivities is proposed based on the relative energies of the Hückel orbitals of benzene and toluene. The (b₁) symmetric antibonding orbital is higher in energy for toluene. Population of this orbital is necessary for formation of the metallanorbornadiene intermediate and does not occur at thermal energies. Reaction with ring labelled toluene-d₅ shows exclusive H₂ or D₂ elimination in reaction with Nb⁺ and H₂, HD, and D₂ elimination in reaction with Ta⁺. Reactions with the picolines show both dehydrogenation and ring cleavage. Isotope labelling studies show facile H/D scrambling occurs in the intermediate ion-molecule complexes with HCN and DCN both eliminated from the methyl-d₃-2-picoline and 4-picoline. The metals react with picoline and pyridine by different mechanisms. The isotope labelling results suggest a metal-hydrido-azepinium structure for the intermediate complex.     

How does a CC double bond cleave in the gas phase? Fragmentation of protonated ketotifen in mass spectrometry

In the literature, it is reported that the protonated ketotifen mainly undergoes C?C double bond cleavage in electrospray ionization tandem mass spectrometry (ESI‐MS/MS); however, there is no explanation on the mechanism of this fragmentation reaction. Therefore, we carried out a combined experimental and theoretical study on this interesting fragmentation reaction. The fragmentation of protonated ketotifen (m/z 310) always generated a dominant fragment ion at m/z 96 in different electrospray ionization mass spectrometers (ion trap, triple quadrupole and linear trap quadrupole (LTQ)‐orbitrap). The mechanism of the generation of this product ion (m/z 96) through the C?C double bond cleavage was proposed to be a sequential hydrogen migration process (including proton transfer, continuous two‐step 1,2‐hydride transfer and ion‐neutral complex‐mediated hydride transfer). This mechanism was supported by density functional theory (DFT) calculations and a deuterium labeling experiment. DFT calculations also showed that the formation of the product ion m/z 96 was most favorable in terms of energy. This study provides a reasonable explanation for the fragmentation of protonated ketotifen in ESI‐MS/MS, and the fragmentation mechanism is suitable to explain other C?C double bond cleavage reactions in mass spectrometry. Copyright © 2016 John Wiley & Sons, Ltd.     

Sequential methyl-fluorine exchange reactions of siloxide ions in the gas phase

Exchange Me for a fluorine: Trimethylsiloxide ions in the presence of NF(3) in the gas?phase undergo an unusual and sequential metathesis-type reaction wherein methyl groups are exchanged for fluorine. Theoretical calculations suggest that the reaction proceeds by a three-step internal-nucleophilic-displacement mechanism which features a pentacoordinated siliconate species as a transition state rather than as an intermediate.     

Do all the protic ionic liquids exist as molecular aggregates in the gas phase?

According to an EI-MS study of 1,1,3,3-tetramethylguanidium-based protic ionic liquids (PILs), it has been concluded that not all PILs exist as molecular aggregates in the gas phase. The detection of both ions of m/z 115.0 and m/z 116.0 for the 1,1,3,3-tetramethylguanidinium trifluoromethylsulfonate (TMGS) protic ionic liquid indicates that both the molecular and ionic aggregates co-exist in the gas phase, which is to say that the TMGS may also evaporate via the ionic aggregates just like aprotic ionic liquids. Furthermore, investigation on triethylamine-based and 1-methylimidazole-based PILs confirmed that the gas phase structure of PILs depends on both the acidity and basicity of the corresponding acid and base.     

Vinylation of trialkylamines with acyl- and cyanoacetylenes via C–N bond cleavage in the presence of water

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N-Perhalofluoroalkylation of secondary amines by the reactions of the amines and amides with perhalofluoroalkanes. Halophilic attack on nitrogen nucleophile on CBr bond.

Secondary amines and amides react spontaneously with perhalofluoroalkanes CF₂BrCFBrX(X = F, Cl, CF₃) to afford N-perhalofluoroalkylated tertiary amines in fair to good yields. Evidence for an anionic chain process initiated by the bromophilic attack of nitrogen nucleophiles on CBr bonds is given.     

Is Se-Se bond cleavage the most favourable process in electron attachment to diselenides? The importance of asymmetry

Accurate ab initio calculations reveal that, in contrast with what has been commonly assumed up to now, electron attachment to diselenides does not always result in a Se-Se bond fission and, in general, the mechanism behind the bond fission may involve the crossing of several states.     

Where does the electron go? Electron distribution and reactivity of peptide cation radicals formed by electron transfer in the gas phase

We report the first detailed analysis at correlated levels of ab initio theory of experimentally studied peptide cations undergoing charge reduction by collisional electron transfer and competitive dissociations by loss of H atoms, ammonia, and N-C alpha bond cleavage in the gas phase. Doubly protonated Gly-Lys, (GK + 2H) (2+), and Lys-Lys, (KK + 2H) (2+), are each calculated to exist as two major conformers in the gas phase. Electron transfer to conformers with an extended lysine chain triggers highly exothermic dissociation by loss of ammonia from the Gly residue, which occurs from the ground ( X ) electronic state of the cation radical. Loss of Lys ammonium H atoms is predicted to occur from the first excited ( A ) state of the charge-reduced ions. The X and A states are nearly degenerate and show extensive delocalization of unpaired electron density over spatially remote groups. This delocalization indicates that the captured electron cannot be assigned to reduce a particular charged group in the peptide cation and that superposition of remote local Rydberg-like orbitals plays a critical role in affecting the cation-radical reactivity. Electron attachment to ion conformers with carboxyl-solvated Lys ammonium groups results in spontaneous isomerization by proton-coupled electron transfer to the carboxyl group forming dihydroxymethyl radical intermediates. This directs the peptide dissociation toward NC alpha bond cleavage that can proceed by multiple mechanisms involving reversible proton migrations in the reactants or ion-molecule complexes. The experimentally observed formations of Lys z (+*) fragments from (GK + 2H) (2+) and Lys c (+) fragments from (KK + 2H) (2+) correlate with the product thermochemistry but are independent of charge distribution in the transition states for NC alpha bond cleavage. This emphasizes the role of ion-molecule complexes in affecting the charge distribution between backbone fragments produced upon electron transfer or capture.     

Can metal ions be used as gas‐phase disulfide bond cleavage reagents? A survey of coinage metal complexes of model peptides containing an intermolecular disulfide bond

The role that a metal ion can have in promoting disulfide bond cleavage has been assessed by surveying the tandem mass spectra of the following metal complexes of model peptides containing an intermolecular disulfide bond: [M--H+Cu(II)](+); [M--H+Cu(II)(bipy)](+); [M+Ag(I)](+); and [M+Au(I)(PMe(3))](+). In comparison to previously studied protonated peptides, these binary and ternary metal complexes generally yield more abundant S--S and/or C--S bond cleavage. In general, [M--H+Cu(II)](+) ions cleave the adjacent C--S bond more readily, while the [M+Au(I)(PMe(3))](+) ion cleaves the S--S bond more readily. The ternary metal complex [M--H+Cu(II)(bipy)](+), on the other hand, fragments by exclusive loss of the bipyridyl ligand for the larger model peptides studied. Of all coinage metal systems studied, Me(3)PAu(+) is superior in promoting disulfide bond cleavage.     

Is allylphosphine a carbon or a phosphorus base in the gas phase?

The gas-phase basicity of allylphosphine (2-propenylphosphine) was measured by means of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry techniques. A complete survey of the allylphosphine-H(+) potential energy surface, carried out through the use of high-level G2(MP2) and B3LYP/6-311+G(3df,2p) calculations, allows us to conclude that, under low-pressure, low-energy ICR conditions, the interaction between the protonated reference base, B(ref)H(+), and allylphosphine leads to a complex in which B(ref)H(+) attaches to the phosphorus atom of allylphosphine, where the electrostatic potential is strongly attractive. Hence, in the first step only the phosphorus protonated species should be formed. Its isomerization to yield the C(beta)-protonated form, which is the global minimum of the potential energy surface, implies a very high activation barrier that cannot be overtaken under normal experimental ICR conditions. Therefore, the main conclusion of our study is that allylphosphine behaves as a phosphorus base in the gas phase, even though the C(beta)-protonated structure is the most stable protonated species. We have also shown that both C(beta)- and C(gamma)-protonation triggers a cyclization of the system. An analysis of the bonding of the different protonated species as compared with that of the neutral system is presented.     

Gas-phase CαCβ double bond cleavage in the dissociation of protonated 2-benzylidenecyclopentanones: Dissociative proton transfer and intramolecular proton-transport catalysis

Among gas-phase dissociation reactions, double bond cleavage reaction appears to happen extremely rare, especially in the case of CC double bond. In the dissociation reaction of protonated 2-benzylidenecyclopentanones in tandem mass spectrometry, the formation of benzyl cations was observed, resulting from the cleavage of C^α=C^β double bonds, which is different from the general cleavage route seen in most α, β-unsaturated ketone cases. A combined experimental and theoretical investigation on intramolecular hydrogen transfers was carried out to illustrate the mechanisms. The external proton is initially localized on the carbonyl oxygen (the thermodynamically-preferred protonation site). Upon collisional activation, the mobile proton stepwise migrates to the C^α position to achieve the reduction and subsequent cleavage of the C^α=C^β double bond. The stepwise proton transfer is achieved via intramolecular proton-transport catalysis with the assistance of the phenyl ring. The ortho position of the phenyl accepts the proton from the carbonyl oxygen via a 1,6-H shift, and then donates it to the C^α stepwise. The conventional 1,3-H shift from the carbonyl oxygen to the C^α position can be excluded in this case due to its significant energy barrier. Further isotope-labeling experiments are applied to confirming the reaction mechanism. Last but not least, the scope-expansion experiments indicates that the aromatic and cycloalkanonyl moieties play a crucial roles in the cleavage reaction of C^α=C^β double bond.     

How difficult are anion-molecule SNAr reactions of unactivated arenes in the gas phase,dimethyl sulfoxide,and methanol solvents?

Nucleophilic substitution on the aromatic ring (S_NAr) is a very important reaction for organic transformations. This kind of reaction is usually difficult to take place, requiring organometallic catalysis or activation of the ring by electron withdrawing groups to turn the nucleophilic attack possible. In this work, the relative importance of intrinsic gas phase barrier and the solvent effect on several S_NAr reactions using theoretical calculations were investigated. The reactions of the anions OH^?, CN^?, and CH₃O^? and the enolates CH₃COCH₂^? and CH₃COCHCOCH₃^? with bromobenzene and (o, m, p)-methoxy bromobenzene in methanol and dimethyl sulfoxide as solvents were considered. The OH^? and CH₃O^? ions are highly reactive in the gas phase. However, the solvent effect induces a high activation barrier in solution, turning the reaction difficult, although feasible. The CN^? and CH₃COCHCOCH₃^? ions have high activation barriers even in the gas phase. The interesting CH₃COCH₂^? ion has a moderate barrier in the gas phase, although the free energy barrier in DMSO solution reaches 33 kcal mol^?1. Our analysis suggests that decreasing the solvent effect, arylation of enolates with unactivated arenes could become possible.

     

N-terminal derivatization and fragmentation of neutral peptides via ion--molecule reactions with acylium ions: toward gas-phase Edman degradation?

The gas-phase ion-molecule reactions of neutral alanylglycine have been examined with various mass-selected acylium ions RCO(+) (R= CH(3), CD(3), C(6)H(5), C(6)F(5) and (CH(3))( 2)N), as well as the transacylation reagent O-benzoylbenzophenone in a Fourier transform ion cyclotron resonance mass spectrometer. Reactions of the gaseous dipeptide with acylium ions trapped in the ICR cell result in the formation of energized [M + RCO](+) adduct ions that fragment to yield N-terminal b-type and C-terminal y-type product ions, including a modified b(1) ion which is typically not observed in the fragmentation of protonated peptides. Judicious choice of the acylium ion employed allows some control over the product ion types that are observed (i.e., b versus y ions). The product ion distributions from these ion--molecule reactions are similar to those obtained by collision-activated dissociation in a triple quadrupole mass spectrometer of the authentic N-acylated alanylglycine derivatives. These data indicate that derivatization of the peptide in the gas-phase occurs at the N-terminal amine. Ab initio molecular orbital calculations, performed to estimate the thermochemistry of the steps associated with adduct formation as well as product ion formation, indicate that (i) the initially formed adduct is energized and hence likely to rapidly undergo fragmentation, and (ii) the likelihood for the formation of modified b(1) ions in preference to y(1) ions is dependent on the R substituent of the acylium ion. The reaction of the tetrapeptide valine--alanine--alanine--phenylalanine with the benzoyl cation was also found to yield a number of product ions, including a modified b(1) ion. This result suggests that the new experimental approach described here may provide a tool to address one of the major limitations associated with traditional mass spectrometric peptide sequencing approaches, that is, determination of the identity and order of the two N-terminal amino acids. Analogies are made between the reactions observed here and the derivatization and N-terminal cleavage reactions employed in the condensed-phase Edman degradation method.     

Cα-Cβ and Cα-N bond cleavage in the dissociation of protonated N-benzyllactams: dissociative proton transfer and intramolecular proton-transport catalysis

In mass spectrometry of protonated N-benzylbutyrolactams, the added proton is initially localized on the carbonyl oxygen, which is the thermodynamically preferred protonation site. Upon collisional activation, dissociative proton transfer takes place leading to the occurrence of fragmentation reactions. The major fragmentations observed are the cleavages of C(α)-C(β) and C(α)-N bonds on the two sides of the methylene linker, which is different to the cleavage of the amide bond itself seen in most amide cases. Theoretical calculations and isotopic labeling experiments demonstrate that the phenyl ring regulates the proton transfer reactions. The proton directly migrates to the C(β) position via a 1,5-H shift leading to the efficient loss of benzene, while it stepwise migrates to the amide nitrogen resulting in the formation of a benzyl cation. The stepwise proton transfer is achieved via intramolecular proton-transport catalysis. The C(γ) position accepts the proton from the carbonyl oxygen via a 1,6-H shift, and then donates it to the amide nitrogen via a 1,4-H shift. The general 1,3-H shift from the carbonyl oxygen to the amide nitrogen can be excluded in this case due to its significant energy barrier. The substituent effects are also applied to explore the reaction mechanism, and it proves that both C(β) and C(γ) are involved in the dissociative proton transfer processes. For monosubstituted N-benzylbutyrolactams, the abundance ratios of the two competing product ions are well correlated with the nature of the substituents.     

Are the radical centers in peptide radical cations mobile? The generation, tautomerism, and dissociation of isomeric alpha-carbon-centered triglycine radical cations in the gas phase

The mobility of the radical center in three isomeric triglycine radical cations[G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) has been investigated theoretically via density functional theory (DFT) and experimentally via tandem mass spectrometry. These radical cations were generated by collision-induced dissociations (CIDs) of Cu(II)-containing ternary complexes that contain the tripeptides YGG, GYG, and GGY, respectively (G and Y are the glycine and tyrosine residues, respectively). Dissociative electron transfer within the complexes led to observation of [Y(*)GG](+), [GY(*)G](+), and [GGY(*)](+); CID resulted in cleavage of the tyrosine side chain as p-quinomethide, yielding [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+), respectively. Interconversions between these isomeric triglycine radical cations have relatively high barriers (> or = 44.7 kcal/mol), in support of the thesis that isomerically pure [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) can be experimentally produced. This is to be contrasted with barriers < 17 kcal/mol that were encountered in the tautomerism of protonated triglycine [Rodriquez C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The CID spectra of [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) were substantially different, providing experimental proof that initially these ions have distinct structures. DFT calculations showed that direct dissociations are competitive with interconversions followed by dissociation.