Gas-phase hydrogen/deuterium exchange as a molecular probe for the interaction of methanol and protonated peptides

The gas-phase hydrogen/deuterium (HID) exchange kinetics of several protonated amino acids and dipeptides under a background pressure of CH₃OD were determined in an external source Fourier transform mass spectrometer. H/D exchange reactions occur even when the gas-phase basicity of the compound is significantly larger (> 20 kcal/mol) than methanol. In addition; greater deuterium incorporation is observed for compounds that have multiple sites of similar basicities. A mechanism is proposed that involves a structurally specific intermediate with extensive interaction between the protonated compound and methanol.     

Methyl guanine isomer distinction by hydrogen / deuterium exchange using a fourier transform mass spectrometer

Analytical Chemistry Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Differentiation of the seven isomers of methyl guanine has been accomplished by monitoring gas-phase hydrogen/deuterium (H/D) exchange reactions of the protonated molecular ions with deuterium oxide (D₂O) in a Fourier transform mass spectrometer. In each case a distinctive reaction rate for the first H/D exchange was observed, and exchanges of up to three deuterium atoms occurred with characteristic ion abundances that could be used to differentiate the isomers. O⁶-Methyl guanine, for example, showed only one slow H/D exchange with D₂O, whereas l-methyl guanine exchanged two hydrogen atoms at a significantly faster rate. On comparison of the possible resonance structures of each protonated isomer with the experimental information about the number and rate of H/D exchanges observed, a reaction mechanism involving a concerted proton abstraction-deuterium cation donation was proposed.     

Gas-phase H/D exchange reactions of polyamine complexes: (M + H)+, (M + alkali metal+), and (M + 2H)2+

Gas-phase hydrogen/deuterium exchange reactions between noncovalent polyamine complexes and D2O, CH3OD, or ND3 are undertaken in a quadrupole ion trap mass spectrometer. Structural features of the protonated polyamines can be differentiated by the rates and overall extent of exchange, specifically the presence of propylene units and/or a cyclic structure noticeably decreases exchange compared to the exchange observed for acyclic polyamines with only ethylene bridges between amino groups. Significant differences are observed for singly protonated vs. doubly protonated complexes, where the doubly protonated complexes undergo more efficient exchange at a higher rate than the analogous singly protonated complexes. Molecular modeling calculations suggest that more diffuse conformations may exist for the higher charge states, thus facilitating H/D exchange. In addition, H/D exchange reactions between the alkali metal cationized complexes and ND3 are nearly quenched, compared to the significant exchange seen for singly protonated complexes. A conformational change or the loss of a low energy reaction pathway may explain the limited exchange reactions seen when a bulky cation replaces a proton in the complex.     

Hydrogen/deuterium exchange of monomers and dimers of leucine enkephalin

Leucine enkephalin has been studied using the combination of electrospray ionization (ESI) with a fast flow technique. ESI of leucine enkephalin produces an isotopic multiplet of peaks beginning at m/z 556. Hydrogen/deuterium exchange of this multiplet with ND₃ has revealed the contribution of two ion populations to this multiplet: The singly protonated monomer and the doubly protonated dimer. These populations were separated through their different kinetic behavior. Whereas the dimers undergo slow exchange the monomers undergo pronounced complexation with ND₃ and display a fast exchange of four labile hydrogens. The results indicate a more compact globular structure for the diprotonated dimer.     

Chemical ionization of fluorophenyl n-propyl ethers: Loss of propene from the metastable [M + D]+ ions

Chemical ionization (CI) mass spectrometry with the reagents D₂O, CD₃OD, and CD₃CN (given in order of increasing proton affinity) has been used to generate metastable [M + D]⁺ ions of a series of mono-, di-, and trifluorophenyl n-propyl ethers and analogs labeled with two deuterium atoms at the β position of the alkyl group. Loss of propene is the main reaction of the [M + D]⁺ ions, whereas dissociation with formation of propyl carbenium ions is of minor importance. The combined results reveal that the deuteron added in the CI process can be incorporated in the propene molecules as well as in the propyl carbenium ions. The extent to which the added deuteron is exchanged with the hydrogen atoms of the propyl group is markedly dependent on the position of the fluorine atom(s) on the ring and the exothermicity of the initial deuteron transfer. For 3-fluorophenyl n-propyl ether, exchange is not observed if D₂O is the CI reagent, and occurs only to a minor extent in the experiments with the CI reagents CD₃OD and CD₃CN. Similar results are obtained for the 3,5-difluoro- and 2,4,6-trifluorophenyl ethers, whereas significant exchange is observed prior to the dissociations of the [M + D]⁺ ions of the 4-fluoro- and 2,6-difluorophenyl n-propyl ethers, irrespective of the nature of the CI reagent. These results are discussed in terms of the occurrence of initial deuteron transfer either to the oxygen atom or the aromatic ring followed by formation of an ion/neutral complex of a fluorine-substituted molecule and a secondary propyl carbenium ion. Initial deuteron transfer to the oxygen atom is suggested to yield complexes that can react by exchange between the added deuteron and the hydrogen atoms of the original propyl group prior to dissociation. By contrast, initial deuteron transfer to the ring is suggested to lead to complexes that react further by loss of propene molecules containing only the hydrogen/deuterium atoms of the original propyl entity.     

Kinetics of gas-phase hydrogen/deuterium exchange and gas-phase structure of protonated phenylalanine, proline, tyrosine and tryptophan

Site-specific rate constants for the gas-phase hydrogen/deuterium (H/D) exchange of four, three, five and five hydrogen atoms in protonated phenylalanine (Phe), proline (Pro), tyrosine (Tyr) and tryptophan (Trp), respectively, were determined from matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) experiments with D(2)O, D(2)S, and CH(3)OD as deuterating agents. No H/D exchange was observed with D(2)S. For exchange with both CD(3)OD and D(2)O, which is about ten times slower in the latter, results indicate for all compounds protonation of the alpha-amino group in agreement with theoretical results. Also, with both reagents, all compounds exchange at the COOH site more than ten times faster than at the protonation site, with OH and NH sites of Tyr and Trp, respectively, exchanging slowest. The observation of H/D exchange despite the high differences in proton affinities between the amino acids and deuterating agent exceeding 200 kJ mol(-1) is in agreement with lowering of the barrier for proton transfer through hydrogen bonding proposed by Lebrilla and coworkers.     

Mechanistic study of hydrogen/deuterium exchange between [M - 1]− ions of chlorinated benzenes and D2O or ND3

Low-energy collisions between [M - 1]^? ions derived from the three isomers of dichlorobenzene and deuterated water and ammonia are found to produce distinctive hydrogen/ deuterium (H/D) exchange reaction product patterns. The predominant products observed for p-, m-, and o-dichlorobenzene are 1, 2, and 3 sequential deuterium exchanges, respectively. The reactivity is substantially higher for D₂O than ND₃ We postulate a mechanism that involves the formation of a five-membered-ring intermediate. The intermediate is thought to be initiated by the attack of ND₃ or D₂O at the localized negative charge site on the aromatic ring. A successful exchange is followed by the relocation of the charge site to the adjacent carbon. Ion products with higher degrees of deuterium substitution than the expected predominant products of their corresponding isomers are believed to be the results of isomerization of the reactant ions occurring in the ion source. The proposed mechanism fuily explains the observed product spectra derived from al1 the isomers of chlorinated benzenes. The trends for the formation of various H/D exchange products represented by the sweated product-time plots based on the proposed mechanism compare well with the similar trends obtained from the experimental product-pressure plots. The reaction is useful for the mass spectrometric differentiation of chlorobenzene isomers.     

Gas phase hydrogen / deuterium exchange in electrospray ionization mass spectrometry as a practical tool for structure elucidation

Two methods for gas phase hydrogen/deuterium exchange have been developed for the analysis of small molecules. Hydrogen/deuterium exchange has been implemented by making simple modifications to the plumbing for the nebulizer and curtain gases on a nebulization-assisted electrospray ion source. The nebulizer gas exchange method has demonstrated deuterium exchange levels of 84–97% for a variety of molecules representing a wide range of structural classes containing up to 51 potentially exchangeable hydrogens; this allowed determination of the number of exchangeable hydrogens for all of the molecules studied containing ≤ 25 labile hydrogens (M _r ≤ 3000). ND₃ gas consumption is minimized in the nebulizer method by toggling the nebulizer from air to ND₃ for only a few scans of the total sample elution period. The curtain gas exchange method is more variable, yielding exchange levels of 32–98% for the same set of molecules; this was still sufficient to allow determination of > 70% of the molecules studied containing ≤ 25 labile hydrogens. Gas consumption is minimized in the curtain method by replacing ≤ 10% of the curtain gas flow with ND₃. Neither the nebulizer nor curtain exchange method requires the use of deuterated or aprotic solvents at typical 2 μL/min flow rates.     

H/D exchange reactions of protonated diglycine; an electrospray ionization–flow tube reactor experiment

The H/D exchange reactions of protonated diglycine, GLY₂H⁺, with ND₃ were studied under thermal conditions with a combination of an electrospray ion source and a flow tube reactor. Consecutive exchange of the five labile hydrogens is observed with increasing flow rate of ND₃. Collision complexes corresponding to the consecutive H/D exchanges are monitored for the first time. The role of multiple exchanges in a single collision event with ND₃ is probed. Results will be discussed in the light of previously suggested mechanisms of H/D exchange of GLY₂H⁺ with deuterated ammonia.     

Formation and reactions of clusters in the gas phase: small peptides and carboxylic acids

The cluster formation of seventeen small dipeptides with different primary structures and vanillic acid was investigated by means of a neutral laser desorption and supersonic beam expansion followed by multi photon ionization time of flight mass spectrometry. The structures of these clusters have been characterized by mass spectrometric methods as well as by DFT calculations. It is shown that the structure of the cluster from a dipeptide and vanillic acid is described by a hydrogen bond between the phenolic group of the vanillic acid and the N-terminal amino function of the dipeptide. The intensity of the cluster ion and the main fragmentation product, the protonated peptide ion, can be linked to the proton affinity of the peptide. Furthermore the fragmentation reactions of the protonated peptide are accompanied by extensive hydrogen rearrangements yielding both a and y fragments. The intensities of these fragments follow the proton affinity of the dipeptide.     

Highly Cytotoxic Bioconjugated Gold(I) Complexes with Cysteine‐Containing Dipeptides

Several gold(I) complexes with cysteine‐containing dipeptides have been prepared starting from cystine by coupling different amino acids and using several orthogonal protections. The first step is the reaction of cystine, where the sulfur centre is protected as disulfide, with Boc₂O in order to protect the amino group, followed by coupling of an amino acid ester; finally the disulfide bridge is broken with mercaptoethanol to afford the dipeptide derivative. Further reaction with [AuCl(PPh₃)] gives the gold‐dipeptide‐phosphine species. Starting from these formally gold(I) thiolate–dipeptide phosphine complexes with the general formula [Au(SR)(PR₃)] different structural modifications, such as change in the type of the amino protecting group, the type of phosphine, the number of gold(I) atoms per molecule, or the use of a non‐proteinogenic conformationally restricted amino acid ester, were introduced in order to evaluate their influence in the biological activity of the final complexes. The cytotoxic activity, in vitro, of these complexes was evaluated against different tumour human cell lines (A549, MiaPaca2 and Jurkat). The complexes show an outstanding cytotoxic activity with IC₅₀ values in the very low micromolar range. Structure–activity relationship studies from the complexes open the possibility of designing more potent and promising gold(I) anticancer agents.     

Study of H/D-exchange reaction kinetics of polypeptides

One of the possible methods for 3D protein structure investigation is the study of gas-phase hydrogen/deuterium (H/D) exchange reaction between protein ions and a D-containing reactant gas, e.g., D₂O or ND₃. A segmented radio frequency quadrupole (RFQ) was used as a molecule-ion reactor to study gasphase H/D-exchange of protonated ions of three different peptides. The ions were produced in an electrospray ion source. The RFQ is a part of ion transport interface of a high resolution orthogonal time-of-fiight mass spectrometer (O-TOF MS). The RFQ was modified for a linear ion trap (LIT) mode of operation to increase a dwell time of target ions inside the RFQ. Phase-sensitive operation of the LIT and the O-TOF MS was controlled by custom developed PC executive program. The reaction mixture of N₂ and ND₃ was injected into the reactor, while keeping its partial pressure in the range of 10⁻³–10⁻² mbar, and corresponding ND3 concentration in the range of 10¹³–10¹⁴ cm⁻³. It was possible to vary the ion dwell time in the reactor between 30 ms and 1 s. H/D-exchange was studied for leucine enkephalin, gramicidin S and apamin. The data analysis based on statistical approach has shown a principal possibility to distinguish different mobile H-atoms of peptides, taking part in H/D-exchange, according to reaction rates.     

Gas-phase noncovalent interactions between vancomycin-group antibiotics and bacterial cell-wall precursor peptides probed by hydrogen/deuterium exchange

Gas-phase structures of noncovalent complexes between the glycopeptide antibiotics vancomycin, eremomycin, ristocetin, and pseudo aglyco-ristocetin and the cell-wall mimicking peptides N-acetyl-D-Alanyl-D-Alanine, N-acetyl-Glycyl-D-Alanine, and N,N′-di-acetyl L-Lysyl-D-Alanyl-D-Alanine have been probed by hydrogen/deuterium (H/D) exchange using ND₃ as reagent gas. The noncovalent complexes were transferred from solution to the vacuum using electrospray ionization. The H/D exchange of the solvent-free ions was studied in a Fourier transform ion cyclotron resonance mass spectrometer. The H/D exchange behavior of the free antibiotics and the free peptides were compared with the exchange observed for the antibiotic–peptide complexes. A general increase was found in the degree of deuterium incorporation upon complex formation with the ligand, which indicates that the peptide binding makes more sites on the antibiotic capable of taking part in the H/D exchange. Apart from H/D exchange, adduct formation with ND₃ was observed, but only for the singly protonated peptides and the doubly protonated [ristocetin+N-acetyl-D-Alanyl-D-Alanine]. This marked difference in chemical reactivity of closely related systems such as [ristocetin+N-acetyl-Glycyl-D-Alanine] and [ristocetin+N-acetyl-D-Alanyl-D-Alanine] indicates that the gas-phase structures of these noncovalent complexes are quite sensitive to small changes in the primary structures of the peptides. The gas-phase structures of the antibiotic–peptide complexes are probably different from the solution-phase structures, with the peptides no longer bound to the characteristic solution-phase binding pockets of the antibiotics.     

Gas phase reactions of protonated 1,3-diphenylpropyne and some isomeric [C15H13]+ ions

Metastable (3-phenyl-2-propynyl)benzenium ions, generated by electron impact induced fragmentation from the appropriately substituted 1,4-dihydrobenzoic acid, react by loss of ˙CH₃ and C₆H₆. The study of deuterated derivatives reveals that hydrogen/deuterium exchanges involving all hydrogen and deuterium atoms precede the fragmentations. The results suggest a skeletal rearrangement by electrophilic ring-closure reactions giving rise to protonated phenylindene and protonated 9,10-methano-9,10-dihydroanthracene prior to the elimination of C₆H₆ and ˙CH₃, respectively. A study of isomeric [C₁₅H₁₃]⁺ ions by collision-induced decomposition and by deuterium labelling shows that these ions interconvert by hydrogen migrations and skeletal rearrangements.     

Elucidation de structure et comportement de produits naturels sous ionisation chimique—II: Aminolyse et substitution nucleophile produites—en phase gazeuse avec l'ammoniac—sur la cinerubine a

The structure of cinerubine A has been studied by chemical ionisation mass spectrometry. In the NH₃/Cl mode, this type of compound with polyfunctional sites undergoes as aminolysis reaction, i.e. hydroxyl and carbonyl groups are substituted by NH₃. The protonated molecular ions formed in the ion source fragment to give intense ions which provide useful structural information. Unimolecular fragmentations in the first field-free region permit determination of the reactive sites. Use of ND₃ as reagent gas provides information on the number of mobile H atoms and permits the assignment of structure for these ionic species.     

Observation of zwitterion formation in the gas-phase H/D-exchange with CH<Subscript>3</Subscript>OD: Solution-phase structures in the gas phase

Infrared spectroscopy of gas-phase singly deuterated [Trp+K]⁺ (formed by H/D exchange with CH₃OD) shows that some (∼20%) kinetically stable zwitterionic (ZW) conformer is formed, based on the diagnostic antisymmetric CO stretch of the deprotonated carboxylate moiety, υ_as(CO₂⁻), at 1680 cm⁻¹. A majority of the deuterated [Trp+K]⁺ is found to be in the charge solvation (CS) conformation, with deuterium exchange occurring on both the acid and amino groups, which is consistent with H/D scrambling. Interestingly, H/D exchange with the more basic ND₃ reagent did not result in the stabilization of a kinetically stable zwitterion, although it is not clear yet what causes this observation. The result for CH₃OD shows that H/D exchange can in fact alter the structure of the analyte and, hence, care needs to be taken when interpreting gas-phase H/D exchange studies. Moreover, this result shows the possibility of forming solution-phase structures that are thermodynamically disfavored in the gas phase, thus opening a new area of study.     

l‐Isoleucyl‐l‐asparagine 1.094‐hydrate: a hybrid hydrogen‐bonding pattern

The title compound, C₁₀H₂₀N₃O₄·1.094H₂O, crystallizes with two dipeptide molecules in the asymmetric unit, each participating in two head‐to‐tail chains with hydrogen bonds between the terminal amino and carboxylate groups. As with many other dipeptides, the resulting structure is divided into distinct layers, but as the amide groups of the two peptide molecules participate in different types of interaction, the observed hydrogen bonds within a peptide main‐chain layer (as distinct from the side‐chain/solvent regions) cannot adapt to any of the four basic patterns observed previously for dipeptides. Instead, a rare hybrid pattern is formed.     

Another Unprecedented Wieland Mechanism Confirmed: Hydrogen Formation from Hydrogen Peroxide,Formaldehyde, and Sodium Hydroxide

In 1923, Wieland and Wingler reported that in the molecular hydrogen producing reaction of hydrogen peroxide with formaldehyde in basic solution, free hydrogen atoms (H^.) are not involved. They postulated that bis(hydroxymethyl)peroxide, HOCH₂OOCH₂OH, is the intermediate, which decomposes to yield H₂ and formate, proposing a mechanism that would nowadays be considered as a “concerted process”. Since then, several other (conflicting) “mechanisms” have been suggested. Our NMR and Raman spectroscopic and kinetic studies, particularly the determination of the deuterium kinetic isotope effect (DKIE), now confirm that in this base‐dependent reaction, both H atoms of H₂ derive from the CH₂ hydrogen atoms of formaldehyde, and not from the OH groups of HOCH₂OOCH₂OH or from water. Quantum‐chemical CBS‐QB3 and W1BD computations show that H₂ release proceeds through a concerted process, which is strongly accelerated by double deprotonation of HOCH₂OOCH₂OH, thereby ruling out a free radical pathway.     

Directive effect of a methyl substituent in the exchange reaction of ring hydrogen with molecular deuterium in dicyclopentadienyltitanium complexes

Hydrogenated (1-methylallyl)dicyclopentadienyltitanium(III) exchanges its ring hydrogen atoms with deuterium gas. The deuterated complex can be oxidized with hydrogen chloride and air to (C₅D₅)₂TiCl₂. In the related methyl-substituted complex, obtained by hydrogenation of allylbis(methylcyclopentadienyl)titanium(III), only the ring hydrogen atoms in β-position to the methyl substituent exchanged with deuterium, the hydrogen in α-position to the substituent proved to be relatively unreactive. In the exchange reaction, an intermediate is proposed having a structure with a bridged π- as well as σ-bonded C₅H₄ or C₅H₃CH₃ group.     

Multiple Site Hydrogen Isotope Labelling of Pharmaceuticals

Radiolabelling is fundamental in drug discovery and development as it is mandatory for preclinical ADME studies and late-stage human clinical trials. Herein, a general, effective, and easy to implement method for the multiple site incorporation of deuterium and tritium atoms using the commercially available and air-stable iridium precatalyst [Ir(COD)(OMe)]₂ is described. A large scope of pharmaceutically relevant substructures can be labelled using this method including pyridine, pyrazine, indole, carbazole, aniline, oxa-/thia-zoles, thiophene, but also electron-rich phenyl groups. The high functional group tolerance of the reaction is highlighted by the labelling of a wide range of complex pharmaceuticals, containing notably halogen or sulfur atoms and nitrile groups. The multiple site hydrogen isotope incorporation has been explained by the in situ formation of complementary catalytically active species: monometallic iridium complexes and iridium nanoparticles.