Unimolecular depurination of protonated deoxyribonucleosides in the gas phase: A fast atom bombardment tandem mass spectrometric investigation

The spontaneous or collision-induced unimolecular dissociations of base-protonated 2′-deoxyribonucleosides afford, in the gas phase and in the absence of solvent, high yields of protonated nucleobases. The release of neutral bases corresponds to a high-energy reaction path and does not compete with the formation of the protonated bases. A determinant solvent effect has to be invoked to explain the opposite behaviour, which is exhibited by the same precursors, dissociating unimolecularly, in aqueous acidic solution.     

Collision induced dissociation of protonated N-nitrosodimethylamine by ion trap mass spectrometry: Ultimate carcinogens in gas phase

Collision induced dissociation of protonated N-nitrosodimethylamine (NDMA) and isotopically labeled N-nitrosodimethyl-d6-amine (NDMA-d6) was investigated by sequential ion trap mass spectrometry to establish mechanisms of gas phase reactions leading to intriguing products of this potent carcinogen. The fragmentation of (NDMA + H⁺) occurs via two dissociation pathways. In the alkylation pathway, homolytic cleavage of the N–O bond of N-dimethyl, N′-hydroxydiazenium ion generates N-dimethyldiazenium distonic ion which reacts further by a CH₃ radical loss to form methanediazonium ion. Both methanediazonium ion and its precursor are involved in ion/molecule reactions. Methanediazonium ion showed to be capable of methylating water and methanol molecules in the gas phase of the ion trap and N-dimethyldiazenium distonic ion showed to abstract a hydrogen atom from a solvent molecule. In the denitrosation pathway, a tautomerization of N-dimethyl, N′-hydroxydiazenium ion to N-nitrosodimethylammonium intermediate ion results in radical cleavage of the N–N bond of the intermediate ion to form N-dimethylaminium radical cation which reacts further through α-cleavage to generate N-methylmethylenimmonium ion. Although the reactions of NDMA in the gas phase are different to those for enzymatic conversion of NDMA in biological systems, each activation method generates the same products. We will show that collision induced dissociation of N-nitrosodiethylamine (NDEA) and N-nitrosodipropylamine (NDPA) is also a feasible approach to gain information on formation, stability, and reactivity of alkylating agents originating from NDEA and NDPA. Investigating such biologically relevant, but highly reactive intermediates in the condensed phase is hampered by the short life-times of these transient species.     

Generation and dissociation pathways of singly and doubly protonated bisguanidines in the gas phase

Para-bisguanidinyl benzene 1 and its N-permethylated derivative 2 are both sufficiently strong bases to afford not only the monocations [1+H]+ and [2+H]+, but also the doubly protonated ions, [1+2H]2+ and [2+2H]2+, in the gas phase. The title ions generated via electrospray ionization are probed by collision-induced dissociation experiments which inter alia reveal that the dicationic species [1+2H]2+ and [2+2H]2+ can even undergo fragmentation reactions with maintenance of the 2-fold charge. Complementary results from density functional theory predict PAs above 1000 kJ mol(-1) for the neutral compounds, i.e., PA(1) = 1025 kJ mol(-1) and PA(2) = 1067 kJ mol(-1). Due to the stabilization of the positive charge in the guanidinium ions and the para-phenylene spacer separating the basic sites, even the monocations bear sizable proton affinities, i.e., PA([1+H]+) = 740 kJ mol(-1) and PA([2+H]+) = 816 kJ mol(-1).     

Methylating peptides to prevent adduct ion formation also directs cleavage in collision-induced dissociation mass spectrometry

We investigated the effect of N-terminal amino group and carboxyl group methylation on peptide analysis by electrospray mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS/MS). Permethylation of the N-terminal amino group and the carboxyl groups can reduce metal ion adducts but does not enhance sensitivity in electrospray as previously observed for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. N-terminal trimethylated peptides exhibit collision-induced dissociation (CID) tandem mass spectra that differ from their unmodified analogs; the results support the mobile proton hypothesis of peptide fragmentation. A permanent positive charge at the N-terminus leads to competition between permanent-charge directed processes and loss of the N-terminal trimethyl amino group. Carboxyl methylation has no effect on fragmentation behavior other than to shift the mass of fragments containing methylated carboxyl groups. Comparison of regular and tandem mass spectra of different methylated peptides allowed probing the location of incomplete methylation, the proton displaced by alkali metal ions and the purity of a mass-selected methylated peptide ion.     

On the formation of protonated acetic acid from ionized n-alkanoic acids in the gas phase

By means of collisional activation mass spectrometry and semi-empirical molecular orbital calculations (MNDO) it is shown that the [C₂H₅O₂]⁺ ions from metastable molecular ions of n-pentanoic and hexanoic acid have the structure of carbonyl protonated acetic acid [CH₃C(OH)₂]⁺. The MNDO calculated geometries of this ion and some other isomeric forms are given together with the ΔH_f⁰ values.     

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Thermochemical data, ΔH _n ^o , ΔS _n ^o , and ΔG _n ^o , for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4–13.1 kcal/mol for the first and 11.2–11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7–13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are “more negative.” The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data.     

Photodissociation of protonated β-diketones in the gas phase

The gas phase photodissociation spectra of four protonated β-diketones were obtained and compared with the absorption spectra of the corresponding ions in solution. Protonated 2,4-pentanedione was observed to undergo the photodissociation process [C₅H₉O₂]⁺ +hν → [CH₃CO]⁺ +C₃H₆O with a λmax at 276±10 nm compared with a solution absorption maximum at 286 nm. Protonated 2,4-hexanedione was observed to undergo the photodissociation processes [C₆H₁₁O₂]⁺ +hν → [CH₃CO]⁺ +C₄H₈O and [C₆H₁₁O₂]⁺ +hν → [C₂H₅CO]⁺ +C₃H₆O with a λmax at 279±10 nm compared with a solution absorption maximum at 288 nm. Protonated 3-methyl-2,4-pentanedione was observed to undergo the photodissociation process [C₆H₁₁O₂]⁺ +hν → [CH₃CO]⁺ +C₄H₈O with a λmax at 295±10 nm compared with a solution absorption maximum at 305 nm. Protonated 1,1,1-trifluoro-2,4-pentanedione was observed to undergo the photodissociation process [C₅H₆F₃O₂]⁺ +hν → CF₃H+[C₄H₅O₂]⁺ with a λmax at 273±10 nm compared with a solution absorption maximum at 288 nm. The [CH₃CO]⁺ and [C₂H₅CO]⁺ produced photochemically with the first three ions react to regenerate the protonated β-diketone leading to a photostationary state. Photodissociation of the protonated alkyl β-diketones is believed to occur from the protonated keto form, whereas photodissociation of protonated 1,1,1-trifluoro-2,4-pentanedione is believed to occur from the protonated enol form. Mechanisms for the observed photodissociation processes are proposed and comparisons with results from related techniques are presented.     

Electron transfer to protonated beta-alanine N-methylamide in the gas phase: an experimental and computational study of dissociation energetics and mechanisms

Ammonium radicals derived from protonated beta-alanine N-methyl amide (BANMA) were generated by femtosecond collisional electron transfer to gas-phase cations prepared by chemical ionization and electrospray. Regardless of the mode of precursor ion preparation, the radicals underwent complete dissociation on the time scale of 5.15 micros. Deuterium isotope labeling and product analysis pointed out several competitive and convergent dissociation pathways that were not completely resolved by experiment. Ab initio calculations, which were extrapolated up to the CCSD(T)/6-311++G(3df,2p) level of theory, provided the proton affinity and gas-phase basicity of BANMA as PA = 971 kJ mol-1 and GB = 932 kJ mol-1 to form the most stable ion structure 1c+ in which the protonated ammonium group was internally solvated by hydrogen bonding to the amide carbonyl. Ion 1c+ was calculated to have an adiabatic recombination energy of 3.33 eV to form ammonium radical 1c*. The potential energy surface for competitive and consecutive isomerizations and dissociations of 1c* was investigated at correlated levels of theory and used for Rice-Ramsperger-Kassel-Marcus (RRKM) calculations. RRKM unimolecular rate constants suggested that dissociations starting from the ground electronic state of radical 1c* were dominated by loss of an ammonium hydrogen atom. In contrast, dissociations starting from the B excited state were predicted to proceed by reversible isomerization to an aminoketyl radical (1f*). The latter can in part dissociate by N-Calpha bond cleavage leading to the loss of the amide methyl group. This indicates that apparently competitive dissociations observed for larger amide and peptide radicals, such as backbone cleavages and losses of side-chain groups, may originate from different electronic states and proceed on different potential energy surfaces.     

Reduction of in-source collision-induced dissociation and thermolysis of sulopenem prodrugs for quantitative liquid chromatography/electrospray ionization mass spectrometric analysis by promoting sodium adduct formation

Six chromatographically resolved sulopenem prodrugs were monitored for their potential to undergo both in-source collision-induced dissociation (CID) and thermolysis. Initial Q1 scans for each prodrug revealed the formation of intense [Prodrug2 + H]+, [Prodrug2 + Na]+, [Prodrug + Na]+, and [Sulopenem + Na]+ ions. Non-adduct-associated sulopenem ([Sulopenem + H]+) along with several additional lower mass ions were also observed. Product ion scans of [Prodrug3 + Na]+ showed the retention of the sodium adduct in the collision cell continuing down to opening of the beta-lactam ring. In-source CID and temperature experiments were conducted under chromatographic conditions while monitoring several of the latter ion transitions (i.e., adducts, dimers and degradants/fragments) for a given prodrug. The resulting ion profiles indicated the regions of greatest stability for temperature and declustering potential (DP) that provided the highest signal intensity for each prodrug and minimized in-source degradation. The heightened stability of adduct ions, relative to their appropriate counterpart (i.e., dimer to dimer adduct and prodrug to prodrug adduct ions), was observed under elevated temperature and DP conditions. The addition of 100 microM sodium to the mobile phase further enhanced the formation of these more stable adduct ions, yielding an optimal [Prodrug + Na]+ ion signal at temperatures from 400 to 600 degrees C. A clinical liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for sulopenem prodrug PF-04064900 in buffered whole blood was successfully validated using sodium-fortified mobile phase and the [PF-04064900 + Na]+ ion for quantitation. A conservative five-fold increase in sensitivity from previously validated preclinical assays using the [PF-04064900 + H]+ precursor ion was achieved.     

Isomerization of the protonated acetone dimer in the gas phase

Mass spectrometry-based methods have been employed in order to study the reactions of non- (h(6)/h(6)), half (d(6)/h(6)), and fully (d(6)/d(6)) deuterium labeled protonated dimers of acetone in the gas phase. Neither kinetic nor thermodynamic isotope effects were found. From MIKES experiments (both spontaneous and collision-induced dissociations), it was found that the relative ion yield (m/z 65 vs m/z 59) from the dissociation reaction of half deuterium labeled (d(6)/h(6)) protonated dimer of acetone is dependent on the internal energy. A relative ion yield (m/z 65 vs m/z 59) close to unity is observed for cold, nonactivated, metastable ions, whereas the ion yield is observed to increase (favoring m/z 65) when the pressure of the collision gas is increased. This is in striking contrast to what would be expected if a kinetic isotope effect were present. A combined study of the kinetics and the thermodynamics of the association reaction between acetone and protonated acetone implicates the presence of at least two isomeric adducts. We have employed G3(MP2) theory to map the potential energy surface leading from the reactants, acetone and protonated acetone, to the various isomeric adducts. The proton-bound dimer of acetone was found to be the lowest-energy isomer, and protonated diacetone alcohol the next lowest-energy isomer. Protonated diacetone alcohol, even though it is an isomer hidden behind many barriers, can possibly account for the observed relative ion yield and its dependence on the mode of activation.     

Equilibrium intermetallic particles in the gas phase — A Knudsen cell mass spectrometric study

Using the Knudsen cell effusion technique it is possible to generate a molecular beam containing intermetallic molecules. Mass spectrometric studies were carried out with the systems: cesium/antimony, cesium/antimony/bismuth, cesium/antimony/indium, cesium/antimony/tin and cesium/antimony/bismuth/tin. In all these systems intermetallic particles with extraordinary stoichiometries could be detected. A brief discussion of the appearance energies and the bonding principle of these molecules or clusters are given.     

Bile salt aggregates in the gas phase: an electrospray ionization mass spectrometric study

Helical and ordered structures have previously been identified by X-ray diffraction analysis in crystals and fibers of bile salts, and proposed as models of the micellar aggregates formed by trimeric or dimeric units of dihydroxy and trihydroxy salts, respectively. These models were supported by the results of studies of micellar bile salt solutions performed with different experimental techniques. The study has now been extended to the gas phase by utilizing electrospray ionization mass spectrometry (ESIMS) to investigate the formation and the composition of aggregates stabilized by noncovalent interactions, including polar (ion-ion, ion-dipole, dipole-dipole, hydrogen bonding etc.) and apolar (van der Waals and repulsive) interactions. The positive and negative ESIMS spectra of sodium glycodeoxycholate (NaGDC), taurodeoxycholate (NaTDC), glycocholate (NaGC), and taurocholate (NaTC) aqueous solutions, recorded under different experimental conditions, show in the first place that aggregates analogous to those present in micellar solutions do also exist in the gas phase. Furthermore, consistently with the condensed-phase model, the positive-ion spectra show that the trimers are the most stable oligomers among the aggregates of dihydroxy salts (NaGDC and NaTDC) whilst the dimers are the most stable among the aggregates of trihydroxy salts (NaGC and NaTC). Moreover, the binding energy of the constituent glycocholate salt units in most gaseous oligomers exceeds that of the corresponding taurocholate units. The ESIMS evidence has been confirmed by vapor-pressure measurements performed on NaGC and NaTC crystals and NaGDC and NaTDC fibers, the results of which show that the evaporation enthalpy of glycocholate exceeds that of taurocholate by some 50 kJ mol(-1).     

The diphosphate monoanion in the gas phase: a joint mass spectrometric and theoretical study

H(3)P(2)O(7) (-) ions were obtained in an electrospray ion source of a Fourier transform ion cyclotron resonance (ESI/FTICR) mass spectrometer from a CH(3)CN/H(2)O (1:1) pyrophosphoric acid solution and in the ionic source of a triple quadrupole (TQ) mass spectrometer from the chemical ionisation (CI) of pyrophosphoric acid introduced by a thermostatically controlled direct insertion probe. The ions were structurally characterised by mass spectrometric techniques and theoretical calculations. Consistent with collisionally activated dissociation (CAD) mass spectrometric results, theoretical calculations identified the linear diphosphate anion (I) as the most stable isomer on the H(3)P(2)O(7) (-) potential energy surface. The joint application of mass spectrometric techniques and theoretical methods provided information on the dissociative processes of diphosphate anions in the gas phase. Finally, this study provides an insight into the structures and stabilities of the [H(3)PO(4).PO(3)](-), [HP(2)O(6).H(2)O](-) and [H(2)PO(4).HPO(3)](-) clusters and allows the stability and structure of the dimetaphosphate anion, HP(2)O(6) (-), to be investigated at the B3LYP6-31+G* and CCSD(T) levels of theory.     

Acid‐catalysed glucose dehydration in the gas phase: a mass spectrometric approach

Understanding on a molecular level the acid‐catalysed decomposition of the sugar monomers from hemicellulose and cellulose (e.g. glucose, xylose), the main constituent of lignocellulosic biomass is very important to increase selectivity and reaction yields in solution, key steps for the development of a sustainable renewable industry. In this work we reported a gas‐phase study performed by electrospray triple quadrupole mass spectrometry on the dehydration mechanism of d ‐glucose. In the gas phase, reactant ions corresponding to protonated d ‐glucose were obtained in the ESI source and were allowed to undergo collisionally activated decomposition (CAD) into the quadrupole collision cell. The CAD mass spectrum of protonated d ‐glucose is characterized by the presence of ionic dehydrated daughter ion (ionic intermediates and products), which were structurally characterized by their fragmentation patterns. In the gas phase d ‐glucose dehydration does not lead to the formation of protonated 5‐hydroxymethyl‐2‐furaldehyde, but to a mixed population of m/z 127 isomeric ions. To elucidate the d ‐glucose dehydration mechanism, 3‐O‐methyl‐d ‐glucose was also submitted to the mass spectrometric study; the results suggest that the C3 hydroxyl group plays a key role in the reaction mechanism. Furthermore, protonated levulinic acid was found to be formed from the monodehydrated d ‐glucose ionic intermediate, an alternative pathway other than the known route consisting of 5‐hydroxymethyl‐2‐furaldehyde double hydration. Copyright © 2015 John Wiley & Sons, Ltd.     

Unimolecular dissociation of protonated trans-1,4-diphenyl-2-butene-1,4-dione in the gas phase: rearrangement versus simple cleavage

Fragmentation mechanisms of trans-1,4-diphenyl-2-butene-1,4-dione were studied using a variety of mass spectrometric techniques. The major fragmentation pathways occur by various rearrangements by loss of H(2)O, CO, H(2)O and CO, and CO(2). The other fragmentation pathways via simple alpha cleavages were also observed but accounted for the minor dissociation channels in both a two-dimensional (2-D) linear ion trap and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The elimination of CO(2) (rather than CH(3)CHO or C(3)H(8)), which was confirmed by an exact mass measurement using the Q-TOF instrument, represented a major fragmentation pathway in the 2-D linear ion trap mass spectrometer. However, the elimination of H(2)O and CO becomes more competitive in the beam-type Q-TOF instrument. The loss of CO is observed in both the MS(2) experiment of m/z 237 and the MS(3) experiment of m/z 219 but via the different transition states. The data suggest that the olefinic double bond in protonated trans-1,4-diphenyl-2-butene-1,4-dione plays a key role in stabilizing the rearrangement transition states and increasing the bond dissociation (cleavage) energy to give favorable rearrangement fragmentation pathways.