Transient Intermediates of Chemical Reactions by Neutralization-Reionization Mass Spectrometry

Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis

Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using ¹⁵N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature. The formation of sequence w₂⁺ ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA⁺, dGGG⁺, dCCC⁺, dTTT⁺, dACA⁺, and dATC⁺ were established by Born-Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA²⁺ and dACA²⁺ revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.

Low scale syringe-made synthesis of 15 N-labelled oligonucleotides

Fast and reasonable low-scale (200 nmol) syringe-made synthesis of ¹⁵ N-labelled oligonucleotides representing DNA trinucleotide codons is communicated. All codons were prepared by solid-phase controlled pore glass synthesis column technique via the phosphoramidite method. Twenty-four labelled oligonucleotides covering the DNA genetic code alphabet were prepared using commercially available reagents and affordable equipment in a reasonably short period of time, with acceptable yields and purity for direct applications in mass spectrometry.

Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms

Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion-ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV-visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion-electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson-Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.

Guanine–adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory

Hydrogen-rich cation radicals (GATT + 2H)⁺˙ and (AGTT + 2H)⁺˙ represent oligonucleotide models of charged hydrogen atom adducts to DNA.

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-C_α bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c₃- and c₄-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm^-1 serves as an important diagnostic feature.

Hydrogen-Rich Cation Radicals of DNA Dinucleotides: Generation and Structure Elucidation by UV-Vis Action Spectroscopy

Hydrogen-rich DNA dinucleotide cation radicals (dGG + 2H)^+•, (dCG + 2H)^+•, and (dGC + 2H)^+• represent transient species comprising protonated and hydrogen atom adducted nucleobase rings that serve as models for proton and radical migrations in ionized DNA. These DNA cation radicals were generated in the gas phase by electron-transfer dissociation of dinucleotide dication-crown-ether complexes and characterized by UV-vis photodissociation action spectra, ab initio calculations of structures and relative energies, and time-dependent density functional theory calculations of UV-vis absorption spectra. Theoretical calculations indicate that (dGG + 2H)^+• cation radicals formed by electron transfer underwent an exothermic conformational collapse that was accompanied by guanine ring stacking and facile internucleobase hydrogen atom transfer, forming 3'-guanine C-8-H radicals. In contrast, exothermic hydrogen transfer from the 5'-cytosine radical onto the guanine ring in (dCG + 2H)^+• was kinetically hampered, resulting in the formation of a mixture of 5'-cytosine and 3'-guanine radicals. Conformational folding and nucleobase stacking were energetically unfavorable in (dGC + 2H)^+• that retained its structure of a 3'-cytosine radical, as formed by one-electron reduction of the dication. Hydrogen-rich guanine (G + H)^• and cytosine (C + H)^• radicals were calculated to have vastly different basicities in water, as illustrated by the respective p K_a values of 20.0 and 4.6, which is pertinent to their different abilities to undergo proton-transfer reactions in solution.

Study of Ion Dynamics by Electron Transfer Dissociation: Alkali Metals as Targets

High energy collision processes for singly charged positive ions using an alkali metal target are confirmed, as a charge inversion mass spectrometry, to occur by electron transfers in successive collisions and the dissociation processes involve the formation of energy-selected neutral species from near-resonant neutralization with alkali metal targets. A doubly charged thermometer molecule was made to collide with alkali metal targets to give singly and doubly charged positive ions. The internal energy resulting from the electron transfer with the alkali metal target was very narrow and centered at a particular energy. This narrow internal energy distribution can be attributed to electron transfer by Landau-Zener potential crossing between the precursor ion and an alkali metal atom, and the coulombic repulsion between singly charged ions in the exit channel. A large cross section of more than 10^-14 cm² was estimated for high-energy electron transfer dissociation (HE-ETD). Doubly protonated phosphorylated peptides obtained by electrospray ionization were collided with Xe and Cs targets to give singly and doubly charged positive ions. Whereas doubly charged fragment ions resulting from CAD were dominant in the case of the Xe target, singly charged fragment ions resulting from ETD were dominant with the Cs target. HE-ETD using the Cs target provided all of the z-type ions by N-C_α bond cleavage without the loss of the phosphate groups. The results demonstrate that HE-ETD with an alkali metal target allowed the position of phosphorylation and the amino acid sequence of peptides with post translational modifications (PTM) to be determined.

Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies

Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.

The Elusive Ethenediselone, Se=C=C=Se

The neutral ethenediselone, Se=C=C=Se, has been characterised by neutralisation–reionisation mass spectrometry, which implies a minimum lifetime of the order of microseconds. Tetraselenafulvalene 1 and tetramethyltetraselenafulvalene 2 were used as precursor molecules. Flash vacuum thermolysis (FVT) of these compounds with isolation of the products in Ar matrices permitted the identification of ethyne, 2-butyne, CSe2, and selenoketene, H2C=C=Se, but at best traces of Se=C=C=Se survived the FVT/matrix isolation experiment. Multiconfigurational calculations indicate that Se=C=C=Se is a ground state triplet molecule with a very small singlet-triplet gap.

MALDI in-source decay mass spectrometry of polyamidoamine dendrimers

We report using MALDI-ISD (in-source decay) mass spectrometry (MS) to characterize highly branched synthetic polymers of polyamidoamine (PAMAM) dendrimer. This inherently monodisperse polymer possesses dendritic branches networked by tertiary amines and an amide functionality in each repeating unit. Among various ISD matrices examined, 2,5-DHB was the most efficient, yielding 33 fragments produced by single- or multiple-bond cleavages. Detailed analysis revealed that cleavages at tertiary amine sites (S- and E-type fragments) were the most pronounced, with various other cleavages around amide groups. The fragmentation mechanism appeared to follow the radical-induced dissociation pathway. In addition, the matrix dependence of PAMAM MALDI-ISD differed from that of peptides/proteins. The observed fragments provided rich structural information, which was suitable to characterize dendritic polymers.

The expanding role of electrospray ionization mass spectrometry for probing reactive intermediates in solution

Within the past decade, electrospray ionization mass spectrometry (ESI-MS) has rapidly occupied a prominent position for liquid-phase mechanistic studies due to its intrinsic advantages allowing for efficient "fishing" (rapid, sensitive, specific and simultaneous detection/identification) of multiple intermediates and products directly from a "real-world" solution. In this review we attempt to offer a comprehensive overview of the ESI-MS-based methodologies and strategies developed up to date to study reactive species in reaction solutions. A full description of general issues involved with probing reacting species from complex (bio)chemical reaction systems is briefly covered, including the potential sources of reactive intermediate (metabolite) generation, analytical aspects and challenges, basic rudiments of ESI-MS and the state-of-the-art technology. The main purpose of the present review is to highlight the utility of ESI-MS and its expanding role in probing reactive intermediates from various reactions in solution, with special focus on current progress in ESI-MS-based approaches for improving throughput, testing reality and real-time detection by using newly developed MS instruments and emerging ionization sources (such as ambient ESI techniques). In addition, the limitations of modern ESI-MS in detecting intermediates in organic reactions is also discussed.

The early life of a peptide cation-radical. Ground and excited-state trajectories of electron-based peptide dissociations during the first 330 femtoseconds

We report a new approach to investigating the mechanisms of fast peptide cation-radical dissociations based on an analysis of time-resolved reaction progress by Ehrenfest dynamics, as applied to an Ala-Arg cation-radical model system. Calculations of stationary points on the ground electronic state that were carried out with effective CCSD(T)/6-311++G(3df,2p) could not explain the experimental branching ratios for loss of a hydrogen atom, ammonia, and N-C(α) bond dissociation in (AR + 2H)(+•). The Ehrenfest dynamics results indicate that the ground and low-lying excited electronic states of (AR + 2H)(+•) follow different reaction courses in the first 330 femtoseconds after electron attachment. The ground (X) state undergoes competing loss of N-terminal ammonia and isomerization to an aminoketyl radical intermediate that depend on the vibrational energy of the charge-reduced ion. The A and B excited states involve electron capture in the Arg guanidine and carboxyl groups and are non-reactive on the short time scale. The C state is dissociative and progresses to a fast loss of an H atom from the Arg guanidine group. Analogous results were obtained by using the B3LYP and CAM-B3LYP density functionals for the excited state dynamics and including the universal M06-2X functional for ground electronic state calculations. The results of this Ehrenfest dynamics study indicate that reaction pathway branching into the various dissociation channels occurs in the early stages of electron attachment and is primarily determined by the electronic states being accessed. This represents a new paradigm for the discussion of peptide dissociations in electron based methods of mass spectrometry.

Studies of cyclization reactions of linear cumulenes and heterocumulenes using the neutralization-reionization procedure and/or ab initio calculations

A number of linear cumulenes and heterocumulenes have been made by charge stripping of anions of known bond connectivity in the source of a mass spectrometer. Some of these reactive molecules have been identified in interstellar molecular clouds. The structures of these neutrals may be investigated by reionization to a decomposing positive ion [the neutralization-reionization technique ((-)NR(+))], and/or by ab initio calculations. Energized linear cumulenes and heterocumulenes may undergo cyclization to form stable cyclic isomers. To cite a selection of the examples described in this review: (i) four-atom systems CCCC and some heterocumulenes CCCX (X=B, N, Al, Si, P) involve the formation of stable four-membered ring rhombic (also called kite and fan) structures. One of the cyclic molecules, cyclo-C(3) Si, has been detected in interstellar molecular clouds, (ii) five-atom cumulene and heterocumulene systems are more complex. Linear CCCCC rearranges the carbon skeleton by forming a C substituted rhomboid system, CCCCO forms a three-membered cyclic isomer, while nitrogen containing five-atom cumulenes effect nitrile to isonitrile interconversion via three-centered cyclized intermediates, and (iii) CCCCCC and CCCCBO cyclize to give unique six-membered ring systems.

A neutralization-reionization and reactivity mass spectrometry study of the generation of neutral hydroxymethylene

Neutral hydroxymethylene HCOH is an important intermediate in several chemical reactions; however, it is difficult to observe due to its high reactivity. In this work, neutral hydroxymethylene and formaldehyde were generated by charge exchange neutralization of their respective ionic counterparts and then were reionized and detected as positive-ion recovery signals in neutralization-reionization mass spectrometry in a magnetic sector instrument of BEE geometry. The reionized species were characterized by their subsequent collision-induced dissociation mass spectra. The transient hydroxymethylene neutral was observed to isomerize to formaldehyde with an experimental time span exceeding 13.9 µs. The vertical neutralization energy of the HCOH(+•) ion has also been assayed using charge transfer reactions between the fast ions and stationary target gases of differing ionization energy. The measured values match the result of ab initio calculations at the QCISD/6-311 + G(d,p) and CCSD(T)/6-311 + + G(3df,2p) levels of theory. Neutral hydroxymethylene was also produced by proton transfer from CH(2) OH(+) to a strong base such as pyridine, confirmed by appropriate isotopic labeling. There is a kinetic isotope effect (KIE) for H(+) versus D(+) transfer from the C atom of the hydroxymethyl cation of ∼3, consistent with a primary KIE of a nearly thermoneutral reaction.

Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H(2)PO(4) radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Ion/neutral, ion/electron, ion/photon, and ion/ion interactions in tandem mass spectrometry: do we need them all? Are they enough?

A range of strategies and tools have been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on the transformation of the ion type prior to dissociation (e.g., electron capture dissociation). A variety of ion interactions have been studied for the purpose of ion dissociation and ion transformation, including ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena have been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structural determination in tandem mass spectrometry: ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation.

Mass Spectrometry of Benzyne and Cyclopentadienylideneketene

The formation of cyclopentadienylideneketene 2 and benzyne 1 in flash vacuum thermolysis reactions is investigated by on-line mass spectrometry. Compounds 13, 14, and 15 all afford ketene 2, which decomposes to benzyne and CO in the high-temperature regime. Cyclopentadienylideneketene 2 is stable on the microsecond time-scale of neutralization-reionization experiments. Collisional activation mass spectrometry of m/z 76 from 14, 15, and 5 indicates that the C6H4•+ ions most likely undergo ring opening in the mass spectrometer.

Electron super-rich radicals. III. On the peculiar behavior of the aminodihydroxymethyl radical in the gas phase

In contrast to previously reported electron-super-rich trihydroxy-, triamino- and diaminohydroxymethyl radicals, the title aminodihydroxymethyl radical (1) generates a fraction of metastable species in the form of their deuterium isotopologues. The lifetimes of metastable radicals produced by femtosecond collisional electron transfer to aminodihydroxymethyl cations exceed 4 mus. The main fraction of 1 dissociates by fast loss of a hydroxyl hydrogen atom to form carbamic acid. Loss of an amino hydrogen atom is less facile and becomes <10% competitive at high internal energies or if the main dissociation is slowed down by deuterium isotope effects. RRKM calculations of unimolecular rate constants on a CCSD(T)/aug-cc-pVTZ potential energy surface gave a reasonably good fit for the competitive dissociations of 1 but not for the fraction of nondissociating radicals. The metastable species are attributed to excited electronic states which are predicted to have favorable Franck-Condon factors for being formed by collisional electron transfer.

Transition metals as electron traps. I. Structures, energetics, electron capture, and electron-transfer-induced dissociations of ternary copper-peptide complexes in the gas phase

Electron-induced dissociations of gas-phase ternary copper-2,2'-bipyridine complexes of Gly-Gly-Gly and Gly-Gly-Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge-reversal ((+)CR(-)) and electron-capture-induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge-reduced intermediates were observed on the short time scale in the (+)CR(-) and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge-reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide-H)bpy](+*) type where it carried a approximately +1 atomic charge. Cu coordination in charge-reduced [Cu(peptide-H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide-H)bpy](-*) products of electron transfer. [Cu(peptide)bpy](2+*) complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri- or tetracoordinated in the [Cu(peptide)bpy](+) charge-reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed.

Gas-phase structure and relative stability of proton-bound homo- and heterochiral clusters of tetra-amide macrocycles with amines

The structure, stability, and CID pattern of proton-bound homochiral and heterochiral complexes, formed in the gas phase by the combination of two molecules of a chiral macrocyclic tetra-amide and an amine B, i.e. CH3NH2, (CH3)2NH, or (S)-(–)-1-phenylethylamine, have been examined by ESI-ITMS-CID mass spectrometry. With B = CH3NH2, the CID pattern is characterized by the predominant loss of B, accompanied by a much less extensive release of one tetra-amide molecule. With (S)-(–)-1-phenylethylamine, loss of a tetra-amide molecule efficiently competes with loss of B. Finally, with (CH3)2NH, loss of a tetra-amide molecule predominates over loss of B. No appreciable isotope and chiral guest configuration effects have been detected in the fragmentation of the homochiral complexes. A distinct configurational effect has been appreciated in the CID of the homo- and the heterochiral complexes with all amines used. The results of this study have been discussed in the light of semi-empirical computational evidence. The differences in the CID patterns of the homo- and the heterochiral complexes have been rationalized in terms of structural factors and of the basicity of amine B.

Differences between collisionally activated and electron-transfer dissociations found for CH(2)X(2)(X = Cl, Br, and I) by using alkali-metal targets

High-energy collisionally activated dissociation (HE-CAD) and high-energy electron- transfer dissociation (HE-ETD) on collisions with alkali-metal targets (Cs, K, and Na) were investigated for CH(2)X(2) (+) (X = Cl, Br, and I) ions by tandem mass spectrometry (MS/MS). In the HE-CAD spectra observed, peaks associated with CH(2)X(+) ions formed by a loss of a halogen atom are always predominant regardless of precursor ions and target metals. The observation of the predominant CH(2)X(+) ions is explained by the lowest energy levels of the fragments of CH(2)X(+) + X among the possible fragment energy levels and internal-energy distribution in HE-CAD. In the charge-inversion spectra, relative peak intensities of the negative ions formed by HE-ETD strongly depend on the precursor ions and the target metals. While the CHCl(2) (-) ion was predominant in the spectra of CH(2)Cl(2) (+) regardless of target species, the most intense peaks in those of CH(2)Br(2) (+) and CH(2)I(2) (+) were ascribed to either Br(-) or CH(2)Br(-) and either I(-) or I(2) (-), respectively, depending on the target metals. The dependence of the relative intensities of the fragment ions by HE-ETD on the precursor ions and target species are discussed on the basis of the energy levels of the neutral fragments and the narrow internal-energy distribution resulting from the near-resonant neutralization. It was demonstrated that HE-ETD using the alkali-metal targets provided rich information on the dissociation of the neutral species.

Atmospheric pressure thermal dissociation of phospho- and sulfopeptides

Several phospho- and sulfopeptides were subjected to atmospheric pressure thermal dissociation (APTD), which was effected by passing peptide ions generated by electrosonic spray ionization (ESSI) through a heated coiled metal tube. Sequence informative fragment ions including a-, b-, c-, and y-types of ions were observed with increased relative intensities under APTD compared with collision-induced dissociation (CID), performed inside the ion trap. A certain degree of preservation of phosphate and sulfate ester moieties was observed for some fragments ions under APTD. The neutral fragments generated outside the mass spectrometer were further analyzed via on-line corona discharge to provide rich and complementary sequence information to that provided by the fragment ions directly obtained from APTD, although complete losses of the modification groups were noted. Improved primary sequence information for phospho- and sulfopeptides was typically obtained by analyzing both ionic and neutral fragments from APTD compared with fragment ions from CID alone. Localization of the modification sites of phospho- and sulfopeptides was achieved by combining the structural information acquired from APTD and CID.

Electron capture in charge-tagged peptides. Evidence for the role of excited electronic states

Electron capture dissociation (ECD) was studied with doubly charged dipeptide ions that were tagged with fixed-charge tris-(2,4,6-trimethoxyphenyl)phosphonium-methylenecarboxamido (TMPP-ac) groups. Dipeptides GK, KG, AK, KA, and GR were each selectively tagged with one TMPP-ac group at the N-terminal amino group while the other charge was introduced by protonation at the lysine or arginine side-chain groups to give (TMPP-ac-peptide + H)(2+) ions by electrospray ionization. Doubly tagged peptide derivatives were also prepared from GK, KG, AK, and KA in which the fixed-charge TMPP-ac groups were attached to the N-terminal and lysine side-chain amino groups to give (TMPP-ac-peptide-ac-TMPP)(2+) dications by electrospray. ECD of (TMPP-ac-peptide + H)(2+) resulted in 72% to 84% conversion to singly charged dissociation products while no intact charge-reduced (TMPP-ac-dipeptide + H)(+) ions were detected. The dissociations involved loss of H, formation of (TMPP + H)(+), and N-C(alpha) bond cleavages giving TMPP-CH(2)CONH(2)(+) (c(0)) and c(1) fragments. In contrast, ECD of (TMPP-ac-peptide-ac-TMPP)(2+) resulted in 31% to 40% conversion to dissociation products due to loss of neutral TMPP molecules and 2,4,6-trimethoxyphenyl radicals. No peptide backbone cleavages were observed for the doubly tagged peptide ions. Ab initio and density functional theory calculations for (Ph(3)P-ac-GK + H)(2+) and (H(3)P-ac-GK + H)(2+) analogs indicated that the doubly charged ions contained the lysine side-chain NH(3)(+) group internally solvated by the COOH group. The distance between the charge-carrying phosphonium and ammonium atoms was calculated to be 13.1-13.2 A in the most stable dication conformers. The intrinsic recombination energies of the TMPP(+)-ac and (GK + H)(+) moieties, 2.7 and 3.15 eV, respectively, indicated that upon electron capture the ground electronic states of the (TMPP-ac-peptide + H)(+*) ions retained the charge in the TMPP group. Ground electronic state (TMPP-ac-GK + H)(+*) ions were calculated to spontaneously isomerize by lysine H-atom transfer to the COOH group to form dihydroxycarbinyl radical intermediates with the retention of the charged TMPP group. These can trigger cleavages of the adjacent N-C(alpha) bonds to give rise to the c(1) fragment ions. However, the calculated transition-state energies for GK and GGK models suggested that the ground-state potential energy surface was not favorable for the formation of the abundant c(0) fragment ions. This pointed to the involvement of excited electronic states according to the Utah-Washington mechanism of ECD.

Electron capture in spin-trap capped peptides. An experimental example of ergodic dissociation in peptide cation-radicals

Electron capture dissociation was studied with tetradecapeptides and pentadecapeptides that were capped at N-termini with a 2-(4'-carboxypyrid-2'-yl)-4-carboxamide group (pepy), e.g., pepy-AEQLLQEEQLLQEL-NH(2), pepy-AQEFGEQGQKALKQL-NH(2), and pepy-AQEGSEQAQKFFKQL-NH(2). Doubly and triply protonated peptide cations underwent efficient electron capture in the ion-cyclotron resonance cell to yield charge-reduced species. However, the electron capture was not accompanied by backbone dissociations. When the peptide ions were preheated by absorption of infrared photons close to the dissociation threshold, subsequent electron capture triggered ion dissociations near the remote C-terminus forming mainly (b(11-14) + 1)(+)* fragment ions that were analogous to those produced by infrared multiphoton dissociation alone. Ab initio calculations indicated that the N-1 and N-1' positions in the pepy moiety had topical gas-phase basicities (GB = 923 kJ mol(-1)) that were greater than those of backbone amide groups. Hence, pepy was a likely protonation site in the doubly and triply charged ions. Electron capture in the protonated pepy moiety produced the ground electronic state of the charge-reduced cation-radical with a topical recombination energy, RE = 5.43-5.46 eV, which was greater than that of protonated peptide residues. The hydrogen atom in the charge-reduced pepy moiety was bound by >160 kJ mol(-1), which exceeded the hydrogen atom affinity of the backbone amide groups (21-41 kJ mol(-1)). Thus, the pepy moiety functioned as a stable electron and hydrogen atom trap that did not trigger radical-type dissociations in the peptide backbone that are typical of ECD. Instead, the internal energy gained by electron capture was redistributed over the peptide moiety, and when combined with additional IR excitation, induced proton-driven ion dissociations which occurred at sites that were remote from the site of electron capture. This example of a spin-remote fragmentation provided the first clear-cut experimental example of an ergodic dissociation upon ECD.

Modeling deoxyribonucleic acid and ribonucleic acid damage in the gas phase

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first- principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.

Degradation of Ionized OV(OCH3)3 in the Gas Phase. From the Neutral Compound All the Way down to the Quasi-terminal Fragments VO+ and VOH+

The consecutive fragmentation of ionized trimethyl vanadate(V), OV(OCH3)3 (1), is examined by experiment and theory. After an elimination of formaldehyde from the molecular ion 1+, subsequent dissociations proceed via losses of first H2 and then two molecules of formaldehyde to finally yield the VOH+ cation; these redox reactions involve the V(II)/V(IV) manifold. At elevated energies, expulsion of CH3O* from 1+ can efficiently compete to afford OV(OCH3)2+, a formal V(V) compound, from which subsequent losses of H2 and two units of CH2O lead to bare VO+, thereby exploring the V(III)/V(V) redox manifold. Experiments using complementary mass spectrometric techniques, i.e., neutralization-reionization experiments and ion/molecule reactions, in conjunction with extensive computational studies provide deep insight into the ion structures and the relative energetics of these dissociation reactions. In particular, a quantitative energetic scheme is obtained that ranges from neutral OV(OCH3)3 all the way down to the quasi-terminal fragment ions VOH+ and VO+, respectively.

Simple b ions have cyclic oxazolone structures. A neutralization-reionization mass spectrometric and computational study of oxazolone radicals

The 2-methyloxazol-5-on-2-yl radical (3) and its deuterium labeled analogs were generated in the gas-phase by femtosecond electron-transfer and studied by neutralization-reionization mass spectrometry and quantum chemical calculations. Radical 3 undergoes fast dissociation by ring opening and elimination of CO and CH(3)CO. Loss of hydrogen is less abundant and involves hydrogen atoms from both the ring and side-chain positions. The experimental results are corroborated by the analysis of the potential energy surface of the ground electronic state in 3 using density functional, perturbational, and coupled-cluster theories up to CCSD(T) and extrapolated to the 6-311 ++ G(3df,2p) basis set. RRKM calculations of radical dissociations gave branching ratios for loss of CO and H that were k(CO)/k(H) > 10 over an 80-300 kJ mol(-1) range of internal energies. The driving force for the dissociations of 3 is provided by large Franck-Condon effects on vertical neutralization and possibly from involvement of excited electronic states. Calculations also provided the adiabatic ionization energy of 3, IE(adiab) = 5.48 eV and vertical recombination energy of cation 3(+), RE(vert) = 4.70 eV. The present results strongly indicate that oxazolone structures can explain fragmentations of b-type peptide ions upon electron capture, contrary to previous speculations.

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.