C-C and C-H bond activation in the fragmentation of the [M + Ni]+ adducts of aliphatic amino acids

The major metal-containing species formed upon fast atom bombardment of amino acid/Ni⁺² mixtures is the [M + Ni]⁺ adduct, involving reduction of the Ni⁺² to the +1 oxidation state. By contrast, electrospray ionization of amino acid/Ni⁺² mixtures produces predominantly [Ni(M ? H)M]⁺; this species, on collisional activation, produces predominantly [M + Ni]⁺ by elimination of [M - H], presumably a carboxylate radical. The unimolecular fragmentation reactions occurring on the metastable ion time scale for the [M + Ni]⁺ adducts of a variety of α-amino acids have been recorded. The adducts with phenylalanine, α-aminoisobutyric acid and α-aminobutyric acid fragment by elimination of H₂O, H₂O + CO and, to a minor extent, by elimination of CO₂. These reactions are similar to those observed for the [M + Cu]⁺ adducts of α-amino acids. A reaction distinctive for the [M + Ni]⁺ adducts involves formation of the immonium ion RCH=NH ₂ ⁺ . By contrast, the [M + Ni]⁺ adducts with leucine, isoleucine, and norleucine show extensive metastable ion fragmentation by elimination of H₂, CH₄, C₂H₄, C₃H₆, and C₄H₈, with the relative importance of the different fragmentation channels depending on the configuration of the C₄H₉ side chain. These results are interpreted in terms of C-C and C-H bond activation of the C₄H₉ side chain by the Ni⁺. The adducts with valine and norvaline fragment in a fashion similar to the adduct with phenylalanine, except that minor elimination of C₃H₆ is observed.     

Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes

A comparative study of molecular balances by NMR spectroscopy indicates that noncovalent functional‐group interactions with an arene dominate over those with an alkene, and that a π‐facial intramolecular hydrogen bond from a hydroxy group to an arene is favored by approximately 1.2 kJ mol^?1. The strongest interaction observed in this study was with the cyano group. Analysis of the series of groups CH₂CH₃, CH?CH₂, C?CH, and C?N shows a correlation between conformational free‐energy differences and the calculated charge on the C^α atom of these substituents, which is indicative of the electrostatic nature of their π interactions. Changes in the free‐energy differences of conformers show a linear dependence on the solvent hydrogen bond acceptor parameter β.     

Radical Stability Directs Electron Capture and Transfer Dissociation of β‐Amino Acids in Peptides

We report on the characteristics of the radical‐ion‐driven dissociation of a diverse array of β‐amino acids incorporated into α‐peptides, as probed by tandem electron‐capture and electron‐transfer dissociation (ECD/ETD) mass spectrometry. The reported results demonstrate a stronger ECD/ETD dependence on the nature of the amino acid side chain for β‐amino acids than for their α‐form counterparts. In particular, only aromatic (e.g., β‐Phe), and to a substantially lower extent, carbonyl‐containing (e.g., β‐Glu and β‐Gln) amino acid side chains, lead to N? C_β bond cleavage in the corresponding β‐amino acids. We conclude that radical stabilization must be provided by the side chain to enable the radical‐driven fragmentation from the nearby backbone carbonyl carbon to proceed. In contrast with the cleavage of backbones derived from α‐amino acids, ECD of peptides composed mainly of β‐amino acids reveals a shift in cleavage priority from the N? C_β to the C_α? C bond. The incorporation of CH₂ groups into the peptide backbone may thus drastically influence the backbone charge solvation preference. The characteristics of radical‐driven β‐amino acid dissociation described herein are of particular importance to methods development, applications in peptide sequencing, and peptide and protein modification (e.g., deamidation and isomerization) analysis in life science research.     

213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns

Characterization of acidic peptides and proteins is greatly hindered due to lack of suitable analytical techniques. Here we present the implementation of 213 nm ultraviolet photodissociation (UVPD) in high-resolution quadrupole-Orbitrap mass spectrometer in negative polarity for peptide anions. Radical-driven backbone fragmentation provides 22 distinctive fragment ion types, achieving the complete sequence coverage for all reported peptides. Hydrogen-deficient radical anion not only promotes the cleavage of C_α–C bond but also stimulates the breaking of N–C_α and C–N bonds. Radical-directed loss of small molecules and specific side chain of amino acids are detected in these experiments. Radical containing side chain of amino acids (Tyr, Ser, Thr, and Asp) may possibly support the N–C_α backbone fragmentation. Proline comprising peptides exhibit the unusual fragment ions similar to reported earlier. Interestingly, basic amino acids such as Arg and Lys also stimulated the formation of abundant b and y ions of the related peptide anions. Loss of hydrogen atom from the charge-reduced radical anion and fragment ions are rationalized by time-dependent density functional theory (TDDFT) calculation, locating the potential energy surface (PES) of ππ* and repulsive πσ* excited states of a model amide system.

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Graphical Abstract ?

     

Oxidation of α-amino acids promoted by the phthalimide N-oxyl radical: A kinetic and product study

A kinetic study of the hydrogen atom transfer (HAT) reaction from a series of N-Boc- or N-Acetyl-protected amino acids to the phthalimide N-oxyl radical (PINO) was carried out to obtain information about reactivity and selectivity patterns. With amino acids containing aliphatic side chains, the 2nd order rate constants are of the same order of magnitude, in agreement with a HAT process involving the Cα?H bond. Proline is the most reactive substrate suggesting that HAT process involves the C_δ?H bond instead of C_α?H bond. These results are confirmed by the product analysis of the aerobic oxidations of the corresponding N-Boc and N-Ac protected amino acids methyl esters promoted by N-hydroxyphthalimide. Comparison of our results with those reported for HAT reactions to other radical species indicates that PINO displays electrophilic characteristics that are intermediate between those observed for the more stable Br radical and the more reactive cumyloxyl radical.     

Dye‐Labeled Cα‐Tetrasubstituted α‐Amino Acids

We report the synthesis of pyrene‐ and carboxyfluorescein labeled C^α‐tetrasubstituted amino acids (TAAs). The fluorescent dye can be coupled to the TAA before or after its incorporation into a peptide sequence using a Suzuki‐type C? C bond formation.     

Collisional activation spectra of field ionised molecules

The collision of field ionised molecular ions of high kinetic energy (8 keV) with neutral target atoms (helium) gives rise to a large variety of fragments. In general the types of fragments, as well as their abundance ratios, closely resemble those formed under 70 eV electron-impact. The differences observed between the collisional activation spectra of several field ionised[C₇H₈]+. ions, as well as the differences observed between several [C₈H₈]+. ions can be rationalised assuming different degrees of isomerisation. The usefulness of collisional fragmentation spectra for structure determination of organic compounds has been demonstrated for a variety of compounds and some mixtures.     

Metastable ion study of organosilicon compounds. Part III—trimethoxyphenylsilane

The unimolecular decomposition of trimethoxyphenylsilane (1) was investigated by mass-analysed ion kinetic energy (MIKE) spectrometry, deuterium-labelling studies and from high resolution data. The characteristic fragmentations of metastable molecular ion of 1 were losses of C₆H₆ and C₇H₇^· with rearrangements. Almost complete H/D scrambling occurred in the molecular ion prior to these decompositions. The other important fragmentation routes corresponded to expulsions of CH₃O^· and C₆H₅^·. These fragmentations were followed by consecutive elimination of an H₂CO molecule, as commonly observed in the mass spectra of alkoxysilanes. In these fragmentation processes, H/D scrambling increased as the internal energy of the molecular ion was lowered. The fragmentations of 1 were compared with those of its carbon analogue, α,α,α-trimethoxytoluene.     

Electron impact ionization mass spectra of lithocholyl amides: Evidence for a C(20) to C(23) rearrangement involving the loss of a C4H9 fragment

Amides of lithocholic acid (3α-hydroxy-5β-cholan-24-oic acid) with 6-aminocaproic acid and 4-aminobutyric acid were prepared and examined by electron impact ionization mass spectrometry. Both these compounds gave an unusual [M ? 57]⁺ fragment. Since the product-ion analysis of [M ? 57]⁺ revealed the presence of fragments corresponding to the intact steroid nucleus in addition to that of the original amino acid (6-aminocaproic acid or 4-aminobutyric acid), we concluded that the integrity of the steroid amide had been retained in this fragment. The absence of this fragment from the product-ion spectrum of [M ? CH₃]⁺ rules out the sequential loss from the molecular ion of 15 + 42 u as the origin of this signal. Mass spectrometry of the 24-¹³C-labelled lithocholylcaproylamide showed the retention of the label in the [M ? 57]⁺ fragment. In contrast, the corresponding compound labelled with deuterium at C(23) showed a significant loss of the label during the formation of this product ion at [M ? 58]⁺. In addition, through a combination of derivatization and tandem mass spectrometry, it was demonstrated that this loss of 57 u represented a rearrangement with the expulsion of a C₄H₉ radical from the side-chain spanning C(20) to C(23) resulting in a truncated steroid-amide fragment. This fragmentation pattern has not been observed in bile acid conjugates with N-α-amino acids.     

Doubly charged fragment ions in the field ionization mass spectra of alkylbenzenes

It is shown that the radical [C₆H₅C_mH_2m]²⁺ fragment ions found in the field ionization mass spectra of alkylbenzenes are formed via a different adsorption state of the singly charged species than in the case of the formation of [M]²⁺ molecular ions. It is further demonstrated that the primary fragmentation of molecules by the cleavage of C? C bonds results not only from decompositions of molecular ions in the gas phase but also from surface reactions.     

RIMS analysis of ion induced fragmentation of molecules sputtered from an enriched U3O8 matrix

Resonance ionization mass spectrometry was used to measure the composition of the sputtered flux from 15 keV Ga⁺, Au⁺, Au₂ ⁺ and Au₃ ⁺ primary ions impacting a ²³⁵U enriched U₃O₈ standard. We demonstrate that molecular fragmentation decreases as the primary ion mass and nuclearity increases. Stopping and range of ions in matter calculations show that cluster ions (Au₂ ⁺ and Au₃ ⁺) deposit more of their energy via direct knock-ons with near-surface target atoms, whereas monatomic ions (Ga⁺ and Au⁺) penetrate much deeper into the target sub-surface region. We correlate these results to the experimental observations by showing that increased cluster ion sputter yields partition the projectile energy over a larger number of sputtered molecules. Therefore, while cluster ions deposit more total energy into the near surface region of the target compared to monatomic ions, the energy per molecule decreases with projectile mass and nuclearity. Less energy per molecule decreases the number of U–O bond breaks and, consequently, leads to a decrease in molecular fragmentation. Additionally, the extent of molecular fragmentation as a function of ion dose was evaluated. We show that molecular fragmentation increases with increased ion dose; primarily as a result of sub-surface chemical damage accumulation. The relative intensity of this effect appears to be projectile independent.     

The molecular structure of fumaric acid and the deformation of carboxyl group geometry on crystallization

The molecular structure of fumaric acid was studied by means of gas electron diffraction at 260° C. The molecular parameters and their standard deviations obtained for a C_2h model are (r_a distances in Å, angles in degrees): CO: 1.202(0.002), C-O: 1.341(0.006), C-C: 1.486(0.004), CC: 1.356(0.016). C-C-O: 112.1(1.0), C-CO: 124.4(1.1), C-CC: 121.8(1.2). From the available data on carboxylic acids the weighted average deformation of the structure of a carboxylic group on crystallization was determined; a significant expansion of the O-H bond (0.040 Å ), the CO bond (0.010 Å ) and the C-C-O bond angle (1.5° ) and a shrinkage of the C-O bond (0.041 Å ), the C_α-C bond (0.012 Å ) and the C-CO bond angle (2.0° ) was found. The energy for these deformations was estimated to be 1.8 kcal mol^?1.     

Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry

The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSⁿ tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at C_β by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at C_α is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd.     

Theoretical evaluation of the nature and strength of the F������F intermolecular interactions present in fluorinated hydrocarbons

The nature, strength and directionality of C?CF···F interactions were theoretically evaluated on all symmetry unique dimers present in the CF₄, C₂F₄ and C₆F₆ crystals and on CF₄, CHF₃, CH₂F₂ and CH₃F model dimers placed in two different geometries. On each dimer, the interaction energy was computed at the MP2/aug-cc-pVDZ level, and also an Atoms in Molecule analysis of the dimer electron density was done to find all intermolecular bonds. The characterization was completed by computing the energy components of the dimer interaction energy, using the SAPT method. The results show that in most dimers found in the CF₄, C₂F₄ and C₆F₆ crystals, there are more than one C?CF···F intermolecular bond and sometimes even a C?CF···?? intermolecular bond. By selecting dimers presenting one C?CF···F bond, the following strength can be estimated for a single C?CF···F bond: ?0.21?kcal/mol in C(sp³) atoms, ?0.25?kcal/mol in C(non-aromatic sp²), ?0.41?kcal/mol in C(aromatic sp²). The interaction energy of the dimer grows almost linearly with the number of C?CF···F bonds present. The relative orientation of the C?CF···F bond affects the bond strength. The SAPT calculations indicate that in collinear dimers, C?CF···F interactions are strongly dominated by the dispersion energetic component, while when in non-collinear conformations the electrostatic component can be as important as the dispersion one.     

VUV photoionisation of free azabenzenes: Pyridine, pyrazine, pyrimidine, pyridazine and s-triazine

Photoionisation mass spectrometry was used to obtain the fragmentation pathways of pyridine, pyridazine, pyrimidine, pyrazine and s-triazine molecules upon absorption of 23.0, 15.7 and 13.8 eV synchrotron photons. The ionic fragments observed vary from molecule to molecule, however C₂H₂⁺, HCN⁺and HCNH⁺ are common to all five molecules at the three photon energies. Furthermore, the presence of C₂H₂N₂⁺, C₃H₃N⁺ and C₄H₄⁺ in the spectra of some of the molecules suggests dissociation pathways via loss of HCN moieties. The respective parent cations, m/q=79, 80 and 81 have a greater yield at low photon energies when compared to the most intense fragment peak in each spectra. We recorded two of the fragment cation yields, as well as the parent photoion yield curves of pyridine, pyridazine, and pyrimidine in the 8–30 eV range. The formation of abundant cation fragments show a strong propensity of the molecules for dissociation after the absorption of VUV photons higher than 14 eV. The differences in relative fragment yields from molecule to molecule, and when changing the excitation energy, suggest significant bond rearrangements and nuclear motion during the dissociation time. Thus, bond cleavage is dependent on the photon energy deposited in the molecule and on intramolecular reactivity. With the aid of photoion yield curves and energy estimations we have assigned major peaks in the spectra and discussed their fragmentation pathways.     

Precise values of the 13C component vicinal coupling constants for calculating side-chain conformations in amino acids

From consideration of ¹H–¹H vicinal coupling constants and ¹³C? ¹H long-range coupling constants in a series of amino acid derivatives, the precise values of ¹³C component vicinal coupling constants have been calculated for the three minimum energy staggered rotamers for the C(α)H? C(β)H₂ side-chains of amino acids.     

Infrared multiphoton and collision-induced dissociation studies of some gaseous alkylamine ions

Collision-induced dissociation and infrared multiphoton dissociation of ions formed in di- and tri-ethylamine, di- and tri-n-propylamine, and di-isopropylamine were investigated by Fourier-transform ion-cyclotron resonance mass spectrometry. Molecular ions of all amines except di-n-propylamine produced similar fragment ions when subjected to either dissociation technique. The initial fragmentation involved C_αC_β bond cleavage, loss of an alkyl radical, and formation of an immonium ions. Subsequent fragmentations of the immonium ions produced by both dissociation mechanisms involved McLafferty-type rearrangements and loss of alkenes. The molecular ion of di-n-propylamine fragmented by a different mechanism when subjected to infrared irradiation. Protonated molecules of di- and tri-n-propylamine yielded C₃H₆ and an ammonium ion upon infrared multiphoton dissociation, while protonated molecules of the other amines did not dissociate when this technique was applied. In contrast, collision-induced dissociation produced fragmentation for all protonated molecules. Explanation of the different fragmentations observed for the two dissociation techniques is given in terms of a mechanism involving a tight transition state for protonated di- and tri-n-propylamine dissociation.     

Investigation of azoles and azines. 76. Mass spectra of 5- and 6-substituted uracils

Peaks of molecular ions that generally have the maximum intensity are observed in the mass spectra of most of the investigated 5- and 6-substituted uracils and 5-substituted orotic acids and their deutero analogs and methylated derivatives. The principal pathway of the fragmentation of the molecular ions is retrodiene fragmentation with the formation of [O=C₍₄₎C₍₅₎R⁵C₍₆₎R₍₆₎N₍₁₎R¹]⁺ (F₁) ions. The stabilities of the latter depend on the nature and position of the substituents attached to the C₍₅₎ and C₍₆₎ atoms. The fragmentation of the F₁ ions can be realized via four principal pathways (B-E) with the detachment of N-CR⁶ (B), O=C=CR⁵ (C), CO (D), and R⁶ (E) fragments. The most general pathway for the fragmentation of 5-substituted uracils is pathway C, whereas the most general pathway for 6-substituted uracils is pathway E. In the spectra of 5-substituted orotic acids the intensities of the molecular-ion peaks are high (100%) only in the case of electron-donor R⁵ and decrease sharply with an increase in the electron-acceptor strength of the substituent. The principal pathways of fragmentation of the molecular ions are decarboxylation (F) and retrodiene fragmentation (A), the contribution of which is appreciably smaller. The M-CO₂ ions formed after decarboxylation undergo fragmentation via a scheme similar to that observed for 5-substituted uracils.See [1] for Communication 75.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 520–531, April, 1990.     

Gas‐Phase Reaction of CeV2O7+ with C2H4: Activation of CC and CH Bonds

The reactivity of metal oxide clusters toward hydrocarbon molecules can be changed, tuned, or controlled by doping. Cerium‐doped vanadium cluster cations CeV₂O₇⁺ are generated by laser ablation, mass‐selected by a quadrupole mass filter, and then reacted with C₂H₄ in a linear ion trap reactor. The reaction is characterized by a reflectron time‐of‐flight mass spectrometer. Three types of reaction channels are observed: 1) single oxygen‐atom transfer , 2) double oxygen‐atom transfer , and 3) C?C bond cleavage. This study provides the first bimetallic oxide cluster ion, CeV₂O₇⁺, which gives rise to C?C bond cleavage of ethene. Neither Ce_xO_y^± nor V_xO_y^± alone possess the necessary topological and electronic properties to bring about such a reaction.     

Laser induced fission of C60 with kinetic energy release

A neutral C₆₀ fullerene beam is ionised by 308 nm laser pulses. For each cluster sizeC _n ⁺ , 0n60 of the typical bimodal mass distributions known from the literature [1] velocity distributions have been determined by a time of flight method. A consistent interpretation of the measured mean velocities is obtained when binary fission of the parent molecule is assumed to be responsible for the fragmentation patterns, the total kinetic energy release being 0.45±0.1 eV independent of fragment mass and of laser fluence.