A2 Ion Research Articles

Rearrangement chemistry of an ions probed by IR spectroscopy

The structure and the dynamics of the isomerization of an ions, which are observed upon low-energy collision induced dissociation of protonated peptides in tandem mass spectrometry (MS/MS), are investigated using a combination of gas phase infrared spectroscopy and theory. IR spectra in the fingerprint region are discussed, but a particular emphasis is given to the NH stretching region which turns out to be highly structurally diagnostic. Overall, theory and infrared spectroscopy provide compelling evidence that an ions undergo cyclisation and/or rearrangement reactions. In the cases of the a2 and a3 ions of oligoglycine, the analysis of the NH stretching region is fully consistent with our previous conclusions based on the IR fingerprint spectra. In the case of the a4 ions of oligoglycine, a band observed near 3550cm−1 provides a clear-cut signature of the permuted imine–amide structure, thus allowing for a better structural assignment. The dynamics of the rearrangement chemistry of the imine–amide structure is discussed in details, and a critical discussion on the influence of the experimental CID conditions is proposed in the case of the YG a2 ion.

7th International Symposium on Enabling Technologies for Life Sciences (ETP)

7^th International Symposium on Enabling Technologies for Life Sciences (ETP)

Design and operations of a load-tolerant external conjugate-T matching system for the A2 ICRH antennas at JET

A load-tolerant external conjugate-T (ECT) impedance matching system for two A2 ion cyclotron resonance heating (ICRH) antennas was successfully put into operation at JET. The system allows continuous injection of the radio-frequency (RF) power into plasma in the presence of strong antenna loading perturbations caused by edge-localized modes (ELMs). Reliable ECT performance was demonstrated under a variety of antenna loading conditions including H-mode plasmas with radial outer gaps (ROGs) in the range 4–14 cm. The high resilience to ELMs predicted during the circuit simulations was fully confirmed experimentally. Dedicated arc-detection techniques and real-time matching algorithms were developed as a part of the ECT project. The new advanced wave amplitude comparison system has proven highly efficient in detection of arcs both between and during ELMs. The ECT system has allowed the delivery of up to 4 MW of RF power without trips into plasmas with type-I ELMs. Together with the 3 dB system and the ITER-like antenna, the ECT has brought the total RF power coupled to ELMy plasma to over 8 MW, considerably enhancing JET research capabilities. This paper provides an overview of the key design features of the ECT system and summarizes the main experimental results achieved so far.

Structures of the a2 ions of Ala-Ala-Ala and Phe-Phe-Phe

IRMPD spectra are reported for a2 ions derived from trialanine (AAA) and triphenylalanine (FFF) and compared with spectra calculated by density functional theory at the B3LYP/6-311++G(d,p) level of theory. At low collision energies the cyclic N1-protonated imidazolidinone ion C1 is dominant, but at higher collision energies the rearranged product, linear protonated imine–amide ion L2, is formed. Theory has been used to explore the potential energy surfaces for the isomers of a2 ion derived from AAA and FFF. For each surface, seven isomeric structures have been located and barriers to interconversions between these structures are reported. The critical transition state in converting C1 into L2 involves a 1,3-proton shift between the two nitrogen atoms of the imidazolidinone ring. This barrier is higher than that for losing CO from C1 via the linear L1 ion. Consequently, attempts at converting the C1 isomer into L2 by sustained off-resonance irradiation failed to produce any L2. DFT calculations show that the barrier to the 1,3-proton shift across the imidazolidinone ring is greatly reduced by employing a water or methanol molecule for proton-switching. The phenyl ring in the side chain of the a2 ion of FFF also catalyzes the C1 to L2 tautomerization, but is less effective than a solvent molecule. A comparison between the calculated spectra for the two possible diastereomers of the cyclic C1 isomer created in the ring-closing reaction and the IRMPD action spectrum suggests that one mode of closing is preferred.

Fragmentation mechanism of product ions from protonated proline-containing tripeptides in electrospray ionization mass spectrometry

The dissociation chemistry of primary fragment ions from the protonated proline-containing tripeptides glycylprolylglycine, prolylglycylglycine, and prolylprolylglycine was investigated by electrospray ionization multi-stage mass spectrometry. Calculations showed the a2 ions generated from b2 ions were cyclic, which is energetically more favorable than the linear form. The prolyl residue in the structure affected the energy hypersurface of the dissociation reaction from the b2 ion to the a2 ion. In the fragmentation of a2 ions, the iminium-imine complex corresponding to loss of CO from the a2 ion was suggested to be an ion-neutral complex (INC). The a1 ion was generated from direct separation of this INC, and the internal iminium ion, which was absent in PGG, was generated from another INC that was formed from the first INC via proton-bridged complex-mediated intramolecular proton transfer. Although these intermediates are unstable, their existence is supported by experiments and density functional theory calculations.

Tyrosine side-chain catalyzed proton transfer in the YG a2 ion revealed by theory and IR spectroscopy in the ‘fingerprint’ and X[sbnd]H (X = C, N, O) stretching regions

IRMPD spectroscopy in the ‘fingerprint’ and XH (X=C, N, O) stretching regions was used to probe the structures of the YG a2 ions generated from protonated YGGFL and doubly protonated YGGFLR. Our experiments indicate a mixture of cyclic and rearranged ‘imine–amide’ structures. The cyclic isomer is generated from the initially formed protonated imine terminated linear structure by head-to-tail cyclization. Proton transfer between the secondary amine of the ring and the amide nitrogen followed by ring opening leads to the rearranged ‘imine–amide’ isomer. Quantum chemical calculations demonstrate that this proton transfer is catalyzed by the tyrosine side chain ring for the YG a2 ion. Isomer specific IRMPD bands observed in the two spectral regions clearly show the presence of the cyclic and rearranged ‘imine–amide’ isomers, the latter being characterized by an IR signature at ∼3545cm−1 associated with the C-terminal amide NH2 asymmetric stretch.

Tandem MS Can Distinguish Hyaluronic Acid from N-Acetylheparosan

Isobaric oligosaccharides enzymatically prepared from hyaluronic acid (HA) and N-acetylheparosan (NAH), were distinguished using tandem mass spectrometry. The only difference between the two series of oligosaccharides was the linkage pattern (in HA 1-->3 and in NAH 1-->4) between glucuronic acid and N-acetylglucosamine residues. Tandem mass spectrometry afforded spectra in which glycosidic cleavage fragment ions were observed for both HA and NAH oligosaccharides. Cross-ring cleavage ions 0,2An and 0,2An-h (n is even number) were observed only in GlcNAc residues of NAH oligosaccharides. One exception was an 0,2A2 ion fragment observed for the disaccharide from HA. These cross-ring cleavage fragment ions are useful to definitively distinguish HA and NAH oligosaccharides.

Evaluation of the dose rate distribution for an air-type 60CO irradiation facility

The dose rate distributions in the 29,000-Ci 60Co irradiation facility in National Tsing Hua University were investigated by measurements and calculations. The dose rate measurements were performed using radiochromic dye films and an Exradin A2 ion chamber mounted on a PC-controlled motorised vertical translation stage. The calculations were made by using the three-dimensional point kernel code QAD-CGGP with detailed source composition and geometry modelling. The scattered gamma rays from the walls of the irradiation cell were also evaluated by using the Monte Carlo code MCNP.

Fragmentation reactions of deprotonated peptides containing proline. The proline effect

The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N-terminal proline are formation of a(3) and y(1) ions. When proline is in the central position of tripeptides, a(3), y(2) and y(1) ions are the primary fragmentation products of [M--H](-), while when the proline is in the C-terminal position, a(3)and y(1) ions are the major primary products. In the latter case, the a(3) ion fragments primarily to the ''b(2) ion; further evidence is presented that the ''b(2) ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N-terminal to proline show a distinct preference for cleavage of the amide bond N-terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline.

Fragmentation Mechanisms of Product Ions from Protonated Tripeptides

Dissociation chemistries of the primary fragment ions from the tripeptides, GAG and AGG, were examined both experimentally and theoretically, and compared with those from GGG [El Aribi, H.; Rodriquez, C. F.; Almeida, D. R. P.; Ling, Y.; Mak, W. W.-N.; Hopkinson, A. C.; Siu, K. W. M. J. Am. Chem. Soc. 2003, 125, 9229−9236]. Findings in this study with GAG and AGG confirm and extend those in the earlier study on GGG. Fragmentation of the b2 to a2 ion from GAG and AGG is qualitatively similar to that from GGG; stabilization by the methyl group, however, results in generally lower energies for GAG. Fragmentation of the a2 ion from GAG produces both the a1 (protonated methanimine) and the internal iminium ion (protonated ethanimine). By contrast, fragmentation of the a2 ion from AGG produces only the a1 ion (protonated ethanimine). In GAG, formation of the internal iminium ion requires an intramolecular proton transfer in the proton-bridged complex after cleavage of CO, which is absent in AGG. The a1 ion from GAG is postulated to form via cleavage of the vibrationally excited proton-bridged complex prior to proton transfer, favored under higher collision-energy conditions. The critical transition state in the fragmentation of the b2 to a1 ion is best described as a complex between the a1 ion and a carbene. Although details differ, in both GAG and AGG, there is a proton transfer from the terminal amino group to the carbene carbon and a second proton transfer from the ring nitrogen back to the terminal amino group. Separation of the components then yields the a1 ion and a neutral oxazolone.

Formation of iminium ions by fragmentation of a2 ions.

Tandem mass spectrometric experiments have been carried out on the protonated amides H-Gly-Ala-NH2, H-Ala-Gly-NH2, H-Ala-Val-NH2, H-Val-Ala-pNA, H-Leu-Phe-NH2, H-Phe-Leu-NH2, H-Phe-Tyr-NH2 and H-Tyr-Phe-NH2 with particular emphasis on the fragmentation of the isomeric a2 ions derived therefrom. Primary fragmentation reactions of the protonated amides involve formation of the y1" and b2 ions with further fragmentation of the b2 ion to form the a2 ion which fragments to form iminium ions. Collision-induced dissociation studies of the mass-selected a2 ions were carried out. For the Gly-Ala, Ala-Gly and Val-Ala a2 ions, weak signals were observed corresponding to loss of CO from the a2 ion. With the exception of the Gly-Ala, Ala-Gly and Val-Ala a2 ions, both possible iminium ions (a1 and the internal iminium ion) are observed with the most abundant being that formed by proton attachment to the imine of higher proton affinity. The results provide strong support for the recently proposed (El Aribi et al. J. Am. Chem. Soc. 2003; 125: 9229) mechanism of fragmentation of a2 ions which involves elimination of CO from the a2 ion to form a proton-bound complex of two imines. Based on this mechanism ab initio calculations of the total energies of the a2 ions and the transition states for fragmentation have been carried out giving the energy barrier for fragmentation of each a2 ion. The experimental results are interpreted in terms of these energetics data, unimolecular rate constants calculated by using the RRKM theory, and the imine proton affinities.

Elucidation of fragmentation mechanisms of protonated Peptide ions and their products: a case study on glycylglycylglycine using density functional theory and threshold collision-induced dissociation.

The fragmentation mechanisms of protonated triglycine and its first-generation dissociation products have been investigated using a combination of density functional theory calculations and threshold collision-induced dissociation experiments. The activation barrier measured for the fragmentation of protonated triglycine to the b(2) ion and glycine is in good agreement with a calculated barrier at the B3LYP/6-31++G(d,p) level of theory reported earlier [Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The b(2) ion fragments to the a(2) ion via a transition state structure that is best described as acylium-like. Contrary to what is commonly assumed, the lowest energy structure of the a(2) ion is not an iminium ion, but a cyclic, protonated 4-imidazolidone. Furthermore, fragmentation of the b(2) to the a(1) ion proceeds not via a mechanism that results in HNCO and H(2)C=C=O as byproducts, as have been postulated, but via a transition state that contains an incipient a(1) ion and an incipient carbene. The fragmentation of a(2) to a(1) proceeds via a transition state structure that contains the a(1) ion, CO and an imine as incipient components.

Fragmentation Reactions of a2 Ions Derived From Deprotonated DipeptidesA Synergy Between Experiment and Theory

The fragmentation reactions of a number of a2 ions ([M−H−CO2]-) derived from dipeptides have been studied by energy-resolved mass spectrometry, isotopic labeling, and MS3 experiments. The general reaction sequence leading eventually to a deprotonated amine, is shown to occur, a reaction sequence first proposed by Styles and O'Hair (Rapid Commun. Mass Spectrom. 1998, 12, 809) from a study of the a2 ion derived from glycylglycine. When an amidic hydrogen (R2 = H) is present, the initial proton-transfer reaction 1 is nonreversible. However, when there is no amidic hydrogen, as in the a2 ions derived from H−Ala−Pro−OH or H−Gly−Sar−OH, the initial proton-transfer reaction 1 becomes reversible, leading to the interchange of N-bonded and C-bonded hydrogens. Ab initio calculations at the MP2/6-31+G(d) level of the energies and interconversion pathways of anions derived by deprotonation of glycine N-methylamide show a barrier of 8 kcal mol-1 for reaction 1, with reaction 2 being 23.8 kcal mol-1 endothermic. When an amidic hydrogen (R2 = H) is present, the amine-deprotonated species formed in reaction 1 abstracts a proton from the amide nitrogen to form the amide-deprotonated species, the most stable species on the potential energy surface. The system effectively becomes trapped in this low-energy well and exits upon activation by reactions 2 and 3 as observed when glycine N-methylamide is deprotonated directly. When no amidic hydrogen is present, this low-energy state does not exist, and reaction 1 becomes reversible, leading to the interchange of N-bonded and C-bonded hydrogens. In these cases, a significant population of the original a2 ion is formed, which fragments by the reaction

Relative Dissociation Energies of Protonated Peptides by Electrospray Ionization/Surface-Induced Dissociation

Relative dissociation energies (RDEs) are obtained for the major fragment ions produced by electrospray ionization/surface-induced dissociation of singly protonated triglycine, tetraglycine, leucine enkephalin, and leucine enkephalin arginine. A previously described data analysis method (Lim, H.; et al. J. Phys. Chem. B 1998, 102, 4753) is employed to analyze the energy-resolved mass spectra by subtracting out the distribution of energy transferred to the surface, integrating over the distribution of the incident ion energy, and taking into account the precursor ion initial internal energy and kinetic energy distributions. These variables are optimized by anchoring the RDE for the lowest energy fragment of a given precursor ion to its literature values and then using these optimized parameters to obtain the other RDEs. The RDEs of the four major fragments of triglycine vary from 2.4 eV for the b(2) fragment ion to 6.0 eV for the a(2) ion. The RDEs of the four major fragments of tetraglycine vary from 3.2 eV for the y(2) ion to 5.7 eV for the a(2) ion. The leucine enkephalin RDEs range from 1.1 eV for the b(4) ion to 2.1 eV for the b(2) ion. The leucine enkephalin arginine RDEs all lay between 2.5 and 3.5 eV. The overall trend of fragmentation order for all peptides is (y(n), b(n)) < a(n) and is consistent with the results from other experiments. The peptide RDEs presented here are only as accurate as the literature values to which they are anchored. Determination of absolute dissociation energies from SID data will require further refinement of the data analysis method.