Spectroscopic evidence for an oxazolone structure of the b2 fragment ion from protonated tri-alanine

Infrared multiple photon dissociation (IRMPD) spectroscopy is used to identify the structure of the b ₂⁺ ion generated from protonated tri-alanine by collision induced dissociation (CID). The IRMPD spectrum of b ₂⁺ differs markedly from that of protonated cyclo-alanine-alanine, demonstrating that the product is not a diketopiperazine. Instead, comparison of the IRMPD spectrum of b ₂⁺ to spectra predicted by density functional theory provides compelling evidence for an oxazolone structure protonated at the oxazolone N-atom.     

Fragmentation of Singly,Doubly, and Triply Charged Hydrogen Deficient Peptide Radical Cations in Infrared Multiphoton Dissociation and Electron Induced Dissociation

Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]^(n+1)+· (n = 0, 1, 2), in MS³ IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS³ CID. Backbone fragmentation in MS³ IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS³ IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS³ CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.     

Infrared multiphoton dissociation of small-interfering RNA anions and cations

Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H]⁺, [A + H]⁺, and [C + H]⁺, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.     

Ionic Pd/NHC Catalytic System Enables Recoverable Homogeneous Catalysis: Mechanistic Study and Application in the Mizoroki–Heck Reaction

N-Heterocyclic carbene (NHC) ligands are ubiquitously utilized in catalysis. A common catalyst design model assumes strong M–NHC binding in this metal–ligand framework. In contrast to this common assumption, we demonstrate here that lability and controlled cleavage of the M−NHC bond (rather than its stabilization) could be more important for high-performance catalysis at low catalyst concentrations. The present study reveals a dynamic stabilization mechanism with labile metal–NHC binding and [PdX₃]⁻[NHC-R]⁺ ion pair formation. Access to reactive anionic palladium intermediates formed by dissociation of the NHC ligands and plausible stabilization of the molecular catalyst in solution by interaction with the [NHC-R]⁺ azolium ion is of particular importance for an efficient and recyclable catalyst. These ionic Pd/NHC complexes allowed for the first time the recycling of the complex in a well-defined form with isolation at each cycle. Computational investigation of the reaction mechanism confirms a facile formation of NHC-free anionic Pd in polar media through either Ph–NHC coupling or reversible H–NHC coupling. The present study formulates novel ideas for M/NHC catalyst design.     

Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps

The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.     

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe₂L₃⁴⁺ ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu^I or Ag^I. The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS³ of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu^I and Ag^I complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe₂^IL₂²⁺ and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.     

A series of (NHC)Pd(N˄O)(OAc) complexes: synthesis,characterization and catalytic activities towards desulfinative Sonogashira coupling of arylsulfonyl hydrazides with arylalkynes

A series of well-defined N-heterocyclic carbene palladium (II) complexes with general formula (NHC)Pd(N^˄O)(OAc) were prepared through reaction of Pd (NHC)(OAc)₂(H₂O) with 1-methyl-1H-pyrazole-3-carboxylic acid or 1-methyl-1H-indazole-3-carboxylic acid in the presence of K₂CO₃. These complexes were then used for desulfinative Sonogashira coupling of arylsulfonyl hydrazides with terminal alkynes. With low catalyst loading, all synthesized palladium compounds exhibited moderate to high catalytic activities for the reactions.     

Increased sequence coverage of thymine‐rich oligodeoxynucleotides by infrared multiphoton dissociation compared to collision‐induced dissociation

Infrared multiphoton dissociation (IRMPD) of thymine‐rich oligodeoxynucleotides in a linear ion‐trap mass spectrometer affords far more extensive fragmentation than conventional collision‐induced dissociation (CID). For oligodeoxynucleotides containing one non‐thymine base, CID results primarily in cleavage on the 3′ side of the non‐thymine nucleobase, whereas IRMPD results in cleavages between all the nucleobases and thus provides complete sequence coverage. Furthermore, for oligodeoxynucleotides containing a single non‐thymine base, it is shown that the full series of diagnostic sequence ions observed in the IRMPD mass spectra arise from secondary dissociation of the two primary products formed from the initial cleavage site located next to the non‐thymine base. Copyright © 2010 John Wiley & Sons, Ltd.     

Imidazole‐coordinated monodentate NHC–Pd(II) complex derived from proline and its application to the coupling reaction of arylboronic acids with carboxylic acid anhydrides in water at room temperature

Cleavage of a C N bond of imidazolium salt derived from N‐phenyl‐substituted proline was observed in this laboratory. A novel imidazole‐coordinated monodentate NHC–Pd(II) complex 5 was obtained as the sole product in good yield in the reaction of imidazolium salt 4 with Pd(OAc)₂ in refluxing THF. The structure of complex 5 was determined unambiguously by an X‐ray diffraction. The complex was found to be a good catalyst in the cross‐coupling reaction of arylboronic acids with carboxylic acid anhydrides in water at room temperature. Copyright © 2011 John Wiley & Sons, Ltd.     

(N-Heterocyclic carbene) ion-pair palladium complexes: Suzuki–Miyaura cross-coupling studies in neat water under mild conditions

The synthesis and characterization of a series of (N-heterocyclic carbene)PdCl₃⁻(NMe₃H)⁺ ion-pair complexes are presented. Applying the quaternary ammonium salt as the function with NHC–Pd(II) complexes yields the new ion-pair complexes. The NHC–Pd(II) ion-pair complexes work well by undergoing the Suzuki–Miyaura reaction with aryl chloride substrates in water under mild conditions in air at room temperature. Twenty products resulting from Suzuki–Miyaura coupling reactions carried out in the presence of the new NHC–Pd(II) ion-pair complex under mild optimal conditions were examined to determine the optimum yields.     

N‐Heterocyclic carbene/phosphite synergistically assisted Pd/C‐catalyzed Suzuki coupling of aryl chlorides

An N‐heterocyclic carbene and phosphite synergistically enhanced Pd/C catalyst system has been developed for Suzuki coupling of aryl chlorides and aryl boronic acids from commercially available Pd/C with sterically demanding N,N′‐bis(2,6‐diisopropylphenyl)imidazolylidene and trimethylphosphite. A remarkable increase in catalytic activity of Pd/C was observed when used along with 1 equiv. N,N′‐bis(2,6‐diisopropylphenyl)imidazolium chloride and 2 equiv. phosphite with respect to palladium in appropriate solvents that were found to play a crucial role in Pd/C‐NHC‐P(OR)₃‐catalyzed Suzuki coupling. A dramatic ortho‐substitution effect of carbonyl and nitrile groups in aryl chlorides was observed and explained by a modified quasi‐heterogeneous catalysis mechanism. The Pd/C catalyst could be easily recovered from reaction mixtures by simple filtration and only low palladium contamination was detected in the biparyl products. A practical process for the synthesis of 4‐biphenylcarbonitrile has therefore been developed using the N‐heterocyclic carbene/phosphite‐assisted Pd/C‐catalyzed Suzuki coupling. Copyright © 2013 John Wiley & Sons, Ltd.     

CID of singly charged antioxidants applied in lubricants by means of a 3D ion trap and a linear ion trap-Orbitrap mass spectrometer

The aim of this study was to investigate the fragmentation behavior induced by low‐energy collision‐induced dissociation (LE‐CID) of four selected antioxidants applied in lubricants, by two different types of ion trap mass spectrometers: a three‐dimensional ion trap (3D‐IT) and a linear IT (LIT) Orbitrap MS. Two sterically hindered phenols and two aromatic amines were selected as model compounds representing different antioxidant classes and were characterized by positive‐ion electrospray ionization (ESI) and LE‐CID. Various types of molecular ions (e.g. [M]^+?, [M + H]⁺, [M + NH₄]⁺ or [M + Na]⁺) were used as precursor ions generating a significant number of structurally relevant product ions. Furthermore, the phenolic compounds were analyzed by negative‐ion ESI. For both IT types applied for fragmentation, the antioxidants exhibited the same unusual LE‐CID behavior: (1) they formed stable radical product ions and (2) C? C bond cleavages of aliphatic substituents were observed and their respective cleavage sites depended on the precursor ion selected. This fragmentation provided information on the type of structural isomer usually not obtainable for branched aliphatic substituents utilizing LE‐CID. Comparing the two instruments, the main benefit of applying the LIT‐Orbitrap was direct access to elemental composition of product ions enabling unambiguous interpretation of fragmentation trees not obtainable by the 3D‐IT device (e.g. loss of isobaric neutrals). It should be emphasized that the types of product ions formed do not depend on the type of IT analyzer applied. For characterizing degradation products of antioxidants, the LIT‐Orbitrap hybrid system, allowing the determination of accurate m/z values for product ions, is the method of choice. Copyright © 2011 John Wiley & Sons, Ltd.     

Topoisomer Differentiation of Molecular Knots by FTICR MS: Lessons from Class II Lasso Peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminal macrolactam ring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collision-induced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECD spectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c•/z from c/z•) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions ( b￠_n ^· ) \left( {b{\prime}_n^{ \bullet }} \right) . We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z• and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture.     

Polycondensation of haloarylketones catalyzed by palladium compounds bearing N-heterocyclic carbene (NHC) ligands

Palladium-catalyzed α-arylation of ketones, which can efficiently give coupling products by using appropriate ligands and bases, could be applied to a polycondensation reaction. Stable N-heterocyclic carbenes (NHC) were used as favorable ligands coordinating the Pd catalysts, which were generated in situ from commercially available palladium compounds such as Pd(OAc)₂ and Pd₂(dba)₃ as suitable catalyst precursors in this polymerization. Using small amounts of binary catalysts, poly(aryl alkyl ketone)s were afforded in high yields from haloarylketones in the presence of a base. A primarily prepared palladium catalyst having an NHC ligand, [Pd(OAc)₂(NHC)], also efficiently catalyzed the polycondensation, whereas a palladium compound bearing two carbene ligands, [PdX₂(NHC)₂], did not.     

Modelling of multifrequency IRMPD for laser isotope separation

The process of infrared multiple photon dissociation (IRMPD) of molecules is of great fundamental importance and has practical significance, such as isotope separation etc. Unfortunately, a clear insight into the process has been hindered by the bewildering array of important variables affecting MPD. The dissociation probability γ (φ) i.e. the yield has been found to be a sensitive function of laser fluence φ along with numerous other parameters like laser frequency, gas pressure etc. We have shown that in single frequency IRMPD, an accurate quantitative characterization of the dissociation probability can be adequately expressed by a ‘power law’ model with two fitting parameters namely critical fluence, φ_c and multiphoton order,m. This model was exploited in analysing our MPD results on various systems. However, the small isotope shift encountered in heavy elements and the sticking phenomenon observed in small light molecules restrict respectively the separation factor and the dissociation yield. These problems can effectively be tackled by irradiation with multifrequency laser beams which can be chosen appropriately on the basis of spectroscopic features. Based on our success in single frequency model, multifrequency IRMPD is modelled by a functional form containing the product of power law terms for individual fluences on irradiation frequencies. This model is successfully benchmarked with our experimental results on multifrequency LIS of tritium. Such knowledge can be utilized for appropriate separation process design, evaluation and optimization.     

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITC-modified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that utilizes 4-sulfophenylisothiocyanate (SPITC) in conjunction with CID and IRMPD.     

C-S bond formation catalyzed by N-heterocylic carbene palladium phosphine complexes

N-Heterocyclic carbenes (NHCs) are known to be useful ligands for palladium-complex catalysis. It was found that [(NHC)Pd(PPh₃)Cl₂] is an effective pre-catalyst in Pd-catalyzed C-S cross coupling reactions to produce the functionalized sulfides in excellent yields. The turn over frequency (TOF) for the coupling of p-CH₃C₆H₄Br with p-CH₃C₆H₄SH reaches to 6.25 (mol of product) (mole of catalyst)⁻¹ h⁻¹.     

Collision-induced dissociation studies of protonated alcohol and alcohol—water clusters by atmospheric pressure ionization tandem mass spectrometry. 1?Methanol

Cluster size distribution and collision-induced dissociation (CID) studies of protonated methanol and protonated methanol—water clusters yield information on the structure and energetics of such ions. Ions were formed at atmospheric pressure in a corona discharge source, and were subjected to CID in the center quadrupole of a triple quadrupole mass spectrometer. Cluster ions containing up to 13 molecules of methanol and/or water were observed and examined using CID experiments. The CID of all (CH₃OH)_n · H₂O · H⁺ clusters, where n ? 8, showed that water loss was statistically favored over methanol loss and that the preferred dissociation channel involved loss of water with methanol molecules. These results support a model employing a chain of hydrogen-bonded solvent molecules rather than one in which fused rings of ligands surround a central hydronium ion. However, CID of larger clusters, where n ? 9, showed that loss of one methanol was equal to or less than loss of water, reflecting a change in structure.     

Electrospray ionization collision induced dissociation of thiocarbocyanine and selenocarbocyanine dyes

The effect of the properties of sulphur and selenium atoms, the composition and location of substituents (―CH₃, ―OCH₃, ―C₂H₅, and ―C₃H₆―((N⁺Br^?)C₅H₅)), and the charge state on the collision induced dissociation (CID) behaviour of ions generated by electrospray ionization (ESI) of thiocarbocyanine and selenocarbocyanine dyes have been investigated. The results show that, for of all the examined singly charged ions, the main dissociation channel was related to the formation of distonic ions, generated as a result of cleavages within the dimethine bridge. In the case of doubly charged ions (with propyl‐pyridinium substituents), competition between fragmentation processes related to charges located at different nitrogen atoms has been observed. The S/Se replacement also has an impact on the CID behaviour of the examined carbocyanine dyes. On the basis of the performed CID MS/MS experiments, general rules for the CID of thiocarbocyanine and selenocarbocyanine dyes have been proposed.     

Quantitative Description of Structural Effects on the Stability of Gold(I) Carbenes

The gas‐phase bond‐dissociation energies of a SO₂–imidazolylidene leaving group of three gold(I) benzyl imidazolium sulfone complexes are reported (E₀=46.6±1.7, 49.6±1.7, and 48.9±2.1 kcal mol^?1). Although these energies are similar to each other, they are reproducibly distinguishable. The energy‐resolved collision‐induced dissociation experiments of the three [L]–gold(I) (L=ligand) carbene precursor complexes were performed by using a modified tandem mass spectrometer. The measurements quantitatively describe the structural and electronic effects a p‐methoxy substituent on the benzyl fragment, and trans [NHC] and [P] gold ligands, have towards gold carbene formation. Evidence for the formation of the electrophilic gold carbene in solution was obtained through the stoichiometric and catalytic cyclopropanation of olefins under thermal conditions. The observed cyclopropane yields are dependent on the rate of gold carbene formation, which in turn is influenced by the ligand and substituent. The donation of electron density to the carbene carbon by the p‐methoxy benzyl substituent and [NHC] ligand stabilizes the gold carbene intermediate and lowers the dissociation barrier. Through the careful comparison of gas‐phase and solution chemistry, the results suggest that even gas‐phase leaving‐group bond‐dissociation energy differences of 2–3 kcal mol^?1 enormously affect the rate of gold carbene formation in solution, especially when there are competing reactions. The thermal decay of the gold carbene precursor complex was observed to follow first‐order kinetics, whereas cyclopropanation was found to follow pseudo‐first‐order kinetics. Density‐functional‐theory calculations at the M06‐L and BP86‐D3 levels of theory were used to confirm the observed gas‐phase reactivity and model the measured bond‐dissociation energies.