Multiphoton Dissociation Research Articles

Instrumental Dependent Dissociations of n-Propyl/Isopropyl Phosphonate Isomers: Evaluation of Resonant and Non-Resonant Vibrational Activations

Structural elucidation and distinction of isomeric neurotoxic agents remain a challenge. Tandem mass spectrometry can be used for this purpose in particular if a "diagnostic" product ion is observed. Different vibrational activation methods were investigated to enhance formation of diagnostic ions through consecutive processes from O,O-dialkyl alkylphosphonates. Resonant and non-resonant collisional activation and infrared multiphoton dissociation (IRMPD) were used with different mass spectrometers: a hybrid quadrupole Fourier transform ion cyclotron resonance (Qh-FTICR) and a hybrid linear ion trap-Orbitrap (LTQ/Orbitrap). Double resonance (DR) experiments, in ion cyclotron resonance (ICR) cell, were used for unambiguous determination of direct intermediate yielding diagnostic ions. From protonated n-propyl and isopropyl O-O-dialkyl-phosphonates, a diagnostic m/z 83 ion characterizes the isopropyl isomer. This ion is produced through consecutive dissociation processes. Conditions to favor its formation and observation using different activation methods were investigated. It was shown that with the LTQ, consecutive experimental steps of isolation/activation with modified trapping conditions limiting the low mass cut off (LMCO) effect were required, whereas with FT-ICR by CID and IRMPD the diagnostic ion detection was provided only by one activation step. Among the different investigated activation methods it was shown that by using low-pressure conditions or using non-resonant methods, efficient and fast differentiation of isomeric neurotoxic agents was obtained. This work constitutes a unique comparison of different activation modes for distinction of isomers showing the instrumental dependence characteristic of the consecutive processes. New insights in the dissociation pathways were obtained based on double-resonance IRMPD experiments using a FT-ICR instrument with limitation at low mass values.

Protonated pyrimidine nucleosides probed by IRMPD spectroscopy

The ESI-formed protonated 2′-deoxycytidine, cytidine, cytarabine, and gemcitabine have been probed using infrared multiphoton dissociation (IRMPD) spectroscopy performed in the 900–2000cm−1 region at CLIO, the Orsay Free Electron Laser facility, and in the 2800–3800cm−1 region using a YAG-laser coupled to a table-top optical parametric oscillator/amplifier (OPO/OPA). The IRMPD spectra are compared of the protonated nucleosides with the IR spectra of their B3LYP/6-311++G(d,p)-optimized isomeric forms. The stability at room temperature of some conformers has been investigated by means of ab initio molecular dynamics simulations. The IRMPD spectra are consistent with the formation in the ESI source of both the N3- and the O2-protonated nucleosides. The most favoured members of both families are characterized by the pyrimidine base oriented anti to the furanose moiety. Concerning the O2-protonated nucleosides, IRMPD spectra and thermochemical considerations support the predominant formation of the structures with the proton oriented up relative to the furanose moiety.

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Inverse Neighboring Group Participation: Explanation of an Unusual S→N Alkyl Migration of Isothiuronium Salts Containing a Lactone Group

A detailed experimental and DFT study of the S to N alkyl migration of substituted S-(1(3H)-isobenzofuranon-3-yl)isothiuronium bromide to N,N'-dimethyl-N-(3-oxo-1,3-dihydro-2-benzofuran-1-yl)thiourea provided evidence for the existence of an unusual double displacement mechanism involving two consecutive back-side S(N)2 reactions where a carboxylate anion has a crucial role both as a leaving group as well as an internal nucleophile. The thiazetidine zwitterionic species that is involved in this mechanism as an intermediate was characterized by infrared multiphoton dissociation spectroscopy and was trapped with methyl iodide. It was found that the intermediate has a structure of a free ion pair. The double-displacement mechanism can be considered as a new type of inverse lactone neighboring group participation.

An Interplay Between Infrared Multiphoton Dissociation Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry and Density Functional Theory Computations in the Characterization of a Tripodal Quinolin-8-Olate Gd(III) Complex

A new hexadentate, tripodal 8-hydroxyquinoline based ligand (QH3) and its gadolinium(III) tris-chelated (GdQ) complex with hemicage structure was investigated by using high resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICRMS). The protonated adduct of the free ligand and its hemicage tripodal Gd(III) complex, [GdQ + H](+), were first observed in experiments of electrospray ionization (ESI) with a linear ion trap (LTQ) mass spectrometer and further investigated by using high resolution FTICRMS. Gas-phase dissociation of the protonated Gd(III) complex, by infrared multiphoton dissociation (IRMPD) FTICR MS, demonstrated a fragmentation pattern with six main product cluster ions labeled as [Fn](+) (n = 1 up to 6). These product ions suggest the elimination of 7-amino-alkyl or 7-alkyl chains of the hemicage moiety. High resolution MS conditions allowed the elucidation of the fragmentation pattern and product ion structures along with the determination, among the isotopic pattern of Gd, of the chemical compositions of closely related species, which differ in terms of hydrogen content. Among the Gd six naturally stable isotopes, (158)Gd is the most abundant, and its peak within each cluster was used as a reference for distinguishing each product ions. Computational DFT investigations were applied to give support to some hypothesis of fragmentation pathways, which could not have been easily justified on the basis of the experimental work. Furthermore, computational studies suggested the coordination geometry of the protonated parent complex and the five- and four-coordinated complexes, which derive from its fragmentation. Furthermore, experimental and computational evidences were collected about the octet spin state of the parent compound.

Influence of N-terminal residue composition on the structure of proline-containing b2+ ions.

To probe the structural implications of the proline residue on its characteristic peptide fragmentation patterns, in particular its unusual cleavage at its C-terminus in formation of a b(2) ion in XxxProZzz sequences, the structures of a series of proline-containing b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy and fragment ion hydrogen-deuterium exchange (HDX). Five different Xxx-Pro b(2)(+) ions were studied, with glycine, alanine, isoleucine, valine, or histidine in the N-terminal position. The residues selected feature different sizes, chain lengths, and gas phase basicities to explore whether the structure of the N-terminal residue influences the Xxx-Pro b(2)(+) ion structure. In proteins, the proline side chain-to-backbone attachment causes its peptide bonds to be in the cis conformation more than any other amino acid, although trans is still favored over cis. However, HP is the only b(2)(+) ion studied here that forms the diketopiperazine exclusively. The GP, AP, IP, and VP b(2)(+) ions formed from protonated tripeptide precursors predominantly featured oxazolone structures with small diketopiperazine contributions. In contrast to the b(2)(+) ions generated from tripeptides, synthetic cyclic dipeptides VP and HP were confirmed to have exclusive diketopiperazine structures.

Quantum control of multi-photon dissociation of HCl+ with intense femtosecond laser pulses

The multi-photon dissociation of HCl(+) through three channels HCl(+)→H(1s|(2)S)+Cl(+)((3)P), H(+)+Cl((2)P(0)), and H((2)S)+Cl(+)((1)D) steered by intense femtosecond laser pulses are investigated theoretically using the quantum wave packet dynamics. The numerical calculations are performed in two cases without and with the coupling between the excited states. The results show that the dissociation is sensitive to the duration τ, peak intensity I(0), and the resonance of driving laser fields. In the case without the coupling, the effect of the permanent dipole moments on the dissociations dominates for τ < 15 fs, while with the increase of τ, the dissociation dynamics is mainly dominated by the transition dipole moment. In the case with the coupling, the above-threshold dissociation process is complex, and the non-resonant (λ = 400 nm) and resonant (λ = 800 and 1200 nm) laser fields lead to different variation of the branching ratios. The angle-resolved energy distribution is also discussed in detail.

Chirality recognition of the protonated serine dimer and octamer by infrared multiphoton dissociation spectroscopy

Infrared multiphoton dissociation (IRMPD) spectroscopy has been used to record IR signatures of chirality recognition in the protonated serine dimer and octamer in the 3200-3800 cm(-1) region. This is the first IRMPD study to investigate the heterochiral biomolecular system by utilizing the isotope-labelled species. Noticeable differences in the homo- versus heterochiral IRMPD spectra have been obtained experimentally for both the dimer and octamer. Different dissociation patterns have been noted not only between the homo- and heterochiral octamers, but also between the two -OH stretching vibrational bands of the same chirality species. Systematic theoretical searches have been carried out to identify the most stable conformers of both the homo- and heterochiral protonated serine dimer and octamer. The final geometry optimization and harmonic vibrational calculations have been performed at the MP2/6-311++G(d,p) level for the homo- and heterochiral protonated serine dimer and at the B3LYP/6-31G(d) level for the homo- and heterochiral protonated serine octamer. For the homo- and heterochiral dimer, good agreement between the experimental and theoretical spectra has been achieved and the major conformers have been identified. For the homo- and heterochiral octamer, the main IR features observed have been satisfactorily reproduced theoretically and the dominant conformers identified. More than one main conformer has been identified for the homochiral octamer. This conclusion has been further supported by the analysis of the wavelength specific dissociation products.

Selected Examples of Gas-Phase Ion Chemistry Studies

Gas-phase ion chemistry is an area in mass spectrometry that has received much research interest since the mid fifties of the last century. Although the focus of mass spectrometric research has shifted the last twenty years largely to life science studies, including proteomics, genomics and metabolomics, there are still several groups in the world active in gas-phase ion chemistry of both positive and negative ions, either unimolecularly and/or bimolecularly. In this tutorial lecture the formation and determination of tautomeric ion structures and intra-ionic catalyzed tautomerization in the gas phase will be discussed. In addition, an example of formation of different tautomeric structures in protic and aprotic solvents under electrospray ionization conditions will be given, as established by gas-phase infrared multiphoton dissociation spectroscopy. This will be followed by presenting an example of time-resolved MS/MS which enables to identify the structure of an ion, generated at a particular molecular ion lifetime. At the end of the lecture the power of ion mobility will be shown in elucidating the mechanism of epimerization of bis-Tröger bases having chiral nitrogen centers.

Formation and infrared absorption of protonated naphthalenes (1-C10H9+and 2-C10H9+) and their neutral counterparts in solid para-hydrogen

Protonated naphthalene (C(10)H(9)(+)) and its neutral counterparts (hydronaphthyl radicals, C(10)H(9)) are important intermediates in the reactions of aromatic compounds and in understanding the unidentified infrared (IR) emissions from interstellar media. We report the IR spectra of 1-C(10)H(9)(+), 2-C(10)H(9)(+), 1-C(10)H(9), and 2-C(10)H(9) trapped in solid para-hydrogen (p-H(2)); the latter three are new. These species were produced upon electron bombardment of a mixture of naphthalene (C(10)H(8)) and p-H(2) during matrix deposition. The intensities of IR features of 1-C(10)H(9)(+) decreased after the matrix was maintained in darkness for 19 h, whereas those of 1-C(10)H(9) and 2-C(10)H(9) increased. Irradiation of this matrix sample with light at 365 nm diminished lines of 1-C(10)H(9)(+) and 2-C(10)H(9) and enhanced lines of 1-C(10)H(9) and 2-C(10)H(9)(+); the latter species was unstable and converted to 1-C(10)H(9)(+) in less than 30 min and 2-C(10)H(9) was converted to 1-C(10)H(9) at 365 nm. Observed wavenumbers and relative intensities of these species agree satisfactorily with the anharmonic vibrational wavenumbers and IR intensities predicted with the B3PW91/6-311++G(2d,2p) method. Compared with spectra recorded previously with IR photodissociation of Ar-tagged C(10)H(9)(+) or IR multiphoton dissociation of C(10)H(9)(+), our method has the advantages of producing high-resolution IR spectra with a wide spectral coverage, true IR intensity and excellent ratio of signal to noise; both protonated species and their neutral counterparts are produced with little interference from other fragments. With these advantages, the IR spectra of 1-C(10)H(9)(+), 2-C(10)H(9)(+), 1-C(10)H(9), and 2-C(10)H(9) are here clearly characterized.

MeCAT – comparing relative quantification of alpha lactalbumin using both molecular and elemental mass spectrometry

Chemical tagging with stable isotopes is one of the best established methods for the quantification of proteins using mass spectrometry, especially in non-proliferating cells and tissue. The absolute quantification of proteins is still a challenge. Metal-coded affinity tagging (MeCAT), used to label proteins and peptides with lanthanide ions, allows both, relative and absolute, quantitative determination. MeCAT loaded with lanthanide ions allows the use of inductively coupled plasma mass spectrometry (ICP-MS) enabling very accurate and sensitive quantification of peptides and proteins based on the metal ion signal. Furthermore, multiplex assays are possible that are not limited to 4- or 8-plex analyses when using different lanthanides. Naturally, different lanthanides also lead to different molecular masses for the same labelled peptides which can be distinguished easily. This enables the relative quantification in electrospray MS based on the relative signal intensities of the differentially labelled peptides. We have studied MeCAT labelled peptides, using LC/ESI-MS and LC/ESI-MS/MS with infrared multiphoton dissociation (IRMPD) to show that both the molecular masses and the specific fragments resulting from the MS/MS experiments can be used for relative quantification. The results are compared with high performance liquid chromatography (HPLC)/ICP-MS and direct ICP-MS analysis as standard methods. We show that the ESI and IRMPD based methods deliver quantitative results comparable to ICP-MS.

Isomer-separated photodissociation of large sized silicon and carbon cluster ions: Drift tube experiment combined with a tandem reflectron mass spectrometer for Si 24 + – Si 27 + and C 32 + –C 38 +

Isomer-resolved multiphoton dissociations (PDs) with 4.66-eV laser photons were applied to carbon and silicon cluster cations, C\hbox{$_{n}^{{+}}$}+n (n = 32, 34, 36, and 38) and Si\hbox{$_{m}^{{+}}$}+m (m = 24–27), in order to investigate correlations between the isomer structures and dissociation reactions. Cyclic and fullerene structures of C\hbox{$_{n}^{{+}}$}+n and prolate and spherical isomers of Si\hbox{$_{m}^{{+}}$}+m, which are the coexisting isomers in these size ranges, were separated by ion mobility spectrometry, followed by photolysis using a tandem reflectron mass spectrometer. Photofragment ion distributions were revealed to depend on the parent isomer structures. Dissociation mechanisms were discussed from the fragment ion distributions.

Comparison of MS/MS Methods for Characterization of DNA/Cisplatin Adducts

The development of activation/dissociation techniques such as ultraviolet photodissociation (UVPD), infrared multiphoton dissociation (IRMPD), and electron transfer dissociation (ETD) as alternatives to collision induced dissociation (CID) has extended the range of strategies for characterizing biologically relevant molecules. Here, we describe a comprehensive comparison of CID, IRMPD, UVPD, ETD, and hybrid processes termed ETcaD and ET-IRMPD (and analogous hybrid methods in the negative mode NETcaD and NET-IRMPD) for generating sequence-specific fragment ions and allowing adduction sites to be pinpointed for DNA/cisplatin adducts. Among the six MS/MS methods, the numerous products generated by the IRMPD and UVPD techniques resulted in the most specific and extensive backbone cleavages. We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra.

Application of parametric equations of motion to study the resonance coalescence in $\text{H}_{2}^{+}$H2+

Recently, occurrence of coalescence point was reported in H(2)(+) undergoing multiphoton dissociation in strong laser field. We have applied parametric equations of motion and smooth exterior scaling method to study the coalescence phenomenon of H(2)(+). The advantage of this method is that one can easily trace the different states that are changing as the field parameters change. It was reported earlier that in the parameter space, only two bound states coalesce [R. Lefebvre, O. Atabek, M. Sindelka, and N. Moiseyev, Phys. Rev. Lett. 103, 123003 (2009)]. However, it is found that increasing the accuracy of the calculation leads to the coalescence between resonance states originating from the bound and the continuum states. We have also reported many other coalescence points.

Scrambling of autoinducing precursor peptides investigated by infrared multiphoton dissociation with electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry

Two synthetic precursor peptides, H(2)N-CVGIW and H(2)N-LVMCCVGIW, involved in the quorum sensing of Lactobacillus plantarum WCFS1, were characterized by mass spectrometry (MS) with electrospray ionization and 7-T Fourier transform ion cyclotron resonance (ESI-FTICR) instrument. Cell-free bacterial supernatant solutions were analyzed by reversed-phase liquid chromatography with ESI-FTICR MS to verify the occurrence of both pentapeptide and nonapeptide in the bacterial broth. The structural characterization of both protonated peptides was performed by infrared multiphoton dissociation using a continuous CO(2) laser source at a wavelength of 10.6 μm. As their fragmentation behavior cannot be directly derived from the primary peptide structure, all anomalous fragments were interpreted as neutral loss of amino acids from the interior of both peptides, i.e., loss of V, G, VG and M, MC, V, CC, from H(2)N-CVGIW and H(2)N-LVMCCVGIW, respectively. Mechanisms of this scrambling are proposed. FTICR MS provides accurate masses of all fragment ions with very low absolute mass errors (<1.6 ppm), which facilitated the reliable assignment of their elemental compositions. The resolving power was more than sufficient to resolve closely isobaric product ions with routine subparts per million mass accuracies. Only the occurrence of pentapeptide was found in the cell-free culture of L. plantarum, grown in Waymouth's medium broth, with a low content of 5.2 ± 2.6 μM by external calibration. Most of it was present as oxidized H(2)N-CVGIW, that is, the soluble disulfide pentapeptide with a level tenfold higher (i.e., 50 ± 4 μM, n = 3).

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H5+ is a weakly bound molecular ion, which is formed from the reaction of H3+ and H2 and that has a very rich vibrational spectrum. In this work, diffusion Monte Carlo (DMC) approaches are used to explore the nature of vibrationally excited states of the proton-transfer mode in H5+. On the basis of these calculations, alternative assignments of the recently reported infrared multiphoton dissociation spectra of H5+ and D5+ [J. Phys. Chem. Lett. 2012, 3, 3160−3166] are suggested. In the proposed assignments, progressions of transitions in the proton-transfer mode with up to nine quanta of excitation are invoked. Reduced dimensional calculations of the spectra of H5+ and D5+ are used to provide an understanding of why such high overtones should be observable through absorption spectroscopy. Implications of how excitations of this mode can provide insights into the H3+ + H2 reaction are also discussed.

Towards analytically useful two-dimensional Fourier transform ion cyclotron resonance mass spectrometry

Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pfändler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field.

Characterization of Modified RNA by Top‐Down Mass Spectrometry

Characterization of Modified RNA by Top‐Down Mass Spectrometry

Excitation energies and multiphoton dissociation–ionization of 1,4-pentadiene at 266 and 355 nm

The photodissociation (PD) and photoionization (PI) of 1,4-pentadiene (PDE), which result in the absorption of multiple photons, were studied both experimentally and theoretically. The PD and PI ions were the result of the interaction of a cooled molecular beam of PDE with laser radiation of wavelengths 266 and 355 nm, measured using a time of flight (TOF) mass spectrometer. There are several differences in the ionization patterns, with the wavelength as a common characteristic in the absence of the parent ion, and on the possible dissociation of the neutral species such as C2H3 and C3H5, which then dissociates and ionizes. To interpret the results, the potential energy surface (PES) of PDE was calculated. Using time-dependent density functional theory (TD-DFT), the excitation energies and potential energy surfaces along the two main dissociative coordinates, namely, C2–C3 and C3–H, were also calculated. Possible mechanisms responsible for the formation of the observed ions are proposed: hydrogen loss, molecular hydrogen formation, simple C–C dissociation, total deprotonation and hydrogen transposition.

Identification of glucosinolates in capers by LC‐ESI‐hybrid linear ion trap with Fourier transform ion cyclotron resonance mass spectrometry (LC‐ESI‐LTQ‐FTICR MS) and infrared multiphoton dissociation

An liquid chromatography-mass spectrometry method using electrospray ionization in negative ion mode coupled with a hybrid quadrupole linear ion trap and Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was applied to characterize of intact glucosinolates (GLSs) in crude sample extracts of wild bud flowers of Capparis spinosa (Capparis species, family Capparaceae). Structural information of GLSs was obtained upon precursor ions' isolation within the FTICR trapping cell and subsequent fragmentation induced by infrared multiphoton dissociation (IRMPD). Such a fragmentation was found very useful in terms of chemical identification of all precursor ions [M-H](-) including sulfur-rich GLSs reported here for the first time. Along with most common GLSs already found in capers such as glucocapparin, isopropyl/n-propyl-GLS, mercapto-glucocapparin, and two indolic GLS, i.e., 4-hydroxyglucobrassicin and glucobrassicin, the occurrence of the uncommon glycinyl-glucocapparin as well as two sulfur-rich GLSs is reported. IRMPD showed an increased selectivity towards disulfide bond cleavages with thiol migration, suggesting the side chain structure of non-targeted compounds, i.e., disulfanyl-glucocapparin and trisulfanyl-glucocapparin. Glucocapparin [2.05 ± 0.25 mg/g, dry weight (dw)] was the most abundant GLS, followed by glucobrassicin (232 ± 18 µg/g, dw) and 4-hydroxyglucobrassicin (89 ± 12 µg/g, dw). All other compounds were present at very low content ranging from 0.5 to 1.5 µg/g dw.