Infrared Multiple Photon Dissociation Research Articles

Benzoxazine Formation Mechanism Evaluation by Direct Observation of Reaction Intermediates.

Benzoxazine formation is a fundamental step in the preparation of polybenzoxazine resins, and a detailed description of the mechanism governing the formation of benzoxazine and side products is vital for improving the properties and performance of these resins. Determination of the nature and properties of reaction intermediates is not trivial. Therefore, a Mannich-type condensation of aniline, formaldehyde, and phenol was evaluated as a potential method to form benzoxazine. Coupling positive mode electrospray ionization mass spectrometry (ESI(+)-MS) with infrared multiple photon dissociation (IRMPD) spectroscopy allowed unambiguous determination of an iminium-based mechanism and the direct observation of iminium intermediates. The benzoxazine formation mechanism was indirectly confirmed by the observation of side products that are relevant to the polymerization step, and directly confirmed by the identification of four distinct reaction intermediates that were completely characterized by IRMPD spectroscopy. The benzoxazine monomer was also shown to undergo isomerization under standard ESI-MS analysis conditions, suggesting the presence of a mixture of three isomers during their usual ESI-MS analysis.

Gas-phase vibrations of the anionic, hydrogen-bonded dimer of 9-methylguanine

The gas-phase InfraRed Multiple Photon Dissociation (IRMPD) spectra in the fingerprint region of the anion (m/z 163) and mono-deprotonated homodimer of 9-methyl-guanine (2, m/z 329) and its d5 analogue (2-d5) are reported here. The anionic dimer is reverse Watson-Crick paired with the hydrogen bonding pattern ADD/DAA (where A stands for acceptor and D stands for donor), in which the site of negative charge is unambiguously found to be N1. The match between experimental vibrational spectra and DFT-computed spectra is good with the exception of the region between 2000 and 2900 cm−1 that contains symmetrical and antisymmetrical N–H stretches of the adjacent hydrogen-bond donor-donor pair.

Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides.

The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.

Co-adsorption of O2 and C2H4 on a Free Gold Dimer Probed via Infrared Photodissociation Spectroscopy.

Infrared multiple photon dissociation (IR-MPD) spectroscopy in conjunction with density functional theory (DFT) calculations has been employed to study the activation of molecular oxygen and ethylene co-adsorbed on a free gold dimer cation Au2+. Both studied complexes, Au2O2(C2H4)+ and Au2O2(C2H4)2+, show distinct features of both intact O2 and ethylene co-adsorbed on the cluster. However, the ethylene C=C double bond is activated, increasing in length by up to 0.07Å compared with the free molecule, and the red shift of the O-O vibration frequency increases with the number of adsorbed ethylene molecules, indicating a small but increasing activation of the O-O bond. The small O2 activation and the rather weak interaction between O2 and C2H4 are also reflected in the calculated electronic structure of the co-adsorption complexes which shows only a small occupation of the empty anti-bonding O2 2π*2p orbital as well as the localization of most of the Kohn-Sham orbitals on O2 and C2H4, respectively, with only limited mixing between O2 and C2H4 orbitals. The results are compared with theoretical studies on neutral AuxO2(C2H4) (x = 3, 5, 7, 9) complexes.

IR ion spectroscopy in a combined approach with MS/MS and IM-MS to discriminate epimeric anthocyanin glycosides (cyanidin 3-O-glucoside and -galactoside)

Anthocyanins are widespread in plants and flowers, being responsible for their different colouring. Two representative members of this family have been selected, cyanidin 3-O-β-glucopyranoside and 3-O-β-galactopyranoside, and probed by mass spectrometry based methods, testing their performance in discriminating between the two epimers. The native anthocyanins, delivered into the gas phase by electrospray ionization, display a comparable drift time in ion mobility mass spectrometry (IM-MS) and a common fragment, corresponding to loss of the sugar moiety, in their collision induced dissociation (CID) pattern. However, the IR multiple photon dissociation (IRMPD) spectra in the fingerprint range show a feature particularly evident in the case of the glucoside. This signature is used to identify the presence of cyanidin 3-O-β-glucopyranoside in a natural extract of pomegranate. In an effort to increase any differentiation between the two epimers, aluminum complexes were prepared and sampled for elemental composition by FT-ICR-MS. CID experiments now display an extensive fragmentation pattern, showing few product ions peculiar to each species. More noteworthy is the IRMPD behavior in the OH stretching range showing significant differences in the spectra of the two epimers. DFT calculations allow to interpret the observed distinct bands due to a varied network of hydrogen bonding and relative conformer stability.

Characterization of protonated AcAlaDab and AcDabAla by IRMPD spectroscopy and molecular modeling

Alanine (Ala) based oligopeptides containing a residue of 2,4-diaminobutyric acid (Dab) serve as a unique model to examine the effect of the side-chain ionization on the conformational changes of the peptide backbone structure. In this work, two isomeric dipeptide ions, AcAlaDabH+ and AcDabAlaH+, are studied by infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical modeling. The IRMPD spectra were recorded in a Fourier transform-ion cyclotron resonance mass spectrometer coupled to an infrared free electron laser. For each peptide ion, seven theoretical infrared (IR) spectra were obtained from a set of unique low-energy conformations calculated at the ωB97X-D/6-311 + G(d,p) level of theory. A manually weighted IR spectrum containing two conformations gives the best prediction for each IRMPD spectrum. An interesting spectral feature is that the frequency of the amide I band of AcAlaDabH+ is about 30 cm−1 lower compared to that of AcDabAlaH+. This redshift of the amide I band implies a stronger hydrogen-bonding interaction between the charged NH3+ group on the side-chain of Dab and the CO group of the backbone in the former ion. The stronger hydrogen-bonding interaction is likely due to a combination of a shorter H⋯O distance and a more favorable alignment of the N–H–O moiety in a unique conformation adopted by AcAlaDabH+, which results in an increased stability of the ion. The results explain an earlier observation that AcAlaDab has a higher proton affinity than AcDabAla.

Ion spectroscopy and guided ion beam studies of protonated asparaginyl-threonine decomposition: Influence of a hydroxyl containing C-Terminal residue on deamidation processes

The spontaneous deamidation of asparagine residues plays a significant role in various biological functions and degenerative, aging diseases. Here, we present a full description of the deamidation reaction (as well as other key dissociation processes) of protonated asparaginyl-threonine, [AsnThr + H]+, via complementary infrared multiple photon dissociation (IRMPD) ion spectroscopy, threshold collision-induced dissociation (TCID), and theoretical studies. IRMPD spectra allow for the clear identification of precursor and product ion structural conformations when compared to theoretically calculated spectra for likely structures. Analysis of kinetic energy dependent cross sections measured via TCID with xenon using a guided ion beam tandem mass spectrometer allows for characterization of the energies involved in the decomposition processes of interest. Threshold energies are compared to relative single point energies of major reaction species calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels of theory, thereby determining important rate-limiting steps involved in [AsnThr + H]+ decomposition. Our studies confirm the formation of a succinimide intermediate via deamidation of [AsnThr + H]+, an observation consistent with condensed-phase deamidation analyses. Interestingly, our spectroscopic results suggest deamidation does not produce furanone isomers even though theoretical results indicate this pathway (exhibited in gas-phase analyses of similar dipeptide systems) should be competitive. Dehydration of [AsnThr + H]+ is also observed, where theory suggests that oxazolone and oxazoline formation are competitive at threshold energies, but IRMPD analyses conclusively confirm the formation of the oxazoline structure. The comprehensive results presented (in addition to complementary studies discussed herein) allow for a valuable analysis of C-terminal residue side-chain effects on the deamidation process.

Metallacyclopropene structures identified by IRMPD spectroscopic investigation of the dehydrogenation reactions of Ta+ and TaO+ with ethene

Species formed in the reactions of Ta+ and TaO+ with ethene are examined spectroscopically using infrared multiple photon dissociation (IRMPD) action spectroscopy. Ta+, TaC2H2+, and TaO+ are all observed to dehydrogenate ethene yielding [Ta,2C,2H]+, [Ta,4C,4H]+, and [Ta,O,2C,2H]+, respectively. For these species, IR action spectra are obtained in the 225–3400 cm−1 range by monitoring fragmentation into the [Ta,2C]+, [Ta,4C,nH]+ (n = 2, 3), and [Ta,O]+ mass channels, respectively. The spectra are assigned to TaC2H2+, Ta(C2H2)2+, and OTaC2H2+ metallacyclopropene species on the basis of comparisons with scaled vibrational spectra from B3LYP/def2-TZVPPD geometry optimized structures. To further elucidate the chemistry observed, complete reaction coordinate pathways having quintet, triplet, and singlet spin for all three dehydrogenation reactions have also been examined.

Structures of [GPGG + H – H2O]+ and [GPGG + H – H2O – NH[dbnd]CH2]+ ions; evidence of rearrangement prior to dissociation

Infrared multiple photon dissociation (IRMPD) spectroscopy shows the [GPGG + H – H2O]+ ion to have an imidazolone structure. Collision-induced dissociation of this [b4]+ ion results in the loss of HNCH2 from the first residue; the IRMPD spectrum of this MS3 product ion is very similar to that of the [b4]+ ion itself, strongly indicating that the [b4 – HNCH2]+ ion also has an imidazolone structure. Losses of CO and glycine are the dominant dissociation pathways for the [b4 – HNCH2]+ ion. The latter loss requires tautomerism of the keto-form of the imidazolone ring to become the lower-energy enol-form, prior to dissociation. Isotopic labelling showed that loss of CO occurs from the ring of the keto-form. Density functional theory calculations were performed at both the B3LYP/6–311++G (d,p) and M06–2X/6–311++G (d,p) levels and the results are in good agreement.

Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy.

Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]+, and as a Cu(ii) complex, [Cu(Cur - H)]+, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm-1) and hydrogen stretching (3100-3750 cm-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]+ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH3 groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]+ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.

Elusive Intermediates in the Breakdown Reactivity Patterns of Prodrug Platinum(IV) Complexes.

Kinetically inert platinum(IV) complexes are receiving growing attention as promising candidates in the effort to develop safe and valid alternatives to classical square-planar Pt(II) complexes currently used in antineoplastic therapy. Their antiproliferative activity requires intracellular Pt(IV)-Pt(II) reduction (activation by reduction). In the present work, a set of five Pt(IV) complexes has been assayed using mass spectrometry-based techniques, i.e., collision-induced dissociation (CID), and IR multiple photon dissociation (IRMPD) spectroscopy, together with ab initio theoretical investigations. Breakdown and reduction mechanisms are observed that lead to Pt(II) species. Evidence is found for typically transient Pt(III) intermediates along the dissociation paths of isolated, negatively charged (electron-rich) Pt(IV) prodrug complexes.

The Sequence of Coronene Hydrogenation Revealed by Gas-phase IR Spectroscopy

Abstract Gas-phase coronene cations ( ) can be sequentially hydrogenated with up to 24 additional H atoms, inducing a gradual transition from a planar, aromatic molecule toward a corrugated, aliphatic species. The mass spectra of hydrogenated coronene cations show that molecules with odd numbers of additional hydrogen atoms (n H) are dominant, with particularly high relative intensity for “magic numbers” n H = 5, 11, and 17, for which hydrogen atoms have the highest binding energies. Reaction barriers and binding energies strongly affect the hydrogenation sequence and its site specificity. In this contribution, we monitor this sequence experimentally by the evolution of infrared multiple-photon dissociation (IRMPD) spectra of gaseous with n H = 3–11, obtained using an infrared free electron laser coupled to a Fourier transform ion cyclotron mass spectrometer. For weakly hydrogenated systems (n H = 3, 5) multiple-photon absorption mainly leads to loss of H atoms (and/or H2). With increasing n H, C2H2 loss becomes more relevant. For n H = 9, 11, the carbon skeleton is substantially weakened and fragmentation is distributed over a large number of channels. A comparison of our IRMPD spectra with density functional theory calculations clearly shows that only one or two hydrogenation isomers contribute to each n H. This confirms the concept of hydrogenation occurring along very specific sequences. Moreover, the atomic sites participating in the first 11 steps of this hydrogenation sequence are clearly identified.

IRMPD action spectroscopy, ER-CID experiments, and theoretical approaches investigate intrinsic L-thymidine properties compared to D-thymidine: Findings support robust methodology

L-Thymidine (L-dThd) is the enantiomer of D-thymidine (dThd), a naturally-occurring pyrimidine nucleoside found within DNA nucleic acids. L-dThd, also known as Telbivudine, does not occur naturally, but in the last decade has found successful application as an antiviral medication for hepatitis B virus infection. In this work, the gas-phase conformers of the protonated and sodium cationized forms of L-dThd, [L-dThd+H]+ and [L-dThd + Na]+, are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy complemented by electronic structure calculations performed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. Comparisons between the experimental IRMPD spectra and theoretical linear IR spectra elucidate the stable low-energy conformations adopted by these L-dThd complexes generated by electrospray ionization. Minor 2,4-dihydroxy tautomers (T) and O2 protonated conformers contribute to the experimental [L-dThd+H]+ population, whereas conformers involving tridentate binding of Na+ to the O2, O4′, and O5′ atoms primarily contribute to the experimental [L-dThd + Na]+ population. Theory predicts a tautomer as the protonated ground conformer of [L-dThd+H]+ with thymine in an anti orientation and a tridentate (O2O4′O5′) sodium cationized ground conformer with a syn thymine orientation, consistent with theoretical predictions for [dThd+H]+ and [dThd + Na]+, respectively. Both protonated and sodium cationized L-dThd and dThd illustrate highly parallel IRMPD spectral features as expected. Survival yield analyses of data from energy-resolved collision-induced dissociation experiments elucidate the relative stabilities of [L-dThd+H]+ and [L-dThd + Na]+ as compared to the corresponding enantiomeric systems. Identical results are exhibited in the survival yield analyses as anticipated for enantiomeric complexes to simple cations. This work employs the same robust methodology that has provided structural characterization and energetic insight for similar systems preceding it to validate the parallel theoretical and experimental behaviors expected for enantiomers.

The structure of proton-bound Triethylammonia (X = F, Cl) Clusters

ABSTRACTIon pair complexes of triethylammonium, [(CH2CH3)3NH]+, and (X = F, Cl) are studied with a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy and density functional theory calculations. IRMPD spectra show that the charge-carrying proton is oriented towards a trigonal face of the halogenated closo-dodecaborate in both derivatives. Resonant IR absorption via or [(CH2CH3)3NH]+ bands in the 800–1600 cm−1 region drives dissociation via the lowest energy proton-transfer fragmentation channel and the charge transfer (i.e. redox) threshold, which is second lowest in energy. By tuning the power of the interrogating laser or the wavenumber (to select specific vibrational transitions), one can control the degree of fragmentation via the two lowest energy dissociation thresholds.

Impact of the 2'- and 3'-Sugar Hydroxyl Moieties on Gas-Phase Nucleoside Structure.

Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogues, those based on 2',3'-dideoxyribose sugars are quite common, particularly in anti-HIV applications. The gas-phase structures of several protonated 2',3'-dideoxyribose nucleosides are examined in this work and compared with those of the analogous protonated DNA, RNA, and arabinose nucleosides to elucidate the influence of the 2'- and combined 2',3'-hydroxyl groups on intrinsic structure. Infrared multiple photon dissociation (IRMPD) action spectra are collected for the protonated 2',3'-dideoxy forms of adenosine, guanosine, cytidine, thymidine and uridine, [ddAdo+H]+, [ddGuo+H]+, [ddCyd+H]+, [ddThd+H]+, and [ddUrd+H]+, in the IR fingerprint and hydrogen-stretching regions. Molecular mechanics conformational searching followed by electronic structure calculations generates low-energy conformers of the protonated 2',3'-dideoxynucleosides and corresponding predicted linear IR spectra to facilitate interpretation of the measured IRMPD action spectra. These experimental IRMPD spectra and theoretical calculations indicate that the absence of the 2'- and 3'-hydroxyls largely preserves the protonation preferences of the canonical forms. The spectra and calculated structures indicate a slight preference for C3'-endo sugar puckering. The presence of the 3'- and further 2'-hydroxyl increases the available intramolecular hydrogen-bonding opportunities and shifts the sugar puckering modes for all nucleosides but the guanosine analogues to a slight preference for C2'-endo over C3'-endo. Graphical Abstract.

Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence-Bond Modeling.

Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO2 (CH2 )n (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.

Structures of Rhodium Oxide Cluster Cations Rh7Om+ (m = 4–7, 12, 14) Revealed by Infrared Multiple Photon Dissociation Spectroscopy

Vibrational spectra of Rh7Om+ (m = 4–7, 12, 14) were measured in the 300–1300 cm–1 range via infrared multiple photon dissociation (IRMPD) spectroscopy. For the oxygen poor cluster sizes, Rh7Om+ (m = 4–7), IRMPD spectra were recorded through photodissociation of Rh7Om+–Ar complexes. IR spectra for Rh7Om+ (m = 12, 14) were recorded via the release of an O2 molecule from Rh7Om+ producing Rh7Om–2+; no O2 loss was observed from Rh7Om+ (m = 4–7, 8, 10). By comparison with the calculated vibrational spectra of several stable isomers obtained using density functional theory, these IR spectra are assigned to geometrical structures. For m = 4–7, all O atoms are bound to Rh atoms only, with a transition of the Rh core from capped octahedral to capped prismatic between m = 5 and m = 6. For the oxygen-rich Rh7O12+ and Rh7O14+, molecular O2 is adsorbed on a bridge site between two Rh atoms. The frequencies of the bands observed bands signal that the O2 molecules are activated, indicating that rhodium oxide clusters with Rh2O3 composition are still capable to donate electrons to activate O–O bonds in adsorbed O2.

Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches.

In this article, we report the results of gas-phase IR spectroscopy of neutral glycylglycine (Gly-Gly) in the 700-1850 cm-1 frequency range. A combination of laser desorption, jet-cooling, and IR multiple-photon dissociation vacuum-ultraviolet (IRMPD-VUV) action spectroscopy is employed, together with extensive quantum chemical calculations that assist in the analysis of the experimental data. As a result, we determined that the most favorable conformer in the low-temperature environment of the supersonic jet is the nearly planar structure with two C5 hydrogen-bonding interactions. Calculations clearly show that this conformer is favored because of its flexibility (considerable entropy stabilization) as well as efficient conformer relaxation processes in the jet. To gain more understanding into the relative stability of the lowest-energy Gly-Gly conformers, the relative strength of hydrogen bonding and steric interactions is analyzed using the noncovalent interactions (NCI) approach.

Spectroscopic diagnostic for the ring-size of carbohydrates in the gas phase: furanose and pyranose forms of GalNAc.

Hexoses are mainly found in nature in the pyranose form (6-membered ring). Yet, furanose forms (5-membered ring) are observed in some rare polysaccharides. Using IRMPD spectroscopy (InfraRed Multiple Photon Dissociation), we propose a straightforward diagnostic of the ring-size of N-acetyl galactosamine ions. The furanose form of N-acetyl galactosamine was synthesized and its protonated ion was isolated in an ion trap to measure its gas phase vibrational spectrum by IRMPD. Comparison with the IRMPD spectrum of its pyranose counterpart reveals that they have distinctive optical fingerprints. This new MS-based diagnostic opens the way to facile identification of the ring-size in oligosaccharides. Our experimental data also provide new insights to support the theoretical description of the conformational behavior of the furanose ring, which is notoriously more flexible than the pyranose form but remains difficult to assess.

Infrared photodissociation spectroscopy of di-manganese oxide cluster cations.

Infrared multiple-photon dissociation (IR-MPD) spectroscopy and density functional theory (DFT) calculations have been employed to elucidate the geometric structure of a series of di-manganese oxide clusters Mn2Ox+ (x = 4-7). The theoretical exploration predicts that all investigated clusters contain a rhombus-like Mn2O2 core with up to four, terminally bound, oxygen atoms. The short Mn-O bond length of the terminal oxygen atoms of ≤1.58 Å indicates triple bond character instead of oxyl radical formation. However, the IR-MPD spectra reveal that higher energy isomers with up to two O2 molecules η2-coordinated to the cluster core can be kinetically trapped under the given experimental conditions. In these complexes, all O2 units are activated to superoxide species. In addition, the sequential increase of the oxygen content in the cluster allows for a controlled increase of the positive charge localized on the Mn atoms reaching a maximum for Mn2O7+.