The Structure of Deprotonated Tri-Alanine and Its a3− Fragment Anion by IR Spectroscopy

We present the first infrared spectra of a mass-selected deprotonated peptide anion (AlaAlaAla) and its decarboxylated fragment anion formed by collision induced dissociation. Spectra are obtained by IRMPD spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Spectra have been recorded over the 800–1800 cm−1 spectral range and compared with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. These experiments suggest a carboxylate anion for [M − H]− and an amide deprotonated (amidate) structure for the a3 fragment anion [M − H − CO2]−. The frequency for the amidate carbonyl stretch occurring around 1555 ± 5 cm−1 has been confirmed by additional spectroscopic studies of the conjugated base of N-methylacetamide, which serves as a simple model system for the deprotonated amide linkage in a peptide anion

Infrared ion spectroscopy at felix: applications in peptide dissociation and analytical chemistry

Infrared free electron lasers such as those in Paris, Berlin and Nijmegen have been at the forefront of the development of infrared ion spectroscopy. In this contribution, I will give an overview of new developments in IR spectroscopy of stored ions at the FELIX Laboratory. In particular, I will focus on recent developments made possible by the coupling of a new commercial ion trap mass spectrometer to the FELIX beamline. The possibility to record IR spectra of mass-selected molecular ions and their reaction products has in recent years shed new light on our understanding of collision induced dissociation (CID) reactions of protonated peptides in mass spectrometry (MS). We now show that it is possible to record IR spectra for the products of electron transfer dissociation (ETD) reactions \begin{equation} [M + nH]^{n+} + A^{-} ~ \rightarrow ~ [M + nH]^{(n-1)+} + A ~ \rightarrow ~ {\rm dissociation~of~analyte} \nonumber \end{equation} \noindent These reactions are now widely used in novel MS-based protein sequencing strategies, but involve complex radical chemistry. The spectroscopic results allow stringent verification of computationally predicted product structures and hence reaction mechanisms and H-atom migration. The sensitivity and high dynamic range of a commercial mass spectrometer also allows us to apply infrared ion spectroscopy to analytes in complex “real-life” mixtures. The ability to record IR spectra with the sensitivity of mass-spectrometric detection is unrivalled in analytical sciences and is particularly useful in the identification of small (biological) molecules, such as in metabolomics. We report preliminary results of a pilot study on the spectroscopic identification of small metabolites in urine and plasma samples

Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.The infrared (IR) spectrum of protonated histamine (histamineH+) was recorded in the 575–1900 cm−1 fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum of mass-selected histamineH+ ions was obtained in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. A variety of isomers were identified and characterized by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. The low-energy isomers are derived from various favourable protonation sites—all of which are N atoms—and different orientations of the ethylamine side chain with respect to the heterocyclic imidazole ring. The measured IRMPD spectrum was monitored in the NH3 loss channel and exhibits 14 bands in the investigated spectral range, which were assigned to vibrational transitions of the most stable isomer, denoted A. This imidazolium-type isomer A with protonation at the imidazole ring and gauche conformation of the ethylamine side chain is significantly stabilized by an intramolecular ionic Nπ–H+⋯Nα hydrogen bond to the ethylamino group. The slightly less stable ammonium-type isomer B with protonation at the ethylamino group is only a few kJ mol−1 higher in energy and may also provide a minor contribution to the observed IRMPD spectrum. Isomer B is derived from A by simple proton transfer from imidazole to the ethylamino group along the intramolecular Nπ–H+⋯Nα hydrogen bond via a low barrier, which is calculated to be of the order of 5–15 kJ mol−1. Significantly, the most stable structure of isolated histamineH+ differs from that in the condensed phase by both the protonation site and the conformation of the side chain, emphasizing the important effects of solvation on the structure and function of this neurotransmitter. The effects of protonation on the geometric and electronic structure of histamine are evaluated by comparing the calculated properties of isomer A with those of the most stable structure of neutral histamine A(n).EC/FP7/226716/EU/European Light Sources Activities - Synchrotrons and Free Electron Lasers/ELIS

The structure and energetics of 3^3He and 4^4He nanodroplets doped with alkaline earth atoms

We present systematic results, based on density functional calculations, for the structure and energetics of $^3$He and $^4$He nanodroplets doped with alkaline earth atoms. We predict that alkaline earth atoms from Mg to Ba go to the center of $^3$He drops, whereas Ca, Sr, and Ba reside in a deep dimple at the surface of $^4$He drops, and Mg is at their center. For Ca and Sr, the structure of the dimples is shown to be very sensitive to the He-alkaline earth pair potentials used in the calculations. The $5s5p\leftarrow5s^2$ transition of strontium atoms attached to helium nanodroplets of either isotope has been probed in absorption experiments. The spectra show that strontium is solvated inside $^3$He nanodroplets, supporting the calculations. In the light of our findings, we emphasize the relevance of the heavier alkaline earth atoms for analyzing mixed $^3$He-$^4$He nanodroplets, and in particular, we suggest their use to experimentally probe the $^3$He-$^4$He interface.Comment: Typeset using Revtex, 20 pages and 8 Postscript file

A Cl− hinge for cyclen macrocycles: Ionic Interactions and tweezer-like complexes

The supramolecular networks derived from the complexation of polyazamacrocycles with halide anions constitute fundamental building blocks of a broad range of modern materials. This study provides insights into the conformational framework that supports the binding of protonated cyclen macrocyles (1,4,7,10-Tetraazacyclododecane) by chloride anions through NH δ+ ···Cl - interactions. The isolated complex comprised of two cyclen hosts linked by one Cl - anion is characterized by means of infrared action spectroscopy and ion mobility mass spectrometry, in combination with quantum chemical computations. The Cl - anion is found to act as a hinge that bridges the protonated NH2+ moieties of the two macrocycles leading to a molecular tweezer configuration. Different types of conformations emerge, depending on whether the trimer adopts an open arrangement, with significant freedom for internal rotation of the cyclen moieties, or it locks in a folded conformation with intermolecular H-bonds between the two cyclen backbones. The ion mobility collision cross section supports that folded configurations of the complex are dominant under isolated conditions in the gas phase. The IRMPD spectroscopy experiments suggest that two qualitatively different families of folded conformations coexist at room temperature, featuring either peripheral or inner positions of the anion with respect to the macrocycle cavities, These findings should have implications in the growth of extended networks in the nanoscale and in sensing applicationsThe research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. This study is part of project P12-FQM-4938 of the research programme of Junta de Andalucia and FEDER

Infrared action spectroscopy of doubly charged PAHs and their contribution to the aromatic infrared bands

The so-called aromatic infrared bands are attributed to emission of polycyclic aromatic hydrocarbons. The observed variations toward different regions in space are believed to be caused by contributions of different classes of PAH molecules, i.e. with respect to their size, structure, and charge state. Laboratory spectra of members of these classes are needed to compare them to observations and to benchmark quantum-chemically computed spectra of these species. In this paper we present the experimental infrared spectra of three different PAH dications, naphthalene$^{2+}$, anthracene$^{2+}$, and phenanthrene$^{2+}$, in the vibrational fingerprint region 500-1700~cm$^{-1}$. The dications were produced by electron impact ionization of the vapors with 70 eV electrons, and they remained stable against dissociation and Coulomb explosion. The vibrational spectra were obtained by IR predissociation of the PAH$^{2+}$ complexed with neon in a 22-pole cryogenic ion trap setup coupled to a free-electron infrared laser at the Free-Electron Lasers for Infrared eXperiments (FELIX) Laboratory. We performed anharmonic density-functional theory calculations for both singly and doubly charged states of the three molecules. The experimental band positions showed excellent agreement with the calculated band positions of the singlet electronic ground state for all three doubly charged species, indicating its higher stability over the triplet state. The presence of several strong combination bands and additional weaker features in the recorded spectra, especially in the 10-15~$\mu$m region of the mid-IR spectrum, required anharmonic calculations to understand their effects on the total integrated intensity for the different charge states. These measurements, in tandem with theoretical calculations, will help in the identification of this specific class of doubly-charged PAHs as carriers of AIBs.Comment: Accepted for publication in A&

Infrared spectroscopy of ionized corannulene in the gas phase

The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H2, and C2Hx losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp3 hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C5v geometry induced by the Jahn-Teller effect as a consequence of the degenerate 2E1 ground electronic state. As indicated by the calculations, the five equivalent Cs minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm−1 region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation

Infrared Multiple-Photon Dissociation Action Spectroscopy of the b(2)(+) Ion from PPG: Evidence of Third Residue Affecting b(2)(+) Fragment Structure

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2 + fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2 + ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2 + ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPGprecursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation

Unravelling the Keto–Enol Tautomer Dependent Photochemistry and Degradation Pathways of the Protonated UVA Filter Avobenzone

Avobenzone (AB) is a widely used UVA filter known to undergo irreversible photodegradation. Here, we investigate the detailed pathways by which AB photodegrades by applying UV laser-interfaced mass spectrometry to protonated AB ions. Gas-phase infrared multiple-photon dissociation (IRMPD) spectra obtained with the free electron laser for infrared experiments, FELIX, (600–1800 cm–1) are also presented to confirm the geometric structures. The UV gas-phase absorption spectrum (2.5–5 eV) of protonated AB contains bands that correspond to selective excitation of either the enol or diketo forms, allowing us to probe the resulting, tautomer-dependent photochemistry. Numerous photofragments (i.e., photodegradants) are directly identified for the first time, with m/z 135 and 161 dominating, and m/z 146 and 177 also appearing prominently. Analysis of the production spectra of these photofragments reveals that that strong enol to keto photoisomerism is occurring, and that protonation significantly disrupts the stability of the enol (UVA active) tautomer. Close comparison of fragment ion yields with the TD-DFT-calculated absorption spectra give detailed information on the location and identity of the dissociative excited state surfaces, and thus provide new insight into the photodegradation pathways of avobenzone, and photoisomerization of the wider class of β-diketone containing molecules