Infrared Multiple Photon Dissociation Spectra Research Articles

IR spectroscopic characterization of 3d transition metal carbene cations, FeCH2+ and CoCH2+: periodic trends and a challenge for DFT approaches.

A combination of IR multiple-photon dissociation (IRMPD) action spectroscopy and quantum chemical calculations was employed to investigate the [M,C,2H]+ (M = Fe and Co) species. These were formed by reacting laser ablated M+ ions with oxirane (ethylene oxide, c-C2H4O) in a room temperature ion trap. IRMPD spectra for the Fe and Co species are very similar and exhibit one major band. Comparison with density functional theory (DFT) and coupled cluster with single and double excitations (CCSD) calculations allows assignment of the spectra to MCH2+ carbene structures. For these 3d transition metal systems, experimental IRMPD spectra compare relatively poorly with DFT calculated IR spectra, but CCSD calculated spectra are a much better match primarily because the M-C stretch gains significant intensity. The origins of this behavior are explored in some detail. The present results are also compared to previous results for the 4d and 5d congeners and the periodic trends in these structures are evaluated.

IR spectroscopic characterization of [M,C,2H]+ (M = Ru and Rh) products formed by reacting 4d transition metal cations with oxirane: Spectroscopic evidence for multireference character in RhCH2.

A combination of infrared multiple-photon dissociation (IRMPD) action spectroscopy and quantum chemical calculations was employed to investigate the [M,C,2H]+ (M = Ru and Rh) species. These ions were formed by reacting laser ablated M+ ions with oxirane (ethylene oxide, c-C2H4O) in a room-temperature ion trap. IRMPD spectra for the Ru species exhibit one major band and two side bands, whereas spectra for the Rh species contain more distinct bands. Comparison with density functional theory (DFT), coupled-cluster (CCSD), and equation-of-motion spin-flip CCSD (EOM-SF-CCSD) calculations allows assignment of the [M,C,2H]+ structures. For the spectrum of [Ru,C,2H]+, a combination of HRuCH+ and RuCH2+ structures reproduces the observed spectrum at all levels of theory. The well-resolved spectrum of [Rh,C,2H]+ could not be assigned unambiguously to any calculated structure using DFT approaches. The EOM-SF-CCSD calculations showed that the ground-state surface has multireference electronic character, and symmetric carbenes in both the 1A1 and 3A2 states are needed to reproduce the observed spectrum.

Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium.

The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.

Vibrational spectroscopy of free di-manganese oxide cluster complexes with di-hydrogen

The reaction of free di-manganese oxide clusters Mn2Ox + (x = 2-7) with hydrogen in a flow tube reactor results in a strongly cluster size dependent complex formation: Mn2O3 + and Mn2O4 + are most reactive and adsorb up to two H2 molecules, the reactivity is reduced for Mn2O2 +/Mn2O5 +, and Mn2O6 +/Mn2O7 + appear to be non-reactive. Infrared multiple-photon dissociation (IR-MPD) spectra of the complexes Mn2O4H2 + and Mn2O5H2 + reveal one band that shifts upon isotopic labelling of hydrogen, whereas the spectra of Mn2O2H2 + and Mn2O3H2 + do not show any clear spectral shifts upon H2/D2 exchange. Detailed analysis of the IR-MPD spectra in conjunction with density functional theory (DFT) calculations strongly indicate the molecular η2-binding of H2 to one of the Mn atoms. H2 dissociation via hydroxylation of the cluster oxo bridges yielding H-Mn(MH)O(OH)O2 + or Mn2(OH)2O2 + appears to be thermodynamically favourable but kinetically hampered.

Protonated Forms of Naringenin and Naringenin Chalcone: Proteiform Bioactive Species Elucidated by IRMPD Spectroscopy, IMS, CID-MS, and Computational Approaches.

Naringenin (Nar) and its structural isomer, naringenin chalcone (ChNar), are two natural phytophenols with beneficial health effects belonging to the flavonoids family. A direct discrimination and structural characterization of the protonated forms of Nar and ChNar, delivered into the gas phase by electrospray ionization (ESI), was performed by mass spectrometry-based methods. In this study, we exploit a combination of electrospray ionization coupled to (high-resolution) mass spectrometry (HR-MS), collision-induced dissociation (CID) measurements, IR multiple-photon dissociation (IRMPD) action spectroscopy, density functional theory (DFT) calculations, and ion mobility-mass spectrometry (IMS). While IMS and variable collision-energy CID experiments hardly differentiate the two isomers, IRMPD spectroscopy appears to be an efficient method to distinguish naringenin from its related chalcone. In particular, the spectral range between 1400 and 1700 cm-1 is highly specific in discriminating between the two protonated isomers. Selected vibrational signatures in the IRMPD spectra have allowed us to identify the nature of the metabolite present in methanolic extracts of commercial tomatoes and grapefruits. Furthermore, comparisons between experimental IRMPD and calculated IR spectra have clarified the geometries adopted by the two protonated isomers, allowing a conformational analysis of the probed species.

5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations.

Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.

Gas-phase spectroscopy of photostable PAH ions from the mid- to far-infrared

ABSTRACT We present gas-phase InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy of cationic phenanthrene, pyrene, and perylene over the 100–1700 cm−1 (6–95 μm) spectral range. This range covers both local vibrational modes involving C–C and C–H bonds in the mid-IR, and large-amplitude skeletal modes in the far-IR. The experiments were done using the 7T Fourier-Transform Ion Cyclotron Resonance (FTICR) mass spectrometer integrated in the Free-Electron Laser for Intra-Cavity Experiments (FELICE), and findings were complemented with Density Functional Theory (DFT) calculated harmonic and anharmonic spectra, matching the experimental spectra well. The experimental configuration that enables this sensitive spectroscopy of the strongly bound, photoresistant Polycyclic Aromatic Hydrocarbons (PAHs) over a wide range can provide such high photon densities that even combination modes with calculated intensities as low as 0.01 km mol−1 near 400 cm−1 (25 μm) can be detected. Experimental frequencies from this work and all currently available IRMPD spectra for PAH cations were compared to theoretical frequencies from the NASA Ames PAH IR Spectroscopic Database to verify predicted trends for far-IR vibrational modes depending on PAH shape and size, and only a relatively small redshift (6–11 cm−1) was found between experiment and theory. The absence of spectral congestion and the drastic reduction in bandwidth with respect to the mid-IR make the far-IR fingerprints viable candidates for theoretical benchmarking, which can aid in the search for individual large PAHs in the interstellar medium.

Unveiling host–guest–solvent interactions in solution by identifying highly unstable host–guest configurations in thermal non-equilibrium gas phase

We propose a novel scheme of examining the host–guest–solvent interactions in solution from their gas phase structures. By adopting the permethylated β-cyclodextrin (perm β-CD)–protonated L-Lysine non-covalent complex as a prototypical system, we present the infrared multiple photon dissociation (IRMPD) spectrum of the gas phase complex produced by electrospray ionization technique. In order to elucidate the structure of perm β-CD)/LysH+ complex in the gas phase, we carry out quantum chemical calculations to assign the two strong peaks at 3,340 and 3,560 cm−1 in the IRMPD spectrum, finding that the carboxyl forms loose hydrogen bonding with the perm β-CD, whereas the ammonium group of L-Lysine is away from the perm β-CD unit. By simulating the structures of perm β-CD/H+/L-Lysine complex in solution using the supramolecule/continuum model, we find that the extremely unstable gas phase structure corresponds to the most stable conformer in solution.

Cation-π Interactions between a Noble Metal and a Polyfunctional Aromatic Ligand: Ag+ (benzylamine).

The structure of an isolated Ag+(benzylamine) complex is investigated by infrared multiple photon dissociation (IRMPD) spectroscopy complemented with quantum chemical calculations of candidate geometries and their vibrational spectra, aiming to ascertain the role of competing cation‐N and cation‐π interactions potentially offered by the polyfunctional ligand. The IRMPD spectrum has been recorded in the 800–1800 cm−1 fingerprint range using the IR free electron laser beamline coupled with an FT‐ICR mass spectrometer at the Centre Laser Infrarouge d'Orsay (CLIO). The resulting IRMPD pattern points toward a chelate coordination (N‐Ag+‐π) involving both the amino nitrogen atom and the aromatic π‐system of the phenyl ring. The gas‐phase reactivity of Ag+(benzylamine) with a neutral molecular ligand (L) possessing either an amino/aza functionality or an aryl group confirms N‐ and π‐binding affinity and suggests an augmented silver coordination in the product adduct ion Ag+(benzylamine)(L) .

IR Spectroscopic Characterization of Methane Adsorption on Copper Clusters Cun+ (n = 2-4).

The interaction of CH4 with cationic copper clusters has been studied with infrared-multiple photon dissociation (IRMPD) spectroscopy. Cun+ (n = 2–4) formed by laser ablation were reacted with CH4. The formed complexes were irradiated with the IR light of the free-electron laser for intracavity experiments (FELICE), and the fragments were mass-analyzed with a reflectron time-of-flight mass spectrometer. The structures of the Cun+–CH4 complexes are assigned on the basis of comparison between the resulting IRMPD spectra to spectra of different isomers calculated with density functional theory (DFT). For all sizes n, the structure found is one with molecularly adsorbed CH4. Only slight deformations of the CH4 molecule have been identified upon adsorption on the clusters, which results in redshifts of the spectroscopic bands. This deformation can be explained by charge transfer from the cluster to the adsorbed methane molecule.

Size-dependent H and H2 formation by infrared multiple photon dissociation spectroscopy of hydrated vanadium cations, V+(H2O)n, n = 3-51.

Infrared spectra of the hydrated vanadium cation (V+(H2O)n; n = 3–51) were measured in the O–H stretching region employing infrared multiple photon dissociation (IRMPD) spectroscopy. Spectral fingerprints, along with size-dependent fragmentation channels, were observed and rationalized by comparing to spectra simulated using density functional theory. Photodissociation leading to water loss was found for cluster sizes n = 3–7, consistent with isomers featuring intact water ligands. Loss of molecular hydrogen was observed as a weak channel starting at n = 8, indicating the advent of inserted isomers, HVOH+(H2O)n−1. The majority of ions for n = 8, however, are composed of two-dimensional intact isomers, concordant with previous infrared studies on hydrated vanadium. A third channel, loss of atomic hydrogen, is observed weakly for n = 9–11, coinciding with the point at which the H and H2O calculated binding energies become energetically competitive for intact isomers. A clear and sudden spectral pattern and fragmentation channel intensity at n = 12 suggest a structural change to inserted isomers. The H2 channel intensity decreases sharply and is not observed for n = 20 and 25–51. IRMPD spectra for clusters sizes n = 15–51 are qualitatively similar indicating no significant structural changes, and are thought to be composed of inserted isomers, consistent with recent electronic spectroscopy experiments.

Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes.

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol−1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.

IRMPD Spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and Corresponding CID Fragment Ions.

Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS2) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]+ and [PC 4:0/4:0 + Na/K - 183]+ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]+, [PC 4:0/4:0 + Na]+, and [PC 4:0/4:0 + K]+, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]+ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.

Cluster Size Dependent Interaction of Free Manganese Oxide Clusters with Acetic Acid and Methyl Acetate

We have employed infrared multiple-photon dissociation (IR-MPD) spectroscopy together with density functional theory (DFT) calculations to study the interaction of series of subnanometer sized manganese oxide clusters, MnxOy+ (x = 1-6, y = 0-9) with acetic acid (HOAc) and methyl acetate (MeOAc). Reaction with HOAc leads to strongly cluster size and composition dependent IR-MPD spectra, indicating molecular adsorption on MnOx+ clusters and thermodynamically favorable but kinetically hampered HOAc dissociation (deprotonation) on Mn2O4+ and Mn3O5+. Other cluster sizes exhibit the preferred formation of a dissociative bidentate chelating structure. In contrast to HOAc, all clusters bind MeOAc via the carbonyl group as an intact molecule, and dissociation appears to be kinetically hindered under the given experimental conditions.

Mid-infrared spectroscopic signatures of dibenzopyrene cations – The effect of symmetry on PAH IR spectroscopy

In this work, we characterize – for the first time – in the gas phase infrared spectra of three isomeric Polycyclic Aromatic Hydrocarbon (PAH) cations of C24H14 composition that belong to distinctly different symmetry groups (C2h, Cs and C1). Mid-infrared (Mid-IR) spectra are recorded by means of infrared multiple photon dissociation (IRMPD) spectroscopy at the free electron laser for infrared experiments (FELIX) laboratory. The measured infrared (IR) band positions compare reasonably well with density functional theory (DFT) calculated values. The number of IR active bands increases as the symmetry of the molecule lowers. The IRMPD spectra of irregular PAHs are found to be dense and do not resemble the sharp signatures typical of astronomical IR bands, but rather look like the broad plateau on which these are perched. This lends credit to the GrandPAH hypothesis that suggests that small and irregular PAHs are weeded out by the strong interstellar radiation field and only large regular PAHs remain.

Structural characterization of [M,C,2H]+ products formed by reaction of 5d metal cations Pt+ and Ir+ with ethylene oxide and Ta+ with methane using messenger spectroscopy

Structural characterization of gas-phase [M,C,2H]+ (M = Ta, Ir, Pt), formed by reacting laser ablation formed M+ with ethylene oxide (c-C2H4O) or methane under multiple collision conditions, is achieved using infrared multiple-photon dissociation (IR-MPD) spectroscopy with the intracavity free-electron laser FELICE. After product formation, part of the product distribution is complexed with Ar, allowing for simultaneous recording of IR-MPD spectra of both bare [M,C,2H]+, which dissociates via dehydrogenation, and [M,C,2H]+∙Ar, which loses Ar. Comparison of the spectra with density functional theory (DFT) calculations allows for an internally consistent assignment of the spectra to the Ta+CH2 (3A′′) distorted carbene, Pt+CH2 (2A1) carbene, and to the HIr+CH (1A′) carbyne-hydride. Evidence for a symmetric Ta+CH2∙Ar (3B2) complex is also obtained. For Pt and Ir, these structures match those found in previous work when these species were formed by reaction of M+ with methane, CH4 and CD4. Under the current conditions, no clear signs of the previously observed Ir+CH2 (3A2) carbene product were found, consistent with its higher energy, especially after Ar complexation. Potential energy surfaces for the reactions of Pt+ and Ir+ with c-C2H4O are also computed.

Infrared multiple photon dissociation action spectroscopy of protonated unsymmetrical dimethylhydrazine and proton-bound dimers of hydrazine and unsymmetrical dimethylhydrazine.

The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser and an optical parametric oscillator laser system. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP-GD3BJ/6-311+G(d,p) level of theory. These comparisons show that protonated UDMH binds the proton at the methylated nitrogen atom (α) with two low-lying α conformers probably being populated. For (UDMH)2H+, the proton is shared between the methylated nitrogen atoms with several low-lying α conformers likely to be populated. Higher-lying conformers of (UDMH)2H+ in which the proton is shared between α and β (unmethylated) nitrogen atoms cannot be ruled out on the basis of the IRPMD spectrum. For (N2H4)2H+, there are four low-lying conformers that all reproduce the IRMPD spectrum reasonably well. As hydrazine and UDMH see usage as fuels for rocket engines, such spectra are potentially useful as a means of remotely monitoring rocket launches, especially in cases of unsuccessful launches where environmental hazards need to be assessed.

Infrared Study of OCS Binding and Size-Selective Reactivity with Gold Clusters, Aun+ (n = 1-10).

OCS binding to and reactivity with isolated gold cluster cations, Aun+ (n = 1-10), has been studied by infrared multiple photon dissociation (IR-MPD) spectroscopy in conjunction with quantum chemical calculations. The distribution of complexes AunSx(OCS)m+ formed reflects the relative reactivity of different cluster sizes with OCS, under the multiple collision conditions of our ablation source. The IR-MPD spectra of Aun(OCS)+ (n = 3-10) clusters are interpreted in terms of either μ1 or μ2 S binding motifs. Analysis of the fragmentation products following infrared excitation of parent Aun(OCS)+ clusters reveals strongly size-selective (odd-even) branching ratios for OCS and CO loss, respectively. CO loss signifies infrared-driven OCS decomposition on the cluster surface and is observed to occur predominantly on even n clusters (i.e., those with odd electron counts). The experimental data, including fragmentation branching ratios, are consistent with calculated potential energy landscapes, in which the initial species trapped are molecularly bound entrance channel complexes, rather than global minimum inserted structures. Attempts to generate Rhn(OCS)+ and Ptn(OCS)+ equivalents failed; only sulfide reaction products were observed in the mass spectrum, even after cooling the cluster source to -100 °C.

Energetic Stabilization of Carboxylic Acid Conformers by Manganese Atoms and Clusters.

Free cationic manganese atoms and clusters Mnx+ (x = 1-3) have been reacted with small carboxylic acids (formic, acetic, and propionic acids) and methyl acetate in a flow tube reactor held at room temperature. The geometry of the thus formed complexes has subsequently been studied via infrared multiple-photon dissociation (IR-MPD) spectroscopy and density-functional theory (DFT) calculations. The IR-MPD spectra of the acid complexes show two signals in the C═O stretch region indicating the coexistence of two conformers. In agreement, the DFT calculations reveal that the-intrinsically less stable-cis-conformer of the carboxylic acids binds more strongly to Mn+ than the trans-conformer, which leads to the energetic stabilization of the former. This stronger binding is attributed to a stronger electrostatic interaction with the manganese cation. A similar stabilization is also predicted for the cis-conformer of methyl acetate; however, the resulting change of the C═O stretch eigenfrequency is too small to be resolved in the experiment. This finding can open up completely new routes for the future room-temperature preparation of the cis-conformers of carboxylic acids and their derivatives.

A Combined Infrared Ion Spectroscopy and Computational Chemistry Study of Hydroxyproline Isomers.

Hydroxyproline is a common variation of proline, with diverse biological roles. The hydroxylation of proline gives rise to several (natural and/or synthetic) isomeric forms, including both positional isomers and stereoisomers. While mass spectrometry is widely touted as a very selective analytical technique, the identification of closely related isomers often poses a challenge. In these cases, allied technologies become helpful in providing full characterization. Here, infrared multiple photon dissociation (IRMPD) spectroscopy is used to differentiate between three isomers, namely cis-3-hydroxyproline, cis-4-hydroxyproline, and trans-4-hydroxyproline. In contrast to the protonated species which show only minor variations in their IRMPD spectra, lithiated species were found to display significant spectral differences, making their differentiation more straightforward. The conformational origin of these spectral differences was investigated by complementary quantum-chemical calculations.