Multiphoton Dissociation Spectra Research Articles

Structural connectivity of 18‐Crown‐6/H+/L‐tryptophan noncovalent complexes in gas phase and in solution: Delineating host–guest–solvent interactions in solution from gas phase structures

AbstractWe investigate the structural correlation of noncovalent crown ether/H+/L‐tryptophan (CR/TrpH+) host–guest complexes in the solution phase with those in the gas phase generated through electrospray ionization/mass spectrometry (ESI/MS) techniques. We perform quantum chemical calculations to determine their structures, relative Gibbs free energies, and infrared spectra. We compare the calculated infrared (IR) spectra with the IR multiphoton dissociation (IRMPD) spectra observed for the 18‐Crown‐6/TrpH+ complex by Polfer and co‐workers [J. Phys. Chem. A 2013, 117, 1181–1188] for assigning the IR bands. We observe that the carboxyl group remains “naked,” lacking hydrogen bonding with the CR unit in the gas phase, and that this most stable conformer originates from the corresponding lowest Gibbs free energy structure in solution. Based on these findings, we propose that gas phase host–guest complexes directly correlate with those in solution, reinforcing the possibility of obtaining invaluable information about host–guest–solvent interactions in solution from the structure of the host–guest pair in the gas phase.

Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies.

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Structure of protonated heterodimer of proline and phenylalanine: Revealed by infrared multiphoton dissociation spectroscopy and theoretical calculations

The infrared multiphoton dissociation (IRMPD) spectrum of the protonated heterodimer of ProPheH+, in the range of 2700-3700 cm−1, has been obtained with a Fourier-transform ion cyclotron mass spectrometer combined with an IR OPO laser. The experimental spectrum shows one peak at 3565 cm−1 corresponding to the free carboxyl O-H stretching vibration, and two broad peaks centered at 2935 and 3195 cm−1. Theoretical calculations were performed on the level of M062X/6-311++G(d,p). Results show that the most stable isomer is characterized by a charge-solvated structure in which the proton is bound to the unit of proline. Its predicted spectrum is in good agreement with the experimental one, although the coexistence of salt-bridged structures cannot be entirely excluded.

Communication: Gas phase vibrational spectroscopy of the azide-water complex.

The vibrational spectra of the azide-water complex, N3 -(H2O), and its fully deuterated isotopologue are studied using infrared photodissociation (IRPD) spectroscopy (800-3800 cm-1) and high-level ab initio computations. The IRPD spectrum of the H2-tagged complex exhibits four fundamental transitions at 3705, 3084, 2003, and 1660 cm-1, which are assigned to the free OH stretching, the hydrogen-bonded O-H stretching, the antisymmetric N3 stretching, and the water bending mode, respectively. The IRPD spectrum is consistent with a planar, singly hydrogen-bonded structure according to an MP2 and CCSD(T) anharmonic analysis via generalized second-order vibrational perturbation theory. The red-shift of the hydrogen-bonded OH stretching fundamental of 623 cm-1 associated with this structure is computed within 6 cm-1 (or 1%) and is used to estimate the proton affinity of azide (1410 kJ mol-1). Born-Oppenheimer molecular dynamics simulations show that large amplitude motions are responsible for the observed band broadening at cryogenic temperature. Temperature-dependent (6-300 K) IR multiphoton dissociation spectra of the untagged complex are also presented and discussed in the context of spectral diffusion observed in the condensed phase.

Endo or Exo? Structures of Gas-Phase Alkali Metal Cation/Aromatic Half-Belt Complexes.

1,1,9,9-Tetramethyl[9](2,11)teropyrenophane (TM9TP), a belt-shaped molecule, has a sizable cavity that molecules or ions could occupy. In this study, the question of whether TM9TP forms gas-phase ion-molecule complexes with metal cations (K+ , Rb+ , Cs+ ) situated inside or outside the TM9TP cavity was addressed using both experimental and computational methods. Complexes were trapped in a Fourier transform ion cyclotron resonance mass spectrometer and their structures were explored by some novel physical chemistry/mass spectrometry methods. Blackbody infrared radiative dissociation kinetics reveal two populations of ions, a fast dissociating fraction and a persistent fraction. Infrared multiphoton dissociation spectra (vibrational spectra) provide very strong evidence that the most abundant population is a complex where the metal cation is inside the TM9TP cavity, endo-TM9TP. Red-shifted C-H stretching bands present in the gas-phase vibrational spectra of these ionic complexes show that there is an interaction between the metal cation and bridge C-H bonds due to the cation sitting inside the cavity of TM9TP. B3LYP/6-31+G(d,p) calculations showed the endo complexes to be the lowest in energy; about 60 kJ mol-1 more thermodynamically stable and more than 120 kJ mol-1 kinetically more stable than the exo complex.

Uranyl/12-crown-4 Ether Complexes and Derivatives: Structural Characterization and Isomeric Differentiation.

The following gas-phase uranyl/12-crown-4 (12C4) complexes were synthesized by electrospray ionization: [UO2(12C4)2]2+ and [UO2(12C4)2(OH)]+. Collision-induced dissociation (CID) of the dication resulted in [UO2(12C4-H)]+ (12C4-H is a 12C4 that has lost one H), which spontaneously adds water to yield [UO2(12C4-H)(H2O)]+. The latter has the same composition as complex [UO2(12C4)(OH)]+ produced by CID of [UO2(12C4)2(OH)]+ but exhibits different reactivity with water. The postulated structures as isomeric [UO2(12C4-H)(H2O)]+ and [UO2(12C4)(OH)]+ were confirmed by comparison of infrared multiphoton dissociation (IRMPD) spectra with computed spectra. The structure of [UO2(12C4-H)]+ corresponds to cleavage of a C-O bond in the 12C4 ring, with formation of a discrete U-Oeq bond and equatorial coordination by three intact ether moieties. Comparison of IRMPD and computed IR spectra furthermore enabled assignment of the structures of the other complexes. Theoretical studies of the chemical bonding features of the complexes provide an understanding of their stabilities and reactivities. The results reveal bonding and structures of the uranyl/12C4 complexes and demonstrate the synthesis and identification of two different isomers of gas-phase uranyl coordination complexes.

Identification of the fragment of the 1-methylpyrene cation by mid-IR spectroscopy

The fragment of the 1-methylpyrene cation, C17H11+, is expected to exist in two isomeric forms, 1-pyrenemethylium PyrCH2+ and the tropylium containing species PyrC7+. We measured the infrared (IR) action spectrum of cold C17H11+ tagged with Ne using a cryogenic ion trap instrument coupled to the FELIX laser. Comparison of the experimental data with density functional theory calculations allows us to identify the PyrCH2+ isomer in our experiments. The IR Multi-Photon Dissociation spectrum was also recorded following the C2H2 loss channel. Its analysis suggests combined effects of anharmonicity and isomerisation while heating the trapped ions, as shown by molecular dynamics simulations.

Spectroscopic Discrimination of Diastereomeric Complexes Involving an Axially Chiral Receptor.

The infrared multiphoton dissociation (IRMPD) spectra of electrospray ionization (ESI)-formed proton-bound complexes between the axially chiral multifunctional macrocycle MaR and d- and l-phenylalanine (PD and PL ) or d- and l-3,4-dihydroxyphenylalanine (DD and DL ) are recorded in the ν˜ =2800-3700 cm-1 region. Whereas the diastereomeric [MaR ⋅H⋅PD ]+ and [MaR ⋅H⋅PL ]+ complexes do not show any significant spectral differences, the spectrum of [MaR ⋅H⋅DD ]+ clearly diverges from that of its [MaR ⋅H⋅DL ]+ diastereomer. A comparison of the experimental spectra with the B3LYP/6-31G**-calculated harmonic vibrational frequencies of a number of stable structures indicates the formation, in the ESI source, of very similar spectroscopically active structures, with the protonated amino acid placed outside the flat cavity of the macrocycle and hydrogen-bonded at its O2 center. Different spectral signatures of the [MaR ⋅H⋅DD ]+ and [MaR ⋅H⋅DL ]+ complexes are attributed to the coexistence of several stable rotamers in the ESI source.

IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions.

Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800-1830 cm-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs+LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M+-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.

IRMPD spectroscopy of metalated flavins: structure and bonding of M(q+)-lumichrome complexes (M(q+) = Li⁺-Cs⁺, Ag⁺, Mg²⁺).

Infrared multiphoton dissociation (IRMPD) spectra of mass selected isolated metal-lumichrome ionic complexes, M(q+)LCn with M(q+) = Li(+), Na(+), K(+), Rb(+), Cs(+), Ag(+) (n = 1), and Mg(2+) (n = 2), are recorded in the fingerprint range. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by density functional theory calculations at the B3LYP/cc-pVDZ level, which provide insight into the structure, binding energy, bonding mechanism, and spectral properties of the complexes. The two major binding sites identified involve metal bonding to the oxygen atoms of the two available carbonyl groups of LC (denoted O2 and O4). The more stable O4 isomer benefits from an additional interaction with the lone pair of the nearby N5 atom of LC. While M(+)LC with alkali metals are mainly stabilized by electrostatic forces, the Ag(+)LC complex reveals additional stabilization arising from partly covalent contributions. Finally, the interaction of Mg(2+) ions with LC is largely enhanced by the doubled positive charge. The frequencies of the C[double bond, length as m-dash]O stretching modes are a sensitive indicator of both the metal binding site and the metal bond strength.

Infrared Multiphoton Dissociation Spectroscopy of Protonated 1,2-Diaminoethane-water Clusters: Vibrational Assignment via the MP2 Method

Infrared multiphoton dissociation (IRMPD) spectra of various protonated 1,2-diaminoethane-water clusters DAE- (n = 1-6) were measured in the wavelength range of 3000-3800 . The IRMPD spectra of the well separated ionic clusters were simulated by the MP2 method employing various basis sets. Comparison of the IRMPD spectra with the theory indicates that each cluster may exist as several low-lying conformers, and the sum spectra of the various conformers reveal almost one to one correspondence between theory and experiment. Free N-H and O-H stretches are observed in the ranges of 3400-3500 and 3600-3800 , respectively. The and stretches are, however, observed in the broad region of 3000-3600 . The theoretical calculations on DAE- (n = 1-4) show gradual decrease of the average binding energy between DAE- and as the cluster size increases, attaining the lowest value of 55 kJ/mol when n = 4. We found a low energy barrier of 21 kJ/mol to the isomerization converting the lowest energy cluster of DAE- to the second lowest one.

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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.

Infrared Multiphoton Dissociation Spectroscopy Study of Protonated p-Aminobenzoic Acid: Does Electrospray Ionization Afford the Amino- or Carboxy-Protonated Ion?

Infrared multiphoton dissociation spectra of protonated p-aminobenzoic acid generated by electrospray ionization (ESI) from aqueous methanol and acetonitrile solutions were recorded in the gas phase from 2800-4000 cm(-1). The O-protonated ion is more stable than the N-protonated structure in the gas phase, whereas the opposite is true in both solutions. When CH(3)OH/H(2)O was used as the ESI solvent, only the O-protonated ion was observed. In contrast, a 70:30 mixture of the O- and N-protonated species were produced from CH(3)CN/H(2)O. These structural assignments are based on an assortment of experimental data (action spectra, photofragments, photofragmentation kinetics, and H/D exchange) and are fully supported by extensive computations. This work shows that ESI can lead to isomerization and that the ionization site may be varied by changing the solvent from which the substrate is analyzed.

Multivariate Analysis of Electron Detachment Dissociation and Infrared Multiphoton Dissociation Mass Spectra of Heparan Sulfate Tetrasaccharides Differing Only in Hexuronic acid Stereochemistry

The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture.

The hydrated Li +–adenine–thymine complex by IRMPD spectroscopy in the N–H/O–H stretching region

The interaction of lithium ions with the nucleic acid bases which make up the A:T base pair, adenine and thymine, as well as the hydration of the complex by one water molecule has been studied in the gas phase. An IRMPD spectrum is reported for [A–T–Li +]–H 2O (A = adenine, T = thymine) over the N–H stretching region, 3200–3800 cm −1. Calculations were performed using the B3LYP density functional and 6-31+G(d,p) basis set as well as MP2/6-311++G(2d,p) theory to model the thermochemistry and infrared spectra of potential structures. Theory and experimental results were used to determine possible structures of each complex. These structures, along with their corresponding thermochemical and spectroscopic data, are reported here. The lithium cation was found to bond most favorably to the O4 oxygen of thymine, and the water molecule was found to bind to the lithium cation. The adenine moiety of the complex is that of the A7 tautomer, leading to an A:T base pair which is not the canonical form. Based on the analysis, a number of low energy, intramolecular hydrogen-bonded structures are suggested as being present in the gas phase and thus responsible for generating the experimental infrared multi-photon dissociation (IRMPD) spectrum.

Structure of Zirconocene Complexes Relevant for Olefin Catalysis: Infrared Fingerprint of the Zr(C5H5)2(OH)(CH3CN)+ Cation in the Gas Phase

Cationic zirconocene complexes are active species in Ziegler-Natta catalysis for olefin polymerization. Their structure and metal-ligand bond strength strongly influence their activity. In the present work, the infrared multiphoton dissociation (IRMPD) spectrum of mass selected Zr(C(5)H(5))(2)(OH)(CH(3)CN)(+) cations was obtained in the 300-1500 cm(-1) fingerprint range by coupling a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization (ESI) source and the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO). The experimental efforts are complemented by quantum chemical calculations at the MP2 and B3LYP levels using the 6-311G* basis set. Vibrational assignments of transitions observed in the IRMPD spectra to modes of the Zr-O-H, C(5)H(5), and CH(3)CN moieties are based on comparison to calculated linear absorption spectra. Both the experimental data and the calculations provide unprecedented information about structure, metal-ligand bonding, charge distribution, and binding energy of the complex.

Redox Processes in the Iron(III)/9,10-Phenanthraquinone System

With the use of the model complexes [(PQ)FeCl(CH(3)O)](+), [(phen)FeCl(CH(3)O)](+), and [(PQ)(phen)FeCl(CH(3)O)](+), where PQ is 9,10-phenanthraquinone and phen is 1,10-phenanthroline, the reactivity of phenanthraquinone in complexes with iron(III) is investigated. It is shown that 9,10-phenanthraquinone takes part in redox processes occurring at iron and thereby allows the oxidation of methanolate to formaldehyde. The oxidation is driven by the reduction of iron(III) to iron(II) and 9,10-phenanthraquinone to the semihydroquinone radical or semiquinolate, if the hydrogen atom is transferred from methanolate to chlorine rather than PQ. 1,10-Phenanthroline, on the other hand, acts as an innocent ligand, and the [(phen)FeCl(CH(3)O)](+) complex shows a typical two-state reactivity. The reactivity of [(PQ)(phen)FeCl(CH(3)O)](+) reveals that the hexacoordination of iron energetically facilitates the oxidation of methanolate, and therefore it is proposed that, in the presence of suitable reductants, the mixture of iron(III) and 9,10-phenanthraquinone can lead to the generation of the semihydroquinone radicals, species responsible for the toxicity of PQ. The fragmentation of [(PQ)(phen)FeCl(CH(3)O)](+) also demonstrates a strong binding of phen toward iron(III), which is a reason for using phen as an iron chelator in biochemistry. The structures and reactivities of the complexes are investigated by means of mass spectrometry, infrared multiphoton dissociation spectra, and density functional theory calculations.

Infrared multiphoton dissociation spectrum of isolated protonated 1-azapyrene

The infrared spectrum of protonated 1-azapyrene has been obtained by infrared multiphoton dissociation (IRMPD) spectroscopy using a Fourier-transform ion cyclotron resonance mass spectrometer coupled to an infrared tunable free electron laser. Found when electrospraying a pyrene/methanol/acetic acid solution, the carrier of the dominant m/z 204 peak was determined by comparison of the IRMPD spectrum with density functional theory calculations (B3LYP/6-31G(d,p)). The greater proton affinity and solubility of 1-azapyrene explains the competitive protonation of azapyrene over pyrene despite its apparent smaller abundance in the electrospray solution. The possible contribution of 1-azapyrene to the interstellar infrared emission bands is briefly discussed.

Density functional theory calculations of vibrational spectra of rhodium oxide clusters

Predicted infrared vibrational spectra of low-energy isomers of rhodium cluster oxides, Rh6Om+(m=1–4), are presented, based on structures calculated using density functional theory. The oxygen stretching frequencies are found to be characteristic of the oxygen binding mode. These simulated spectra provide a guide to future experimental measurements of the infrared multi-photon dissociation spectra, enabling assignment of the binding sites of oxygen atoms on the cluster. In favourable cases these calculations suggest that a determination of the underlying metal framework structure is possible.

Electron Detachment Dissociation of Neutral and Sialylated Oligosaccharides

Electron detachment dissociation (EDD) has recently been shown by Amster and coworkers to constitute a valuable analytical approach for structural characterization of glycosaminoglycans. Here, we extend the application of EDD to neutral and sialylated oligosaccharides. Both branched and linear structures are examined, to determine whether branching has an effect on EDD fragmentation behavior. EDD spectra are compared to collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) spectra of the doubly and singly deprotonated species. Our results demonstrate that EDD of both neutral and sialylated oligosaccharides provides structural information that is complementary to that obtained from both CAD and IRMPD. In all cases, EDD resulted in additional cross-ring cleavages. In most cases, cross-ring fragmentation obtained by EDD is more extensive than that obtained from IRMPD or CAD. Our results also indicate that branching does not affect EDD fragmentation, contrary to what has been observed for electron capture dissociation (ECD).