Infrared Photodissociation Spectra Research Articles

IR and UV Spectroscopy of Gas-Phase Monohydrated Protonated Guanine.

We use UV and infrared photodissociation spectroscopy to study monohydrated protonated guanine in a dual cryogenic ion trap spectrometer. The monohydrated complexes are formed through helium-mediated collisions between bare electrosprayed protonated guanine and low-pressure water vapor in a clustering trap maintained at 180 K, before being transferred to a quadrupole ion trap at 10 K. The spectrum of the monohydrated complex exhibits sharp vibronic transitions at the band origin and becomes broader and higher in intensity further in blue, which is very similar to protonated guanine but with a notable blue shift of ∼1850 cm-1 (∼0.23 eV). The UV hole-burning experiments showed that the vibronic bands recorded in the region of the band origin belong to a single conformer under our experimental conditions. The IR photodissociation spectrum in the 3000-3600 cm-1 range, with the aid of theoretical calculations (SCS-CC2/aug-cc-pVDZ), allowed us to assign the structure to the lowest energy N7-O conformer.

Cryogenic Ion Vibrational Spectroscopy of Protonated Valine: Messenger Tag Effects.

We report the infrared photodissociation spectrum of tagged protonated valine in the range 1000-1900 cm-1, prepared in a cryogenic ion trap. Comparison of experimental results with calculated infrared spectra based on density functional theory shows that the hydroxyl group of the carboxylic acid functionality and the protonated amine group adopt a trans configuration. Nitrogen and methane molecules were used as messenger tags with optimal tagging temperatures of 30 K for N2 and 60 K for CH4. While the calculated infrared spectra of the tagged ion suggest only a weak influence of the messenger tag on the frequency positions of ValH+, the measured intensities for N2-tagged ValH+ appear strongly suppressed for all but the highest frequency feature at 1773 cm-1. We trace this behavior to the binding energy of the N2 tag, which is significantly higher than that of CH4, based on density functional and coupled cluster calculations and rate estimates for photoinduced unimolecular dissociation from statistical theory.

Internal Energy Dependence of the Pyrrole Dimer Cation Structures Formed in a Supersonic Plasma Expansion: Charge-Resonance and Hydrogen-Bonded Isomers.

The structures of the pyrrole dimer cation (Py2+) formed in an electron-ionization-driven supersonic plasma expansion of Py seeded in Ar or N2 are probed as a function of its internal energy by infrared photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. The IRPD spectra recorded in the CH and NH stretch ranges are analyzed by dispersion-corrected density functional theory (DFT) calculations at the B3LYP-D3/aug-cc-pVTZ level. The spectra of the cold Ar/N2-tagged Py2+ clusters, Py2+Ln (n = 1-5 for Ar, n = 1 for N2), indicate the exclusive formation of the most stable antiparallel π-stacked Py2+ structure under cold conditions, which is stabilized by charge-resonance interaction. The bare Py2+ dimers produced in the ion source have higher internal energy, and the observation of additional transitions in their IRPD spectra suggests a minor population of less stable hydrogen-bonded isomers composed of heterocyclic Py/Py+ structures formed after intramolecular H atom transfer and ring opening. These intermolecular isomers differ from the chemically bonded structures proposed earlier in the analysis of IRPD spectra of Py2+ generated by VUV ionization of neutral Pyn clusters.

IR spectrum of SiH3OH2+SiH4: cationic OH⋯HSi dihydrogen bond versus charge-inverted SiH⋯Si hydrogen bond.

The low electronegativity of Si gives rise to a variety of nonconventional intermolecular interactions in clusters of silanes and their derivatives, which have not been well characterized yet. Herein, we characterize the structures of various isomers of bare and Ar-tagged SiH3OH2+SiH4 dimers composed of protonated silanol and silane by infrared photodissociation (IRPD) of mass-selected ions and dispersion-corrected density functional calculations (B3LYP-D3/aug-cc-pVTZ). The analysis of the IRPD spectra recorded in the OH stretch range reveals the competition between two types of nonconventional hydrogen bonds (H-bonds). The first one represents a OH⋯HSi ionic dihydrogen bond (DHB), in which SiH4 interacts with the H2O moiety of SiH3OH2+. The second one represents a charge-inverted SiH⋯Si ionic H-bond (CIHB), in which the SiH4 ligand interacts with the SiH3 moiety of SiH3OH2+. The latter may also be considered as a weak three-centre two-electron (3c-2e) bond. Although both types of H-bonds are computed to have comparable interaction strengths for SiH3OH2+SiH4 (D0 ≈ 35-40 kJ mol-1), DHB isomers dominate the population in the supersonic plasma expansion, while the abundance of CIHB isomers is roughly one order of magnitude lower, probably as a result of entropic factors.

Observation of Slow Eigen-Zundel Interconversion in H+(H2O)6 Clusters upon Isomer-Selective Vibrational Excitation and Buffer Gas Cooling in a Cryogenic Ion Trap.

The formation of isomers when trapping floppy cluster ions in a temperature-controlled ion trap is a generally observed phenomenon. This involves collisional quenching of the ions initially formed at high temperature by buffer gas cooling until their internal energies fall below the barriers in the potential energy surface that separate them. Here we explore the kinetics at play in the case of the two isomers adopted by the H+(H2O)6 cluster ion that differ in the proton accommodation motif. One of these is most like the Eigen cation with a tricoordinated hydronium motif (denoted E), and the other is most like the Zundel ion with the proton equally shared between two water molecules (denoted Z). After initial cooling to about 20 K in the radiofrequency (Paul) trap, the relative populations of these two spectroscopically distinct isomers are abruptly changed through isomer-selective photoexcitation of bands in the OH stretching region with a pulsed (∼6 ns) infrared laser while the ions are in the trap. We then monitor the relaxation of the vibrationally excited clusters and reformation of the two cold isomers by recording infrared photodissociation spectra with a second IR laser as a function of delay time from the initial excitation. The latter spectra are obtained after ejecting the trapped ions into a time-of-flight photofragmentation mass spectrometer, thus enabling long (∼0.1 s) delay times. Excitation of the Z isomer is observed to display long-lived vibrationally excited states that are collisionally cooled on a ms time scale, some of which quench into the E isomer. These excited E species then display spontaneous interconversion to the Z form on a ∼10 ms time scale. These qualitative observations set the stage for a series of experimental measurements that can provide quantitative benchmarks for theoretical simulations of cluster dynamics and the potential energy surfaces that underlie them.

Microhydration of the Pyrrole Cation (Py+) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py+(H2O)2

Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py+) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py+(H2O)2 and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py+(H2O)2 is formed by stepwise hydration of the acidic NH group of Py+ by a hydrogen-bonded (H2O)2 chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py+H2O and (H2O)2, respectively. The linear chain structure of the Py+(H2O)2 cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H2O)2 global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py+ and the π-bonded OH hydrogen of (H2O)2, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.

Dinitrogen Activation in the Gas Phase: Spectroscopic Characterization of C-N Coupling in the V3 C+ +N2 Reaction.

We report on cluster-mediated C-N bond formation in the gas phase using N2 as a nitrogen source. The V3 C+ +N2 reaction is studied by a combination of ion-trap mass spectrometry with infrared photodissociation (IRPD) spectroscopy and complemented by electronic structure calculations. The proposed reaction mechanism is spectroscopically validated by identifying the structures of the reactant and product ions. V3 C+ exhibits a pyramidal structure of C1 -symmetry. N2 activation is initiated by adsorption in an end-on fashion at a vanadium site, followed by spontaneous cleavage of the N≡N triple bond and subsequent C-N coupling. The IRPD spectrum of the metal nitride product [NV3 (C=N)]+ exhibits characteristic C=N double bond (1530 cm-1 ) and V-N single bond (770, 541 and 522 cm-1 ) stretching bands.

Carbon dioxide activation by discandium dioxide cations in the gas phase: a combined investigation of infrared photodissociation spectroscopy and DFT calculations.

We present a combined computational and experimental study of CO2 activation at the Sc2O2+ metal oxide ion center in the gas phase. Density functional theory calculations on the structures of [Sc2O2(CO2)n]+ (n = 1-4) ion-molecule complexes reveal a typical end-on binding motif as well as bidentate and tridentate carbonate-containing configurations. As the number of attached CO2 molecules increases, activated forms tend to dominate the isomeric populations. Distortion energies are unveiled to account for the conversion barriers from molecularly bound isomers to carbonate structures, and show a monotonically decreasing trend with successive CO2 ligand addition. The infrared photodissociation spectra of target ion-molecule complexes were recorded in the 2100-2500 cm-1 frequency region and interpreted by comparison with simulated IR spectra of low-lying isomers representing distinct configurations, demonstrating a high possibility of carbonate structure formation in current experiments.

Infrared spectrum of the 1-cyanoadamantane cation: evidence of hydrogen transfer and cage-opening upon ionization.

The radical cations of diamondoids are important intermediates in their functionalization reactions and are also candidates as carriers for astronomical absorption and emission features. Although neutral diamondoids have been studied extensively, information regarding their radical cations is largely lacking, particularly for functionalized diamondoid derivatives. Herein, we characterize the structure of the 1-cyanoadamantane radical cation (C10H15CN+, AdCN+) using infrared photodissociation (IRPD) spectroscopy of mass selected AdCN+N2 clusters in the XH stretch range (2400-3500 cm-1) and dispersion-corrected density functional theory calculations (B3LYP-D3BJ/cc-pVTZ). A group of three distinct CH stretch bands are observed in the 2800-3000 cm-1 range, in addition to a highly redshifted absorption at 2580 cm-1 attributed to the acidic CH proton predicted by calculations. An unexpected broad absorption peaking at 3320 cm-1 is also detected and assigned to an NH stretch mode based on its width and frequency. Calculations indicate that hydrogen atom transfer (HAT) from the adamantyl cage (C10H15, Ady) to the N atom of the CN group yields lower energy structures, with an open-cage isomer exhibiting such hydrogen transfer being the global minimum on the potential energy surface. The energy barriers involved in the formation of this open-cage isomer are also lower than those calculated for generation of the analogous open-cage 1-amantadine cation isomer which has previously been identified by IRPD. The combined consideration of IRPD spectra and calculations indicates a major population of the nascent canonical closed-cage isomer and a smaller population of the global minimum isomer featuring both cage-opening and hydrogen transfer.

An Infrared Study of Gas-Phase Metal Nitrosyl Ion–Molecule Complexes

We present a combined experimental and quantum chemical study of gas-phase group 9 metal nitrosyl complexes, M(NO)n+ (M = Co, Rh, Ir). Experimental infrared photodissociation spectra of mass-selected ion-molecule complexes are presented in the region 1600 cm-1 to 2000 cm-1 which includes the NO stretch. These are interpreted by comparison with the simulated spectra of energetically low-lying structures calculated using density functional theory. A mix of linear and nonlinear ligand binding is observed, often within the same complex, and clear evidence of coordination shell closing is observed at n = 4 for Co(NO)n+ and Ir(NO)n+. Calculations of Rh(NO)n+ complexes suggest additional low-lying five-coordinate structures. In all cases, once a second coordination shell is occupied, new spectral features appear which are assigned to (NO)2 dimer moieties. Further evidence of such motifs comes from differences in the spectra recorded in the dissociation channels corresponding to single and double ligand loss.

Impact of anion polarizability on ion pairing in microhydrated salt clusters.

Despite longstanding interest in the mechanism of salt dissolution in aqueous media, a molecular level understanding remains incomplete. Here, cryogenic ion trap vibrational action spectroscopy is combined with electronic structure calculations to track salt hydration in a gas phase model system one water molecule at a time. The infrared photodissociation spectra of microhydrated lithium dihalide anions [LiXX'(H2O) n ]- (XX' = I2, ClI and Cl2; n = 1-3) in the OH stretching region (3800-2800 cm-1) provide a detailed picture of how anion polarizability influences the competition among ion-ion, ion-water and water-water interactions. While exclusively contact ion pairs are observed for n = 1, the formation of solvent-shared ion pairs, identified by markedly red-shifted OH stretching bands (<3200 cm-1), originating from the bridging water molecules, is favored already for n = 2. For n = 3, Li+ reaches its maximum coordination number of four only in [LiI2(H2O)3]-, in accordance with the hard and soft Lewis acid and base principle. Water-water hydrogen bond formation leads to a different solvent-shared ion pair motif in [LiI2(H2O)3]- and network formation even restabilizes the contact ion pair motif in [LiCl2(H2O)3]-. Structural assignments are exclusively possible after the consideration of anharmonic effects. Molecular dynamics simulations confirm that the significance of large amplitude motion (of the water molecules) increases with increasing anion polarizability and that needs to be considered already at cryogenic temperatures.

Cryo spectroscopy of N2 on cationic iron clusters.

Infrared photodissociation (IR-PD) spectra of iron cluster dinitrogen adsorbate complexes [Fen(N2)m]+ for n = 8-20 reveal slightly redshifted IR active bands in the region of 2200-2340 cm-1. These bands mostly relate to stretching vibrations of end-on coordinated N2 chromophores, a μ1,end end-on binding motif. Density Functional Theory (DFT) modeling and detailed analysis of n = 13 complexes are consistent with an icosahedral Fe13 + core structure. The first adsorbate shell closure at (n,m) = (13,12)-as recognized by the accompanying paper on the kinetics of N2 uptake by cationic iron clusters-comes with extensive IR-PD band broadening resulting from enhanced couplings among adjacent N2 adsorbates. DFT modeling predicts spin quenching by N2 adsorption as evidenced by the shift of the computed spin minima among possible spin states (spin valleys). The IR-PD spectrum of (17,1) surprisingly reveals an absence of any structure but efficient non-resonant fragmentation, which might indicate some weakly bound (roaming) N2 adsorbate. The multiple and broad bands of (17,m) for all other cases than (17,1) and (17,7) indicate a high degree of variation in N2 binding motifs and couplings. In contrast, the (17,7) spectrum of six sharp bands suggests pairwise equivalent N2 adsorbates. The IR-PD spectra of (18,m) reveal additional features in the 2120-2200 cm-1 region, which we associate with a μ1,side side-on motif. Some additional features in the (18,m) spectra at high N2 loads indicate a μ1,tilt tilted end-on adsorption motif.

The Chemical Nature of Ti4O10-: Vibrational Predissociation Spectroscopy Combined with Global Structure Optimization.

The gas-phase infrared spectrum of Ti4O10- is studied in the spectral range from 400 cm-1 to 1250 cm-1 using cryogenic ion trap vibrational spectroscopy, in combination with density functional theory (DFT). The infrared photodissociation (IRPD) spectrum of D2-tagged Ti4O10- provides evidence for a structure of lower symmetry that contains a superoxo group (1121 cm-1) and two terminal Ti=O moieties. DFT combined with a genetic algorithm for global structure optimization predicts two isomers which feature a superoxo group: the Cs symmetric global minimum-energy structure and a similar isomer (C1) that is slightly higher in energy. Coupled cluster calculations confirm the relative stability. Comparison of the harmonic DFT spectra (different functionals) with the IRPD spectrum suggests that both of these isomers contribute. Earlier assignments to the adamantane-like C3v isomer with three terminal Ti-O• - groups in a quartet state are not confirmed. They were based on the infrared multiple photon photodissociation (IRMPD) spectrum of bare Ti4O10- and local DFT structure optimizations.

Structural Characterization of Nickel-Doped Aluminum Oxide Cations by Cryogenic Ion Trap Vibrational Spectroscopy.

Isolated nickel-doped aluminum oxide cations (NiOm)(Al2O3)n(AlO)+ with m = 1-2 and n = 1-3 are investigated by infrared photodissociation (IRPD) spectroscopy in combination with density functional theory and the single-component artificial force-induced reaction method. IRPD spectra of the corresponding He-tagged cations are reported in the 400-1200 cm-1 spectral range and assigned based on a comparison to calculated harmonic IR spectra of low-energy isomers. Simulated spectra of the lowest energy structures generally match the experimental spectra, but multiple isomers may contribute to the spectra of the m = 2 series. The identified structures of the oxides (m = 1) correspond to inserting a Ni-O moiety into an Al-O bond of the corresponding (Al2O3)1-3(AlO)+ cluster, yielding either a doubly or triply coordinated Ni2+ center. The m = 2 clusters prefer similar structures in which the additional O atom either is incorporated into a peroxide unit, leaving the oxidation state of the Ni2+ atom unchanged, or forms a biradical comprising a terminal oxygen radical anion Al-O•- and a Ni3+ species. These clusters represent model systems for under-coordinated Ni sites in alumina-supported Ni catalysts and should prove helpful in disentangling the mechanism of selective oxidative dehydrogenation of alkanes by Ni-doped catalysts.

Infrared Spectroscopy of Solvation in the TaO2+ Hydrolysis Reaction.

The solvent effect of the TaO2+ reaction with water molecules in the gas phase is examined. Stoichiometric TaO2(H2O)n+ cations are generated by the laser vaporization of a tantalum metal target in the pulsed supersonic expansion of H2O/He mixed gas. The infrared photodissociation spectra of TaO2(H2O)n+ cations are measured using the argon-tagging technology in the 2800-3850 cm-1 region. Density functional theory calculations are carried out to identify the observed infrared bands and elucidate the reaction mechanism. In the TaO2+ reaction with one H2O molecule, both the hydrated adduct H2O-TaO2+ and dihydroxide TaO(OH)2+ are generated. The coexistence of tetrahydroxide Ta(OH)4+ and hydrated dihydroxide H2O-TaO(OH)2+ is seen when the second H2O molecule is involved. However, only the hydrated H2O-Ta(OH)4+ product is obtained in the TaO2 reaction with three H2O molecules. Theoretical calculations indicate that in the reaction, the formation of a six-membered cyclic transition state through the hydrogen bond lowers the energy barrier significantly, which promotes the transfer of the hydrogen of hydrated adducts to generate di- and tetrahydroxides.

Vacuum Ultraviolet Photoionization Induced Proton Migration and Formation of a New C-N Bond in Pyridine Clusters Revealed by Infrared Spectroscopy and Mass Spectrometry.

The structures and reactions of pyridine (Pyd) cluster cations in a supersonic molecular beam generated upon photoionization at 9.2-9.4 eV were investigated by infrared (IR) action spectroscopy. The mass spectrum showed prominent peaks of (Pyd)m+ and H+(Pyd)m, m = 1-5. In the pyridine/pyridine-d5 mixture, the mass pattern indicated that H+ and D+ migrated during the formation and dissociation of the cluster cations. The IR photodissociation spectra of both (Pyd)2+ and H+(Pyd)2 revealed a N-H stretching band near 3400 cm-1, indicating that their structures are 1-(2-pyridyl)pyridin-1-ium and pyridinium-pyridine, respectively. Observation of the former product implies that the reaction proceeds via an α-distonic cation intermediate, while the latter product is formed via proton migration. The IR spectra of (Pyd)m+ and H+(Pyd)m, m ≥ 3, suggested that these clusters consist of a covalently bound (Pyd)2+ or H+(Pyd)2 core, respectively, with additional pyridines attached to them via hydrogen bonds and/or weak dispersive interactions.

Rovibrational spectroscopy of the CH+-He and CH+-He4 complexes

A cryogenic 22-pole ion trap apparatus is used in combination with a table-top pulsed IR source to probe weakly bound CH+-Heand CH+-He4 complexes by predissociation spectroscopy at 4 K. The infrared photodissociation spectra of the C–H stretching vibrations are recorded in the range of 2720–2800 cm−1. The spectrum of CH+-Heexhibits perpendicular transitions of a near prolate top with a band origin at 2745.9 cm−1, and thus confirms it to have a T-shaped structure. For CH+-He4, the C-H stretch along the symmetry axis of this oblate top results in parallel transitions.

Infrared photodissociation spectroscopic and theoretical study of H n C4O+ (n = 1, 2) cation clusters in the gas phase

The carbon chain cations H n C4O+ (n = 1, 2) were generated via pulsed laser vaporisation of a graphite target in supersonic expansions of helium seeded with carbon monoxide and acetylene. The infrared spectra were measured via mass-selected infrared photodissociation spectroscopy of their CO-tagged complexes [H n C4O·CO]+ (n = 1, 2). Their geometric and electronic structures were determined by gas-phase infrared photodissociation spectra combined with theoretical calculations. The results show that the H n C4O+ (n = 1, 2) core cations are linear carbon chain derivatives which are terminated with hydrogen/dihydrogen and oxygen atoms. The HC4O+ cation has 3Σ− electronic ground state with cumulene-like carbon chain structure, while H2C4O+ cation has 2B1 electronic ground state with polyyne-like carbon chain structure. The CH and CH2 terminal groups have different influence on the type of carbon-carbon bonds in the carbon chain derivatives, due to the sp and sp2 hybridisation property. The carbon chain cations H n C4O+ (n = 1, 2) are studied by gas-phase infrared photodissociation spectra of CO-tagged complexes [H n C4O·CO]+ (n = 1, 2) combined with theoretical calculations. Studies show that the structures of the H n C4O+ (n = 1, 2) core cations are linear carbon chain derivatives which are terminated with hydrogen/dihydrogen and oxygen atoms. The spectrum of [HC4O·CO]+ shows two bands above 3000 cm−1, suggesting possible isomers.

Potassium and sodium ion complexes with a partial peptide of the selectivity filter in K+ channels studied by cold ion trap infrared spectroscopy: the effect of hydration.

Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks Na+. The presence of water in the SF during ion translocation remains under debate due to the experimental and computational challenges in characterizing the interactions between water, ions, and the SF. Our bottom-up approach has been applied to a system composed of a partial peptide of the SF (Ac-tyrosine-NHMe) with a metal ion and a single water molecule to probe these interactions. The IR photodissociation spectra of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water molecule binding sites are ion-dependent. In addition, the ion-peptide distances are elongated significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule. This striking structural difference with the water molecule is discussed in relation to ion selectivity and translocation within the K+ channel.

Effects of Temperature on Cs+(H2O)20 Clathrate Structure.

Clusters consisting of 20 water molecules and a single cesium ion are especially stable due to their clathrate structure that is composed exclusively of three-coordinate water molecules. Clathrate stability was investigated using infrared photodissociation (IRPD) spectroscopy in the free-OH stretching region (∼3600-3800 cm-1) at ion cell temperatures between 135 and 355 K. At 275 K and colder, IRPD spectra of Cs+(H2O)20 have just one acceptor-acceptor-donor band. At higher temperatures, a higher-energy acceptor-donor band emerges and grows in intensity. Non-clathrate Na+(H2O)20 structures contain both of these bands, which do not change significantly in intensity over the temperature range. These results indicate a rapid onset in the conversion from clathrate to non-clathrate structures with temperature and suggest that some clathrate population remains even at the highest temperatures investigated. These results provide new insights into the role of entropy in clathrate stability.