IRPD Spectra Research Articles

Cryo-IR spectroscopy and cryo-kinetics of cluster N2 adsorbate complexes of tantalum cluster cations Ta5-8.

We present an IR-PD study of tantalum cluster adsorbate complexes [Tan(N2)m]+, abbreviated (n,m), n = 5-8. We utilize infrared spectroscopy of isolated and size selected clusters as prepared and characterized by a cryogenic tandem ion trap setup, and we augment our experiments with quantum chemical simulations at the level of density functional theory. The cluster adsorbate complexes (n,m) reveal vibrational bands above 2000cm-1, which indicate end-on coordinated μ1-N2 oscillators, and bands below 2000cm-1, which indicate side-on μ2-κN:κN,N coordinated ones. We observe a general increase in spectral complexity and an inhomogeneous broadening, mainly towards the red, at certain points of N2 loading m, which originates from an increasingly higher amount of double and triple N2 coordination at Ta sites, eventually at all of them. Other than the small tantalum clusters Tan+, n = 2-4, the IR-PD spectra of the initial N2 adsorbate species (n,1), n = 5-8, provide strong evidence for a lack of spontaneous N2 cleavage. Spontaneous N2 cleavage by Tan+, n = 5-8, seems suppressed. Therefore, the ability of a small Ta cluster to cleave dinitrogen disappears with one more tantalum core atom. The study of stepwise N2 adsorption on size selected Tan+, n = 5-8 clusters revealed adsorption limits m(max) of [Tan(N2)m]+ that are independent of cluster size within this size range. Cryo-adsorption kinetics at 26K allowed for kinetic fits to consecutive N2 adsorption steps, and the fits revealed significant N2 desorption rates upon higher N2 loads, and the cluster adsorbate complexes eventually reached equilibrium. Some enhanced N2 desorption rates point towards likely adsorbate shell reorganization, and there is also some evidence for the coexistence of isomeric cluster adsorbate complexes.

Microhydration of ionized building blocks of DNA/RNA: infrared spectra of pyrimidine^{+}-(hbox {H}_{2}hbox {O})_{text {1-3}} clusters

Hydration of biomolecules is an important physiological process that governs their structure, stability, and function. Herein, we probe the microhydration structure of cationic pyrimidine (Pym), a common building block of DNA/RNA bases, by infrared photodissociation spectroscopy (IRPD) of mass-selected microhydrated clusters, hbox {Pym}^{+}-hbox {W}_{n} (W=hbox {H}_{2}hbox {O}), in the size range n=1–3. The IRPD spectra recorded in the OH and CH stretch range are sensitive to the evolution of the hydration network. Analysis with density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level provides a consistent picture of the most stable structures and their energetic and vibrational properties. The global minima of hbox {Pym}^{+}-hbox {W}_{n} predicted by the calculations are characterized by H-bonded structures, in which the H-bonded hbox {W}_{n} solvent cluster is attached to the most acidic C4–H proton of hbox {Pym}^{+} via a single CH...O ionic H-bond. These isomers are identified as predominant carrier of the IRPD spectra, although less stable local minima provide minor contributions. In general, the formation of the H-bonded solvent network (exterior ion solvation) is energetically preferred to less stable structures with interior ion solvation because of cooperative nonadditive three-body polarization effects. Progressive hydration activates the C4–H bond, along with increasing charge transfer from hbox {Pym}^{+} to hbox {W}_{n}, although no proton transfer is observed in the size range nleqslant 3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic hbox {N}_{2} ligands, which strongly prefer interior ion solvation by uppi stacking interactions. Comparison of hbox {Pym}^{+}-W with Pym-W and hbox {H}^{+}Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction.Graphic

Structure and Vibrational Spectra of ArnH+ (n = 2-3).

The structure and vibrational spectra of protonated Ar clusters ArnH+ (n = 2-3) are studied using potential energy surfaces at the CCSD(T)/aug-cc-pVTZ level and basis set. Ar binding energies, as well as position isomerism in Ar3H+, were investigated. In our previous work, the spectra of Ar2H+ reveal a strong progression of combination bands, which involves the asymmetric Ar-H+ stretch with multiple quanta of the symmetric Ar-H+ stretch. In this work, insights on the origin of such progression were examined using an adiabatic model. In addition, contributions from mechanical and electrical anharmonicity on the progressions' intensities were also examined. Comparison of the calculated spectrum for the bare and Ar-tagged ions reveals that the reduction of the symmetry group, from D∞h to either C∞v or C2v, results in a richer vibrational structure in the 500-1700 cm-1 region. When compared with previously reported action spectra (D. C. McDonald III, D. T. Mauney, D. Leicht, J. H. Marks, J. A. Tan, J.-L. Kuo, and M. A. Duncan, J. Chem. Phys., 2016, 145, 231,101), it appears that the position isomers, because of the binding of the weakly bound Ar messenger, are needed to account for the additional bands in the infrared photodissociation spectrum for Ar3H+. These findings demonstrate the active role of the messenger atom in relaxing some of the selection rules for the bare ion's vibrational transitions - resulting in an augmentation of the bands in the action spectrum.

Cryo IR Spectroscopy of N2 and H2 on Ru8+: The Effect of N2 on the H-Migration

We present the cryo IR-PD spectra of the coadsorbed [Ru8(H2)1(N2)4]+ and [Ru8(N2)4(H2)1]+ species differing in the adsorption sequence of H2 and N2, which we record via application of tandem cryo ion trapping. We observe strong evidence for dissociative H2 adsorption, and the spectra reveal differences in the Ru-H stretching region, which we assign to distal and proximal hydrogen atom locations on the Ru8+ cluster, their migration likely hindered by preloaded nitrogen molecules and unaffected by subsequent N2 adsorption.

Conformation of protonated glutamic acid at room and cryogenic temperatures.

Recognition properties of biologically relevant molecules depend on their conformation. Herein, the conformation of protonated glutamic acid (H+Glu) isolated in quadruple ion traps is characterized by vibrational spectroscopy at room and cryogenic temperatures and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. The infrared multiple photon dissociation (IRMPD) spectrum recorded in the fingerprint range at room temperature using an IR free electron laser is attributed to the two most stable and nearly isoenergetic conformations (1-cc and 2-cc) with roughly equal population (ΔG298 = 0.0 kJ mol-1). Both have bridging C[double bond, length as m-dash]O(HNH)+O[double bond, length as m-dash]C ionic H-bonds of rather different strengths but cannot be distinguished by their similar IRMPD spectra. In contrast, the higher-resolution single-photon IRPD spectrum of H2-tagged H+Glu recorded in the conformation-sensitive X-H stretch range in a trap held at 10 K distinguishes both conformers. At low temperature, 1-cc is roughly twice more abundant than 2-cc, in line with its slightly lower calculated energy (ΔE0 = 0.5 kJ mol-1). This example illustrates the importance of cryogenic cooling, single-photon absorption conditions, and the consideration of the X-H stretch range for the identification of biomolecular conformations involving hydrogen bonds.

Helium Tagging Infrared Photodissociation Spectroscopy of Reactive Ions.

The interrogation of reaction intermediates is key for understanding chemical reactions; however their direct observation and study remains a considerable challenge. Mass spectrometry is one of the most sensitive analytical techniques, and its use to study reaction mixtures is now an established practice. However, the information that can be obtained is limited to elemental analysis and possibly to fragmentation behavior, which is often challenging to analyze. In order to extend the available experimental information, different types of spectroscopy in the infrared and visible region have been combined with mass spectrometry. Spectroscopy of mass selected ions usually utilizes the powerful sensitivity of mass spectrometers, and the absorption of photons is not detected as such but rather translated to mass changes. One approach to accomplish such spectroscopy involves loosely binding a tag to an ion that will be removed by absorption of one photon. We have constructed an ion trapping instrument capable of reaching temperatures that are sufficiently low to enable tagging by helium atoms in situ, thus permitting infrared photodissociation spectroscopy (IRPD) to be carried out. While tagging by larger rare gas atoms, such as neon or argon is also possible, these may cause significant structural changes to small and reactive species, making the use of helium highly beneficial. We discuss the "innocence" of helium as a tag in ion spectroscopy using several case studies. It is shown that helium tagging is effectively innocent when used with benzene dications, not interfering with their structure or IRPD spectrum. We have also provided a case study where we can see that despite its minimal size there are systems where He has a huge effect. A strong influence of the He tagging was shown in the IRPD spectra of HCCl(2+) where large spectral shifts were observed. While the presented systems are rather small, they involve the formation of mixtures of isomers. We have therefore implemented two-color experiments where one laser is employed to selectively deplete a mixture by one (or more) isomer allowing helium tagging IRPD spectra of the remaining isomer(s) to be recorded via the second laser. Our experimental setup, based on a linear wire quadrupole ion trap, allows us to deplete almost 100% of all helium tagged ions in the trap. Using this special feature, we have developed attenuation experiments for determination of absolute photofragmentation cross sections. At the same time, this approach can be used to estimate the representation of isomers in a mixture. The ultimate aim is the routine use of this instrument and technique to study a wide range of reaction intermediates in catalysis. To this end, we present a study of hypervalent iron(IV)-oxo complexes ([(L)Fe(O)(NO3)](+)). We show that we can spectroscopically differentiate iron complexes with S = 1 and S = 2 according to the stretching vibrations of a nitrate counterion.

Stepwise microhydration of aromatic amide cations: formation of water solvation network revealed by infrared spectra of formanilide(+)-(H2O)(n) clusters (n ≤ 5).

Hydration of peptides and proteins has a strong impact on their structure and function. Infrared photodissociation spectra (IRPD) of size-selected clusters of the formanilide cation, FA(+)-(H2O)n (n = 1-5), are analyzed by density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the sequential microhydration of this prototypical aromatic amide cation. IRPD spectra are recorded in the hydride stretch and fingerprint ranges to probe the preferred interaction motifs and the cluster growth. IRPD spectra of cold Ar-tagged clusters, FA(+)-(H2O)n-Ar, reveal the important effects of temperature and entropy on the observed hydration motifs. At low temperature, the energetically most stable isomers are prominent, while at higher temperature less stable but more flexible isomers become increasingly populated because of entropy. In the most stable structures, the H2O ligands form a hydrogen-bonded solvent network attached to the acidic NH proton of the amide, which is stabilized by large cooperative effects arising from the excess positive charge. In larger clusters, hydration bridges the gap between the NH and CO groups (n ≥ 4) solvating the amide group rather than the more positively charged phenyl ring. Comparison with neutral FA-(H2O)n clusters reveals the strong impact of ionization on the acidity of the NH proton, the strength and topology of the interaction potential, and the structure of the hydration shell.

Structural elucidation of hydrated CuOH + complexes using IR action spectroscopy and theoretical modeling

Complexes of CuOH+ (H2O)n where n=2–9 are examined using infrared photodissociation spectroscopy (IRPD) with frequencies between ~2700 and 3900cm−1. Structural characterization is achieved through comparison between experimental and theoretical spectra. Geometry optimizations and frequency calculations are performed on a myriad of possible low-energy structures at the B3LYP/6-311+G(d,p) level. Subsequent single- point energy calculations are performed at the B3LYP, B3P86, M06, and MP2(full) levels of theory using a 6-311+G(2d,2p) basis set to obtain relative free energies. The IRPD spectra of all complexes where n≥3 are consistent with structures having a coordination number (CN) of 4 although broad features in the CuOH+ (H2O)5 and CuOH+(H2O) 6 spectra accommodate structures having both CN=4 and CN=5. For CuOH+(H2O) 7, spectral bands in the free-OH region narrow, revealing fine structure that confirms the presence of both CN=4 and CN=5 isomers. Conformational assignments are made on the basis of asymmetric stretching frequencies of free-OH water molecules specific to each CN. Relative intensities of these bands are generally in good agreement with relative energies predicted by MP2(full) and not those of the other levels. MP2(full) and M06 single-point energies for the 4 and 5-coordinate isomers are typically within 5kJ/mol of each other suggesting possible equilibration between the two if isomerization barriers are low.

Infrared spectroscopy of trapped molecular dications below 4 K

First results from a new ion trap instrument are presented. With this instrument, ions can be cooled to temperatures below 4K using helium buffer gas. Low temperatures and high densities lead to efficient formation of helium-tagged ions allowing us to record infrared predissociation spectra of highly reactive species. After a short description of the instrument and its special features, the first IRPD spectrum of a small hydrocarbon dication, C7H62+, is presented. The spectral features observed between 2900 and 3200cm−1 indicate that this dication corresponds to doubly ionized cycloheptatrienylidene. Several DFT methods and the MP2 method are applied to study the effect of helium tagging. The results suggest that the effect of helium on the structure as well as on the IR spectrum of the dication is only minor; most probably in the range of the errors of the theoretical models.

Theoretical Study of Nascent Hydration in the Fe+(H2O)n System

The interactions of the iron monocation with water molecules and argon atoms in the gas phase were studied computationally to elucidate recent infrared vibrational spectroscopy on this system. These calculations employ first-principles all-electron methods performed with B3LYP/DZVP density functional theory. The ground state of Fe(+)(H(2)O) is found to be a quartet (M = 2S + 1 = 4, S is the total spin). Different binding sites for the addition of one or two argon atoms produce several low-lying states of different geometry and multiplicity in a relatively small energy range for Fe(+)(H(2)O)-Ar(2) and Fe(+)(H(2)O)(2)-Ar. In both species, quartet states are lowest in energy, and sextets and doublets lie at higher energies from the respective ground states. These results are consistent with the conclusion that the experimentally determined infrared photodissociation spectra (IRPD) of Fe(+)(H(2)O)-Ar(2) and Fe(+)(H(2)O)(2)-Ar are complicated because of the presence of multiple isomeric structures. The estimated IR bands for the symmetric and asymmetric O-H stretches from different isomers provide new insight into the observed IRPD spectra.

Structures of Thermal, Mass-Selected Water Clusters Probed with Hydrophobic Ion Tags and Infrared Photodissociation Spectroscopy

The structures of tetramethylammonium (TMA(+)) and phenyltrimethylammonium (PTMA(+)) with 1-8 water molecules attached were investigated using infrared photodissociation spectroscopy (IRPD), blackbody infrared radiative dissociation, and theory to elucidate the effects of ion-water interactions and water-water hydrogen bonding in clusters containing these hydrophobic ions. Several pieces of evidence suggest that these ions have only a small effect on water structure. The binding energy of a water molecule to TMA(+) is 44 kJ/mol, a value that is significantly lower than that reported for other cations and close to the condensation energy of bulk water. The OH asymmetric stretch of the water molecule in TMA(+).(H(2)O)(1) at 3718 cm(-1) is less red-shifted from that of an isolated water molecule (3756 cm(-1)) than for those of other cations, and water-water hydrogen bonding is extensive for all clusters with two or more water molecules. These results indicate that charge transfer from water to these hydrophobic ions is much less than that for other cations. There are two predominant structures for these ions with three water molecules: one in which water molecules form a chain and one with a cyclic structure analogous to that of neutral water trimer. With four water molecules attached, water forms a cyclic structure similar to that of neutral water tetramer. The spectra of the larger clusters follow trends reported for neutral water molecule clusters, which indicates that these hydrophobic ions have only a minimal effect on the structure of water in clusters with four or more water molecules. These results suggest that these hydrophobic ions can be used as "tags" that could make possible acquisition of IRPD spectra of even larger clusters, such as clathrates, for which precise mass selection of neutral clusters is not possible by other methods.

IRMPD spectroscopy shows that AGG forms an oxazolone b2+ ion.

Infrared multiple photon dissociation (IRMPD) spectroscopy combined with theoretical vibrational spectra provides a powerful tool for probing structure. This technique has been used to probe the structure of protonated cyclic AG and the b(2)(+) ion from AGG. The experimental spectrum for protonated cyclo AG compares very well with the theoretical spectra for a diketopiperazine. The spectrum corresponds best to a combination of two structures protonation at the alanine and glycine amide oxygens. The experimental spectrum for the b(2)(+) ion from protonated AGG matches best to the theoretical spectrum for an oxazolone structure protonated on the ring nitrogen. In particular, the carbonyl stretching band at 1970 cm(-1) is blue-shifted by approximately 200 cm(-1) compared to the experimental spectrum for protonated cAG, indicating that these two structures are distinct. This is the first time that an IRPD spectrum of a b(2)(+) ion has been obtained and, for this ion, the oxazolone structure proposed based on prior calculations and experiments is confirmed by the spectroscopic method.

Structure of Protonated Carbon Dioxide Clusters: Infrared Photodissociation Spectroscopy and ab Initio Calculations

The infrared photodissociation spectra (IRPD) in the 700 to 4000 cm(-1) region are reported for H+ (CO2)n clusters (n = 1-4) and their complexes with argon. Weakly bound Ar atoms are attached to each complex upon cluster formation in a pulsed electric discharge/supersonic expansion cluster source. An expanded IRPD spectrum of the H+ (CO2)Ar complex, previously reported in the 2600-3000 cm(-1) range [Dopfer, O.; Olkhov, R.V.; Roth, D.; Maier, J.P. Chem. Phys. Lett. 1998, 296, 585-591] reveals new vibrational resonances. For n = 2 to 4, the vibrational resonances involving the motion of the proton are observed in the 750 to 1500 cm(-1) region of the spectrum, and by comparison to the predictions of theory, the structure of the small clusters are revealed. The monomer species has a nonlinear structure, with the proton binding to the lone pair of an oxygen. In the dimer, this nonlinear configuration is preserved, with the two CO2 units in a trans configuration about the central proton. Upon formation of the trimer, the core CO2 dimer ion undergoes a rearrangement, producing a structure with near C2v symmetry, which is preserved upon successive CO2 solvation. While the higher frequency asymmetric CO2 stretch vibrations are unaffected by the presence of the weakly attached Ar atom, the dynamics of the shared proton motions are substantially altered, largely due to the reduction in symmetry of each complex. For n = 2 to 4, the perturbation due to Ar leads to blue shifts of proton stretching vibrations that involve motion of the proton mostly parallel to the O-H+-O axis of the core ion. Moreover, proton stretching motions perpendicular to this axis exhibit smaller shifts, largely to the red. Ab initio (MP2) calculations of the structures, complexation energies, and harmonic vibrational frequencies are also presented, which support the assignments of the experimental spectra.

Infrared Photodissociation Spectroscopy of Electrosprayed Ions in a Fourier Transform Mass Spectrometer

Previous gas-phase methods for infrared photodissociation spectroscopy (IRPD) require sample volatility. Our method instead uses electrospray ionization to introduce even large nonvolatile molecules into a Fourier transform mass spectrometer, where extended (>15 s) ion storage makes possible high sensitivity spectral measurements with an OPO laser over a range of 3050-3800 cm(-1). The spectra of 22 gaseous proton-bound amino acid complexes are generally correlated with the H-stretching frequencies established for O-H and N-H functional groups in solution. For theoretical structure predictions of the Gly2H+ and N-acylated Asp2H+ dimers, IRPD spectra clearly differentiate between the predicted lowest energy conformers. In contrast to solution, in the gas phase the glycine zwitterion is approximately 20 kcal/mol less stable than the neutral; however, glycine is clearly zwitterionic in the gaseous GlyLysH+ dimer. The level of theory is inadequate for the larger Lys2H+ dimer, as all low energy predicted structures have free carboxyl O-H groups, in contrast to the IR spectrum. IRPD appears to be a promising new technique for providing unique information on a broad range of biomolecular and other gaseous ions, especially on noncovalent bonding involving O-H and N-H groups.