IR spectroscopy has become a frequently used tool to characterize gas-phase peptides and proteins. In many experiments, ions are m/z selected, irradiated by intense and tunable IR light and fragmentation is monitored as a function of IR wavelength. The presence of different conformers can, however, complicate the interpretation, as the resulting spectra represent the sum of the spectra of the individual components. We constructed a setup, in which ion mobility methods are used to obtain m/z selected ions of defined shape on which are then further investigated by IR spectroscopy. First results on peptide aggregates are presented and for some of those, the IR spectra show a transition from helical or random coil to beta sheet structures.
In a different experiment, peptide or protein ions are captures in liquid helium droplets prior to IR spectroscopic investigation. The conditions inside a helium droplet are isothermal at 0.38 K and the interaction between the helium matrix and the molecules are weak so that only small perturbations on the molecule are expected. IR spectra for m/z selected peptides with up to 10 aminoacids and proteins containing more than 100 aminoacids have been measured. The spectra of the smaller species show resolved bands of individual oscillators, which can be used for structure assignment. For the larger species, band envelopes are obtained and for the case of highly charged proteins, a transition form helical to extended structures is observed.

Most of the work on peptide radical cations has involved protons as the source of charge. Nonetheless, using metal ions as charge sources often offers advantages like stabilization of the structure via multidentate coordination and the elimination of the “mobile proton”. Moreover, characterization of metal-bound amino acids is of general interest as the interaction of peptide side chains with metal ions in biological systems is known to occur extensively. In the current study, we generate thiyl radicals of cysteine and homocysteine in the gas phase complexed to alkali metal ions. Subsequently, we utilize infrared multiple-photon dissociation (IRMPD) and ion-molecule reactions (IMR) to characterize the structure and reactivity of these radical ions. Our group has worked extensively with the cysteine-based radical cations and anions, characterizing the gas-phase reactivity and rearrangement of the amino acid and several of its derivatives. In a continuation of this work, we are perusing the effects of metal ions as the charge bearing species on the reactivity of the sulfur radical. Our S-nitroso chemistry can easily be used in conjunction with metal ion coordination to produce initial S-based radicals in peptide radical-metal ion complexes. In all cases we have been able to achieve radical formation with significant yield to study reactivity. Ion-molecule reactions of metallated radicals with allyl iodide, dimethyl disulfide, and allyl bromide have all shown decreasing reactivity going down group 1A. Recently, we determined the experimental IR spectra for the homocysteine radical cation with Li+, Na+, and K+ as the charge bearing species at the FELIX facility. For comparison, the protonated IR spectrum of homocysteine has previously been obtained by our group. A preliminary match of the IR spectra has been confirmed. Finally, calculations are underway to determine the bond distances of all the metal adduct structures.

Investigations of molecular structure and conformational isomerism are at the forefront of today’s biophysics and biochemistry. In particular, vibrations excited by far-IR radiation can be highly sensitive to the molecular 3D structure as they are delocalized over large parts of the molecule. Current theoretical predictions of vibrational frequencies in the far-IR range are not accurate enough because of the non-local character and anharmonicity of these vibrations. Therefore experimental studies in the far-IR are vital to guide theory towards improved methodology. In this work we present the conformer-specific far-IR spectra of aminophenol and ethylvanillin molecules in the range of 220-800 cm⁻¹utilizing ion-dip action spectroscopy carried out at the free electron laser FELIX in Nijmegen, Netherlands. The systems studied are aromatic molecules with important functional groups such as the hydroxyl (OH) and amino (NH₂) groups in aminophenol, and the hydroxyl, ethoxy (OCH₂CH₃) and formyl (CHO) groups in ethylvanillin. The experimental spectra show well resolved conformer-specific vibrational bands. In the case of ethylvanillin only two planar conformers have been observed under supersonic jet expansion conditions. Despite the fact that these conformers differ only in the position of oxygen of the formyl group with respect to ethoxy group, they are well distinguishable in far-IR spectra. The capability of numerical methods based on density functional theory (DFT) for predicting vibrational frequencies in this spectral region within the harmonic approximation has been investigated by using several hybrid-functionals such as B3LYP, PBE0, B2PLYP and CAM-B3LYP. An anharmonic correction based on vibrational second order perturbation theory approachV. Barone, Anharmonic vibrational properties by a fully automated second-order perturbative approach, J. Chem. Phys. 122 (2005) 014108.as also applied. We have found that the methods we considered are well suited for the assignment of far-IR vibrational features except the modes which are strongly anharmonic, like the NH₂ wagging mode in aminophenol which is likely to be due to double well potential governing this motion. V. Barone, Anharmonic vibrational properties by a fully automated second-order perturbative approach, J. Chem. Phys. 122 (2005) 014108.w

The VLS-PGM beamline at the Canadian Light Source cover the energy range from 12eV to 250eV with a resolving power better than 10⁴ throughout this range. Associated with this beamline are two endstations designed for gas phase spectroscopy. The first is a dual toroid electrostatic particle energy analyser. Each toroid can (independently) measure the energy and angular distribution of charged particles emitted from the interaction region and can be set for either positive ions or electrons. This allows both photoelectron and ion kinetic energy spectra to be recorded. Recent results from this instrument will be presented including both high resolution photoelectron spectra and photoelectron asymmetry parameter (β) spectra. Coincidence circuitry exists to allow, in favourable circumstances,the measurement of molecular frame photoelectron angular distributions (MFPADs) where the detection of an ion fragment allows orientation of the parent molecule to be deduced. The second is a Wiley-McLaren Time-of-Flight mass spectrometer equipped with multihit electronics. This allows partial ion yield (PIY) spectra to be recorded as well as multi-ion coincidence spectra (PePIPICO). Again recent results will be presented looking at double ionisation in benzene like molecules.

Benzyl radical (C₆H₅CH₂) and two other C₇H₇ radicals are commonly encountered in the combustion of substituted aromatic compounds found in biofuels and gasoline. High temperature pyrolysis of benzyl radical requires isomerization to other C₇H₇ radicals that may include cycloheptatrienyl (tropyl) radical (cyc-C₇H₇) and norbornadienyl radical. The thermal decomposition of all three radicals has now been investigated using a micro-reactor that heats dilute gas-phase samples up to 1600 K and has a residence time of about 100 μ-sec. The pyrolysis products exit the reactor into a supersonic expansion and are detected using synchrotron-based photoionization mass spectrometry and matrix-isolation IR spectroscopy. The products of the pyrolysis of benzyl radical (C₆H₅CH₂) along with three isotopomers (C₆H₅¹³CH₂, C₆D₅CH₂, and C₆H₅CD₂) were detected and identifiedBuckingham, G. T., Ormond, T. K., Porterfield, J. P., Hemberger, P., Kostko, O., Ahmed, M., Robichaud, D. J., Nimlos, M. R., Daily, J. W., Ellison, G. B. 2015, Journal of Chemical Physics 142 044307 The distribution of ¹³C atoms and D atoms indicate that multiple different decomposition pathways are active. l0pt Figure

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Footnotes:

Buckingham, G. T., Ormond, T. K., Porterfield, J. P., Hemberger, P., Kostko, O., Ahmed, M., Robichaud, D. J., Nimlos, M. R., Daily, J. W., Ellison, G. B. 2015, Journal of Chemical Physics 142 044307.

With the advent of third-generation synchrotron light sources, it has been demonstrated that higher-order corrections to the dipole approximation are necessary for the description of light-matter interactions in the soft x-ray range. These effects, known as ‘nondipole effects’, present themselves as asymmetries in the angular distributions of photoelectrons. Chiral molecules, known to have asymmetries in photoelectron angular distributions when exposed to circularly polarized light, have been proposed to demonstrate a chiral-specific nondipole effect when exposed to linearly polarized light. We present the first-ever measurement of nondipole chiral angular distributions for the case of each enantiomer of camphor in the photon energy range 296-343eV.

Fourier transform spectrometers (FTS) are usually based upon amplitude division interferometers through beamsplitters (BS) as in the Michelson interferometer geometry. However, the manufacture of broadband BS is difficult and even impossible in the far VUV (below λ = 140 nm). We therefore conceived an instrument based upon an original design involving only reflective plane surfaces, giving access to the whole VUV range without the restrictions associated with BS. The VUV– FTS is a permanent endstation connected to one of the three experimental branches of the DESIRS beamlineNahon et al., J. Synchrotron Radiat., 19, 508(2012)nd devoted to high resolution photoabsorption in the UV-VUV spectral range, typically between λ = 300 and 40 nmDe Oliveira et al., Nat. Photonics, 5, 149(2011) Since 2008, a large international community of users interested in laboratory measurements with applications in astrophysics, molecular physics or planetary atmospheres has been attracted by the VUV - FTS capabilities including its efficiency in terms of signal to noise ratio, even when high spectral resolution was not an issue. A large number of dedicated gas phase sample environments have been developed including a windowless cell that can be cooled down, a heated windowless cell, a free molecular jet set-up and various windowed cells. Besides, a new discharge gas cell for production and study of transient species gave recently its first results. As an illustration, the VUV absorption spectrum of the CH₃ radical down to 140 nm will be shown in this presentation.

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Footnotes:

Nahon et al., J. Synchrotron Radiat., 19, 508(2012)a De Oliveira et al., Nat. Photonics, 5, 149(2011).

The predissociation of N₂ excited levels is enabled by the presence of optically-inaccessible triplet states. We have recorded vacuum ultraviolet (VUV) spectra at the SOLEIL synchrotron which reveal these states through their perturbation of allowed transitions or their direct appearance due to intensity borrowing. Some of these measurements were recorded at 900 K in order to access high-rotational levels, other measurements investigated weak forbidden transitions at high column density. Following careful analysis, significant new information has been obtained elucidating the states responsible for the astrochemically and atmospherically signficant N₂ predissociation mechanism, and allowing for improvements in its quantitiative modelling.

The high-resolution (0.001 cm⁻¹) spectrum of thiirane has been recorded using the infrared beamline at the Australian synchrotron facility. Spectra have been recorded between 750 cm⁻¹ to 1120 cm⁻¹ and ro-vibrational transitions associated with four bands have been observed and assigned. Coriolis coupling was observed between the ν₄ (1024 cm⁻¹) and the ν₁₄(1050 cm⁻¹) fundamentals as well as between ν₁₁ (825 cm⁻¹) and the ν₈ (895 cm⁻¹) fundamentals. The ν₁₀ (945 cm⁻¹) fundamental was also observed and was found to have no significant perturbations associated with it. For each of the observed bands rotational, centrifugal distortion and Coriolis interaction parameters have been determined. The ground state constants have also been further refined.

Rotationally-resolved vibrational spectra of two planar conformers of 2-fluorophenol have been collected from 100-1000 cm⁻¹ using the Bruker IFS125HR FTIR spectrometer at the Canadian Light Source with a resolution of 0.000959 cm⁻¹. The cis conformer is lower in energy by  2.9 kcal/mol (MP2/aug-cc-pvDZ) and is thought to be stabilized by an intramolecular hydrogen bond between the hydroxyl group and neighbouring fluorine atom on the ring. The OH out-of-plane torsion bands below 400 cm⁻¹ provide the best fingerprint to distinguish between the two conformers in the gas phase spectrum as the c-type band origin of the cis conformer is blue-shifted by  36 cm⁻¹ from that of the trans conformer as result of the intramolecular interaction. In this talk, we will discuss the progress of the analysis of this complex far infrared spectrum of 2-fluorophenol.

Classical explosives such as RDX or TNT exhibit a very low vapor pressure at room temperature and their detection in air requires very sensitive techniques with levels usually better than 1 ppb. To overcome this difficulty, it is not the explosive itself which is detected, but another compound more volatile present in the explosive. J. C. Oxley, J. L. Smith, W. Luo, J. Brady, Prop. Explos. Pyrotec. 34 (2009) 539–543his volatile compound can exist naturally in the explosive due to the manufacturing process. For example, in the case of DiNitroToluene (DNT), the molecule is a degradation product of TNT and is required for its manufacture. Ortho-Mononitrotoluene (2-NT) and para-mononitrotoluene (4-NT) can be also used as detection taggants for explosive detection. In this study, using the exceptional properties of the SOLEIL synchrotron source, and adapted multipass-cells, gas phase Far-IR rovibrational spectra of different isomers of mononitrotoluene and dinitrotoluene have been investigated. Room temperature Far-IR cross-sections of the 3 isomer forms of mononitrotoluene have been determined for the lowest frequency vibrational bands located below 700 cm⁻¹.A. Cuisset, S. Gruet, O. Pirali, G. Mouret, Spectrochimica Acta Part A, 132 (2014) 838-845.ross sections and their temperature dependences have been also measured in the Mid-IR using conventional FTIR spectroscopy probing the nitro-derivatives vapors in a heated multipass-cell.

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Footnotes:

J. C. Oxley, J. L. Smith, W. Luo, J. Brady, Prop. Explos. Pyrotec. 34 (2009) 539–543T A. Cuisset, S. Gruet, O. Pirali, G. Mouret, Spectrochimica Acta Part A, 132 (2014) 838-845.C

Tetrahydrofuran (THF) is a prototype biofuel and a common intermediate in combustion of alkanes and alkenes. Photolytic Cl atom-initiated oxidation of THF was studied with multiplexed photoionization mass spectrometry (MPIMS) technique at temperatures 400-650 K and pressures 0.005-2 bar. Photoionization spectra and kinetic time traces were recorded simultaneously for all mass channels. Photoionization spectra, recorded with tunable VUV synchrotron radiation, were used to separate and identify isomers with the same nominal molecular formula, providing mechanistic insight into the the underlying kinetics. Our study suggests that formation of alkylperoxy radicals and their subsequent isomerization to hydroperoxyalkyl radicals plays an important role in low temperature oxidation of THF, while ring opening of THF_−H radical (which dominates THF oxidation at T > 800 K) is less important at our conditions.