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  • 1. Bull, James N.
    et al.
    Buntine, Jack T.
    Scholz, Michael S.
    Carrascosa, Eduardo
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Bieske, Evan J.
    Photodetachment and photoreactions of substituted naphthalene anions in a tandem ion mobility spectrometer2019In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 217, p. 34-46Article in journal (Refereed)
    Abstract [en]

    Substituted naphthalene anions (deprotonated 2-naphthol and 6-hydroxy-2-naphthoic acid) are spectroscopically probed in a tandem drift tube ion mobility spectrometer (IMS). Target anions are selected according to their drift speed through nitrogen buffer gas in the first IMS stage before being exposed to a pulse of tunable light that induces either photodissociation or electron photodetachment, which is conveniently monitored by scavenging the detached electrons with trace SF6 in the buffer gas. The photodetachment action spectrum of the 2-naphtholate anion exhibits a band system spanning 380-460 nm with a prominent series of peaks spaced by 440 cm(-1), commencing at 458.5 nm, and a set of weaker peaks near the electron detachment threshold corresponding to transitions to dipole-bound states. The two deprotomers of 6-hydroxy-2-naphthoic acid are separated and spectroscopically probed independently. The molecular anion formed from deprotonation of the hydroxy group gives rise to a photodetachment action spectrum similar to that of the 2-naphtholate anion with an onset at 470 nm and a maximum at 420 nm. Near the threshold, the photoreaction with SF6 is observed with displacement of an OH group by an F atom. In contrast, the anion formed from deprotonation of the carboxylic acid group gives rise to a photodissociation action spectrum, recorded on the CO2 loss channel, lying at much shorter wavelengths with an onset at 360 nm and maximum photoresponse at 325 nm.

  • 2. Bull, James N.
    et al.
    Carrascosa, Eduardo
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Bieske, Evan J.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics. University of Melbourne, Australia.
    Ion mobility action spectroscopy of flavin dianions reveals deprotomer-dependent photochemistry2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 29, p. 19672-19681Article in journal (Refereed)
    Abstract [en]

    The intrinsic optical properties and photochemistry of flavin adenine dinucleotide (FAD) dianions are investigated using a combination of tandem ion mobility spectrometry and action spectroscopy. Two principal isomers are observed, the more stable form being deprotonated on the isoalloxazine group and a phosphate (N-3,PO4 deprotomer), and the other on the two phosphates (PO4,PO4 deprotomer). Ion mobility data and electronic action spectra suggest that photo-induced proton transfer occurs from the isoalloxazine group to a phosphate group, converting the PO4,PO4 deprotomer to the N-3,PO4 deprotomer. Comparisons of the isomer selective action spectra of FAD dianions and flavin monoanions with solution spectra and gas-phase photodissociation action spectra suggests that solvation shifts the electronic absorption of the deprotonated isoalloxazine group to higher energy. This is interpreted as evidence for significant charge transfer in the lowest optical transition of deprotonated isoalloxazine. Overall, this work demonstrates that the site of deprotonation of flavin anions strongly affects their electronic absorptions and photochemistry.

  • 3.
    de Ruette, Nathalie
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Alexander, John D.
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Haag, Nicole
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    DESIREE electrospray ion source test bench and setup for collision induced dissociation experiments2018In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 89, no 7, article id 075102Article in journal (Refereed)
    Abstract [en]

    In this paper, we give a detailed description of an electrospray ion source test bench and a single-pass setup for ion fragmentation studies at the Double ElectroStatic Ion Ring ExpEriment infrastructure at Stockholm University. This arrangement allows for collision-induced dissociation experiments at the center-of-mass energies between 10 eV and 1 keV. Charged fragments are analyzed with respect to their kinetic energies (masses) by means of an electrostatic energy analyzer with a wide angular acceptance and adjustable energy resolution.

  • 4.
    Gatchell, Michael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics. Aarhus University, Denmark.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Chen, Tao
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Nascimento, Rodrigo F.
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Anderson, Emma K.
    Stockholm University, Faculty of Science, Department of Physics.
    Delaunay, R.
    Vizcaino, V.
    Rousseau, P.
    Adoui, L.
    Huber, B. A.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Failure of hydrogenation in protecting polycyclic aromatic hydrocarbons from fragmentation2015In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 92, no 5, article id 050702Article in journal (Refereed)
    Abstract [en]

    A recent study of soft x-ray absorption in native and hydrogenated coronene cations, C24H12+m + m = 0-7, led to the conclusion that additional hydrogen atoms protect (interstellar) polycyclic aromatic hydrocarbon (PAH) molecules from fragmentation [Reitsma et al., Phys. Rev. Lett. 113, 053002 (2014)]. The present experiment with collisions between fast (30-200 eV) He atoms and pyrene (C16H10+m +, m = 0, 6, and 16) and simulations without reference to the excitation method suggests the opposite. We find that the absolute carbon-backbone fragmentation cross section does not decrease but increases with the degree of hydrogenation for pyrene molecules.

  • 5.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Collision- and photon-induced dynamics of complex molecular ions in the gas phase2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I report experiments probing collision- and photon-induced molecular dynamics in the gas phase. Excited molecules formed in such interactions may relax by emitting electrons or photons, isomerization or fragmentation. For complex molecular systems, these processes typically occur on timescales exceeding picoseconds following statistical redistribution of the excitation energy across the internal degrees of freedom. However, energy transfer to molecules through ion/atom impact may in some cases lead to prompt atom knockout in Rutherford-type scattering processes on much faster timescales. Another example of such a non-statistical process is photon-induced excited-state proton transfer, a structural rearrangement occurring on the femtosecond timescale.

    In this work, I investigate the competition between statistical and non-statistical fragmentation processes for a range of molecules colliding with He at center-of-mass energies in the sub-keV range. I show that heavy atom knockout is an important process for systems containing aromatic rings such as Polycyclic Aromatic Hydrocarbons (PAHs) or porphyrins, while statistical fragmentation processes dominate for less stable and/or smaller systems such as adenine or hydrogenated PAHs. Furthermore, I present the first measurements of the threshold energies for prompt single atom knockout from isolated molecules. The experimental results are interpreted with the aid of Molecular Dynamics (MD) simulations which allow us to extract the energy deposited into the system during a collision, knockout cross sections, fragmentation pathways and the structures of the fragments. The results presented in this work may be important for understanding the response of complex molecules to energetic processes in e.g. astrophysical environments.

    Furthermore, I present the results of photodissociation and luminescence experiments probing flavin mono-anions in the gas phase. These are compared against calculations and previously measured spectra in solution. The discrepancies between the present results and the theoretical values suggest that more consideration of the vibronic structure is needed to model the photoabsorption and emission in flavins. Finally, I present the results of photoisomerisation experiments of flavin di-anions where two different isomers have been found and I discuss the proton transfer mechanisms which govern the structural changes.

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  • 6.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    The role of knockout driven fragmentation in collision with isolated complex molecular systems2018Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This licentiate thesis covers results from collision induced dissociation (CID) experiments of Polycyclic Aromatic Hydrocarbons (PAHs), hydrogentated PAHs (HPAHs) and porphyrins. PAHs and HPAHs are believed to play key roles in the evolution of complex molecules in space, while porphyrins are essential for various functions in living organisms. The experiments were carried out in the Electrospray Ion Source Laboratory (EIS-LAB) at the Double ElectroStatic Ion-Ring ExpEriment (DESIREE) infrastructure, Stockholm University.  In these studies, molecular ions collide with neutral targets at center-of-mass energies from a few tens to a few hundreds of eV. In this energy regime, fragmentation is mainly driven by nuclear scattering processes (nuclear stopping) rather than by interactions with the molecular electronic clouds (electronic stopping). Thus, knockout of single heavy atoms from the molecule in prompt billiard-ball type collision processes may occur in competition with statistical fragmentation processes in which the excitation energy is redistributed across all degrees of freedom before the decay. In this thesis, we have investigated the importance of knockout driven fragmentation processes in a series of experiments with markedly different molecular structures ranging from pure sp2-hybridized to pure sp3-hybridized systems. The experiments are interpreted in view of molecular structure and molecular dynamics simulations. These studies show that knockout processes are important for any molecular system, but they are in general difficult to isolate by means of mass spectrometric techniques. We have seen clear fingerprints of single carbon-atom loss in the collision experiments for PAHs and porphyrins. In contrast, in the case of the hydrogenated PAHs the fragmentation is dominated by the statistical loss of single carbon atoms due to their lower dissociation energy. We further report the threshold displacement energy for PAH, hydrogenated PAHs and porphyrin molecules--the key intrinsic property determining the cross section for prompt atom knockout.

  • 7.
    Giacomozzi, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    D'Angelo, Giovanna
    Stockholm University, Faculty of Science, Department of Physics. Universidad Autónoma de Madrid, Spain.
    Diaz-Tendero, S.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Alcami, M.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Decay pathways for protonated and deprotonated adenine molecules2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 4, article id 044306Article in journal (Refereed)
    Abstract [en]

    We have measured fragment mass spectra and total destruction cross sections for protonated and deprotonated adenine following collisions with He at center-of-mass energies in the 20-240 eV range. Classical and ab initio molecular dynamics simulations are used to provide detailed information on the fragmentation pathways and suggest a range of alternative routes compared to those reported in earlier studies. These new pathways involve, for instance, losses of HNC molecules from protonated adenine and losses of NH2 or C3H2N2 from deprotonated adenine. The present results may be important to advance the understanding of how biomolecules may be formed and processed in various astrophysical environments.

  • 8.
    Giacomozzi, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    D'Angelo, Giovanna
    Stockholm University, Faculty of Science, Department of Physics.
    Diaz-Tendero, Sergio
    de Ruette, Nathalie
    Stockett, Mark
    Stockholm University, Faculty of Science, Department of Physics.
    Alcamí, Manuel
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Decay pathways for protonated and deprotonated Adenine moleculesManuscript (preprint) (Other academic)
  • 9.
    Giacomozzi, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    D'Angelo, Giovanna
    Stockholm University, Faculty of Science, Department of Physics. Universidade do Porto, Portugal; Universidad Autónoma de Madrid, Spain.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Knockout driven fragmentation of porphyrins2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 30, p. 19750-19755Article in journal (Refereed)
    Abstract [en]

    We have studied collisions between tetraphenylporphyrin cations and He or Ne at center-of-mass energies in the range 50-110 eV. The experimental results were interpreted in view of density functional theory calculations of dissociation energies and classical molecular dynamics simulations of how the molecules respond to the He/Ne impact. We demonstrate that prompt atom knockout strongly contributes to the total destruction cross sections. Such impulse driven processes typically yield highly reactive fragments and are expected to be important for collisions with any molecular system in this collision energy range, but have earlier been very difficult to isolate for biomolecules.

  • 10.
    Giacomozzi, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kjaer, C.
    Langeland Knudsen, J.
    Andersen, L. H.
    Brøndsted Nielsen, S.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 21, article id 214309Article in journal (Refereed)
    Abstract [en]

    We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using photo-induced dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0 eV (210-550 nm). The S-0 -> S-2 transition is strongly blue shifted relative to aqueous solution, supporting the view that this transition has a significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima cannot be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions in vacuo. The gas-phase Stokes shift for S-1 is 3000 cm(-1), which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of the vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.

  • 11.
    Kulyk, Kostiantyn
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Vegvari, Akos
    Kovalenko, Oleksandr
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Wendt, Ola
    Zubarev, Roman
    Schmidt, T. Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Collision Induced Dissociation of the retinal chromophore Schiff base from sub-eV to keV collision energiesIn: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed)
    Abstract [en]

    The gas-phase fragmentation of the protonated n-butylamine Schiff base of all-trans-retinal (NB-RPSB) was measured in low- and high-energy collisional activation modes. The protonated n-butyl β-ionone Schiff base (NB-BISB) peak at m/z = 248, known to be formed as a result of a complex gas-phase rearrangement reaction, has been reported to dominate in mass spectra of NB-RPSB after photo- and collisionally activated fragmentation processes. Earlier reported high-energy collision (50 keV) mass spectra have shown a broad distribution of the fragments with the peak at m/z = 248 present but not dominating. We observed the formation of a peak at m/z = 248 only in collisional activation of NB-RPSB parent ion below a few eV, which shows that the rearrangement process is extremely efficient and happens in a very narrow energy range. On the other hand, our high-energy collision induced dissociation experiments yielded fragmentation patterns, which are fully accounted for simple bond cleavages of the NB-RPSB molecular backbone. We do not observe any peak corresponding to the formation of NB-BISB in the 10 eV – 1 keV collision energy range. This leaves the question open why this fragment reappears in the mass spectra at much higher energies.

  • 12.
    Stockett, Mark H.
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Aarhus University, Denmark.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Chen, Tao
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Threshold Energies for Single-Carbon Knockout from Polycyclic Aromatic Hydrocarbons2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 22, p. 4504-4509Article in journal (Refereed)
    Abstract [en]

    We have measured absolute cross sections for ultrafast (femtosecond) single-carbon knockout from polycyclic aromatic hydrocarbon (PAR) cations as functions of He-PAR center-of-mass collision energy in the 10-200 eV range. Classical molecular dynamics (MD) simulations cover this range and extend up to 105 eV. The shapes of the knockout cross sections are well-described by a simple analytical expression yielding experimental and MD threshold energies of E-th(Exp) = 32.5 +/- 0.4 eV and E-th(MD) = 41.0 +/- 0.3 eV, respectively. These are the first measurements of knockout threshold energies for molecules isolated in vacuo. We further deduce semiempirical (SE) and MD displacement energies, i.e., the energy transfers to the PAH molecules at the threshold energies for knockout, of T-disp(SE) = 23.3 +/- 0.3 eV and T-disp(MD) = 27.0 +/- 0.3 eV. The semiempirical results compare favorably with measured displacement energies for graphene (T-disp = 23.6 eV).

  • 13.
    Stockett, Mark H.
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Aarhus University, Denmark.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Chen, Tao
    Stockholm University, Faculty of Science, Department of Physics.
    Rousseau, P.
    Maclot, S.
    Chesnel, J. -Y.
    Adoui, L.
    Huber, B. A.
    Berzins, U.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Isomer effects in fragmentation of Polycyclic Aromatic Hydrocarbons2015In: International Journal of Mass Spectrometry, ISSN 1387-3806, E-ISSN 1873-2798, Vol. 392, p. 58-62Article in journal (Refereed)
    Abstract [en]

    We have observed significant differences in the fragmentation patterns of isomeric Polycyclic Aromatic Hydrocarbon (PAH) cations following collisions with helium atoms at center-of-mass energies around 100 eV. This is in contrast to the situation at other collision energies or in photo-absorption experiments where isomeric effects are very weak and where the lowest-energy dissociation channels (H- and C2H2-loss) domihate in statistical fragmentation processes. In the 100 eV range, non-statistical fragmentation also competes and is uniquely linked to losses of single carbon atoms (CHx-losses). We find that such CHx-losses are correlated with the ionic ground state energy within a given group of isomers. We present results for three C16H10+, four C18H12+ and five C20H12+ isomers colliding with He.

  • 14.
    Wolf, Michael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, H. Mark
    Stockholm University, Faculty of Science, Department of Physics. Aarhus University, Denmark.
    Schmidt, T. Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Hydrogenated pyrene: Statistical single-carbon loss below the knockout threshold2016In: European Physical Journal D: Atomic, Molecular and Optical Physics, ISSN 1434-6060, E-ISSN 1434-6079, Vol. 70, no 4, article id 85Article in journal (Refereed)
    Abstract [en]

    An ongoing discussion revolves around the question of what effect hydrogenation has oncarbon backbone fragmentation in polycyclic aromatic hydrocarbons (PAHs). In order to shedmore light on this issue, we have measured absolute single carbon loss cross sections incollisions between native or hydrogenated pyrene cations (C16H+ 10+m , m = 0, 6, 16) and He as functions of center-of-massenergies down to 20 eV. Classical molecular dynamics (MD) simulations give further insightinto energy transfer processes and also yield m-dependent threshold energies for prompt(femtoseconds) carbon knockout. Such fast, non-statistical fragmentation processesdominate CH x -loss for native pyrene (m = 0), while much slowerstatistical fragmentation processes contribute significantly to single-carbon loss for thehydrogenated molecules (m =6 and m =16). The latter is shown by measurements of large CH x -loss crosssections far below the MD knockout thresholds for C16H+ 16 and C16H+ 26.

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