Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Low-temperature nitrogen-bearing polycyclic aromatic hydrocarbon formation routes validated by infrared spectroscopy

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are abundant in many regions of the Universe, representing a major reservoir for cosmic carbon. However, their formation pathways in cold regions of space remain elusive. Recent astronomical detections show that current astrochemical models drastically underestimate the abundance of aromatic molecules and suggest that additional formation pathways such as ion–molecule reactions need to be considered. Here we reveal efficient low-temperature formation pathways towards nitrogen-containing PAHs via exothermic pyridine+ and acetylene ion–molecule reactions. The experimental approach combines kinetics with spectroscopic probing and unambiguously identifies key reaction intermediates and the final nitrogen-containing PAH product quinolizinium+, a structure that is thought to contribute to the 6.2 μm interstellar emission feature. This study not only provides competing formation pathways relevant in the chemistry of the interstellar medium and Titan’s atmosphere, but also delivers information to verify in-silico potential energy surfaces, astrochemical models and infrared observations.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Schematic overview of the global reaction pathways to N-PAHs as observed and discussed throughout this study.
Fig. 2: Exemplary mass spectra and kinetic profiles of the molecules involved in the ion–molecule reaction of pyridine+ with acetylene.
Fig. 3: Experimental IRMPD fingerprint spectra of the reaction products.
Fig. 4: Calculated potential energy surfaces of the pyridine+-with-acetylene reaction via the nitrogen (N) and carbon (C) atom.
Fig. 5: Comparison of an interstellar infrared emission spectrum and infrared fingerprints of relevant cationic N-PAHs.

Data availability

Source data are provided with this paper. These source data and the log files of the quantum-chemical calculations are available at: https://doi.org/10.34973/m9mn-d172. Additional data are available from the corresponding author upon request.

Code availability

The code used for data reduction in this work can be found here: https://github.com/aravindhnivas/FELion_GUI3.

References

  1. Allamandola, L. J., Tielens, G. G. M. & Barker, J. R. Interstellar polycyclic aromatic hydrocarbons—the infrared emission bands, the excitation/emission mechanism, and the astrophysical implications. Astrophys. J. Suppl. Ser. 71, 733–775 (1989).

    Article  ADS  Google Scholar 

  2. Li, A. Spitzer’s perspective of polycyclic aromatic hydrocarbons in galaxies. Nat. Astron. 4, 339–351 (2020).

    Article  ADS  Google Scholar 

  3. Cernicharo, J. et al. Pure hydrocarbon cycles in TMC-1: Discovery of ethynyl cyclopropenylidene, cyclopentadiene, and indene. Astron. Astrophys. 649, L15 (2021).

    Article  ADS  Google Scholar 

  4. McGuire, B. A. et al. Detection of two interstellar polycyclic aromatic hydrocarbons via spectral matched filtering. Science 371, 1265–1269 (2021).

    Article  ADS  Google Scholar 

  5. Vuitton, V., Yelle, R. V. & McEwan, M. J. Ion chemistry and N-containing molecules in Titan’s upper atmosphere. Icarus 191, 722–742 (2007).

    Article  ADS  Google Scholar 

  6. Ali, A., Sittler, E. C., Chornay, D., Rowe, B. R. & Puzzarini, C. Organic chemistry in Titan’s upper atmosphere and its astrobiological consequences: I. Views towards Cassini plasma spectrometer (CAPS) and ion neutral mass spectrometer (INMS) experiments in space. Planet. Space Sci. 109–110, 46–63 (2015).

    Article  ADS  Google Scholar 

  7. Zhen, J., Castellanos, P., Paardekooper, D. M., Linnartz, H. & Tielens, A. G. G. M. Laboratory formation of fullerenes from PAHs: top-down interstellar chemistry. Astrophys. J. Lett. 797, 30 (2014).

    Article  ADS  Google Scholar 

  8. Berne, O. & Tielens, A. G. G. M. Formation of buckminsterfullerene (C60) in interstellar space. Proc. Natl Acad. Sci. USA 109, 401–406 (2012).

    Article  ADS  Google Scholar 

  9. Parker, D. S. N. et al. Low temperature formation of nitrogen-substituted polycyclic aromatic hydrocarbons (PANHs)—barrierless routes to dihydro(iso)quinolines. Astrophys. J. 815, 115 (2015).

    Article  ADS  Google Scholar 

  10. Lemmens, A. K., Rap, D. B., Thunnissen, J. M. M., Willemsen, B. & Rijs, A. M. Polycyclic aromatic hydrocarbon formation chemistry in a plasma jet revealed by IR-UV action spectroscopy. Nat. Commun. 11, 269 (2020).

    Article  ADS  Google Scholar 

  11. Lee, K. L. K., McGuire, B. A. & McCarthy, M. C. Gas-phase synthetic pathways to benzene and benzonitrile: a combined microwave and thermochemical investigation. Phys. Chem. Chem. Phys. 21, 2946–2956 (2019).

    Article  Google Scholar 

  12. Mccabe, M. N., Hemberger, P., Reusch, E., Bodi, A. & Bouwman, J. Off the beaten path: almost clean formation of indene from the ortho-benzyne + allyl reaction. J. Phys. Chem. Lett. 11, 2859–2863 (2020).

    Article  Google Scholar 

  13. Doddipatla, S. et al. Low-temperature gas-phase formation of indene in the interstellar medium. Sci. Adv. 7, eabd4044 (2021).

    Article  ADS  Google Scholar 

  14. Parker, D. S. N. & Kaiser, R. I. On the formation of nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) in circumstellar and interstellar environments. Chem. Soc. Rev. 46, 452–463 (2017).

    Article  Google Scholar 

  15. Parker, D. S. N. et al. Low temperature formation of naphthalene and its role in the synthesis of PAHs (polycyclic aromatic hydrocarbons) in the interstellar medium. Proc. Natl Acad. Sci. USA 109, 53–58 (2012).

    Article  ADS  Google Scholar 

  16. Parker, D. S. N. et al. Gas phase synthesis of (iso)quinoline and its role in the formation of nucleobases in the interstellar medium. Astrophys. J. 803, 53 (2015).

    Article  ADS  Google Scholar 

  17. Larsson, M., Geppert, W. D. & Nyman, G. Ion chemistry in space. Rep. Prog. Phys. 75, 066901 (2012).

    Article  ADS  Google Scholar 

  18. Huntress, W. T. Jr. Laboratory studies of bimolecular reactions of positive ions in interstellar clouds, in comets, and in planetary atmospheres of reducing composition. Astrophys. J. Suppl. Ser. 33, 495–514 (1977).

    Article  ADS  Google Scholar 

  19. Snow, T. P., Le Page, V., Keheyan, Y. & Bierbaum, V. M. The interstellar chemistry of PAH cations. Nature 391, 259–260 (1998).

    Article  ADS  Google Scholar 

  20. Gerlich, D. Experimental investigations of ion–molecule reactions relevant to interstellar chemistry. J. Chem. Soc. Faraday Trans. 89, 2199–2208 (1993).

    Article  Google Scholar 

  21. Herbst, E., Adams, N. G. & Smith, D. Laboratory measurements of ion–molecule reactions pertaining to interstellar hydrocarbon synthesis. Astrophys. J. 269, 329–333 (1983).

    Article  ADS  Google Scholar 

  22. Asvany, O., Schlemmer, S. & Gerlich, D. Deuteration of CHn+ (n = 3–5) in collisions with HD measured in a low-temperature ion trap. Astrophys. J. 617, 685–692 (2004).

    Article  ADS  Google Scholar 

  23. Shiels, O., Kelly, P., Blanksby, S., da Silva, G. & Trevitt, A. J. Barrierless reactions of three benzonitrile radical cations with ethylene. Aust. J. Chem. 73, 705–713 (2020).

    Article  Google Scholar 

  24. Shiels, O. J. et al. Reactivity trends in the gas-phase addition of acetylene to the N-protonated aryl radical cations of pyridine, aniline, and benzonitrile. J. Am. Soc. Mass. Spectrom. 32, 537–547 (2021).

    Article  Google Scholar 

  25. Soliman, A. R., Hamid, A. M., Attah, I., Momoh, P. & El-Shall, M. S. Formation of nitrogen-containing polycyclic cations by gas-phase and intracluster reactions of acetylene with the pyridinium and pyrimidinium ions. J. Am. Chem. Soc. 135, 155–166 (2013).

    Article  Google Scholar 

  26. Jusko, P. et al. The FELion cryogenic ion trap beam line at the FELIX free-electron laser laboratory: infrared signatures of primary alcohol cations. Faraday Discuss. 217, 172–202 (2019).

    Article  ADS  Google Scholar 

  27. Rap, D. B., Marimuthu, A. N., Redlich, B. & Brünken, S. Stable isomeric structures of the pyridine cation (C5H5N•+) and protonated pyridine (C5H5NH+) elucidated by cold ion infrared spectroscopy. J. Mol. Spectrosc. 373, 111357 (2020).

    Article  Google Scholar 

  28. Dunbar, R. C. Polyatomic ion–molecule radiative association: theoretical framework and predictions: observations of NO+ + C6H5CN as an example. Int. J. Mass Spectrom. Ion Process. 100, 423–443 (1990).

    Article  ADS  Google Scholar 

  29. Oepts, D., van der Meer, A. F. G. & van Amersfoort, P. W. The free-electron-laser user facility FELIX. Infrared Phys. Technol. 36, 297–308 (1995).

    Article  ADS  Google Scholar 

  30. Kislov, V. V., Islamova, N. I., Kolker, A. M., Lin, S. H. & Mebel, A. M. Hydrogen abstraction acetylene addition and Diels–Alder mechanisms of PAH formation: a detailed study using first principles calculations. J. Chem. Theory Comput. 1, 908–924 (2005).

    Article  Google Scholar 

  31. Frenklach, M., Clary, D. W., Gardiner, W. C. & Stein, S. E. Detailed kinetic modeling of soot formation in shock-tube pyrolysis of acetylene. Symp. Combust. 20, 887–901 (1985).

    Article  Google Scholar 

  32. Yim, M. K. & Choe, J. C. Formation of C4H4•+ from the pyridine radical cation: a theoretical mechanistic and kinetic study. J. Phys. Chem. A 115, 3087–3094 (2011).

    Article  Google Scholar 

  33. Feng, J. Y., Lee, Y. P., Witek, H. A. & Ebata, T. Vacuum ultraviolet photoionization induced proton migration and formation of a new C–N bond in pyridine clusters revealed by infrared spectroscopy and mass spectrometry. J. Phys. Chem. Lett. 12, 4936–4943 (2021).

    Article  Google Scholar 

  34. Bohme, D. K. Proton transport in the catalyzed gas-phase isomerization of protonated molecules. Int. J. Mass Spectrom. Ion Process. 115, 95–110 (1992).

    Article  ADS  Google Scholar 

  35. Tu, Y. P. & Holmes, J. L. The chemistry of solvated distonic ions: preparation, isomerization, and fragmentation. J. Am. Chem. Soc. 122, 5597–5602 (2000).

    Article  Google Scholar 

  36. Ibrahim, Y., Mabrouki, R., Meot-Ner, M. & El-Shall, M. S. Hydrogen bonding interactions of pyridine•+ with water: stepwise solvation of distonic cations. J. Phys. Chem. A 111, 1006–1014 (2007).

    Article  Google Scholar 

  37. Anicich, V. G., Milligan, D. B., Fairley, D. A. & McEwan, M. J. Termolecular ion–molecule reactions in Titan’s atmosphere. I: principal ions with principal neutrals. Icarus 146, 118–124 (2000).

    Article  ADS  Google Scholar 

  38. Anicich, V. G. & McEwan, M. J. Ion–molecule chemistry in Titan’s ionosphere. Planet. Space Sci. 45, 897–921 (1997).

    Article  ADS  Google Scholar 

  39. Milligan, D. B. et al. Termolecular ion–molecule reactions in Titan’s atmosphere. II: the structure of the association adducts of HCNH+ with C2H2 and C2H4. J. Am. Soc. Mass. Spectrom. 12, 557–564 (2001).

    Article  Google Scholar 

  40. Eichelberger, B. R., Snow, T. P. & Bierbaum, V. M. Collision rate constants for polarizable ions. J. Am. Soc. Mass. Spectrom. 14, 501–505 (2003).

    Article  Google Scholar 

  41. Waite, J. H. et al. Planetary science: the process of tholin formation in Titan’s upper atmosphere. Science 316, 870–875 (2007).

    Article  ADS  Google Scholar 

  42. Vinatier, S. et al. Vertical abundance profiles of hydrocarbons in Titan’s atmosphere at 15° S and 80° N retrieved from Cassini/CIRS spectra. Icarus 188, 120–138 (2007).

    Article  ADS  Google Scholar 

  43. Sagan, C. & Khare, B. N. Tholins: organic chemistry of interstellar grains and gas. Nature 277, 102–107 (1979).

    Article  ADS  Google Scholar 

  44. Crary, F. J. et al. Heavy ions, temperatures and winds in Titan’s ionosphere: combined Cassini CAPS and INMS observations. Planet. Space Sci. 57, 1847–1856 (2009).

    Article  ADS  Google Scholar 

  45. Hudgins, D. M., Bauschlicher, C. W. Jr. & Allamandola, L. J. Variations in the peak position of the 6.2 μm interstellar emission feature: a tracer of N in the interstellar polycyclic aromatic hydrocarbon population. Astrophys. J. 632, 316–332 (2005).

    Article  ADS  Google Scholar 

  46. Canelo, C. M., Friaça, A. C. S., Sales, D. A., Pastoriza, M. G. & Ruschel-Dutra, D. Variations in the 6.2 μm emission profile in starburst-dominated galaxies: a signature of polycyclic aromatic nitrogen heterocycles (PANHs)? Mon. Not. R. Astron. Soc. 475, 3746–3763 (2018).

    Article  ADS  Google Scholar 

  47. Hudgins, D. M. & Allamandola, L. J. The spacing of the interstellar 6.2 and 7.7 micron emission features as an indicator of polycyclic aromatic hydrocarbon size. Astrophys. J. 513, L69–L73 (1999).

    Article  ADS  Google Scholar 

  48. Yang, Y. et al. Laboratory formation and photochemistry of covalently bonded polycyclic aromatic nitrogen heterocycle (PANH) clusters in the gas phase. Mon. Not. R. Astron. Soc. 498, 1–11 (2020).

    Article  ADS  Google Scholar 

  49. Jiao, C. Q., Boatz, J. A., DeJoseph, C. A. & Garscadden, A. Condensation reaction of C4H4+ with pyridine. Int. J. Mass Spectrom. 288, 22–35 (2009).

    Article  Google Scholar 

  50. Gaussian 16 (Gaussian Inc., 2016).

  51. Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993).

    Article  ADS  Google Scholar 

  52. Barone, V., Cimino, P. & Stendardo, E. Development and validation of the B3LYP/N07D computational model for structural parameter and magnetic tensors of large free radicals. J. Chem. Theory Comput. 4, 751–764 (2008).

    Article  Google Scholar 

  53. Lee, C., Yang, W. & Parr, R. G. Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785–789 (1988).

    Article  ADS  Google Scholar 

  54. Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H–Pu. J. Chem. Phys. 132, 134105 (2010).

    Article  Google Scholar 

  55. Panchagnula, S. et al. Structural investigation of doubly-dehydrogenated pyrene cations. Phys. Chem. Chem. Phys. 22, 21651–21663 (2020).

    Article  Google Scholar 

  56. Lemmens, A. K. et al. Anharmonicity in the mid-infrared spectra of polycyclic aromatic hydrocarbons: molecular beam spectroscopy and calculations. Astron. Astrophys. 628, A130 (2019).

    Article  Google Scholar 

  57. Hohenstein, E. G., Chill, S. T. & Sherrill, C. D. Assessment of the performance of the M05#2X and M06#2X exchange correlation functionals for noncovalent interactions in biomolecules. J. Chem. Theory Comput. 4, 1996–2000 (2008).

    Article  Google Scholar 

  58. Kozuch, S. & Martin, J. M. L. DSD-PBEP86: in search of the best double-hybrid DFT with spin-component scaled MP2 and dispersion corrections. Phys. Chem. Chem. Phys. 13, 20104–20107 (2011).

    Article  Google Scholar 

  59. Kozuch, S. & Martin, J. M. L. Spin-component-scaled double hybrids: an extensive search for the best fifth-rung functionals blending DFT and perturbation theory. J. Comput. Chem. 34, 2327–2344 (2013).

    Google Scholar 

  60. Sloan, G. C., Kraemer, K. E., Price, S. D. & Shipman, R. F. A uniform database of 2.4–45.4 micron spectra from the Infrared Space Observatory Short Wavelength Spectrometer. Astrophys. J. Suppl. Ser. 147, 379–401 (2003).

    Article  ADS  Google Scholar 

  61. Oomens, J., Sartakov, B. G., Tielens, A. G. G. M., Meijer, G. & von Helden, G. Gas-phase infrared spectrum of the coronene cation. Astrophys. J. 560, L99–L103 (2001).

    Article  ADS  Google Scholar 

  62. Oomens, J., Tielens, A. G. G. M., Sartakov, B. G., von Helden, G. & Meijer, G. Laboratory infrared spectroscopy of cationic polycyclic aromatic hydrocarbon molecules. Astrophys. J. 591, 968–985 (2003).

    Article  ADS  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge the support of Radboud University and of the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), for providing the required beam time at the FELIX laboratory and the skilful assistance of the FELIX staff. This work was sponsored by NWO Exact and Natural Sciences as part of the research programme ROSAA (NWO START-UP grant 740.018.010; S.B., A.N.M.) and through the use of supercomputer facilities at SURFsara in Amsterdam (NWO Rekentijd grant 2021.055). We thank the Cologne Laboratory Astrophysics group for providing the FELion ion trap instrument for the current experiments and the Cologne Center for Terahertz Spectroscopy funded by the Deutsche Forschungsgemeinschaft (grant SCHL 341/15-1) for supporting its operation. We thank J. Oomens for helpful discussion.

Author information

Authors and Affiliations

Authors

Contributions

D.B.R. contributed to the conception and design of the work, data collection, data analysis and interpretation, performing quantum-chemical calculations and drafting and editing of the article. J.G.M.S. contributed to the data collection, performing quantum-chemical calculations and editing of the article. A.N.M. developed data analysis and interpretation tools. B.R. contributed to data interpretation and editing of the article. S.B. contributed to the conception and design of the work, data collection, data analysis and interpretation and drafting and editing of the article. All authors discussed the manuscript.

Corresponding author

Correspondence to Sandra Brünken.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Astronomy thanks Adam Trevitt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 First order reaction rate constants obtained from the kinetic profiles of (a) m/z 104, (b) m/z 105, (c) m/z 106 and (d) m/z 130 plotted against the acetylene number density.

Second order reaction rate coefficients are obtained using a linear fit to obtain (a) k2, (b) kRA, (c) kproto and (d) k2,C7. When using large acetylene number densities, required for the measurements on m/z 106 and 130, the reaction towards m/z 104 and 105 has almost proceeded completely during the helium pulse phase (which is not included in the fit) and yields a larger fit error for the latter. The error bars indicate the 1σ errors and the grey shaded bands define the 2σ uncertainty regions of the fits.

Extended Data Fig. 2 Exemplary kinetic profile of the reaction of pyridine+ with acetylene in a continuous high-pressure regime at 150 K.

An ion pulse length of 5 ms and acetylene number densities of 1.8 x 109 to 3.1 x 109 have been used. Measurements are shown as points with 1σ error bars from multiple iterations on each datapoint. The solid lines display the results of the fitted reaction equation model. The grey area is not included in the fit, as the ions are still being thermalized after entering the trap. The value for k2 that describes the bimolecular reaction to m/z 104 is fixed to 4.9 x 10−10 cm3 molecule−1 s−1 as determined from low pressure regime scans.

Extended Data Fig. 3 Experimental IRMPD infrared spectrum of m/z 105 (grey) and comparison with scaled harmonic infrared spectra of different C7H7N•+ isomers (coloured sticks).

The vibrational frequencies have been calculated for (a) two conformers of 2-vinyl-β-distonic-H-pyridine+ (Ca-3, blue sticks), (b) two conformers of 2-acetylene-H-pyridine+ (Ca-2 and Cb-2, pink sticks), (c) pyridine-C2H2+ complex (C-1, blue-green sticks) and 2-vinyl-pyridine+ (Cb-3, green sticks) and (d) N-acetylene-pyridine+ (N-1, purple sticks) and N-vinyl-α-distonic-pyridine+ (N-2, dark-purple sticks) at the B3LYP/N07D-GD3 level of theory. The assigned structures for m/z 105 are shown in panel (a).

Extended Data Fig. 4 Comparison between the experimental IRMPD spectrum of m/z 130 produced in the reaction in the ion trap (grey) and the IRPD spectrum of m/z 130 formed inside the ion storage source (red).

To evaluate the B3LYP/N07D level of theory, the calculated anharmonic infrared spectra of quinolizinium+ (N-5) and H-quinoline+ (Ca-6) are plotted as orange and green sticks, respectively.

Extended Data Fig. 5 Calculated potential energy surface of the first part of the C formation pathway (black) as shown in Fig. 5 and an alternative route via N-acetylene-pyridine+ (N-1).

The energies are zero-point energy corrected and calculated with respect to the entrance energy of pyridine+ and acetylene at the B3LYP/6-311++G(d,p) level of theory. Energies obtained from additional calculations at the DSD-PBEP86-GD3BJ/aug-cc-pVQZ//M06-2X/6-31++G(2df,p) level of theory for the transition states TS-NC-2 and TS-Cb-1 and the product Cb-2 are shown next to it.

Extended Data Fig. 6 Experimental IRMPD infrared spectrum of m/z 104 (grey) and comparison with scaled harmonic infrared spectra of different C7H6N+ isomers (coloured sticks).

The vibrational frequencies have been calculated for (a) 2-ethynyl-H-pyridine+ (Ca-7, red sticks), (b) N-ethynyl-pyridine+ (N-6, blue sticks) and (c) 3 and 4-ethynyl-H-pyridine+ (green and orange sticks, respectively) at the B3LYP/N07D-GD3 level of theory. The assigned structure for m/z 104 is shown in panel (a).

Supplementary information

Supplementary Information

Ordinary differential equations model, Supplementary Table 1 and Figs. 1 and 2.

Source data

Source Data Fig. 2

Mass spectra and kinetic plots.

Source Data Fig. 3

Experimental and calculated infrared spectra.

Source Data Fig. 5

Experimental and calculated infrared spectra.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rap, D.B., Schrauwen, J.G.M., Marimuthu, A.N. et al. Low-temperature nitrogen-bearing polycyclic aromatic hydrocarbon formation routes validated by infrared spectroscopy. Nat Astron 6, 1059–1067 (2022). https://doi.org/10.1038/s41550-022-01713-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41550-022-01713-z

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing