Low-temperature formation of pyridine and (iso)quinoline via neutral–neutral reactions | Nature Astronomy

Nature Astronomy volume 8, pages 856–864 (2024)Cite this article

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Aromatic molecules represent fundamental building blocks in prebiotic chemistry and are contemplated as vital precursors to DNA and RNA nitrogen bases. However, despite the identification of some 300 molecules in extraterrestrial environments, the pathways to pyridine (C5H5N), pyridinyl (C5H4N·) and (iso)quinoline (C9H7N)—the simplest representative mono- and bicyclic aromatic molecules carrying nitrogen—are elusive. Here we afford compelling evidence on the gas-phase formation of methylene amidogen (H2CN·) and cyanomethyl (H2CCN·) radicals via molecular beam studies and electronic structure calculations. The modelling of the chemistries of the Taurus molecular cloud (TMC-1) and Titan’s atmosphere contemplates a complex chain of reactions synthesizing pyridine, pyridinyl and (iso)quinoline from H2CN· and H2CCN· at levels of up to 75%. This study affords unique entry points to precursors of DNA and RNA nitrogen bases in hydrocarbon-rich extraterrestrial environments thus changing the way we think about the origin of prebiotic molecules in our Galaxy.

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Pizzarello, S., Huang, Y. & Fuller, M. The carbon isotopic distribution of Murchison amino acids. Geochim. Cosmochim. Acta 68, 4963–4969 (2004).

ADS Google Scholar

Smith, K. E., Callahan, M. P., Gerakines, P. A., Dworkin, J. P. & House, C. H. Investigation of pyridine carboxylic acids in CM2 carbonaceous chondrites: potential precursor molecules for ancient coenzymes. Geochim. Cosmochim. Acta 136, 1–12 (2014).

ADS Google Scholar

Martins, Z. et al. Extraterrestrial nucleobases in the Murchison meteorite. Earth Planet. Sci. Lett. 270, 130–136 (2008).

ADS Google Scholar

Burton, A. S., Stern, J. C., Elsila, J. E., Glavin, D. P. & Dworkin, J. P. Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites. Chem. Soc. Rev. 41, 5459–5472 (2012).

Google Scholar

Andrews, H., Candian, A. & Tielens, A. G. G. M. Hydrogenation and dehydrogenation of interstellar PAHs: spectral characteristics and H2 formation. Astron. Astrophys. 595, A23 (2016).

ADS Google Scholar

Tsuge, M., Bahou, M., Wu, Y.-J., Allamandola, L. & Lee, Y.-P. The infrared spectrum of protonated ovalene in solid para-hydrogen and its possible contribution to interstellar unidentified infrared emission. Astrophys. J. 825, 96 (2016).

ADS Google Scholar

Tielens, A. G. G. M. Interstellar polycyclic aromatic hydrocarbon molecules. Annu. Rev. Astron. Astrophys. 46, 289–337 (2008).

ADS Google Scholar

Knorke, H., Langer, J., Oomens, J. & Dopfer, O. Infrared spectra of isolated protonated polycyclic aromatic hydrocarbon molecules. Astrophys. J. 706, L66 (2009).

ADS Google Scholar

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 (2005).

ADS Google Scholar

Herbst, E. & Van Dishoeck, E. F. Complex organic interstellar molecules. Annu. Rev. Astron. Astrophys. 47, 427–480 (2009).

ADS Google Scholar

Kaiser, R. I. & Hansen, N. An aromatic universe—a physical chemistry perspective. J. Phys. Chem. A 125, 3826–3840 (2021).

Google Scholar

Peeters, Z., Botta, O., Charnley, S. B., Ruiterkamp, R. & Ehrenfreund, P. The astrobiology of nucleobases. Astrophys. J. 593, L129 (2003).

ADS Google Scholar

Hörst, S. M. Titan’s atmosphere and climate. J. Geophys. Res. 122, 432–482 (2017).

Google Scholar

Vuitton, V., Yelle, R. V., Klippenstein, S. J., Hörst, S. M. & Lavvas, P. Simulating the density of organic species in the atmosphere of Titan with a coupled ion–neutral photochemical model. Icarus 324, 120–197 (2019).

ADS Google Scholar

Loison, J. C. et al. The neutral photochemistry of nitriles, amines and imines in the atmosphere of Titan. Icarus 247, 218–247 (2015).

ADS Google Scholar

Kislov, V. V., Nguyen, T. L., Mebel, A. M., Lin, S. H. & Smith, S. C. Photodissociation of benzene under collision-free conditions: an ab initio/Rice–Ramsperger–Kassel–Marcus study. J. Chem. Phys. 120, 7008–7017 (2004).

ADS Google Scholar

Lin, M.-F. et al. Photodissociation dynamics of pyridine. J. Chem. Phys. 123, 054309 (2005).

ADS Google Scholar

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

ADS Google Scholar

Ricca, A., Bauschlicher, C. W. Jr & Bakes, E. A computational study of the mechanisms for the incorporation of a nitrogen atom into polycyclic aromatic hydrocarbons in the Titan haze. Icarus 154, 516–521 (2001).

ADS Google Scholar

Soorkia, S. et al. Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction. Phys. Chem. Chem. Phys. 12, 8750–8758 (2010).

Google Scholar

López-Puertas, M. et al. Large abundances of polycyclic aromatic hydrocarbons in Titan’s upper atmosphere. Astrophys. J. 770, 132 (2013).

ADS Google Scholar

Anderson, C. M. & Samuelson, R. E. Titan’s aerosol and stratospheric ice opacities between 18 and 500 μm: vertical and spectral characteristics from Cassini CIRS. Icarus 212, 762–778 (2011).

ADS Google Scholar

Sebree, J. A., Trainer, M. G., Loeffler, M. J. & Anderson, C. M. Titan aerosol analog absorption features produced from aromatics in the far infrared. Icarus 236, 146–152 (2014).

ADS Google Scholar

Ali, A., Sittler, E. C. Jr, 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, 46–63 (2015).

ADS Google Scholar

Mathé, C., Gautier, T., Trainer, M. G. & Carrasco, N. Detection opportunity for aromatic signature in Titan’s aerosols in the 4.1–5.3 μm range. Astrophys. J. Lett. 861, L25 (2018).

ADS Google Scholar

Zhao, L. et al. Gas-phase synthesis of corannulene—a molecular building block of fullerenes. Phys. Chem. Chem. Phys. 23, 5740–5749 (2021).

Google Scholar

Kaiser, R. I. et al. Gas-phase synthesis of racemic helicenes and their potential role in the enantiomeric enrichment of sugars and amino acids in meteorites. Phys. Chem. Chem. Phys. 24, 25077–25087 (2022).

Google Scholar

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).

Google Scholar

Zhao, L. et al. A molecular beam and computational study on the barrierless gas phase formation of (iso)quinoline in low temperature extraterrestrial environments. Phys. Chem. Chem. Phys. 23, 18495–18505 (2021).

Google Scholar

Broadfoot, A. L. et al. Ultraviolet spectrometer observations of Neptune and Triton. Science 246, 1459–1466 (1989).

ADS Google Scholar

Moores, J. E., Smith, C. L., Toigo, A. D. & Guzewich, S. D. Penitentes as the origin of the bladed terrain of Tartarus Dorsa on Pluto. Nature 541, 188–190 (2017).

ADS Google Scholar

Yang, Z. et al. Gas-phase formation of 1, 3, 5, 7-cyclooctatetraene (C8H8) through ring expansion via the aromatic 1, 3, 5-cyclooctatrien-7-yl radical (C8H9•) transient. J. Am. Chem. Soc. 144, 22470–22478 (2022).

Google Scholar

Yang, Z. et al. Gas-phase formation of the resonantly stabilized 1-indenyl (C9H7•) radical in the interstellar medium. Sci. Adv. 9, eadi5060 (2023).

Google Scholar

Zhang, J. & Valeev, E. F. Prediction of reaction barriers and thermochemical properties with explicitly correlated coupled-cluster methods: a basis set assessment. J. Chem. Theory Comput. 8, 3175–3186 (2012).

Google Scholar

Adler, T. B., Knizia, G. & Werner, H.-J. A simple and efficient CCSD(T)-F12 approximation. J. Chem. Phys. 127, 221106 (2007).

ADS Google Scholar

Bourgalais, J. et al. The C(3P) + NH3 reaction in interstellar chemistry. I. Investigation of the product formation channels. Astrophys. J. 812, 106 (2015).

ADS Google Scholar

Chiba, S., Honda, T., Kondo, M. & Takayanagi, T. Direct dynamics study of the N(4S)+ CH3(2A2″) reaction. Comput. Theor. Chem. 1061, 46–51 (2015).

Google Scholar

Mebel, A. M., Georgievskii, Y., Jasper, A. W. & Klippenstein, S. J. Pressure-dependent rate constants for PAH growth: formation of indene and its conversion to naphthalene. Faraday Discuss. 195, 637–670 (2016).

ADS Google Scholar

Jasper, A. W. & Hansen, N. Hydrogen-assisted isomerizations of fulvene to benzene and of larger cyclic aromatic hydrocarbons. Proc. Combust. Inst. 34, 279–287 (2013).

Google Scholar

Lau, K.-C., Li, W.-K., Ng, C. Y. & Chiu, S.-W. A Gaussian-2 study of isomeric C2H2N and C2H2N+. J. Phys. Chem. A 103, 3330–3335 (1999).

Google Scholar

Willacy, K., Allen, M. & Yung, Y. A new astrobiological model of the atmosphere of Titan. Astrophys. J. 829, 79 (2016).

ADS Google Scholar

Cui, J. et al. Analysis of Titan’s neutral upper atmosphere from Cassini Ion Neutral Mass Spectrometer measurements. Icarus 200, 581–615 (2009).

ADS Google Scholar

Hickson, K. M. et al. The C(3P) + NH3 reaction in interstellar chemistry. II. Low temperature rate constants and modeling of NH, NH2, and NH3 abundances in dense interstellar clouds. Astrophys. J. 812, 107 (2015).

ADS Google Scholar

Pope, C. J. & Miller, J. A. Exploring old and new benzene formation pathways in low-pressure premixed flames of aliphatic fuels. Proc. Combust. Inst. 28, 1519–1527 (2000).

Google Scholar

Zhao, L. et al. Gas-phase synthesis of benzene via the propargyl radical self-reaction. Sci. Adv. 7, eabf0360 (2021).

ADS Google Scholar

Pearce, B. K. D., Ayers, P. W. & Pudritz, R. E. A consistent reduced network for HCN chemistry in early earth and Titan atmospheres: quantum calculations of reaction rate coefficients. J. Phys. Chem. A 123, 1861–1873 (2019).

Google Scholar

Pearce, B. K. D., He, C. & Hörst, S. M. An experimental and theoretical investigation of HCN production in the Hadean Earth atmosphere. ACS Earth Space Chem. 6, 2385–2399 (2022).

ADS Google Scholar

Marston, G., Nesbitt, F. L., Nava, D. F., Payne, W. A. & Stief, L. J. Temperature dependence of the reaction of nitrogen atoms with methyl radicals. J. Phys. Chem. 93, 5769–5774 (1989).

Google Scholar

Marston, G., Nesbitt, F. L. & Stief, L. J. Branching ratios in the N + CH3 reaction: formation of the methylene amidogen (H2CN) radical. J. Chem. Phys. 91, 3483–3491 (1989).

ADS Google Scholar

Dobrijevic, M., Loison, J. C., Hickson, K. M. & Gronoff, G. 1D-coupled photochemical model of neutrals, cations and anions in the atmosphere of Titan. Icarus 268, 313–339 (2016).

ADS Google Scholar

Loison, J. C., Dobrijevic, M. & Hickson, K. M. The photochemical production of aromatics in the atmosphere of Titan. Icarus 329, 55–71 (2019).

ADS Google Scholar

Benne, B., Dobrijevic, M., Cavalié, T., Loison, J.-C. & Hickson, K. M. A photochemical model of Triton’s atmosphere with an uncertainty propagation study. Astron. Astrophys. 667, A169 (2022).

Google Scholar

Vanuzzo, G. et al. Reaction N(2D) + CH2CCH2 (allene): an experimental and theoretical investigation and implications for the photochemical models of Titan. ACS Earth Space Chem. 6, 2305–2321 (2022).

ADS Google Scholar

Teolis, B. D. et al. A revised sensitivity model for Cassini INMS: Results at Titan. Space Sci. Rev. 190, 47–84 (2015).

ADS Google Scholar

Gladstone, G. R. & Young, L. A. New Horizons observations of the atmosphere of Pluto. Annu. Rev. Earth Planet. Sci. 47, 119–140 (2019).

ADS Google Scholar

Rap, D. B., Schrauwen, J. G., Marimuthu, A. N., Redlich, B. & Brünken, S. Low-temperature nitrogen-bearing polycyclic aromatic hydrocarbon formation routes validated by infrared spectroscopy. Nat. Astron. 6, 1059–1067 (2022).

ADS Google Scholar

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

ADS Google Scholar

McElroy, D. et al. The UMIST database for astrochemistry 2012. Astron. Astrophys. 550, A36 (2013).

Google Scholar

Ohishi, M., McGonagle, D., Irvine, W. M., Yamamoto, S. & Saito, S. Detection of a new interstellar molecule, H2CN. Astrophys. J. 427, L51–L54 (1994).

ADS Google Scholar

Thaddeus, P., Vrtilek, J. M. & Gottlieb, C. A. Laboratory and astronomical identification of cyclopropenylidene, C3H2. Astrophys. J. 299, L63–L66 (1985).

ADS Google Scholar

Cernicharo, J. et al. Discovery of CH2CHCCH and detection of HCCN, HC4N, CH3CH2CN, and, tentatively, CH3CH2CCH in TMC-1. Astron. Astrophys. 647, L2 (2021).

ADS Google Scholar

Tennis, J. D. et al. Detection and modelling of CH3NC in TMC-1. Mon. Not. R. Astron. Soc. 525, 2154–2171 (2023).

ADS Google Scholar

Stoks, P. G. & Schwartz, A. W. Basic nitrogen-heterocyclic compounds in the Murchison meteorite. Geochim. Cosmochim. Acta 46, 309–315 (1982).

ADS Google Scholar

Sephton, M. A. Organic compounds in carbonaceous meteorites. Nat. Prod. Rep. 19, 292–311 (2002).

Google Scholar

Dangi, B. B., Maity, S., Kaiser, R. I. & Mebel, A. M. A combined crossed beam and ab initio investigation of the gas phase reaction of dicarbon molecules (C2; X1Σg+/a3Πu) with propene (C3H6; X1A′): identification of the resonantly stabilized free radicals 1-and 3-vinylpropargyl. J. Phys. Chem. A 117, 11783–11793 (2013).

Google Scholar

Werner, H. et al. MOLPRO, version 2015.1, a package of ab initio programs (Univ. Cardiff Chemistry Consultants (UC3), 2015).

Knowles, P. J., Hampel, C. & Werner, H. J. Coupled cluster theory for high spin, open shell reference wave functions. J. Chem. Phys. 99, 5219–5227 (1993).

ADS Google Scholar

Dunning, T. H. Jr Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007–1023 (1989).

ADS Google Scholar

Peterson, K. A., Adler, T. B. & Werner, H.-J. Systematically convergent basis sets for explicitly correlated wavefunctions: the atoms H, He, B–Ne, and Al–Ar. J. Chem. Phys. 128, 084102 (2008).

ADS Google Scholar

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

ADS Google Scholar

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 (1988).

ADS Google Scholar

Frisch, M. J. et al. Gaussian 16, revision C.1 (Gaussian Inc., Wallingford CT, 2016).

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This work was supported by the US Department of Energy, Basic Energy Sciences, by grant no. DE-FG02-03ER15411 to the University of Hawaii at Manoa. The support of Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant nos. 311508/2021-9 and 405524/2021-8, is also acknowledged. We acknowledge fruitful discussions on the fractional abundances of ammonia with C. A. Nixon (NASA Goddard) and K. Willacy (JPL).

Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA

Zhenghai Yang, Chao He, Shane J. Goettl & Ralf I. Kaiser

Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA

Alexander M. Mebel

Centro Federal de Educação Tecnológica de Minas Gerais, CEFET-MG, Belo Horizonte, Brazil

Paulo F. G. Velloso, Márcio O. Alves & Breno R. L. Galvão

Institut des Sciences Moléculaires, CNRS, Université de Bordeaux, Talence, France

Jean-Christophe Loison & Kevin M. Hickson

Laboratoire d’Astrophysique de Bordeaux, Université de Bordeaux, CNRS, Pessac, France

Michel Dobrijevic

Xinjiang Astronomical Observatory, Chinese Academy of Sciences, Urumqi, P. R. China

Xiaohu Li

Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, Urumqi, P. R. China

Xiaohu Li

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R.I.K. designed the experiments. Z.Y., C.H. and S.J.G. preformed the experiments. A.M.M., P.F.G.V., M.O.A. and B.R.L.G. conducted the electronic structure calculations. J.-C.L, K.M.H. and M.D. conducted the atmospheric modelling of Titan. X.L. performed the astrochemical modelling of TMC-1. Z.Y. and R.I.K. analysed the data and wrote the paper. All authors discussed the data.

Correspondence to Alexander M. Mebel, Breno R. L. Galvão, Jean-Christophe Loison, Xiaohu Li or Ralf I. Kaiser.

The authors declare no competing interests.

Nature Astronomy thanks Ben Pearce and Gianmarco Vanuzzo for their contribution to the peer review of this work.

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Temperature and energy dependence of the thermal rate constant k(T) and k(E) for the p3 + H in the C + NH3 reaction. TST methods are utilized in the calculation.

Singlet and triplet surfaces of the C2-NH3 system involving different routes to the final products.

Distinct pyridinyl radicals and pyridine can be formed from reactions of methylene amidogen (H2CN) with i/n-C4H3 isomers and the cyanomethyl (H2CCN) with propargyl (C3H3).

Distinct pyridinyl radicals and pyridine can be formed from reactions of cis-iminomethyl (HCNH) with i/n-C4H3 isomers.

Supplementary Notes 1–4, Figs. 1–3 and Tables 1–4.

Optimized Cartesian coordinates (Å) and vibrational frequencies (cm−1) for the intermediates, transition states, reactants and products involved in the reactions of C–NH3 and C2–NH3, and the pathways from H2CN·, cis-HCNH and H2CCN· to pyridine and pyridinyl radicals.

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Yang, Z., He, C., Goettl, S.J. et al. Low-temperature formation of pyridine and (iso)quinoline via neutral–neutral reactions. Nat Astron 8, 856–864 (2024). https://doi.org/10.1038/s41550-024-02267-y

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Received: 21 February 2023

Accepted: 09 April 2024

Published: 13 May 2024

Issue Date: July 2024

DOI: https://doi.org/10.1038/s41550-024-02267-y

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