New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited

• Published in: ACS Physical Chemistry Au Vol. 2; no. 3; pp. 225 - 236
• Main Authors: Garay-Ruiz, Diego, Álvarez-Moreno, Moises, Bo, Carles, Martínez-Núñez, Emilio
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 25-05-2022
• Subjects: visualization; indole; pyrolysis; data analysis; automated mechanism discovery; reaction networks; astrochemistry
• ISSN: 2694-2445; 2694-2445
• DOI: 10.1021/acsphyschemau.1c00051

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD­(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.