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.