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

Abstract

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.

Computational Prediction of Speciation Diagrams and Nucleation Mechanisms: Molecular Vanadium, Niobium, and Tantalum Oxide Nanoclusters in Solution

“…43 Recently, there has been an increase of automated methods that are being applied to different fields such as prebiotics, 44 combustion, 45 solid-state synthesis, 46 and decomposition reactions. 47 Following this trend, we have recently reported the development of a new method, called POMSimulator, that automatically generates the CRN for a set of metal-oxo-clusters from raw quantum chemical results and predicts both speciation diagrams and the corresponding reaction mechanism. 48 Hitherto, we have applied this method to polyoxomolybdates and -tungstanates with excellent results.…”

Chemical Reaction Network Knowledge Graphs: the OntoRXN Ontology

“…As mentioned before, recent additions to ioChem-BD allow for the construction of reaction network graphs from reaction energy profiles built in the platform. 28 These reaction networks are an ideal starting point for the generation of KGs: all information about the individual calculations can be easily fetched from the CML files, and structured according to the corresponding network topology. Eventually, it would be possible to add the knowledge-graphbuilding machinery as an additional module in the platform, thus allowing the user to painlessly create OntoRXN-compliant graphs.…”

“…In this line, one area of application where a semantic-based organization could be useful is the study of reaction mechanisms and chemical networks. Recent efforts by our group have been devoted to the development of novel open-source tools for the treatment and processing of reaction networks through graphbased approaches: amk-tools 28 and gTOFfee. 29 The latter is an application of the energy span model (ESM) developed by Sebastian Kozuch and collaborators 30,31 extended to manage reaction networks as undirected graphs.…”

Theoretical chemical reaction database construction based on quantum chemistry-aided retrosynthetic analysis

“…Generally, a reaction-path network is constructed first, and the corresponding reaction is then studied by kinetic simulations. [40][41][42][43][44] However, examining each reaction individually through this two-step procedure requires enormous effort. Therefore, creating a theoretical database of reactions rather than elementary steps remains a major challenge in chemistry.…”