Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM

Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM This archive contains all data and software to reproduce the results of Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM, Moritz Bensberg, Silvia Alessandrini, Cristina Puzzarini, and Markus Reiher, **to be submitted**, 2025. Citation Please cite this repository and Ref. [1] when reusing the data. Database The reaction network is saved as a MongoDB database. It can be restored from the unpacked tar file using `mongorestore`. ├──oxirane-ch-3.tar.xz : The database containing the reaction network and all calculation input/output.| ├──calculations.bson : The calculation input/output.| ├──calculations.metadata.json : The calculation input/output.| ├──compounds.bson : Molecules specified as compounds.| ├──compounds.metadata.json : Molecules specified as compounds.| ├──elementary_steps.bson : Elementary steps/minimum energy paths between structures.| ├──elementary_steps.metadata.json : Elementary steps/minimum energy paths between structures.| ├──flasks.bson : Species containing more than one molecule/weakly interacting complexes.| ├──flasks.metadata.json : Species containing more than one molecule/weakly interacting complexes.| ├──properties.bson : Properties of the molecules (energies, Hessians, etc.)| ├──properties.metadata.json : Species containing more than one molecule/weakly interacting complexes.| ├──reactions.bson : Reactions connecting compounds and/or flasks.| ├──reactions.metadata.json : Reactions connecting compounds and/or flasks.| ├──structures.bson : Cartesian coordinates of individual structures, including information on their properties.| └──structures.metadata.json : Cartesian coordinates of individual structures, including information on their properties. Software This directory contains the software necessary to reproduce the exploration. ├──software.tar.xz| ├──puffin : Code for the "puffin" clients to be run on an HPC cluster.| ├──euler.oxirane-ch.sif : Singularity image file with "puffin" and all its dependencies installed.| ├──chemoton : The software running/monitoring the exploration.| ├──utils-open-source : The scine_utilities version used with chemoton in this project.| ├──database : The scine_database MongoDB wrapper used with chemoton in this project.| ├──network_analysis : The Python scripts used for generating the degree distribution plot.| └──main-scripts : The input scripts for scine_chemoton| ├──main.py : The chemoton input script for the exploration.| ├──credentials.py : This file encodes the settings for the elementary step trials used in the exploration.| ├──elementary_steps.py : This file encodes the settings for the elementary step trials used in the exploration.| ├──advanced.py : Definition of gears for the exploration.| ├──basics.py : Definition of gears for the exploration.| ├──refinement.py : Definition of gears for the exploration.| ├──setup_start.py : This file provides functions to read the input for the exploration.| └──start-structures : Optimized input structures of oxirane and the CH radical. Mess Input files This directory contains the input files for the program `Master Equation System Solver` (MESS). ├──mess.tar.gz | | ├── mess.inp : The input file for the mess calculation at T=100K and p=1e-7 atm is reported using as a string for reactants, products, ts, and intermediates are indicated using the ID of Chemoton. The simulation was run using the GitHub version of MESS (commit hash: 8cd1f7b7a152bb561acc7b3237417ba0146e3717). References [1] Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM, Moritz Bensberg, Silvia Alessandrini, Cristina Puzzarini, and Markus Reiher, **to be submitted**, 2025.