DOI: 10.5281/zenodo.17131467
title: Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM

description: 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.