Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM
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| author | Bensberg, Moritz Alessandrini, Silvia Melosso, Mattia Puzzarini, Cristina Reiher, Markus |
| author_facet | Bensberg, Moritz Alessandrini, Silvia Melosso, Mattia Puzzarini, Cristina Reiher, Markus |
| contents | <h1>Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM</h1> <p>This archive contains all data and software to reproduce the results of</p> <p>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.</p> <h3>Citation</h3> <p>Please cite this repository and Ref. [1] when reusing the data.</p> <h3>Database</h3> <p>The reaction network is saved as a MongoDB database. It can be restored from the unpacked tar file using `mongorestore`.</p> <p>├──oxirane-ch-3.tar.xz : The database containing the reaction network and all calculation input/output.<br>| ├──calculations.bson : The calculation input/output.<br>| ├──calculations.metadata.json : The calculation input/output.<br>| ├──compounds.bson : Molecules specified as compounds.<br>| ├──compounds.metadata.json : Molecules specified as compounds.<br>| ├──elementary_steps.bson : Elementary steps/minimum energy paths between structures.<br>| ├──elementary_steps.metadata.json : Elementary steps/minimum energy paths between structures.<br>| ├──flasks.bson : Species containing more than one molecule/weakly interacting complexes.<br>| ├──flasks.metadata.json : Species containing more than one molecule/weakly interacting complexes.<br>| ├──properties.bson : Properties of the molecules (energies, Hessians, etc.)<br>| ├──properties.metadata.json : Species containing more than one molecule/weakly interacting complexes.<br>| ├──reactions.bson : Reactions connecting compounds and/or flasks.<br>| ├──reactions.metadata.json : Reactions connecting compounds and/or flasks.<br>| ├──structures.bson : Cartesian coordinates of individual structures, including information on their properties.<br>| └──structures.metadata.json : Cartesian coordinates of individual structures, including information on their properties.</p> <h3>Software</h3> <p>This directory contains the software necessary to reproduce the exploration.</p> <p>├──software.tar.xz<br>| ├──puffin : Code for the "puffin" clients to be run on an HPC cluster.<br>| ├──euler.oxirane-ch.sif : Singularity image file with "puffin" and all its dependencies installed.<br>| ├──chemoton : The software running/monitoring the exploration.<br>| ├──utils-open-source : The scine_utilities version used with chemoton in this project.<br>| ├──database : The scine_database MongoDB wrapper used with chemoton in this project.<br>| ├──network_analysis : The Python scripts used for generating the degree distribution plot.<br>| └──main-scripts : The input scripts for scine_chemoton<br>| ├──main.py : The chemoton input script for the exploration.<br>| ├──credentials.py : This file encodes the settings for the elementary step trials used in the exploration.<br>| ├──elementary_steps.py : This file encodes the settings for the elementary step trials used in the exploration.<br>| ├──advanced.py : Definition of gears for the exploration.<br>| ├──basics.py : Definition of gears for the exploration.<br>| ├──refinement.py : Definition of gears for the exploration.<br>| ├──setup_start.py : This file provides functions to read the input for the exploration.<br>| └──start-structures : Optimized input structures of oxirane and the CH radical.</p> <h3>Mess Input files</h3> <p>This directory contains the input files for the program `Master Equation System Solver` (MESS).</p> <p>├──mess.tar.gz |<br> | ├── 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).</p> <h2>References</h2> <p>[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.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17131468 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM Bensberg, Moritz Alessandrini, Silvia Melosso, Mattia Puzzarini, Cristina Reiher, Markus <h1>Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM</h1> <p>This archive contains all data and software to reproduce the results of</p> <p>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.</p> <h3>Citation</h3> <p>Please cite this repository and Ref. [1] when reusing the data.</p> <h3>Database</h3> <p>The reaction network is saved as a MongoDB database. It can be restored from the unpacked tar file using `mongorestore`.</p> <p>├──oxirane-ch-3.tar.xz : The database containing the reaction network and all calculation input/output.<br>| ├──calculations.bson : The calculation input/output.<br>| ├──calculations.metadata.json : The calculation input/output.<br>| ├──compounds.bson : Molecules specified as compounds.<br>| ├──compounds.metadata.json : Molecules specified as compounds.<br>| ├──elementary_steps.bson : Elementary steps/minimum energy paths between structures.<br>| ├──elementary_steps.metadata.json : Elementary steps/minimum energy paths between structures.<br>| ├──flasks.bson : Species containing more than one molecule/weakly interacting complexes.<br>| ├──flasks.metadata.json : Species containing more than one molecule/weakly interacting complexes.<br>| ├──properties.bson : Properties of the molecules (energies, Hessians, etc.)<br>| ├──properties.metadata.json : Species containing more than one molecule/weakly interacting complexes.<br>| ├──reactions.bson : Reactions connecting compounds and/or flasks.<br>| ├──reactions.metadata.json : Reactions connecting compounds and/or flasks.<br>| ├──structures.bson : Cartesian coordinates of individual structures, including information on their properties.<br>| └──structures.metadata.json : Cartesian coordinates of individual structures, including information on their properties.</p> <h3>Software</h3> <p>This directory contains the software necessary to reproduce the exploration.</p> <p>├──software.tar.xz<br>| ├──puffin : Code for the "puffin" clients to be run on an HPC cluster.<br>| ├──euler.oxirane-ch.sif : Singularity image file with "puffin" and all its dependencies installed.<br>| ├──chemoton : The software running/monitoring the exploration.<br>| ├──utils-open-source : The scine_utilities version used with chemoton in this project.<br>| ├──database : The scine_database MongoDB wrapper used with chemoton in this project.<br>| ├──network_analysis : The Python scripts used for generating the degree distribution plot.<br>| └──main-scripts : The input scripts for scine_chemoton<br>| ├──main.py : The chemoton input script for the exploration.<br>| ├──credentials.py : This file encodes the settings for the elementary step trials used in the exploration.<br>| ├──elementary_steps.py : This file encodes the settings for the elementary step trials used in the exploration.<br>| ├──advanced.py : Definition of gears for the exploration.<br>| ├──basics.py : Definition of gears for the exploration.<br>| ├──refinement.py : Definition of gears for the exploration.<br>| ├──setup_start.py : This file provides functions to read the input for the exploration.<br>| └──start-structures : Optimized input structures of oxirane and the CH radical.</p> <h3>Mess Input files</h3> <p>This directory contains the input files for the program `Master Equation System Solver` (MESS).</p> <p>├──mess.tar.gz |<br> | ├── 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).</p> <h2>References</h2> <p>[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.</p> |
| title | Supplemental Material: Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM |
| url | https://doi.org/10.5281/zenodo.17131468 |