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{
"metadata": {
"edited_by": 576,
"owner": 1211,
"_oai": {
"id": "oai:materialscloud.org:2296"
},
"description": "Simulations of chemical reactivity in condensed phase systems represent an ongoing challenge in computational chemistry, where traditional quantum chemical approaches typically struggle with both the size of the system and the potential complexity of the reaction. Here, we introduce a workflow aimed at efficiently training neural network potentials (NNPs) to explore energy barriers in solution at the hybrid density functional theory level. The computational burden associated with training at the PBE0-D3(BJ) level is bypassed through the use of active and transfer learning techniques, whereas extensive sampling of the transition state region is accelerated by well-tempered metadynamics simulations using multiple time-step integration. These NNPs serve to explore a puzzling solute--solvent reactivity route involving the ring opening of N-enoxyphthalimide experimentally observed in methanol but not in 2,2,2-trifluoroethanol (TFE). This reaction represents a challenging example characterized by intricate hydrogen bonding networks and structurally ambiguous solvent-sensitive transition states. The methodology successfully delivers detailed free energy surfaces and relative energy barriers in quantitative agreement with experiment. These barriers are associated with an ensemble of transition states involving direct participation of up to five solvent molecules. While this picture contrasts with the single transition state structure assumed by current static models, no drastic qualitative difference is observed between the formed hydrogen bonding networks and the number of participating solvent molecules in methanol or TFE. The dichotomy between the two solvents thus essentially arises from an electronic effect (i.e., distinct nucleophilicity) and from the larger conformational entropy contributions in methanol. This example underscores the critical role dynamic simulations at the ab initio levels play in capturing the full complexity of solute-solvent interactions.\n\nThe files used in our studies are listed below, ensuring reproducibility and providing resources for future studies related to this work.",
"mcid": "2024.135",
"id": "2296",
"license": "Creative Commons Attribution 4.0 International",
"license_addendum": null,
"references": [
{
"citation": "F. C\u00e9lerse, V. Juraskova, S. Das, M.D. Wodrich, C. Corminboeuf, chemRxiv",
"type": "Preprint"
}
],
"doi": "10.24435/materialscloud:fq-k5",
"keywords": [
"machine learning",
"molecular dynamics simulation",
"free energy",
"ERC"
],
"contributors": [
{
"affiliations": [
"Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne, Switzerland"
],
"familyname": "C\u00e9lerse",
"givennames": "Fr\u00e9d\u00e9ric"
},
{
"affiliations": [
"Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne, Switzerland"
],
"familyname": "Juraskova",
"givennames": "Veronika"
},
{
"affiliations": [
"Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne, Switzerland"
],
"familyname": "Das",
"givennames": "Shubhajit"
},
{
"affiliations": [
"Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne, Switzerland",
"National Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland"
],
"familyname": "Wodrich",
"email": "matthew.wodrich@epfl.ch",
"givennames": "Matthew D."
},
{
"affiliations": [
"Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne, Switzerland",
"National Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland",
"National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland"
],
"familyname": "Corminboeuf",
"email": "clemence.corminboeuf@epfl.ch",
"givennames": "Cl\u00e9mence"
}
],
"conceptrecid": "2295",
"version": 1,
"publication_date": "Sep 09, 2024, 11:41:06",
"is_last": true,
"status": "published",
"_files": [
{
"size": 2670,
"checksum": "md5:b918f5c9a569d2c5a9defbeaafbaef1d",
"description": "CP2K input files for reproducing PBE-D3BJ and PBE0-D3BJ computations",
"key": "CP2K.zip"
},
{
"size": 1477,
"checksum": "md5:97c884a79c000eb89dafff0c8cd0ff49",
"description": "json file for doing NN trainings with the DeepMD software",
"key": "DeepMD_training_example.json"
},
{
"size": 19955,
"checksum": "md5:9de6fbca938ac06c650f048a9ed1abbd",
"description": "Files for running MD simulations with the Lammps software",
"key": "MD_with_lammps.zip"
},
{
"size": 163244,
"checksum": "md5:96c22e421d08a9e40a601792cc91dead",
"description": "Files for running MTS simulations",
"key": "MTS-MD.zip"
},
{
"size": 1332673221,
"checksum": "md5:e58cad381f46c46676ce060224d47153",
"description": "NNPs files for PBE-D3BJ and PBE0-D3BJ (in .pb format) used in our NN-MD simulations",
"key": "NNPs.zip"
},
{
"size": 1379504755,
"checksum": "md5:e447b0f236110edc79bd612ee32f5ffb",
"description": "PBE-D3BJ databases used for MeOH and TFE, in raw format suitable for DeepMD",
"key": "PBE_databases.zip"
},
{
"size": 966206929,
"checksum": "md5:7ea1477054487befe46beaaf14f797bb",
"description": "PBE0-D3BJ databases used for MeOH and TFE, in raw format suitable for DeepMD",
"key": "PBE0_databases.zip"
},
{
"size": 33689,
"checksum": "md5:e747f83e10e05f55f7afb8e36e57e98f",
"description": "Plumed files with examples used in this study",
"key": "PLUMED.zip"
},
{
"size": 139767190,
"checksum": "md5:10af919a44aacad9c4357e9281440f13",
"description": "Chemiscope file containing the structures represented in Figure 5 of the related article",
"key": "MeOH-chemiscope.json.gz"
},
{
"size": 109539545,
"checksum": "md5:afab6c9f8750a35113c9f95a94f29de7",
"description": "Chemiscope file containing the structures represented in Figure 6 of the related article",
"key": "TFE-chemiscope.json.gz"
},
{
"size": 1001,
"checksum": "md5:921b814009cf4765b8e5e95858a21e03",
"description": "Example file used to create the chemiscope files",
"key": "create_chemiscope.py"
}
],
"title": "Capturing dichotomic solvent behavior in solute\u2013solvent reactions with neural network potentials"
},
"id": "2296",
"updated": "2024-09-09T09:41:06.099628+00:00",
"created": "2024-08-09T13:04:51.900032+00:00",
"revision": 6
}