Atomic-level structure determination of amorphous molecular solids by NMR
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{
"id": "1832",
"updated": "2023-11-06T17:01:38.559506+00:00",
"metadata": {
"version": 1,
"contributors": [
{
"givennames": "Manuel",
"affiliations": [
"Institut des Sciences et Ing\u00e9nierie Chimiques, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland"
],
"email": "manuel.cordova@epfl.ch",
"familyname": "Cordova"
},
{
"givennames": "Pinelopi",
"affiliations": [
"Institut des Sciences et Ing\u00e9nierie Chimiques, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland"
],
"familyname": "Moutzouri"
},
{
"givennames": "Sten O.",
"affiliations": [
"Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden"
],
"familyname": "Nilsson Lill"
},
{
"givennames": "Alexander",
"affiliations": [
"Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK"
],
"familyname": "Cousen"
},
{
"givennames": "Martin",
"affiliations": [
"Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK"
],
"familyname": "Kearns"
},
{
"givennames": "Stefan T.",
"affiliations": [
"Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden"
],
"familyname": "Norberg"
},
{
"givennames": "Anna",
"affiliations": [
"Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden"
],
"familyname": "Svensk Ankarberg"
},
{
"givennames": "James",
"affiliations": [
"Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK"
],
"familyname": "McCabe"
},
{
"givennames": "Arthur C.",
"affiliations": [
"Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden"
],
"familyname": "Pinon"
},
{
"givennames": "Staffan",
"affiliations": [
"Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden"
],
"email": "Staffan.Schantz@astrazeneca.com",
"familyname": "Schantz"
},
{
"givennames": "Lyndon",
"affiliations": [
"Institut des Sciences et Ing\u00e9nierie Chimiques, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland"
],
"email": "lyndon.emsley@epfl.ch",
"familyname": "Emsley"
}
],
"title": "Atomic-level structure determination of amorphous molecular solids by NMR",
"_oai": {
"id": "oai:materialscloud.org:1832"
},
"keywords": [
"MARVEL/DD1",
"NMR",
"Amorphous solids",
"machine learning",
"molecular dynamics simulation",
"structure determination"
],
"publication_date": "Jul 25, 2023, 09:47:56",
"_files": [
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"key": "Experimental_spectra.zip",
"description": "Raw NMR data of the experimental spectra measured.",
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{
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"description": "PDB files containing the snapshots extracted from the MD simulations of the amorphous sample.",
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"size": 1057967457
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{
"key": "ML_shifts.zip",
"description": "Numpy arrays containing the chemical shifts predicted using ShiftML2 on the MD snapshots.",
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"key": "Extracted_ftrs.zip",
"description": "JSON files containing the geometric features extracted from the MD snapshots.",
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{
"key": "nmr_scoring.zip",
"description": "JSON and Numpy files containing the scores obtained for molecular environments from the MD snapshots to match the NMR experiments.",
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{
"key": "Random_structures.zip",
"description": "XYZ files of 8000 randomly selected molecular environments from the MD snapshots. Each environment is represented by three files, \"_cen\" for the central molecule, \"_env\" for the neighbouring molecules, and \"_all\" for the complete environment.",
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{
"key": "Selected_structures.zip",
"description": "XYZ files of the 10107 NMR-selected molecular environments from the MD snapshots. Each environment is represented by three files, \"_cen\" for the central molecule, \"_env\" for the neighbouring molecules, and \"_all\" for the complete environment.",
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"description": "Input and output files of the DFTB energy computation performed on the randomly selected molecular environments.",
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"key": "Selected_structures_DFTB.zip",
"description": "Input and output files of the DFTB energy computation performed on the NMR-selected molecular environments.",
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"key": "PDFs.zip",
"description": "Raw data of the pairwise distribution function (PDF) measurements of the amorphous sample in Gudrun format.",
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"size": 106576
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"key": "Simulated_PDFs.zip",
"description": "Numpy arrays containing the simulated pairwise distribution function (PDF) from the MD snapshots and NMR-selected molecular environments.",
"checksum": "md5:39c3d62d68991fff67ba71e0e9caadbf",
"size": 202623
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{
"key": "Clouds.zip",
"description": "Interaction maps obtained for amorphous AZD4625",
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{
"key": "viz_structures.zip",
"description": "XYZ and VMD files used to visualize the structure of amorphous AZD4625.",
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{
"key": "Libraries.zip",
"description": "Python libraries necessary to run the analysis scripts.",
"checksum": "md5:d1310ba236178bce8aed0c78613efc46",
"size": 158399
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{
"key": "Scripts.zip",
"description": "Jupyter notebooks containing the Python scripts used to analyse the data.",
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],
"references": [
{
"comment": "Paper in which the method is described",
"doi": "10.1038/s41467-023-40853-2",
"citation": "M. Cordova, P. Moutzouri, S. O. Nilsson Lill, A. Cousen, M. Kearns, S. T. Norberg, A. Svensk Ankarberg, J. McCabe, A. C. Pinon, S. Schantz, L. Emsley, Nat. Commun. 14, 5138 (2023)",
"url": "https://doi.org/10.1038/s41467-023-40853-2",
"type": "Journal reference"
}
],
"description": "Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to both a high degree of overlap between measured signals, resulting in challenges for spectral assignment, and prevents the unambiguous identification of a single modelled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract preferred conformations and intermolecular interactions in the amorphous sample, and analyze the structure in terms of the hydrogen bonding and conformational factors that stabilize the amorphous form of the drug.",
"status": "published",
"license": "Creative Commons Attribution Share Alike 4.0 International",
"conceptrecid": "1831",
"is_last": true,
"mcid": "2023.112",
"edited_by": 339,
"id": "1832",
"owner": 339,
"license_addendum": null,
"doi": "10.24435/materialscloud:gk-51"
},
"revision": 4,
"created": "2023-07-21T12:32:04.756656+00:00"
}