Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach
The enormous structural and chemical diversity of metal–organic frameworks (MOFs) forces researchers to actively use simulation techniques as often as experiments. MOFs are widely known for their outstanding adsorption properties, so a precise description of the host–guest interactions is essential...
Gespeichert in:
Veröffentlicht in: | Journal of chemical information and modeling 2021-12, Vol.61 (12), p.5774-5784 |
---|---|
Hauptverfasser: | , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 5784 |
---|---|
container_issue | 12 |
container_start_page | 5774 |
container_title | Journal of chemical information and modeling |
container_volume | 61 |
creator | Korolev, Vadim V Nevolin, Yuriy M Manz, Thomas A Protsenko, Pavel V |
description | The enormous structural and chemical diversity of metal–organic frameworks (MOFs) forces researchers to actively use simulation techniques as often as experiments. MOFs are widely known for their outstanding adsorption properties, so a precise description of the host–guest interactions is essential for high-throughput screening aimed at ranking the most promising candidates. However, highly accurate ab initio calculations cannot be routinely applied to model thousands of structures due to the demanding computational costs. Furthermore, methods based on force field (FF) parametrization suffer from low transferability. To resolve this accuracy–efficiency dilemma, we applied a machine learning (ML) approach: extreme gradient boosting. The trained models reproduced the atom-in-material quantities, including partial charges, polarizabilities, dispersion coefficients, quantum Drude oscillator, and electron cloud parameters, with accuracy similar to the reference data set. The aforementioned FF precursors make it possible to thoroughly describe noncovalent interactions typical for MOF–adsorbate systems: electrostatic, dispersion, polarization, and short-range repulsion. The presented approach can also readily facilitate hybrid atomistic simulation/ML workflows. |
doi_str_mv | 10.1021/acs.jcim.1c01124 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2598536876</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2598536876</sourcerecordid><originalsourceid>FETCH-LOGICAL-a364t-931e6d1e4abd7c95fe1677f1e61971402c256b72a9f2a7d3ae91b9c1d051dfd03</originalsourceid><addsrcrecordid>eNp1kUFvEzEQhS0EoqVw54QsceFAgsfeteNjVRFASimHVuJmee3Z4rBrB3sjRE_9D_xDfgkOSTggcZrR0_feWH6EPAc2B8bhjXVlvnZhnINjALx5QE6hbfRMS_b54XFvtTwhT0pZMyaElvwxORGNWqhGsFMyfrLZjjjlcGenkCJNPf2YYpeiR0-XKTuky4CDp9eYx0L7lOklTnb4df_zKt_aGBxd7hK-p_y10JsS4i29tO5LiEhXaHPcCeebTU5VfEoe9XYo-Owwz8jN8u31xfvZ6urdh4vz1cwK2UwzLQClB2xs55XTbY8gleqrCFpBw7jjrewUt7rnVnlhUUOnHXjWgu89E2fk1T63nv22xTKZMRSHw2Ajpm0xvNWLVsiFkhV9-Q-6Ttsc6-sMl7BoKqpVpdiecjmVkrE3mxxGm38YYGZXhalVmF0V5lBFtbw4BG-7Ef1fw_HvK_B6D_yxHo_-N-831GiWRg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2618425997</pqid></control><display><type>article</type><title>Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach</title><source>ACS Publications</source><source>MEDLINE</source><creator>Korolev, Vadim V ; Nevolin, Yuriy M ; Manz, Thomas A ; Protsenko, Pavel V</creator><creatorcontrib>Korolev, Vadim V ; Nevolin, Yuriy M ; Manz, Thomas A ; Protsenko, Pavel V</creatorcontrib><description>The enormous structural and chemical diversity of metal–organic frameworks (MOFs) forces researchers to actively use simulation techniques as often as experiments. MOFs are widely known for their outstanding adsorption properties, so a precise description of the host–guest interactions is essential for high-throughput screening aimed at ranking the most promising candidates. However, highly accurate ab initio calculations cannot be routinely applied to model thousands of structures due to the demanding computational costs. Furthermore, methods based on force field (FF) parametrization suffer from low transferability. To resolve this accuracy–efficiency dilemma, we applied a machine learning (ML) approach: extreme gradient boosting. The trained models reproduced the atom-in-material quantities, including partial charges, polarizabilities, dispersion coefficients, quantum Drude oscillator, and electron cloud parameters, with accuracy similar to the reference data set. The aforementioned FF precursors make it possible to thoroughly describe noncovalent interactions typical for MOF–adsorbate systems: electrostatic, dispersion, polarization, and short-range repulsion. The presented approach can also readily facilitate hybrid atomistic simulation/ML workflows.</description><identifier>ISSN: 1549-9596</identifier><identifier>EISSN: 1549-960X</identifier><identifier>DOI: 10.1021/acs.jcim.1c01124</identifier><identifier>PMID: 34787430</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Accuracy ; Adsorbates ; Adsorption ; Dispersion ; Electron clouds ; Machine Learning ; Machine Learning and Deep Learning ; Metal-Organic Frameworks ; Parameterization ; Quantum Theory ; Static Electricity</subject><ispartof>Journal of chemical information and modeling, 2021-12, Vol.61 (12), p.5774-5784</ispartof><rights>2021 American Chemical Society</rights><rights>Copyright American Chemical Society Dec 27, 2021</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a364t-931e6d1e4abd7c95fe1677f1e61971402c256b72a9f2a7d3ae91b9c1d051dfd03</citedby><cites>FETCH-LOGICAL-a364t-931e6d1e4abd7c95fe1677f1e61971402c256b72a9f2a7d3ae91b9c1d051dfd03</cites><orcidid>0000-0001-6117-5662 ; 0000-0002-1503-3679 ; 0000-0002-4033-9864</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c01124$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.jcim.1c01124$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34787430$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Korolev, Vadim V</creatorcontrib><creatorcontrib>Nevolin, Yuriy M</creatorcontrib><creatorcontrib>Manz, Thomas A</creatorcontrib><creatorcontrib>Protsenko, Pavel V</creatorcontrib><title>Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach</title><title>Journal of chemical information and modeling</title><addtitle>J. Chem. Inf. Model</addtitle><description>The enormous structural and chemical diversity of metal–organic frameworks (MOFs) forces researchers to actively use simulation techniques as often as experiments. MOFs are widely known for their outstanding adsorption properties, so a precise description of the host–guest interactions is essential for high-throughput screening aimed at ranking the most promising candidates. However, highly accurate ab initio calculations cannot be routinely applied to model thousands of structures due to the demanding computational costs. Furthermore, methods based on force field (FF) parametrization suffer from low transferability. To resolve this accuracy–efficiency dilemma, we applied a machine learning (ML) approach: extreme gradient boosting. The trained models reproduced the atom-in-material quantities, including partial charges, polarizabilities, dispersion coefficients, quantum Drude oscillator, and electron cloud parameters, with accuracy similar to the reference data set. The aforementioned FF precursors make it possible to thoroughly describe noncovalent interactions typical for MOF–adsorbate systems: electrostatic, dispersion, polarization, and short-range repulsion. The presented approach can also readily facilitate hybrid atomistic simulation/ML workflows.</description><subject>Accuracy</subject><subject>Adsorbates</subject><subject>Adsorption</subject><subject>Dispersion</subject><subject>Electron clouds</subject><subject>Machine Learning</subject><subject>Machine Learning and Deep Learning</subject><subject>Metal-Organic Frameworks</subject><subject>Parameterization</subject><subject>Quantum Theory</subject><subject>Static Electricity</subject><issn>1549-9596</issn><issn>1549-960X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kUFvEzEQhS0EoqVw54QsceFAgsfeteNjVRFASimHVuJmee3Z4rBrB3sjRE_9D_xDfgkOSTggcZrR0_feWH6EPAc2B8bhjXVlvnZhnINjALx5QE6hbfRMS_b54XFvtTwhT0pZMyaElvwxORGNWqhGsFMyfrLZjjjlcGenkCJNPf2YYpeiR0-XKTuky4CDp9eYx0L7lOklTnb4df_zKt_aGBxd7hK-p_y10JsS4i29tO5LiEhXaHPcCeebTU5VfEoe9XYo-Owwz8jN8u31xfvZ6urdh4vz1cwK2UwzLQClB2xs55XTbY8gleqrCFpBw7jjrewUt7rnVnlhUUOnHXjWgu89E2fk1T63nv22xTKZMRSHw2Ajpm0xvNWLVsiFkhV9-Q-6Ttsc6-sMl7BoKqpVpdiecjmVkrE3mxxGm38YYGZXhalVmF0V5lBFtbw4BG-7Ef1fw_HvK_B6D_yxHo_-N-831GiWRg</recordid><startdate>20211227</startdate><enddate>20211227</enddate><creator>Korolev, Vadim V</creator><creator>Nevolin, Yuriy M</creator><creator>Manz, Thomas A</creator><creator>Protsenko, Pavel V</creator><general>American Chemical Society</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SC</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-6117-5662</orcidid><orcidid>https://orcid.org/0000-0002-1503-3679</orcidid><orcidid>https://orcid.org/0000-0002-4033-9864</orcidid></search><sort><creationdate>20211227</creationdate><title>Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach</title><author>Korolev, Vadim V ; Nevolin, Yuriy M ; Manz, Thomas A ; Protsenko, Pavel V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a364t-931e6d1e4abd7c95fe1677f1e61971402c256b72a9f2a7d3ae91b9c1d051dfd03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Accuracy</topic><topic>Adsorbates</topic><topic>Adsorption</topic><topic>Dispersion</topic><topic>Electron clouds</topic><topic>Machine Learning</topic><topic>Machine Learning and Deep Learning</topic><topic>Metal-Organic Frameworks</topic><topic>Parameterization</topic><topic>Quantum Theory</topic><topic>Static Electricity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Korolev, Vadim V</creatorcontrib><creatorcontrib>Nevolin, Yuriy M</creatorcontrib><creatorcontrib>Manz, Thomas A</creatorcontrib><creatorcontrib>Protsenko, Pavel V</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Computer and Information Systems Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of chemical information and modeling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Korolev, Vadim V</au><au>Nevolin, Yuriy M</au><au>Manz, Thomas A</au><au>Protsenko, Pavel V</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach</atitle><jtitle>Journal of chemical information and modeling</jtitle><addtitle>J. Chem. Inf. Model</addtitle><date>2021-12-27</date><risdate>2021</risdate><volume>61</volume><issue>12</issue><spage>5774</spage><epage>5784</epage><pages>5774-5784</pages><issn>1549-9596</issn><eissn>1549-960X</eissn><abstract>The enormous structural and chemical diversity of metal–organic frameworks (MOFs) forces researchers to actively use simulation techniques as often as experiments. MOFs are widely known for their outstanding adsorption properties, so a precise description of the host–guest interactions is essential for high-throughput screening aimed at ranking the most promising candidates. However, highly accurate ab initio calculations cannot be routinely applied to model thousands of structures due to the demanding computational costs. Furthermore, methods based on force field (FF) parametrization suffer from low transferability. To resolve this accuracy–efficiency dilemma, we applied a machine learning (ML) approach: extreme gradient boosting. The trained models reproduced the atom-in-material quantities, including partial charges, polarizabilities, dispersion coefficients, quantum Drude oscillator, and electron cloud parameters, with accuracy similar to the reference data set. The aforementioned FF precursors make it possible to thoroughly describe noncovalent interactions typical for MOF–adsorbate systems: electrostatic, dispersion, polarization, and short-range repulsion. The presented approach can also readily facilitate hybrid atomistic simulation/ML workflows.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>34787430</pmid><doi>10.1021/acs.jcim.1c01124</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0001-6117-5662</orcidid><orcidid>https://orcid.org/0000-0002-1503-3679</orcidid><orcidid>https://orcid.org/0000-0002-4033-9864</orcidid></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1549-9596 |
ispartof | Journal of chemical information and modeling, 2021-12, Vol.61 (12), p.5774-5784 |
issn | 1549-9596 1549-960X |
language | eng |
recordid | cdi_proquest_miscellaneous_2598536876 |
source | ACS Publications; MEDLINE |
subjects | Accuracy Adsorbates Adsorption Dispersion Electron clouds Machine Learning Machine Learning and Deep Learning Metal-Organic Frameworks Parameterization Quantum Theory Static Electricity |
title | Parametrization of Nonbonded Force Field Terms for Metal–Organic Frameworks Using Machine Learning Approach |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T11%3A23%3A07IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Parametrization%20of%20Nonbonded%20Force%20Field%20Terms%20for%20Metal%E2%80%93Organic%20Frameworks%20Using%20Machine%20Learning%20Approach&rft.jtitle=Journal%20of%20chemical%20information%20and%20modeling&rft.au=Korolev,%20Vadim%20V&rft.date=2021-12-27&rft.volume=61&rft.issue=12&rft.spage=5774&rft.epage=5784&rft.pages=5774-5784&rft.issn=1549-9596&rft.eissn=1549-960X&rft_id=info:doi/10.1021/acs.jcim.1c01124&rft_dat=%3Cproquest_cross%3E2598536876%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2618425997&rft_id=info:pmid/34787430&rfr_iscdi=true |