A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules
Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembl...
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| Veröffentlicht in: | Journal of computational chemistry 2024-11, Vol.45 (29), p.2431-2445 |
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| container_title | Journal of computational chemistry |
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| creator | King, Nathanael J. LeBlanc, Ian D. Brown, Alex |
| description | Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. We term this new algorithm a low‐energy diversity‐enhanced variant on CREST, or LEDE‐CREST. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach. The utility of the algorithm is highlighted by generating ensembles for a variety of noncovalent clusters of flexible or rigid monomers using both CREST and LEDE‐CREST.
Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach. |
| doi_str_mv | 10.1002/jcc.27458 |
| format | Article |
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Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach.</description><identifier>ISSN: 0192-8651</identifier><identifier>ISSN: 1096-987X</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.27458</identifier><identifier>PMID: 38944673</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>algorithm ; Algorithms ; Clusters ; Computational chemistry ; conformer search ; degrees of freedom ; ensemble generation ; noncovalent interactions ; Software</subject><ispartof>Journal of computational chemistry, 2024-11, Vol.45 (29), p.2431-2445</ispartof><rights>2024 The Author(s). published by Wiley Periodicals LLC.</rights><rights>2024 The Author(s). Journal of Computational Chemistry published by Wiley Periodicals LLC.</rights><rights>2024. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2788-ad7d58a957ad2febc52bd0ba575ceefcd57b4e4e349e9147a47bbe805b21a3eb3</cites><orcidid>0000-0001-6734-5300 ; 0000-0002-5384-9222</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjcc.27458$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjcc.27458$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38944673$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>King, Nathanael J.</creatorcontrib><creatorcontrib>LeBlanc, Ian D.</creatorcontrib><creatorcontrib>Brown, Alex</creatorcontrib><title>A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules</title><title>Journal of computational chemistry</title><addtitle>J Comput Chem</addtitle><description>Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. We term this new algorithm a low‐energy diversity‐enhanced variant on CREST, or LEDE‐CREST. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach. The utility of the algorithm is highlighted by generating ensembles for a variety of noncovalent clusters of flexible or rigid monomers using both CREST and LEDE‐CREST.
Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach.</description><subject>algorithm</subject><subject>Algorithms</subject><subject>Clusters</subject><subject>Computational chemistry</subject><subject>conformer search</subject><subject>degrees of freedom</subject><subject>ensemble generation</subject><subject>noncovalent interactions</subject><subject>Software</subject><issn>0192-8651</issn><issn>1096-987X</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><recordid>eNp10EFLHDEYxvEgim6tB7-ABLzYw2gySTbJUcZtVSyC3YK3kGTe0VkyE01mtH57x671IPT0Xn48vPwR2qfkmBJSnqy8Py4lF2oDzSjR80IrebuJZoTqslBzQXfQl5xXhBAm5nwb7TClOZ9LNkPLU_xkU2v7AcceD_eAq5vFryVufy7PsA13MbXDfYebmHAfex-fbIDJ-jDmAVLGscFNgD-tC4C7GMCPAfJXtNXYkGHv_e6i398Xy-q8uLr-cVGdXhW-lEoVtpa1UFYLaeuyAedF6WrirJDCAzS-FtJx4MC4Bk25tFw6B4oIV1LLwLFddLTefUjxcYQ8mK7NHkKwPcQxG0Ykk7Tkmk_08BNdxTH103eGUUq50lTRSX1bK59izgka85DazqYXQ4l5S22m1OZv6skevC-OroP6Q_5rO4GTNXhuA7z8f8lcVtV68hWM6ofu</recordid><startdate>20241105</startdate><enddate>20241105</enddate><creator>King, Nathanael J.</creator><creator>LeBlanc, Ian D.</creator><creator>Brown, Alex</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>JQ2</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-6734-5300</orcidid><orcidid>https://orcid.org/0000-0002-5384-9222</orcidid></search><sort><creationdate>20241105</creationdate><title>A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules</title><author>King, Nathanael J. ; LeBlanc, Ian D. ; Brown, Alex</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2788-ad7d58a957ad2febc52bd0ba575ceefcd57b4e4e349e9147a47bbe805b21a3eb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>algorithm</topic><topic>Algorithms</topic><topic>Clusters</topic><topic>Computational chemistry</topic><topic>conformer search</topic><topic>degrees of freedom</topic><topic>ensemble generation</topic><topic>noncovalent interactions</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>King, Nathanael J.</creatorcontrib><creatorcontrib>LeBlanc, Ian D.</creatorcontrib><creatorcontrib>Brown, Alex</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Wiley Online Library Free Content</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Computer Science Collection</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>King, Nathanael J.</au><au>LeBlanc, Ian D.</au><au>Brown, Alex</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J Comput Chem</addtitle><date>2024-11-05</date><risdate>2024</risdate><volume>45</volume><issue>29</issue><spage>2431</spage><epage>2445</epage><pages>2431-2445</pages><issn>0192-8651</issn><issn>1096-987X</issn><eissn>1096-987X</eissn><abstract>Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. We term this new algorithm a low‐energy diversity‐enhanced variant on CREST, or LEDE‐CREST. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach. The utility of the algorithm is highlighted by generating ensembles for a variety of noncovalent clusters of flexible or rigid monomers using both CREST and LEDE‐CREST.
Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer‐rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. As with CREST, the energies are evaluated using the semiempirical GFN2‐xTB extended tight binding approach.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>38944673</pmid><doi>10.1002/jcc.27458</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0001-6734-5300</orcidid><orcidid>https://orcid.org/0000-0002-5384-9222</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | algorithm Algorithms Clusters Computational chemistry conformer search degrees of freedom ensemble generation noncovalent interactions Software |
| title | A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules |
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