Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution
Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, parti...
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creator | Summers, Thomas J. Zhang, Difan Sobrinho, Josiane A. de Bettencourt-Dias, Ana Rousseau, Roger Glezakou, Vassiliki-Alexandra Cantu, David C. |
description | Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes. |
doi_str_mv | 10.1021/acs.jcim.4c01769 |
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However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.</description><identifier>ISSN: 1549-9596</identifier><identifier>ISSN: 1549-960X</identifier><identifier>EISSN: 1549-960X</identifier><identifier>DOI: 10.1021/acs.jcim.4c01769</identifier><identifier>PMID: 39575913</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Acetonitrile ; Acetonitriles - chemistry ; Adaptive algorithms ; Algorithms ; Computational Chemistry ; Coordination compounds ; Coordination numbers ; Fine structure ; Global optimization ; Lanthanoid Series Elements - chemistry ; Ligands ; Machine learning ; Molecular dynamics ; Molecular Dynamics Simulation ; Optimization algorithms ; Potential energy ; Pyridines - chemistry ; Search engines ; Shells (structural forms) ; Solutions ; Solvation ; Spectra ; X ray absorption ; X-Ray Absorption Spectroscopy</subject><ispartof>Journal of chemical information and modeling, 2024-12, Vol.64 (23), p.8926-8936</ispartof><rights>2024 American Chemical Society</rights><rights>Copyright American Chemical Society Dec 9, 2024</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-a247t-c35b5e658fc28e1775c1fae36e34c9bf9c352c9cbbb14f9dcb7cf38b1bf3d7b73</cites><orcidid>0000-0002-4243-6078 ; 0000-0003-1947-0478 ; 0000-0001-6028-7021 ; 0000-0001-9584-5062 ; 0000-0001-7530-2378 ; 0000-0001-5162-2393</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.4c01769$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.jcim.4c01769$$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/39575913$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Summers, Thomas J.</creatorcontrib><creatorcontrib>Zhang, Difan</creatorcontrib><creatorcontrib>Sobrinho, Josiane A.</creatorcontrib><creatorcontrib>de Bettencourt-Dias, Ana</creatorcontrib><creatorcontrib>Rousseau, Roger</creatorcontrib><creatorcontrib>Glezakou, Vassiliki-Alexandra</creatorcontrib><creatorcontrib>Cantu, David C.</creatorcontrib><title>Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution</title><title>Journal of chemical information and modeling</title><addtitle>J. Chem. Inf. Model</addtitle><description>Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.</description><subject>Acetonitrile</subject><subject>Acetonitriles - chemistry</subject><subject>Adaptive algorithms</subject><subject>Algorithms</subject><subject>Computational Chemistry</subject><subject>Coordination compounds</subject><subject>Coordination numbers</subject><subject>Fine structure</subject><subject>Global optimization</subject><subject>Lanthanoid Series Elements - chemistry</subject><subject>Ligands</subject><subject>Machine learning</subject><subject>Molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Optimization algorithms</subject><subject>Potential energy</subject><subject>Pyridines - chemistry</subject><subject>Search engines</subject><subject>Shells (structural forms)</subject><subject>Solutions</subject><subject>Solvation</subject><subject>Spectra</subject><subject>X ray absorption</subject><subject>X-Ray Absorption Spectroscopy</subject><issn>1549-9596</issn><issn>1549-960X</issn><issn>1549-960X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kcFLwzAUxoMobk7vniTgxYOdSdO0zXGMbQqDCVPYrSRZumW0zUxSxP31Zm7zIHh57x1-3_ce7wPgFqM-RjF-4tL1N1LX_UQinKXsDHQxTVjEUrQ4P82UpR1w5dwGIUJYGl-CDmE0owyTLpCvXFvdrCCHk8oIXsHZ1uta77jXpoGDamWs9usafoYKR4vBeA69gcM1t1x6ZfVOwSlv_Jo3eqng3NtW-tYqqBs4N1W7d7kGFyWvnLo59h54H4_ehs_RdDZ5GQ6mEY-TzEeSUEFVSvNSxrnCWUYlLrkiqSKJZKJkAYglk0IInJRsKUUmS5ILLEqyzERGeuDh4Lu15qNVzhe1dlJVFW-UaV1BMME5TdIEBfT-D7oxrW3CdYFKwpvinMSBQgdKWuOcVWWxtbrm9qvAqNgHUIQAin0AxTGAILk7GreiVstfwenjAXg8AD_S09J__b4B3jCS6w</recordid><startdate>20241209</startdate><enddate>20241209</enddate><creator>Summers, Thomas J.</creator><creator>Zhang, Difan</creator><creator>Sobrinho, Josiane A.</creator><creator>de Bettencourt-Dias, Ana</creator><creator>Rousseau, Roger</creator><creator>Glezakou, Vassiliki-Alexandra</creator><creator>Cantu, David C.</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/0000-0002-4243-6078</orcidid><orcidid>https://orcid.org/0000-0003-1947-0478</orcidid><orcidid>https://orcid.org/0000-0001-6028-7021</orcidid><orcidid>https://orcid.org/0000-0001-9584-5062</orcidid><orcidid>https://orcid.org/0000-0001-7530-2378</orcidid><orcidid>https://orcid.org/0000-0001-5162-2393</orcidid></search><sort><creationdate>20241209</creationdate><title>Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution</title><author>Summers, Thomas J. ; Zhang, Difan ; Sobrinho, Josiane A. ; de Bettencourt-Dias, Ana ; Rousseau, Roger ; Glezakou, Vassiliki-Alexandra ; Cantu, David C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a247t-c35b5e658fc28e1775c1fae36e34c9bf9c352c9cbbb14f9dcb7cf38b1bf3d7b73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Acetonitrile</topic><topic>Acetonitriles - chemistry</topic><topic>Adaptive algorithms</topic><topic>Algorithms</topic><topic>Computational Chemistry</topic><topic>Coordination compounds</topic><topic>Coordination numbers</topic><topic>Fine structure</topic><topic>Global optimization</topic><topic>Lanthanoid Series Elements - chemistry</topic><topic>Ligands</topic><topic>Machine learning</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Optimization algorithms</topic><topic>Potential energy</topic><topic>Pyridines - chemistry</topic><topic>Search engines</topic><topic>Shells (structural forms)</topic><topic>Solutions</topic><topic>Solvation</topic><topic>Spectra</topic><topic>X ray absorption</topic><topic>X-Ray Absorption Spectroscopy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Summers, Thomas J.</creatorcontrib><creatorcontrib>Zhang, Difan</creatorcontrib><creatorcontrib>Sobrinho, Josiane A.</creatorcontrib><creatorcontrib>de Bettencourt-Dias, Ana</creatorcontrib><creatorcontrib>Rousseau, Roger</creatorcontrib><creatorcontrib>Glezakou, Vassiliki-Alexandra</creatorcontrib><creatorcontrib>Cantu, David C.</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>Summers, Thomas J.</au><au>Zhang, Difan</au><au>Sobrinho, Josiane A.</au><au>de Bettencourt-Dias, Ana</au><au>Rousseau, Roger</au><au>Glezakou, Vassiliki-Alexandra</au><au>Cantu, David C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution</atitle><jtitle>Journal of chemical information and modeling</jtitle><addtitle>J. Chem. Inf. Model</addtitle><date>2024-12-09</date><risdate>2024</risdate><volume>64</volume><issue>23</issue><spage>8926</spage><epage>8936</epage><pages>8926-8936</pages><issn>1549-9596</issn><issn>1549-960X</issn><eissn>1549-960X</eissn><abstract>Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>39575913</pmid><doi>10.1021/acs.jcim.4c01769</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-4243-6078</orcidid><orcidid>https://orcid.org/0000-0003-1947-0478</orcidid><orcidid>https://orcid.org/0000-0001-6028-7021</orcidid><orcidid>https://orcid.org/0000-0001-9584-5062</orcidid><orcidid>https://orcid.org/0000-0001-7530-2378</orcidid><orcidid>https://orcid.org/0000-0001-5162-2393</orcidid></addata></record> |
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subjects | Acetonitrile Acetonitriles - chemistry Adaptive algorithms Algorithms Computational Chemistry Coordination compounds Coordination numbers Fine structure Global optimization Lanthanoid Series Elements - chemistry Ligands Machine learning Molecular dynamics Molecular Dynamics Simulation Optimization algorithms Potential energy Pyridines - chemistry Search engines Shells (structural forms) Solutions Solvation Spectra X ray absorption X-Ray Absorption Spectroscopy |
title | Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution |
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