Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods
We investigate ligand-exchange reactions of a biomimetic Co(II)-based heterocubane complex in aqueous solution by means of various approaches for consideration of solvent effects. Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with sever...
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Veröffentlicht in: | Journal of chemical theory and computation 2017-07, Vol.13 (7), p.3348-3358 |
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creator | Hodel, Florian H Deglmann, Peter Luber, Sandra |
description | We investigate ligand-exchange reactions of a biomimetic Co(II)-based heterocubane complex in aqueous solution by means of various approaches for consideration of solvent effects. Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with several explicit solvent molecules have been carried out as well as density functional theory (DFT)-based molecular dynamics simulations. In addition, reaction pathways and barriers have been elucidated via nudged elastic band calculations and metadynamics. The results show that static approaches with approximate consideration of the solvent environment lead to reaction energies, which may change drastically depending on the method employed. A more sophisticated approach is DFT-molecular dynamics at ambient conditions with full solvation, i.e. enough solvent molecules to retain bulk water properties far from the solute, which, however, comes with a much higher computational cost. The investigated example of the exchange of an acetate ligand by a hydroxide demonstrates that entropic contributions can be vital and consideration of electronic energies alone may be a rather rough approximation. |
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Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with several explicit solvent molecules have been carried out as well as density functional theory (DFT)-based molecular dynamics simulations. In addition, reaction pathways and barriers have been elucidated via nudged elastic band calculations and metadynamics. The results show that static approaches with approximate consideration of the solvent environment lead to reaction energies, which may change drastically depending on the method employed. A more sophisticated approach is DFT-molecular dynamics at ambient conditions with full solvation, i.e. enough solvent molecules to retain bulk water properties far from the solute, which, however, comes with a much higher computational cost. The investigated example of the exchange of an acetate ligand by a hydroxide demonstrates that entropic contributions can be vital and consideration of electronic energies alone may be a rather rough approximation.</description><identifier>ISSN: 1549-9618</identifier><identifier>EISSN: 1549-9626</identifier><identifier>DOI: 10.1021/acs.jctc.7b00214</identifier><identifier>PMID: 28609105</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Biomimetics ; Computer simulation ; Continuum modeling ; Density functional theory ; Exchanging ; Ligands ; Molecular chains ; Molecular dynamics ; Solvation ; Solvents</subject><ispartof>Journal of chemical theory and computation, 2017-07, Vol.13 (7), p.3348-3358</ispartof><rights>Copyright © 2017 American Chemical Society</rights><rights>Copyright American Chemical Society Jul 11, 2017</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a364t-cfa8dc471f9132f9adfbd7e599c1c381426f9238d00b0880917df7209ee5fee73</citedby><cites>FETCH-LOGICAL-a364t-cfa8dc471f9132f9adfbd7e599c1c381426f9238d00b0880917df7209ee5fee73</cites><orcidid>0000-0002-6203-9379</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.jctc.7b00214$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.jctc.7b00214$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,780,784,2765,27076,27924,27925,56738,56788</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28609105$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hodel, Florian H</creatorcontrib><creatorcontrib>Deglmann, Peter</creatorcontrib><creatorcontrib>Luber, Sandra</creatorcontrib><title>Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods</title><title>Journal of chemical theory and computation</title><addtitle>J. Chem. Theory Comput</addtitle><description>We investigate ligand-exchange reactions of a biomimetic Co(II)-based heterocubane complex in aqueous solution by means of various approaches for consideration of solvent effects. Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with several explicit solvent molecules have been carried out as well as density functional theory (DFT)-based molecular dynamics simulations. In addition, reaction pathways and barriers have been elucidated via nudged elastic band calculations and metadynamics. The results show that static approaches with approximate consideration of the solvent environment lead to reaction energies, which may change drastically depending on the method employed. A more sophisticated approach is DFT-molecular dynamics at ambient conditions with full solvation, i.e. enough solvent molecules to retain bulk water properties far from the solute, which, however, comes with a much higher computational cost. The investigated example of the exchange of an acetate ligand by a hydroxide demonstrates that entropic contributions can be vital and consideration of electronic energies alone may be a rather rough approximation.</description><subject>Biomimetics</subject><subject>Computer simulation</subject><subject>Continuum modeling</subject><subject>Density functional theory</subject><subject>Exchanging</subject><subject>Ligands</subject><subject>Molecular chains</subject><subject>Molecular dynamics</subject><subject>Solvation</subject><subject>Solvents</subject><issn>1549-9618</issn><issn>1549-9626</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNp1kEtLAzEURoMotlb3riTgxoVT85rJZCl1fEBFsIrLkMkk7ZR51MlMaf-9qX0sBFe5gfN993IAuMRoiBHBd0q74Vy3eshT5P_sCPRxyEQgIhIdH2Yc98CZc3OEKGWEnoIeiSMkMAr74CtZLYq6yaspnNTFUrV5XcHEWqNbB_MKjvOpqrIgWemZqqYGvhulN4yDy1zBSesDGnoCPqwrVfr51bSzOnPn4MSqwpmL3TsAn4_Jx-g5GL89vYzux4GiEWsDbVWcacaxFZgSK1Rm04ybUAiNNY0xI5EVhMYZQimKY380zywnSBgTWmM4HYCbbe-iqb8741pZ5k6bolCVqTsnsUCCM0EF8uj1H3Red03lr5MEMcpZiAn2FNpSuqmda4yViyYvVbOWGMmNdOmly410uZPuI1e74i4tTXYI7C174HYL_Eb3S__t-wGVPIzg</recordid><startdate>20170711</startdate><enddate>20170711</enddate><creator>Hodel, Florian H</creator><creator>Deglmann, Peter</creator><creator>Luber, Sandra</creator><general>American Chemical Society</general><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/0000-0002-6203-9379</orcidid></search><sort><creationdate>20170711</creationdate><title>Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods</title><author>Hodel, Florian H ; Deglmann, Peter ; Luber, Sandra</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a364t-cfa8dc471f9132f9adfbd7e599c1c381426f9238d00b0880917df7209ee5fee73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Biomimetics</topic><topic>Computer simulation</topic><topic>Continuum modeling</topic><topic>Density functional theory</topic><topic>Exchanging</topic><topic>Ligands</topic><topic>Molecular chains</topic><topic>Molecular dynamics</topic><topic>Solvation</topic><topic>Solvents</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hodel, Florian H</creatorcontrib><creatorcontrib>Deglmann, Peter</creatorcontrib><creatorcontrib>Luber, Sandra</creatorcontrib><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 theory and computation</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hodel, Florian H</au><au>Deglmann, Peter</au><au>Luber, Sandra</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods</atitle><jtitle>Journal of chemical theory and computation</jtitle><addtitle>J. Chem. Theory Comput</addtitle><date>2017-07-11</date><risdate>2017</risdate><volume>13</volume><issue>7</issue><spage>3348</spage><epage>3358</epage><pages>3348-3358</pages><issn>1549-9618</issn><eissn>1549-9626</eissn><abstract>We investigate ligand-exchange reactions of a biomimetic Co(II)-based heterocubane complex in aqueous solution by means of various approaches for consideration of solvent effects. Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with several explicit solvent molecules have been carried out as well as density functional theory (DFT)-based molecular dynamics simulations. In addition, reaction pathways and barriers have been elucidated via nudged elastic band calculations and metadynamics. The results show that static approaches with approximate consideration of the solvent environment lead to reaction energies, which may change drastically depending on the method employed. A more sophisticated approach is DFT-molecular dynamics at ambient conditions with full solvation, i.e. enough solvent molecules to retain bulk water properties far from the solute, which, however, comes with a much higher computational cost. The investigated example of the exchange of an acetate ligand by a hydroxide demonstrates that entropic contributions can be vital and consideration of electronic energies alone may be a rather rough approximation.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>28609105</pmid><doi>10.1021/acs.jctc.7b00214</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-6203-9379</orcidid></addata></record> |
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subjects | Biomimetics Computer simulation Continuum modeling Density functional theory Exchanging Ligands Molecular chains Molecular dynamics Solvation Solvents |
title | Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods |
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