Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water
Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-...
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Veröffentlicht in: | The journal of physical chemistry. B 2015-01, Vol.119 (3), p.883-895 |
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description | Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters. |
doi_str_mv | 10.1021/jp505875v |
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The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.</description><identifier>ISSN: 1520-6106</identifier><identifier>ISSN: 1520-5207</identifier><identifier>EISSN: 1520-5207</identifier><identifier>DOI: 10.1021/jp505875v</identifier><identifier>PMID: 25145273</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Charging ; divalent metals ; Electrons ; energy ; Fluid dynamics ; Free energy ; Mathematical models ; Metal ions ; Metals - chemistry ; Models, Molecular ; Nanoarchaeota - enzymology ; Oxidoreductases - chemistry ; Parametrization ; physical chemistry ; Physical simulation ; Protein Conformation ; Structural members ; Water - chemistry</subject><ispartof>The journal of physical chemistry. B, 2015-01, Vol.119 (3), p.883-895</ispartof><rights>Copyright © 2014 American Chemical Society</rights><rights>Copyright © 2014 American Chemical Society 2014 American Chemical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a537t-e8413739487c922e7cca0814fcdd263956e26f919d89b7647f8d21ed64a4c6063</citedby><cites>FETCH-LOGICAL-a537t-e8413739487c922e7cca0814fcdd263956e26f919d89b7647f8d21ed64a4c6063</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/jp505875v$$EPDF$$P50$$Gacs$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/jp505875v$$EHTML$$P50$$Gacs$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25145273$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Pengfei</creatorcontrib><creatorcontrib>Song, Lin Frank</creatorcontrib><creatorcontrib>Merz, Kenneth M</creatorcontrib><title>Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water</title><title>The journal of physical chemistry. B</title><addtitle>J. Phys. Chem. B</addtitle><description>Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.</description><subject>Charging</subject><subject>divalent metals</subject><subject>Electrons</subject><subject>energy</subject><subject>Fluid dynamics</subject><subject>Free energy</subject><subject>Mathematical models</subject><subject>Metal ions</subject><subject>Metals - chemistry</subject><subject>Models, Molecular</subject><subject>Nanoarchaeota - enzymology</subject><subject>Oxidoreductases - chemistry</subject><subject>Parametrization</subject><subject>physical chemistry</subject><subject>Physical simulation</subject><subject>Protein Conformation</subject><subject>Structural members</subject><subject>Water - chemistry</subject><issn>1520-6106</issn><issn>1520-5207</issn><issn>1520-5207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>N~.</sourceid><sourceid>EIF</sourceid><recordid>eNqFkctuEzEUhi1ERUthwQsgb5BgMeC7ZzZIKCq0KFwWrVhajn0mcTSxp_akIqx4BV6xT9KJkkYgIXVh2dL59Pmc8yP0gpK3lDD6btlLImstbx6hEyoZqcajH-_fihJ1jJ6WsiSESVarJ-iYSSok0_wELb_bbFcwQA6_7BBSxKnF52G-6DZ4srB5Dh5_gcF2-CLFgq9KiHM8LABTVqnb338Enn6uLjc94K8pzlL0Wz556HCI-Oxn3wUXBvzDjh88Q0et7Qo839-n6Orj2eXkvJp--3Qx-TCtrOR6qKAWlGveiFq7hjHQzllSU9E675nijVTAVNvQxtfNTCuh29ozCl4JK5wiip-i9ztvv56twDuIQ7ad6XNY2bwxyQbzbyWGhZmnGyM4UaJho-D1XpDT9RrKYFahOOg6GyGti2GEEEmp5upBlGrFRqnk4mFUSTZO3Yit9c0OdTmVkqE9NE-J2SZuDomP7Mu_pz2Q9xGPwKsdYF0xy7TOcVz-f0R3ix2xdw</recordid><startdate>20150122</startdate><enddate>20150122</enddate><creator>Li, Pengfei</creator><creator>Song, Lin Frank</creator><creator>Merz, Kenneth M</creator><general>American Chemical Society</general><scope>N~.</scope><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>7X8</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20150122</creationdate><title>Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water</title><author>Li, Pengfei ; Song, Lin Frank ; Merz, Kenneth M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a537t-e8413739487c922e7cca0814fcdd263956e26f919d89b7647f8d21ed64a4c6063</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Charging</topic><topic>divalent metals</topic><topic>Electrons</topic><topic>energy</topic><topic>Fluid dynamics</topic><topic>Free energy</topic><topic>Mathematical models</topic><topic>Metal ions</topic><topic>Metals - chemistry</topic><topic>Models, Molecular</topic><topic>Nanoarchaeota - enzymology</topic><topic>Oxidoreductases - chemistry</topic><topic>Parametrization</topic><topic>physical chemistry</topic><topic>Physical simulation</topic><topic>Protein Conformation</topic><topic>Structural members</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Pengfei</creatorcontrib><creatorcontrib>Song, Lin Frank</creatorcontrib><creatorcontrib>Merz, Kenneth M</creatorcontrib><collection>American Chemical Society (ACS) Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</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>Advanced Technologies Database with Aerospace</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Pengfei</au><au>Song, Lin Frank</au><au>Merz, Kenneth M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water</atitle><jtitle>The journal of physical chemistry. B</jtitle><addtitle>J. Phys. Chem. B</addtitle><date>2015-01-22</date><risdate>2015</risdate><volume>119</volume><issue>3</issue><spage>883</spage><epage>895</epage><pages>883-895</pages><issn>1520-6106</issn><issn>1520-5207</issn><eissn>1520-5207</eissn><abstract>Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>25145273</pmid><doi>10.1021/jp505875v</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Charging divalent metals Electrons energy Fluid dynamics Free energy Mathematical models Metal ions Metals - chemistry Models, Molecular Nanoarchaeota - enzymology Oxidoreductases - chemistry Parametrization physical chemistry Physical simulation Protein Conformation Structural members Water - chemistry |
title | Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water |
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