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-...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:The journal of physical chemistry. B 2015-01, Vol.119 (3), p.883-895
Hauptverfasser: Li, Pengfei, Song, Lin Frank, Merz, Kenneth M
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 895
container_issue 3
container_start_page 883
container_title The journal of physical chemistry. B
container_volume 119
creator Li, Pengfei
Song, Lin Frank
Merz, Kenneth M
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
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4306492</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1762064534</sourcerecordid><originalsourceid>FETCH-LOGICAL-a537t-e8413739487c922e7cca0814fcdd263956e26f919d89b7647f8d21ed64a4c6063</originalsourceid><addsrcrecordid>eNqFkctuEzEUhi1ERUthwQsgb5BgMeC7ZzZIKCq0KFwWrVhajn0mcTSxp_akIqx4BV6xT9KJkkYgIXVh2dL59Pmc8yP0gpK3lDD6btlLImstbx6hEyoZqcajH-_fihJ1jJ6WsiSESVarJ-iYSSok0_wELb_bbFcwQA6_7BBSxKnF52G-6DZ4srB5Dh5_gcF2-CLFgq9KiHM8LABTVqnb338Enn6uLjc94K8pzlL0Wz556HCI-Oxn3wUXBvzDjh88Q0et7Qo839-n6Orj2eXkvJp--3Qx-TCtrOR6qKAWlGveiFq7hjHQzllSU9E675nijVTAVNvQxtfNTCuh29ozCl4JK5wiip-i9ztvv56twDuIQ7ad6XNY2bwxyQbzbyWGhZmnGyM4UaJho-D1XpDT9RrKYFahOOg6GyGti2GEEEmp5upBlGrFRqnk4mFUSTZO3Yit9c0OdTmVkqE9NE-J2SZuDomP7Mu_pz2Q9xGPwKsdYF0xy7TOcVz-f0R3ix2xdw</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1652394946</pqid></control><display><type>article</type><title>Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water</title><source>ACS Publications</source><source>MEDLINE</source><creator>Li, Pengfei ; Song, Lin Frank ; Merz, Kenneth M</creator><creatorcontrib>Li, Pengfei ; Song, Lin Frank ; Merz, Kenneth M</creatorcontrib><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><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>
fulltext fulltext
identifier ISSN: 1520-6106
ispartof The journal of physical chemistry. B, 2015-01, Vol.119 (3), p.883-895
issn 1520-6106
1520-5207
1520-5207
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4306492
source ACS Publications; MEDLINE
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
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T04%3A48%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Parameterization%20of%20Highly%20Charged%20Metal%20Ions%20Using%20the%2012-6%E2%80%914%20LJ-Type%20Nonbonded%20Model%20in%20Explicit%20Water&rft.jtitle=The%20journal%20of%20physical%20chemistry.%20B&rft.au=Li,%20Pengfei&rft.date=2015-01-22&rft.volume=119&rft.issue=3&rft.spage=883&rft.epage=895&rft.pages=883-895&rft.issn=1520-6106&rft.eissn=1520-5207&rft_id=info:doi/10.1021/jp505875v&rft_dat=%3Cproquest_pubme%3E1762064534%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1652394946&rft_id=info:pmid/25145273&rfr_iscdi=true