optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework
For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (...
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Veröffentlicht in: | Journal of computational chemistry 2010-11, Vol.31 (14), p.2628-2641 |
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creator | Koyano, Yoshiyuki Takenaka, Norio Nakagawa, Yukinori Nagaoka, Masataka |
description | For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH₃---H₂O molecule pair and a MM solvent H₂O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 Å, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 Å in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press). |
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II. Primary importance of reproducing electrostatic interaction in the QM/MM framework</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><creator>Koyano, Yoshiyuki ; Takenaka, Norio ; Nakagawa, Yukinori ; Nagaoka, Masataka</creator><creatorcontrib>Koyano, Yoshiyuki ; Takenaka, Norio ; Nakagawa, Yukinori ; Nagaoka, Masataka</creatorcontrib><description>For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH₃---H₂O molecule pair and a MM solvent H₂O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 Å, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 Å in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press).</description><identifier>ISSN: 0192-8651</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.21558</identifier><identifier>PMID: 20740563</identifier><identifier>CODEN: JCCHDD</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Ammonia - chemistry ; ammonia ionization ; Approximation ; Chemical reactions ; direct dynamics calculation ; Electrostatics ; ESP charge ; free energy gradient method ; Molecular Dynamics Simulation ; Molecules ; NDDO approximation ; NDDO-SSRP method ; PM3-MAIS-SSRP method ; QM/MM-MD method ; Quantum Theory ; semiempirical MO method ; solution chemistry ; Solutions ; Static Electricity ; Water - chemistry</subject><ispartof>Journal of computational chemistry, 2010-11, Vol.31 (14), p.2628-2641</ispartof><rights>Copyright © 2010 Wiley Periodicals, Inc.</rights><rights>2010 Wiley Periodicals, Inc.</rights><rights>Copyright John Wiley and Sons, Limited Nov 15, 2010</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4798-7c6b8950cb8db8b1e3e0c0dcce61785bc0dd2704aa3e7433c8ed3211359c04d63</citedby><cites>FETCH-LOGICAL-c4798-7c6b8950cb8db8b1e3e0c0dcce61785bc0dd2704aa3e7433c8ed3211359c04d63</cites></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.21558$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjcc.21558$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20740563$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Koyano, Yoshiyuki</creatorcontrib><creatorcontrib>Takenaka, Norio</creatorcontrib><creatorcontrib>Nakagawa, Yukinori</creatorcontrib><creatorcontrib>Nagaoka, Masataka</creatorcontrib><title>optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework</title><title>Journal of computational chemistry</title><addtitle>J. Comput. Chem</addtitle><description>For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH₃---H₂O molecule pair and a MM solvent H₂O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 Å, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 Å in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press).</description><subject>Ammonia - chemistry</subject><subject>ammonia ionization</subject><subject>Approximation</subject><subject>Chemical reactions</subject><subject>direct dynamics calculation</subject><subject>Electrostatics</subject><subject>ESP charge</subject><subject>free energy gradient method</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecules</subject><subject>NDDO approximation</subject><subject>NDDO-SSRP method</subject><subject>PM3-MAIS-SSRP method</subject><subject>QM/MM-MD method</subject><subject>Quantum Theory</subject><subject>semiempirical MO method</subject><subject>solution chemistry</subject><subject>Solutions</subject><subject>Static Electricity</subject><subject>Water - chemistry</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc1u1DAUhSMEokNhwQuAxaZikRk7jmNniSJaBnWgiFbtznKcmxlPk3iwHZV5Jx4ST9N2gcTKf9859_qeJHlL8JxgnC22Ws8zwph4lswILou0FPzmeTLDpMxSUTBylLzyfosxpqzIXyZHGeY5ZgWdJX_sLph-7JEPTgVY71FrHfK2G4OxA9Ib6E182qPRm2GNfDxCvzPOaNWh3nagx045ZF1twuEGwsY2c7RcztGFM72KStPvrAtq0IBsixzsnG1GfXCDKA_O-qCC0cgMAZzS93XNgMIG0I_VYrVCrVM93Fl3-zp50arOw5uH9Ti5Ov18WX1Jz7-fLatP56nOeSlSrotalAzrWjS1qAlQwBo3WkNBuGB13DcZx7lSFHhOqRbQ0IwQykqN86agx8nJ5Btb_TWCDzIOQUPXqQHs6CXPRVlSXpBIfviH3NrRDbG5CHGSYUZFhD5OkI5_9Q5auZtGIwmWhwBlDFDeBxjZdw-GY91D80Q-JhaBxQTcmQ72_3eSX6vq0TKdFDFI-P2kUO5WFpxyJq-_nckLfsnxzTWTVeTfT3yrrFRrZ7y8-plhQjERggrM6V_f9cEp</recordid><startdate>20101115</startdate><enddate>20101115</enddate><creator>Koyano, Yoshiyuki</creator><creator>Takenaka, Norio</creator><creator>Nakagawa, Yukinori</creator><creator>Nagaoka, Masataka</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><general>Wiley Subscription Services, Inc</general><scope>FBQ</scope><scope>BSCLL</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>JQ2</scope><scope>7X8</scope></search><sort><creationdate>20101115</creationdate><title>optimum strategy for solution chemistry using semiempirical molecular orbital method. 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Primary importance of reproducing electrostatic interaction in the QM/MM framework</title><author>Koyano, Yoshiyuki ; Takenaka, Norio ; Nakagawa, Yukinori ; Nagaoka, Masataka</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4798-7c6b8950cb8db8b1e3e0c0dcce61785bc0dd2704aa3e7433c8ed3211359c04d63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Ammonia - chemistry</topic><topic>ammonia ionization</topic><topic>Approximation</topic><topic>Chemical reactions</topic><topic>direct dynamics calculation</topic><topic>Electrostatics</topic><topic>ESP charge</topic><topic>free energy gradient method</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecules</topic><topic>NDDO approximation</topic><topic>NDDO-SSRP method</topic><topic>PM3-MAIS-SSRP method</topic><topic>QM/MM-MD method</topic><topic>Quantum Theory</topic><topic>semiempirical MO method</topic><topic>solution chemistry</topic><topic>Solutions</topic><topic>Static Electricity</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Koyano, Yoshiyuki</creatorcontrib><creatorcontrib>Takenaka, Norio</creatorcontrib><creatorcontrib>Nakagawa, Yukinori</creatorcontrib><creatorcontrib>Nagaoka, Masataka</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</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>Koyano, Yoshiyuki</au><au>Takenaka, Norio</au><au>Nakagawa, Yukinori</au><au>Nagaoka, Masataka</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J. Comput. Chem</addtitle><date>2010-11-15</date><risdate>2010</risdate><volume>31</volume><issue>14</issue><spage>2628</spage><epage>2641</epage><pages>2628-2641</pages><issn>0192-8651</issn><eissn>1096-987X</eissn><coden>JCCHDD</coden><abstract>For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH₃---H₂O molecule pair and a MM solvent H₂O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 Å, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 Å in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press).</abstract><cop>Hoboken</cop><pub>Wiley Subscription Services, Inc., A Wiley Company</pub><pmid>20740563</pmid><doi>10.1002/jcc.21558</doi><tpages>14</tpages></addata></record> |
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subjects | Ammonia - chemistry ammonia ionization Approximation Chemical reactions direct dynamics calculation Electrostatics ESP charge free energy gradient method Molecular Dynamics Simulation Molecules NDDO approximation NDDO-SSRP method PM3-MAIS-SSRP method QM/MM-MD method Quantum Theory semiempirical MO method solution chemistry Solutions Static Electricity Water - chemistry |
title | optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework |
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