Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations
The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) mo...
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description | The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions. |
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Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/1.4934880</identifier><identifier>PMID: 26547162</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>Activation energy ; Chemical reactions ; Chloride ions ; CHLORINE IONS ; COMPARATIVE EVALUATIONS ; Computer simulation ; ELECTROSTATICS ; FREE ENERGY ; FUNCTIONS ; HAMILTONIANS ; INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ; INTERACTIONS ; Ion association ; Molecular dynamics ; MOLECULAR DYNAMICS METHOD ; Molecular Dynamics Simulation ; Organic chemistry ; Physics ; POTENTIAL ENERGY ; QUANTUM MECHANICS ; Quantum Theory ; SIMULATION ; SOLUTIONS ; Static Electricity ; Stress, Mechanical ; SYMMETRY</subject><ispartof>The Journal of chemical physics, 2015-11, Vol.143 (17), p.174111-174111</ispartof><rights>2015 AIP Publishing LLC.</rights><rights>Copyright © 2015 AIP Publishing LLC 2015 AIP Publishing LLC</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c431t-661ce3c6a546b1ad939b837e0ff8e175ce6f28c3d5225cad61becbabd96c1efe3</citedby><cites>FETCH-LOGICAL-c431t-661ce3c6a546b1ad939b837e0ff8e175ce6f28c3d5225cad61becbabd96c1efe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27922,27923</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26547162$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/22493193$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Ojeda-May, Pedro</creatorcontrib><creatorcontrib>Pu, Jingzhi</creatorcontrib><title>Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations</title><title>The Journal of chemical physics</title><addtitle>J Chem Phys</addtitle><description>The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.</description><subject>Activation energy</subject><subject>Chemical reactions</subject><subject>Chloride ions</subject><subject>CHLORINE IONS</subject><subject>COMPARATIVE EVALUATIONS</subject><subject>Computer simulation</subject><subject>ELECTROSTATICS</subject><subject>FREE ENERGY</subject><subject>FUNCTIONS</subject><subject>HAMILTONIANS</subject><subject>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</subject><subject>INTERACTIONS</subject><subject>Ion association</subject><subject>Molecular dynamics</subject><subject>MOLECULAR DYNAMICS METHOD</subject><subject>Molecular Dynamics Simulation</subject><subject>Organic chemistry</subject><subject>Physics</subject><subject>POTENTIAL ENERGY</subject><subject>QUANTUM MECHANICS</subject><subject>Quantum Theory</subject><subject>SIMULATION</subject><subject>SOLUTIONS</subject><subject>Static Electricity</subject><subject>Stress, Mechanical</subject><subject>SYMMETRY</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkU9v1DAQxS1ERZfCgS-ALHGBQ4rHTpz4goQq_lSqxKWIo-U4k66r2G5th6rfHq92WcrJ8szTb2beI-QNsHNgUnyE81aJdhjYM7IBNqiml4o9JxvGODRKMnlKXuZ8yxiDnrcvyCmXXduD5BsSrxOa4sINxQVtSTGX-rWZPriypb_iMtO8el9rMVAXqI1-dAEner-aUFZPPdqtCc6ahZowUR8rZl1MetrIztfSDpFfkZPZLBlfH94z8vPrl-uL783Vj2-XF5-vGtsKKI2UYFFYabpWjmAmJdQ4iB7ZPA8IfWdRznywYuo476yZJIxoRzNOSlrAGcUZ-bTn3q2jx8liKMks-i45b9Kjjsbp_zvBbfVN_K1bKWSrhgp4twdUR5zO1pV6j40hVJc059VwUKKq3h_GpHi_Yi7au2xxWUzAuGYNveCC9b2S_4BH6W1cU6gmaA5cDDU4thv7Ya-yNYqccD6uDEzvwtagD2FX7dunNx6Vf9MVfwDVn6dE</recordid><startdate>20151107</startdate><enddate>20151107</enddate><creator>Ojeda-May, Pedro</creator><creator>Pu, Jingzhi</creator><general>American Institute of Physics</general><general>AIP Publishing LLC</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>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20151107</creationdate><title>Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations</title><author>Ojeda-May, Pedro ; Pu, Jingzhi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c431t-661ce3c6a546b1ad939b837e0ff8e175ce6f28c3d5225cad61becbabd96c1efe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Activation energy</topic><topic>Chemical reactions</topic><topic>Chloride ions</topic><topic>CHLORINE IONS</topic><topic>COMPARATIVE EVALUATIONS</topic><topic>Computer simulation</topic><topic>ELECTROSTATICS</topic><topic>FREE ENERGY</topic><topic>FUNCTIONS</topic><topic>HAMILTONIANS</topic><topic>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</topic><topic>INTERACTIONS</topic><topic>Ion association</topic><topic>Molecular dynamics</topic><topic>MOLECULAR DYNAMICS METHOD</topic><topic>Molecular Dynamics Simulation</topic><topic>Organic chemistry</topic><topic>Physics</topic><topic>POTENTIAL ENERGY</topic><topic>QUANTUM MECHANICS</topic><topic>Quantum Theory</topic><topic>SIMULATION</topic><topic>SOLUTIONS</topic><topic>Static Electricity</topic><topic>Stress, Mechanical</topic><topic>SYMMETRY</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ojeda-May, Pedro</creatorcontrib><creatorcontrib>Pu, Jingzhi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ojeda-May, Pedro</au><au>Pu, Jingzhi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations</atitle><jtitle>The Journal of chemical physics</jtitle><addtitle>J Chem Phys</addtitle><date>2015-11-07</date><risdate>2015</risdate><volume>143</volume><issue>17</issue><spage>174111</spage><epage>174111</epage><pages>174111-174111</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><abstract>The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>26547162</pmid><doi>10.1063/1.4934880</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Activation energy Chemical reactions Chloride ions CHLORINE IONS COMPARATIVE EVALUATIONS Computer simulation ELECTROSTATICS FREE ENERGY FUNCTIONS HAMILTONIANS INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY INTERACTIONS Ion association Molecular dynamics MOLECULAR DYNAMICS METHOD Molecular Dynamics Simulation Organic chemistry Physics POTENTIAL ENERGY QUANTUM MECHANICS Quantum Theory SIMULATION SOLUTIONS Static Electricity Stress, Mechanical SYMMETRY |
title | Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations |
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