Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method
Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detac...
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Veröffentlicht in: | The Journal of chemical physics 2020-09, Vol.153 (10), p.104104-104104 |
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creator | Kitoh-Nishioka, Hirotaka Shigeta, Yasuteru Ando, Koji |
description | Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin. |
doi_str_mv | 10.1063/5.0018423 |
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The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/5.0018423</identifier><identifier>CODEN: JCPSA6</identifier><language>eng</language><publisher>Melville: American Institute of Physics</publisher><subject>Computational chemistry ; Continuum modeling ; Coordination compounds ; Copper ; Covalence ; Covalent bonds ; Density functional theory ; Electron transfer ; Electrons ; Molecular orbitals ; Physics ; Proteins ; Ruthenium ; Solvation ; Transition metals</subject><ispartof>The Journal of chemical physics, 2020-09, Vol.153 (10), p.104104-104104</ispartof><rights>Author(s)</rights><rights>2020 Author(s). 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The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.</description><subject>Computational chemistry</subject><subject>Continuum modeling</subject><subject>Coordination compounds</subject><subject>Copper</subject><subject>Covalence</subject><subject>Covalent bonds</subject><subject>Density functional theory</subject><subject>Electron transfer</subject><subject>Electrons</subject><subject>Molecular orbitals</subject><subject>Physics</subject><subject>Proteins</subject><subject>Ruthenium</subject><subject>Solvation</subject><subject>Transition metals</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNp90U1rGzEQBmBRUqjj9tB_IOglKWw6-lztMYQ0CRh6Sc_LWKuNN-xKrqTF8a0_vXJscsihpxmYh2GGl5CvDK4YaPFDXQEwI7n4QBYMTFPVuoEzsgDgrGo06E_kPKVnKKrmckH-Ps7eu3HwT3TCHIcX6kY3OZ8p-o7mt-EW82aH-0RDT7cxZDf4g7Q5Bk9zRJ96F6nF0c4jZtfR3ZA3FGkf8el13RSKLrNIQ1wPGUc6ubwJ3WfysccxuS-nuiS_f94-3txXq193DzfXq8oKrnJlagvWCFAc0bHaCK16yVTfKQTppF5DJ4VhWjYSS4PG8EaLWnblZw5WiCW5OO4t1_-ZXcrtNCTrxhG9C3NquZRCcW4UL_TbO_oc5ujLdQcFtTSas6Iuj8rGkFJ0fbuNw4Rx3zJoD1m0qj1lUez3o022vJ6H4P-D_wGxLIlZ</recordid><startdate>20200914</startdate><enddate>20200914</enddate><creator>Kitoh-Nishioka, Hirotaka</creator><creator>Shigeta, Yasuteru</creator><creator>Ando, Koji</creator><general>American Institute of Physics</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3219-6007</orcidid><orcidid>https://orcid.org/0000-0002-6102-0019</orcidid><orcidid>https://orcid.org/0000-0002-6210-3641</orcidid></search><sort><creationdate>20200914</creationdate><title>Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method</title><author>Kitoh-Nishioka, Hirotaka ; Shigeta, Yasuteru ; Ando, Koji</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c325t-87c0c83052aae178365f415fd5a04e46b0d43816494a438a88296374d96020c33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Computational chemistry</topic><topic>Continuum modeling</topic><topic>Coordination compounds</topic><topic>Copper</topic><topic>Covalence</topic><topic>Covalent bonds</topic><topic>Density functional theory</topic><topic>Electron transfer</topic><topic>Electrons</topic><topic>Molecular orbitals</topic><topic>Physics</topic><topic>Proteins</topic><topic>Ruthenium</topic><topic>Solvation</topic><topic>Transition metals</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kitoh-Nishioka, Hirotaka</creatorcontrib><creatorcontrib>Shigeta, Yasuteru</creatorcontrib><creatorcontrib>Ando, Koji</creatorcontrib><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kitoh-Nishioka, Hirotaka</au><au>Shigeta, Yasuteru</au><au>Ando, Koji</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method</atitle><jtitle>The Journal of chemical physics</jtitle><date>2020-09-14</date><risdate>2020</risdate><volume>153</volume><issue>10</issue><spage>104104</spage><epage>104104</epage><pages>104104-104104</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><coden>JCPSA6</coden><abstract>Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.</abstract><cop>Melville</cop><pub>American Institute of Physics</pub><doi>10.1063/5.0018423</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-3219-6007</orcidid><orcidid>https://orcid.org/0000-0002-6102-0019</orcidid><orcidid>https://orcid.org/0000-0002-6210-3641</orcidid></addata></record> |
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subjects | Computational chemistry Continuum modeling Coordination compounds Copper Covalence Covalent bonds Density functional theory Electron transfer Electrons Molecular orbitals Physics Proteins Ruthenium Solvation Transition metals |
title | Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method |
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