Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems
We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation cal...
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Veröffentlicht in: | The Journal of chemical physics 2011-06, Vol.134 (21), p.214114-214114-9 |
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creator | Send, Robert Kaila, Ville R. I. Sundholm, Dage |
description | We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
in the correlation calculation introduces errors in the excitation energies that are smaller than
\documentclass[12pt]{minimal}\begin{document}$0.1\,\rm eV$\end{document}
0.1
eV
. By using a RVS energy threshold of
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an
ab initio
alternative to quantum mechanics/molecular mechanics separation schemes. |
doi_str_mv | 10.1063/1.3596729 |
format | Article |
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\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
in the correlation calculation introduces errors in the excitation energies that are smaller than
\documentclass[12pt]{minimal}\begin{document}$0.1\,\rm eV$\end{document}
0.1
eV
. By using a RVS energy threshold of
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an
ab initio
alternative to quantum mechanics/molecular mechanics separation schemes.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/1.3596729</identifier><identifier>PMID: 21663351</identifier><identifier>CODEN: JCPSA6</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>Bacterial Proteins - chemistry ; Benzyl Compounds - chemistry ; Cluster Analysis ; Coumaric Acids - chemistry ; Energy Transfer ; Green Fluorescent Proteins - chemistry ; Imidazolines - chemistry ; Models, Chemical ; Molecular Dynamics Simulation ; Photoreceptors, Microbial - chemistry ; Quantum Theory ; Retinaldehyde - chemistry ; Rhodopsin - chemistry ; Theoretical Methods and Algorithms</subject><ispartof>The Journal of chemical physics, 2011-06, Vol.134 (21), p.214114-214114-9</ispartof><rights>2011 American Institute of Physics</rights><rights>Copyright © 2011 American Institute of Physics 2011 American Institute of Physics</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c429t-bfbf52de62644b6b963ee02ca857faab32028774427bc2c60bace19704565fa93</citedby><cites>FETCH-LOGICAL-c429t-bfbf52de62644b6b963ee02ca857faab32028774427bc2c60bace19704565fa93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,790,881,1553,4497,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21663351$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Send, Robert</creatorcontrib><creatorcontrib>Kaila, Ville R. I.</creatorcontrib><creatorcontrib>Sundholm, Dage</creatorcontrib><title>Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems</title><title>The Journal of chemical physics</title><addtitle>J Chem Phys</addtitle><description>We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
in the correlation calculation introduces errors in the excitation energies that are smaller than
\documentclass[12pt]{minimal}\begin{document}$0.1\,\rm eV$\end{document}
0.1
eV
. By using a RVS energy threshold of
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an
ab initio
alternative to quantum mechanics/molecular mechanics separation schemes.</description><subject>Bacterial Proteins - chemistry</subject><subject>Benzyl Compounds - chemistry</subject><subject>Cluster Analysis</subject><subject>Coumaric Acids - chemistry</subject><subject>Energy Transfer</subject><subject>Green Fluorescent Proteins - chemistry</subject><subject>Imidazolines - chemistry</subject><subject>Models, Chemical</subject><subject>Molecular Dynamics Simulation</subject><subject>Photoreceptors, Microbial - chemistry</subject><subject>Quantum Theory</subject><subject>Retinaldehyde - chemistry</subject><subject>Rhodopsin - chemistry</subject><subject>Theoretical Methods and Algorithms</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kUtLJDEUhYOMaPtY-AeG7AYXpXlUJZWNIDLqgCCIrkOSumlrSFXapErGfz9R2x5n4Spwc865h_shdETJCSWCn9IT3ighmdpCC0paVUmhyDe0IITRSgkidtFezr8JIVSyegftMioE5w1doPEOutlNfRxx9Hh6BPzcp2k2AeeVcYB9TNjFeRWgq1yY8wQJwx_XT-bNAyOkZQ_51RxMWgIeYgA3hzIyY4dhsNB10OH8UqxDPkDb3oQMh-t3Hz1c_ry_uK5ubq9-XZzfVK5maqqst75hHQgm6toKqwQHIMyZtpHeGMsZYa2Udc2kdcwJYktXqiSpG9F4o_g-OnvPXc12gM7BOCUT9Cr1g0kvOppe__8z9o96GZ81p-UuQpaAH-uAFJ9myJMe-uwgBDNCnLNuWyKpbFVTlMfvSpdizgn8Zgsl-hWPpnqNp2i_f661UX7w-Nc7f5z467QNOR29LuR0Icf_AveIoxA</recordid><startdate>20110607</startdate><enddate>20110607</enddate><creator>Send, Robert</creator><creator>Kaila, Ville R. I.</creator><creator>Sundholm, Dage</creator><general>American Institute of Physics</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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20110607</creationdate><title>Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems</title><author>Send, Robert ; Kaila, Ville R. I. ; Sundholm, Dage</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c429t-bfbf52de62644b6b963ee02ca857faab32028774427bc2c60bace19704565fa93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Bacterial Proteins - chemistry</topic><topic>Benzyl Compounds - chemistry</topic><topic>Cluster Analysis</topic><topic>Coumaric Acids - chemistry</topic><topic>Energy Transfer</topic><topic>Green Fluorescent Proteins - chemistry</topic><topic>Imidazolines - chemistry</topic><topic>Models, Chemical</topic><topic>Molecular Dynamics Simulation</topic><topic>Photoreceptors, Microbial - chemistry</topic><topic>Quantum Theory</topic><topic>Retinaldehyde - chemistry</topic><topic>Rhodopsin - chemistry</topic><topic>Theoretical Methods and Algorithms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Send, Robert</creatorcontrib><creatorcontrib>Kaila, Ville R. I.</creatorcontrib><creatorcontrib>Sundholm, Dage</creatorcontrib><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>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>Send, Robert</au><au>Kaila, Ville R. I.</au><au>Sundholm, Dage</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems</atitle><jtitle>The Journal of chemical physics</jtitle><addtitle>J Chem Phys</addtitle><date>2011-06-07</date><risdate>2011</risdate><volume>134</volume><issue>21</issue><spage>214114</spage><epage>214114-9</epage><pages>214114-214114-9</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><coden>JCPSA6</coden><abstract>We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
in the correlation calculation introduces errors in the excitation energies that are smaller than
\documentclass[12pt]{minimal}\begin{document}$0.1\,\rm eV$\end{document}
0.1
eV
. By using a RVS energy threshold of
\documentclass[12pt]{minimal}\begin{document}$50\,\rm eV$\end{document}
50
eV
, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an
ab initio
alternative to quantum mechanics/molecular mechanics separation schemes.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>21663351</pmid><doi>10.1063/1.3596729</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Bacterial Proteins - chemistry Benzyl Compounds - chemistry Cluster Analysis Coumaric Acids - chemistry Energy Transfer Green Fluorescent Proteins - chemistry Imidazolines - chemistry Models, Chemical Molecular Dynamics Simulation Photoreceptors, Microbial - chemistry Quantum Theory Retinaldehyde - chemistry Rhodopsin - chemistry Theoretical Methods and Algorithms |
title | Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems |
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