Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine
Identifieur interne : 001207 ( Istex/Corpus ); précédent : 001206; suivant : 001208Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine
Auteurs : Jaroslav V. Burda ; Manoj K. Shukla ; Jerzy LeszczynskiSource :
- Journal of Molecular Modeling [ 1610-2940 ] ; 2005-09-01.
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Abstract
Abstract: Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers’ stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu–O(aqua) interactions were estimated to be about 60 kcal mol−1 and for Cu–N7 bonding in the range of 75–83 kcal mol−1. The broad range in Cu–N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.
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DOI: 10.1007/s00894-005-0269-2
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Burda</name><affiliation><mods:affiliation>Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: burda@karlov.mff.cuni.cz</mods:affiliation></affiliation></author><author><name sortKey="Shukla, Manoj K" sort="Shukla, Manoj K" uniqKey="Shukla M" first="Manoj K." last="Shukla">Manoj K. Shukla</name><affiliation><mods:affiliation>Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J. R. 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For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers’ stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu–O(aqua) interactions were estimated to be about 60 kcal mol−1 and for Cu–N7 bonding in the range of 75–83 kcal mol−1. The broad range in Cu–N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.</div></front></TEI><istex><corpusName>springer-journals</corpusName><author><json:item><name>Jaroslav V. Burda</name><affiliations><json:string>Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic</json:string><json:string>E-mail: burda@karlov.mff.cuni.cz</json:string></affiliations></json:item><json:item><name>Manoj K. Shukla</name><affiliations><json:string>Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J. R. 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TocLevels="0"><VolumeIDStart>11</VolumeIDStart><VolumeIDEnd>11</VolumeIDEnd><VolumeIssueCount>6</VolumeIssueCount></VolumeInfo><Issue IssueType="Combined"><IssueInfo TocLevels="0"><IssueIDStart>4</IssueIDStart><IssueIDEnd>5</IssueIDEnd><IssueHistory><OnlineDate><Year>2005</Year><Month>10</Month><Day>28</Day></OnlineDate><CoverDate><Year>2005</Year><Month>9</Month></CoverDate></IssueHistory><IssueCopyright><CopyrightHolderName>Springer-Verlag</CopyrightHolderName><CopyrightYear>2005</CopyrightYear></IssueCopyright></IssueInfo><Article ID="Art1" OutputMedium="All"> <ArticleInfo Language="En" ArticleType="OriginalPaper" NumberingStyle="Unnumbered" TocLevels="0" ContainsESM="No"> <ArticleID>269</ArticleID><ArticleDOI>10.1007/s00894-005-0269-2</ArticleDOI><ArticleSequenceNumber>16</ArticleSequenceNumber><ArticleTitle Language="En">Theoretical model of the aqua-copper [Cu(H<Subscript>2</Subscript>O)<Subscript>5</Subscript>]<Superscript>+</Superscript>cation interactions with guanine</ArticleTitle><ArticleCategory>Original Paper</ArticleCategory><ArticleFirstPage>362</ArticleFirstPage><ArticleLastPage>369</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2005</Year><Month>4</Month><Day>5</Day></RegistrationDate><Received><Year>2004</Year><Month>11</Month><Day>21</Day></Received><Accepted><Year>2005</Year><Month>1</Month><Day>31</Day></Accepted><OnlineDate><Year>2005</Year><Month>6</Month><Day>1</Day></OnlineDate></ArticleHistory><ArticleCopyright><CopyrightHolderName>Springer-Verlag</CopyrightHolderName><CopyrightYear>2005</CopyrightYear></ArticleCopyright><ArticleGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Jaroslav</GivenName><GivenName>V.</GivenName><FamilyName>Burda</FamilyName></AuthorName><Contact><Email>burda@karlov.mff.cuni.cz</Email></Contact></Author><Author AffiliationIDS="Aff2"><AuthorName DisplayOrder="Western"><GivenName>Manoj</GivenName><GivenName>K.</GivenName><FamilyName>Shukla</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff2"><AuthorName DisplayOrder="Western"><GivenName>Jerzy</GivenName><FamilyName>Leszczynski</FamilyName></AuthorName></Author><Affiliation ID="Aff1"><OrgDivision>Department of Chemical Physics and Optics, Faculty of Mathematics and Physics</OrgDivision><OrgName>Charles University</OrgName><OrgAddress><Street>Ke Karlovu 3</Street><Postcode>121 16</Postcode><City>Prague 2</City><Country>Czech Republic</Country></OrgAddress></Affiliation><Affiliation ID="Aff2"><OrgDivision>Computational Center for Molecular Structure and Interactions, Department of Chemistry</OrgDivision><OrgName>Jackson State University</OrgName><OrgAddress><Street>1325 J. R. Lynch Street</Street><City>Jackson</City><State>MS</State><Postcode>39217-0510</Postcode><Country>USA</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers’ stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu–O(aqua) interactions were estimated to be about 60 kcal mol<Superscript>−1</Superscript> and for Cu–N7 bonding in the range of 75–83 kcal mol<Superscript>−1</Superscript>. The broad range in Cu–N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.</Para></Abstract><KeywordGroup Language="En"><Heading>Keywords</Heading><Keyword>DFT calculations</Keyword><Keyword>Copper complexes</Keyword><Keyword>DNA base</Keyword><Keyword>Metal hydration</Keyword></KeywordGroup></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine</title></titleInfo><name type="personal" displayLabel="corresp"><namePart type="given">Jaroslav</namePart><namePart type="given">V.</namePart><namePart type="family">Burda</namePart><affiliation>Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic</affiliation><affiliation>E-mail: burda@karlov.mff.cuni.cz</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Manoj</namePart><namePart type="given">K.</namePart><namePart type="family">Shukla</namePart><affiliation>Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J. R. Lynch Street, 39217-0510, Jackson, MS, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jerzy</namePart><namePart type="family">Leszczynski</namePart><affiliation>Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J. R. Lynch Street, 39217-0510, Jackson, MS, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>Springer-Verlag; http://www.springer.de</publisher><place><placeTerm type="text">Berlin/Heidelberg</placeTerm></place><dateCreated encoding="w3cdtf">2004-11-21</dateCreated><dateIssued encoding="w3cdtf">2005-09-01</dateIssued><copyrightDate encoding="w3cdtf">2005</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers’ stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu–O(aqua) interactions were estimated to be about 60 kcal mol−1 and for Cu–N7 bonding in the range of 75–83 kcal mol−1. The broad range in Cu–N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.</abstract><note>Original Paper</note><subject lang="en"><genre>Keywords</genre><topic>DFT calculations</topic><topic>Copper complexes</topic><topic>DNA base</topic><topic>Metal hydration</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Molecular Modeling</title><subTitle>Computational chemistry, life science, advanced materials, new methods</subTitle></titleInfo><titleInfo type="abbreviated"><title>J Mol Model</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2005-10-28</dateIssued><copyrightDate encoding="w3cdtf">2005</copyrightDate></originInfo><subject><genre>Chemistry</genre></subject><identifier type="ISSN">1610-2940</identifier><identifier type="eISSN">0948-5023</identifier><identifier type="JournalID">894</identifier><identifier type="VolumeIssueCount">6</identifier><part><date>2005</date><detail type="volume"><number>11</number><caption>vol.</caption></detail><detail type="issue"><number>4-5</number><caption>no.</caption></detail><extent unit="pages"><start>362</start><end>369</end></extent></part><recordInfo><recordOrigin>Springer-Verlag, 2005</recordOrigin></recordInfo></relatedItem><identifier type="istex">67C9291B58ED953CE1839CFFBD0BDBBFAE09B49A</identifier><identifier type="ark">ark:/67375/VQC-56RT0G51-H</identifier><identifier type="DOI">10.1007/s00894-005-0269-2</identifier><identifier type="ArticleID">269</identifier><identifier type="ArticleID">Art1</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer-Verlag, 2005</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Springer-Verlag, 2005</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-56RT0G51-H/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine
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