Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.
Identifieur interne : 001944 ( Main/Exploration ); précédent : 001943; suivant : 001945Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.
Auteurs : Haiyun Jin [États-Unis] ; Puja Goyal [États-Unis] ; Akshaya Kumar Das [Suisse] ; Michael Gaus [États-Unis] ; Markus Meuwly [Suisse] ; Qiang Cui [États-Unis]Source :
- The journal of physical chemistry. B [ 1520-5207 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Cuivre, Eau, Plastocyanine, Populus, Protéines végétales.
- Domaine catalytique, Oxydoréduction, Simulation de dynamique moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Copper, Plant Proteins, Plastocyanin, Water.
- chemistry : Populus.
- Catalytic Domain, Molecular Dynamics Simulation, Oxidation-Reduction.
Abstract
We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable.
DOI: 10.1021/acs.jpcb.5b09656
PubMed: 26624804
PubMed Central: PMC5705190
Affiliations:
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wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706</wicri:regionArea><wicri:noRegion>Wisconsin 53706</wicri:noRegion></affiliation></author><author><name sortKey="Das, Akshaya Kumar" sort="Das, Akshaya Kumar" uniqKey="Das A" first="Akshaya Kumar" last="Das">Akshaya Kumar Das</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation></author><author><name sortKey="Gaus, Michael" sort="Gaus, Michael" uniqKey="Gaus M" first="Michael" last="Gaus">Michael Gaus</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706</wicri:regionArea><wicri:noRegion>Wisconsin 53706</wicri:noRegion></affiliation></author><author><name sortKey="Meuwly, Markus" sort="Meuwly, Markus" uniqKey="Meuwly M" first="Markus" last="Meuwly">Markus Meuwly</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation></author><author><name sortKey="Cui, Qiang" sort="Cui, Qiang" uniqKey="Cui Q" first="Qiang" last="Cui">Qiang Cui</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706</wicri:regionArea><wicri:noRegion>Wisconsin 53706</wicri:noRegion></affiliation></author></analytic><series><title level="j">The journal of physical chemistry. B</title><idno type="eISSN">1520-5207</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Catalytic Domain (MeSH)</term><term>Copper (chemistry)</term><term>Molecular Dynamics Simulation (MeSH)</term><term>Oxidation-Reduction (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plastocyanin (chemistry)</term><term>Populus (chemistry)</term><term>Water (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cuivre (composition chimique)</term><term>Domaine catalytique (MeSH)</term><term>Eau (composition chimique)</term><term>Oxydoréduction (MeSH)</term><term>Plastocyanine (composition chimique)</term><term>Populus (composition chimique)</term><term>Protéines végétales (composition chimique)</term><term>Simulation de dynamique moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Copper</term><term>Plant Proteins</term><term>Plastocyanin</term><term>Water</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Cuivre</term><term>Eau</term><term>Plastocyanine</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Catalytic Domain</term><term>Molecular Dynamics Simulation</term><term>Oxidation-Reduction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Domaine catalytique</term><term>Oxydoréduction</term><term>Simulation de dynamique moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26624804</PMID><DateCompleted><Year>2016</Year><Month>11</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-5207</ISSN><JournalIssue CitedMedium="Internet"><Volume>120</Volume><Issue>8</Issue><PubDate><Year>2016</Year><Month>Mar</Month><Day>03</Day></PubDate></JournalIssue><Title>The journal of physical chemistry. B</Title><ISOAbbreviation>J Phys Chem B</ISOAbbreviation></Journal><ArticleTitle>Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.</ArticleTitle><Pagination><MedlinePgn>1894-910</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/acs.jpcb.5b09656</ELocationID><Abstract><AbstractText>We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jin</LastName><ForeName>Haiyun</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Goyal</LastName><ForeName>Puja</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Das</LastName><ForeName>Akshaya Kumar</ForeName><Initials>AK</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaus</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meuwly</LastName><ForeName>Markus</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cui</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM106443</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01-GM106443</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>12</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Phys Chem B</MedlineTA><NlmUniqueID>101157530</NlmUniqueID><ISSNLinking>1520-5207</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>059QF0KO0R</RegistryNumber><NameOfSubstance UI="D014867">Water</NameOfSubstance></Chemical><Chemical><RegistryNumber>789U1901C5</RegistryNumber><NameOfSubstance UI="D003300">Copper</NameOfSubstance></Chemical><Chemical><RegistryNumber>9014-09-9</RegistryNumber><NameOfSubstance UI="D010970">Plastocyanin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003300" MajorTopicYN="N">Copper</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056004" MajorTopicYN="N">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010084" MajorTopicYN="N">Oxidation-Reduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010970" MajorTopicYN="N">Plastocyanin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014867" MajorTopicYN="N">Water</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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