Sparkle/PM7 Lanthanide Parameters for the Modeling of Complexes and Materials.
Identifieur interne : 000234 ( PubMed/Corpus ); précédent : 000233; suivant : 000235Sparkle/PM7 Lanthanide Parameters for the Modeling of Complexes and Materials.
Auteurs : José Diogo L. Dutra ; Manoel A M. Filho ; Gerd B. Rocha ; Ricardo O. Freire ; Alfredo M. Simas ; James J P. StewartSource :
- Journal of chemical theory and computation [ 1549-9626 ] ; 2013.
Abstract
The recently published Parametric Method number 7, PM7, is the first semiempirical method to be successfully tested by modeling crystal structures and heats of formation of solids. PM7 is thus also capable of producing results of useful accuracy for materials science, and constitutes a great improvement over its predecessor, PM6. In this article, we present Sparkle Model parameters to be used with PM7 that allow the prediction of geometries of metal complexes and materials which contain lanthanide trications. Accordingly, we considered the geometries of 224 high-quality crystallographic structures of complexes for the parameterization set and 395 more for the validation of the parameterization for the whole lanthanide series, from La(III) to Lu(III). The average unsigned error for Sparkle/PM7 for the distances between the metal ion and its coordinating atoms is 0.063Å for all lanthanides, ranging from a minimum of 0.052Å for Tb(III) to 0.088Å for Ce(III), comparable to the equivalent errors in the distances predicted by PM7 for other metals. These distance deviations follow a gamma distribution within a 95% level of confidence, signifying that they appear to be random around a mean, confirming that Sparkle/PM7 is a well-tempered method. We conclude by carrying out a Sparkle/PM7 full geometry optimization of two spatial groups of the same thulium-containing metal organic framework, with unit cells accommodating 376 atoms, of which 16 are Tm(III) cations; the optimized geometries were in good agreement with the crystallographic ones. These results emphasize the capability of the use of the Sparkle Model for the prediction of geometries of compounds containing lanthanide trications within the PM7 semiempirical model, as well as the usefulness of such semiempirical calculations for materials modeling. Sparkle/PM7 is available in the software package MOPAC2012, at no cost for academics and can be obtained from http://openmopac.net.
DOI: 10.1021/ct301012h
PubMed: 24163641
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Dutra</name><affiliation><nlm:affiliation>Departamento de Química, Universidade Federal de Sergipe, 49.100-000 - São Cristóvão, SE, Brazil.</nlm:affiliation></affiliation></author><author><name sortKey="Filho, Manoel A M" sort="Filho, Manoel A M" uniqKey="Filho M" first="Manoel A M" last="Filho">Manoel A M. Filho</name></author><author><name sortKey="Rocha, Gerd B" sort="Rocha, Gerd B" uniqKey="Rocha G" first="Gerd B" last="Rocha">Gerd B. Rocha</name></author><author><name sortKey="Freire, Ricardo O" sort="Freire, Ricardo O" uniqKey="Freire R" first="Ricardo O" last="Freire">Ricardo O. Freire</name></author><author><name sortKey="Simas, Alfredo M" sort="Simas, Alfredo M" uniqKey="Simas A" first="Alfredo M" last="Simas">Alfredo M. Simas</name></author><author><name sortKey="Stewart, James J P" sort="Stewart, James J P" uniqKey="Stewart J" first="James J P" last="Stewart">James J P. Stewart</name></author></analytic><series><title level="j">Journal of chemical theory and computation</title><idno type="eISSN">1549-9626</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The recently published Parametric Method number 7, PM7, is the first semiempirical method to be successfully tested by modeling crystal structures and heats of formation of solids. PM7 is thus also capable of producing results of useful accuracy for materials science, and constitutes a great improvement over its predecessor, PM6. In this article, we present Sparkle Model parameters to be used with PM7 that allow the prediction of geometries of metal complexes and materials which contain lanthanide trications. Accordingly, we considered the geometries of 224 high-quality crystallographic structures of complexes for the parameterization set and 395 more for the validation of the parameterization for the whole lanthanide series, from La(III) to Lu(III). The average unsigned error for Sparkle/PM7 for the distances between the metal ion and its coordinating atoms is 0.063Å for all lanthanides, ranging from a minimum of 0.052Å for Tb(III) to 0.088Å for Ce(III), comparable to the equivalent errors in the distances predicted by PM7 for other metals. These distance deviations follow a gamma distribution within a 95% level of confidence, signifying that they appear to be random around a mean, confirming that Sparkle/PM7 is a well-tempered method. We conclude by carrying out a Sparkle/PM7 full geometry optimization of two spatial groups of the same thulium-containing metal organic framework, with unit cells accommodating 376 atoms, of which 16 are Tm(III) cations; the optimized geometries were in good agreement with the crystallographic ones. These results emphasize the capability of the use of the Sparkle Model for the prediction of geometries of compounds containing lanthanide trications within the PM7 semiempirical model, as well as the usefulness of such semiempirical calculations for materials modeling. Sparkle/PM7 is available in the software package MOPAC2012, at no cost for academics and can be obtained from http://openmopac.net.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">24163641</PMID><DateCreated><Year>2013</Year><Month>10</Month><Day>28</Day></DateCreated><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1549-9626</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>8</Issue><PubDate><Year>2013</Year><Month>Aug</Month><Day>13</Day></PubDate></JournalIssue><Title>Journal of chemical theory and computation</Title><ISOAbbreviation>J Chem Theory Comput</ISOAbbreviation></Journal><ArticleTitle>Sparkle/PM7 Lanthanide Parameters for the Modeling of Complexes and Materials.</ArticleTitle><Pagination><MedlinePgn>3333-3341</MedlinePgn></Pagination><Abstract><AbstractText>The recently published Parametric Method number 7, PM7, is the first semiempirical method to be successfully tested by modeling crystal structures and heats of formation of solids. PM7 is thus also capable of producing results of useful accuracy for materials science, and constitutes a great improvement over its predecessor, PM6. In this article, we present Sparkle Model parameters to be used with PM7 that allow the prediction of geometries of metal complexes and materials which contain lanthanide trications. Accordingly, we considered the geometries of 224 high-quality crystallographic structures of complexes for the parameterization set and 395 more for the validation of the parameterization for the whole lanthanide series, from La(III) to Lu(III). The average unsigned error for Sparkle/PM7 for the distances between the metal ion and its coordinating atoms is 0.063Å for all lanthanides, ranging from a minimum of 0.052Å for Tb(III) to 0.088Å for Ce(III), comparable to the equivalent errors in the distances predicted by PM7 for other metals. These distance deviations follow a gamma distribution within a 95% level of confidence, signifying that they appear to be random around a mean, confirming that Sparkle/PM7 is a well-tempered method. We conclude by carrying out a Sparkle/PM7 full geometry optimization of two spatial groups of the same thulium-containing metal organic framework, with unit cells accommodating 376 atoms, of which 16 are Tm(III) cations; the optimized geometries were in good agreement with the crystallographic ones. These results emphasize the capability of the use of the Sparkle Model for the prediction of geometries of compounds containing lanthanide trications within the PM7 semiempirical model, as well as the usefulness of such semiempirical calculations for materials modeling. Sparkle/PM7 is available in the software package MOPAC2012, at no cost for academics and can be obtained from http://openmopac.net.</AbstractText></Abstract><AuthorList><Author><LastName>Dutra</LastName><ForeName>José Diogo L</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>Departamento de Química, Universidade Federal de Sergipe, 49.100-000 - São Cristóvão, SE, Brazil.</Affiliation></AffiliationInfo></Author><Author><LastName>Filho</LastName><ForeName>Manoel A M</ForeName><Initials>MA</Initials></Author><Author><LastName>Rocha</LastName><ForeName>Gerd B</ForeName><Initials>GB</Initials></Author><Author><LastName>Freire</LastName><ForeName>Ricardo O</ForeName><Initials>RO</Initials></Author><Author><LastName>Simas</LastName><ForeName>Alfredo M</ForeName><Initials>AM</Initials></Author><Author><LastName>Stewart</LastName><ForeName>James J P</ForeName><Initials>JJ</Initials></Author></AuthorList><Language>ENG</Language><GrantList><Grant><GrantID>R44 GM083178</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="">JOURNAL ARTICLE</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><MedlineTA>J Chem Theory Comput</MedlineTA><NlmUniqueID>101232704</NlmUniqueID><ISSNLinking>1549-9618</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>10</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>10</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>10</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1021/ct301012h</ArticleId><ArticleId IdType="pubmed">24163641</ArticleId><ArticleId IdType="pmc">PMC3806451</ArticleId><ArticleId IdType="mid">NIHMS507342</ArticleId></ArticleIdList><pmc-dir>nihms</pmc-dir>
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