Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
Identifieur interne : 002289 ( PubMed/Corpus ); précédent : 002288; suivant : 002290Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
Auteurs : Sidney P. Elmer ; Sanghyun Park ; Vijay S. PandeSource :
- The Journal of chemical physics [ 0021-9606 ] ; 2005.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Acetonitriles, Acetylene, Chloroform, Methanol, Solvents, Water.
- Computer Simulation, Markov Chains, Models, Chemical, Models, Molecular, Molecular Conformation.
Abstract
In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.
DOI: 10.1063/1.2001648
PubMed: 16392592
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pubmed:16392592Le document en format XML
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Pande</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16392592</idno><idno type="pmid">16392592</idno><idno type="doi">10.1063/1.2001648</idno><idno type="wicri:Area/PubMed/Corpus">002289</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002289</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.</title><author><name sortKey="Elmer, Sidney P" sort="Elmer, Sidney P" uniqKey="Elmer S" first="Sidney P" last="Elmer">Sidney P. Elmer</name><affiliation><nlm:affiliation>Department of Chemistry, Stanford University, California 94305-5080, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Park, Sanghyun" sort="Park, Sanghyun" uniqKey="Park S" first="Sanghyun" last="Park">Sanghyun Park</name></author><author><name sortKey="Pande, Vijay S" sort="Pande, Vijay S" uniqKey="Pande V" first="Vijay S" last="Pande">Vijay S. Pande</name></author></analytic><series><title level="j">The Journal of chemical physics</title><idno type="ISSN">0021-9606</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acetonitriles (chemistry)</term><term>Acetylene (chemistry)</term><term>Chloroform (chemistry)</term><term>Computer Simulation</term><term>Markov Chains</term><term>Methanol (chemistry)</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Molecular Conformation</term><term>Solvents (chemistry)</term><term>Water (chemistry)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Acetonitriles</term><term>Acetylene</term><term>Chloroform</term><term>Methanol</term><term>Solvents</term><term>Water</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Markov Chains</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Molecular Conformation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16392592</PMID><DateCompleted><Year>2007</Year><Month>07</Month><Day>26</Day></DateCompleted><DateRevised><Year>2019</Year><Month>06</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0021-9606</ISSN><JournalIssue CitedMedium="Print"><Volume>123</Volume><Issue>11</Issue><PubDate><Year>2005</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>The Journal of chemical physics</Title><ISOAbbreviation>J Chem Phys</ISOAbbreviation></Journal><ArticleTitle>Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.</ArticleTitle><Pagination><MedlinePgn>114902</MedlinePgn></Pagination><Abstract><AbstractText>In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Elmer</LastName><ForeName>Sidney P</ForeName><Initials>SP</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Stanford University, California 94305-5080, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Sanghyun</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Pande</LastName><ForeName>Vijay S</ForeName><Initials>VS</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Chem Phys</MedlineTA><NlmUniqueID>0375360</NlmUniqueID><ISSNLinking>0021-9606</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000097">Acetonitriles</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012997">Solvents</NameOfSubstance></Chemical><Chemical><RegistryNumber>059QF0KO0R</RegistryNumber><NameOfSubstance UI="D014867">Water</NameOfSubstance></Chemical><Chemical><RegistryNumber>7V31YC746X</RegistryNumber><NameOfSubstance UI="D002725">Chloroform</NameOfSubstance></Chemical><Chemical><RegistryNumber>OC7TV75O83</RegistryNumber><NameOfSubstance UI="D000114">Acetylene</NameOfSubstance></Chemical><Chemical><RegistryNumber>Y4S76JWI15</RegistryNumber><NameOfSubstance UI="D000432">Methanol</NameOfSubstance></Chemical><Chemical><RegistryNumber>Z072SB282N</RegistryNumber><NameOfSubstance UI="C032159">acetonitrile</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000097" MajorTopicYN="N">Acetonitriles</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000114" MajorTopicYN="N">Acetylene</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002725" MajorTopicYN="N">Chloroform</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008390" MajorTopicYN="N">Markov Chains</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000432" MajorTopicYN="N">Methanol</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="Y">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008968" MajorTopicYN="N">Molecular Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012997" MajorTopicYN="N">Solvents</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 PubStatus="pubmed"><Year>2006</Year><Month>1</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>7</Month><Day>27</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>1</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16392592</ArticleId><ArticleId IdType="doi">10.1063/1.2001648</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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