Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
Identifieur interne : 000392 ( Ncbi/Curation ); précédent : 000391; suivant : 000393Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
Auteurs : Sidney P. Elmer [États-Unis] ; Sanghyun Park ; Vijay S. PandeSource :
- The Journal of chemical physics [ 0021-9606 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
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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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 wicri:level="1"><nlm:affiliation>Department of Chemistry, Stanford University, California 94305-5080, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Stanford University, California 94305-5080</wicri:regionArea><wicri:noRegion>California 94305-5080</wicri:noRegion></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="KwdFr" xml:lang="fr"><term>Acétonitriles ()</term><term>Acétylène ()</term><term>Chaines de Markov</term><term>Chloroforme ()</term><term>Conformation moléculaire</term><term>Eau ()</term><term>Modèles chimiques</term><term>Modèles moléculaires</term><term>Méthanol ()</term><term>Simulation numérique</term><term>Solvants ()</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><keywords scheme="MESH" xml:lang="fr"><term>Acétonitriles</term><term>Acétylène</term><term>Chaines de Markov</term><term>Chloroforme</term><term>Conformation moléculaire</term><term>Eau</term><term>Modèles chimiques</term><term>Modèles moléculaires</term><term>Méthanol</term><term>Simulation numérique</term><term>Solvants</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></record>Pour manipuler ce document sous Unix (Dilib)
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