Modeling of structural, energetic, and dynamic properties of few-atom silver clusters embedded in polynucleotide strands by using molecular dynamics

Research output: Contribution to journalArticle

Abstract

This work concerns the study of the structural, energetic, and dynamic properties of fluorescent systems composed of silver clusters stabilized by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER force field. Molecular dynamics simulations allowed analysis of the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandrantype maps.

Original languageEnglish
Pages (from-to)360-369
Number of pages10
JournalChemPhysChem
Volume16
Issue number2
DOIs
Publication statusPublished - 2 Feb 2015

Fingerprint

polynucleotides
Polynucleotides
Silver
strands
dynamic characteristics
Molecular dynamics
silver
molecular dynamics
Atoms
atoms
oligomers
Oligomers
radial distribution
assemblies
field theory (physics)
Distribution functions
flexibility
distribution functions
interactions
Computer simulation

Keywords

  • Molecular dynamics
  • Molecular modeling
  • Polynucleotides
  • Silver

Cite this

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abstract = "This work concerns the study of the structural, energetic, and dynamic properties of fluorescent systems composed of silver clusters stabilized by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER force field. Molecular dynamics simulations allowed analysis of the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandrantype maps.",
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author = "Nicolas Staelens and Laurence Leherte and Beno{\^i}t Champagne and Vercauteren, {Daniel P.}",
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T1 - Modeling of structural, energetic, and dynamic properties of few-atom silver clusters embedded in polynucleotide strands by using molecular dynamics

AU - Staelens, Nicolas

AU - Leherte, Laurence

AU - Champagne, Benoît

AU - Vercauteren, Daniel P.

PY - 2015/2/2

Y1 - 2015/2/2

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AB - This work concerns the study of the structural, energetic, and dynamic properties of fluorescent systems composed of silver clusters stabilized by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER force field. Molecular dynamics simulations allowed analysis of the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandrantype maps.

KW - Molecular dynamics

KW - Molecular modeling

KW - Polynucleotides

KW - Silver

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