title: Modeling of structural, energetic, and dynamic properties of few-atom silver clusters embedded in polynucleotide strands by using molecular dynamics.
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 Ramachandran-type maps.
authors.affiliation: Laboratoire de Physico-Chimie Informatique (PCI), Unité de Chimie Physique Théorique et Structurale (UCPTS), Université de Namur, Rue de Bruxelles 61, 5000 Namur (Belgium). nicolas.staelens@unamur.com.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Staelens
authors.forename: Laurence
authors.initials: L
authors.lastname: Leherte
authors.forename: Benoît
authors.initials: B
authors.lastname: Champagne
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Vercauteren
mesh_terms: D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011119:Polynucleotides / Q000737:chemistry*; D012834:Silver / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011119:Polynucleotides; D012834:Silver
keywords: molecular dynamics; molecular modeling; polynucleotides; silver