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Modeling of Structural, Energetic, and Dynamic Properties of Few‐Atom Silver Clusters Embedded in Polynucleotide Strands by Using Molecular Dynamics
Author(s) -
Staelens Nicolas,
Leherte Laurence,
Champagne Benoît,
Vercauteren Daniel P.
Publication year - 2015
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201402632
Subject(s) - molecular dynamics , polynucleotide , ramachandran plot , chemistry , supramolecular chemistry , chemical physics , force field (fiction) , cationic polymerization , nucleic acid , crystallography , nanotechnology , computational chemistry , materials science , protein structure , physics , crystal structure , biochemistry , organic chemistry , quantum mechanics
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.