Computational studies on structural and optical properties of single-stranded DNA encapsulated silver/gold clusters

Abstract

Using a combined approach of molecular dynamics (MD) and density functional theoretical (DFT) calculations, we perform the investigation of structures, energetics and optical properties of Ag12 and Au12 clusters in the presence of single-stranded DNA (ssDNA) scaffold of various nucleobase sequences (i.e. ssdA12, ssdT12, ssdG12 and ssdC12). The individual ssDNA undergoes various conformational changes in the presence of different metal clusters during the course of 1.5 ns MD simulations in aqueous media. We find that ssdG12 interacts strongly with the Ag12 cluster while ssdA12 shows greater binding affinity towards the Au12 cluster. We also find that the two different kinds of binding modes of a nucleobase play a key role in deciding the overall structure and stability of the complex while interacting with metal clusters. The metal clusters form nanocomposites with ssDNA either via π-stacking and/or by the interaction mediated through specific atoms (nitrogen and/or oxygen) present in the nucleobases. The optical response properties of these Ag12/Au12–ssDNA composites together with the bare metal clusters are calculated with the MD simulated structures alone, which are comparable with experimental results. The optical absorption characteristics of metal clusters are little affected by the presence of ssDNA scaffold due to the frontier orbital localization mainly on the metal clusters or ssDNA.