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 Ag 12 and Au 12 clusters in the presence of single-stranded DNA (ssDNA) scaffold of various nucleobase sequences (i.e. ssdA 12 , ssdT 12 , ssdG 12 and ssdC 12 ). 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 ssdG 12 interacts strongly with the Ag 12 cluster while ssdA 12 shows greater binding affinity towards the Au 12 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 p-stacking and/or by the interaction mediated through specific atoms (nitrogen and/or oxygen) present in the nucleobases. The optical response properties of these Ag 12 /Au 12 -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.

Self-Assembly of Silver Metal Clusters of Small Atomicity on Cyclic Peptide Nanotubes

“…17,23,25 Corma et al have recently reported the interesting catalytic properties of tricomponent systems made of polyallylamine surfactants, multiwall carbon nanotubes (MWCNTs) and subnanometric gold (0) clusters, although they did not go into details about the interactions of the metal clusters with the surfactant-stabilized MWCNTs. 3,24,26 The interaction of cationic silver (Ag + ) with anionic DNA has also been employed for the size selective synthesis of silver clusters by the in situ reduction of the corresponding ionic salts. 1,5,[18][19][20][21][27][28][29] In these reported synthetic protocols, the macromolecular hosts (e.g.…”

“…13,23 The same type of templated salt reduction has been described for the size selective preparation of gold nanoparticles in the presence of cyclodextrins templates. 16,24 The adsorption of ligand-coordinated metal clusters into zeolite pores followed by thermal ligand removal has been elegantly applied for the synthesis of neat metal clusters. 17,23,25 Corma et al have recently reported the interesting catalytic properties of tricomponent systems made of polyallylamine surfactants, multiwall carbon nanotubes (MWCNTs) and subnanometric gold (0) clusters, although they did not go into details about the interactions of the metal clusters with the surfactant-stabilized MWCNTs.…”

Biomediated Atomic Metal Nanoclusters: Synthesis and Theory

“…Application of the biological-metal potentials on these style systems may show interesting results. As demonstrated in the last work, however, whatever shortcomings of a classical simulation, used correctly they can generate reasonable results and are often improved by further study with quantum simulation [97].…”

“…It follows then, that the most direct -albeit inaccurate -way of simulating a system with metal and biological components is to use general e and r min parameters that represent the relative energetic and mechanical properties of the metal lattice and allow combining rules to dictate the energies of biological-metal interactions. Studies of DNA on gold surfaces, nanoparticles, and nanoclusters use this method with LJ metal parameters from Rice et al [94][95][96][97]. There are, however, more robust biological-metal potentials using the LJ form and fitted to ab initio simulations.…”

“…They also note an increase in sodium ion concentration around the nanoparticle, which they remark may explain the increase in melting temperature of DNA nanoparticle aggregates. Finally, on a smaller scale, gold and silver nanocluster interaction with ssDNA of homogenous nucleobase sequences were simulated classically, and the optical properties of the resulting nanocluster configuration were computed using ab initio software [97]. The authors determined that ssDNA-A 12 , ssDNA-G 12 , and ssDNA-C 12 exhibited p À bonding to the Ag and Au nanoclusters; however, ssDNA-T 12 showed oxygen atom interaction with Ag and Au nanoclusters.…”