Atomistic Simulation View on Gold Nanocluster Functionalities via Ligand Shell Dynamics
Gold nanoclusters have been traditionally extensively studied by experimental and DFT methods. The past results have revealed their character as an interesting species at the limit of bulk and atomic, with properties tunable for numerous potential applications. Especially, biological and medical applications have raised interest with gold nanoclusters acting as potential labels for imaging, and as drug carriers. To understand in detail their behavior in solvent and protein environments at atomic scale, simulations complementing the experimental data are needed. While such size and time scales are for the most parts beyond reach for DFT methods, such systems are well within capabilities of all-atom MD simulations. In this thesis, the force field parameters for performing such simulations are developed, and applied for different types of gold nanocluster systems to study their functionalities. MD simulations were successfully applied in revealing ligand shell conformations to explain structural functionalities of gold nanoclusters with unknown ligand shell structure. Considering larger systems, MD simulations were applied in investigating solvent and protonation conditions for gold nanocluster self-assembly and superstructure formation. Furthering complexity, simulations with gold nanoclusters and a full enterovirus were performed to study atomic scale interactions between the two. Also free energy calculations were performed to shed light on binding affinities of various drug-based molecules to the virus, and implications of adding the gold nanoclusters to the picture were concluded. Altogether, the results show that MD simulations fill a niche in investigating such systems alongside experimental and DFT methods. Keywords: Gold nanocluster, Molecular dynamics, Simulations, Force field ...
- Artikkeli I: Pohjolainen, E., Chen, X., Malola, S., Groenhof, G., & Häkkinen, H. (2016). A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters. Journal of Chemical Theory and Computation, 12 (3), 1342-1350. DOI: 10.1021/acs.jctc.5b01053
- Artikkeli II: Tero, T.-R., Malola, S., Koncz, B., Pohjolainen, E., Lautala, S., Mustalahti, S., . . . Häkkinen, H. (2017). Dynamic Stabilization of the Ligand-Metal Interface in Atomically Precise Gold Nanoclusters Au68 and Au144 Protected by meta-Mercaptobenzoic Acid. ACS Nano, 11 (12), 11872-11879. DOI: 10.1021/acsnano.7b07787
- Artikkeli III: Pohjolainen, E., Malola, S., Groenhof, G., & Häkkinen, H. (2017). Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjugate Chemistry, 28 (9), 2327-2339. DOI: 10.1021/acs.bioconjchem.7b00367
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Dynamic Stabilization of the Ligand-Metal Interface in Atomically Precise Gold Nanoclusters Au68 and Au144 Protected by meta-Mercaptobenzoic Acid Tero, Tiia-Riikka; Malola, Sami; Koncz, Benedek; Pohjolainen, Emmi; Lautala, Saara; Mustalahti, Satu; Permi, Perttu; Groenhof, Gerrit; Pettersson, Mika; Häkkinen, Hannu (American Chemical Society, 2017)Ligand-stabilized, atomically precise gold nanoclusters with a metal core of a uniform size of just 1-3 nm constitute an interesting class of nanomaterials with versatile possibilities for applications due to their ...
Bulky Surface Ligands Promote Surface Reactivities of [Ag141X12(S-Adm)40]3+ (X=Cl, Br, I) Nanoclusters: Models for Multiple-Twinned Nanoparticles Ren, Liting; Yuan, Peng; Su, Haifeng; Malola, Sami; Lin, Shuichao; Tang, Zichao; Teo, Boon K.; Häkkinen, Hannu; Zheng, Lansun; Zheng, Nanfeng (American Chemical Society, 2017)Surface ligands play important roles in controlling the size and shape of metal nanoparticles and their surface properties. In this work, we demonstrate that the use of bulky thiolate ligands, along with halides, as the ...
Analysis of the Electronic Structure of Non-Spherical Ligand-Protected Metal Nanoclusters : The Case of a Box-Like Ag67 Juarez Mosqueda, Rosalba; Kaappa, Sami; Malola, Sami; Häkkinen, Hannu (American Chemical Society, 2017)In this work we introduce a new strategy to investigate the electronic shell structure of ligand-protected metal nanoclusters of polyhedral core shape. The central idea is to identify the symmetry of the Kohn–Sham molecular ...
Dynamics of weak interactions in the ligand layer of meta-mercaptobenzoic acid protected gold nanoclusters Au68(m-MBA)32 and Au144(m-MBA)40 Mammen, Nisha; Malola, Sami; Honkala, Karoliina; Häkkinen, Hannu (Royal Society of Chemistry (RSC), 2020)Atomically precise metal nanoclusters, stabilized and functionalized by organic ligands, are emerging nanomaterials with potential applications in plasmonics, nano-electronics, bio-imaging, nanocatalysis, and as therapeutic ...
Elucidating the ligand shell structure and dynamics of Au683MBA32 gold nanocluster using molecular dynamics simulations Lautala, Saara (2017)Synthesising novel gold nanoparticles and -clusters can be often easier than characterising them, and after experimental analysis many options for the possible molecular formula of the cluster may remain as equally valid ...