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dc.contributor.authorPohjolainen, Emmi
dc.date.accessioned2019-05-28T13:55:52Z
dc.date.available2019-05-28T13:55:52Z
dc.date.issued2019
dc.identifier.isbn978-951-39-7781-8
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/64255
dc.description.abstractGold 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 fielden
dc.relation.ispartofseriesJYU dissertations
dc.relation.haspart<b>Artikkeli I:</b> Pohjolainen, E., Chen, X., Malola, S., Groenhof, G., & Häkkinen, H. (2016). A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters. <i>Journal of Chemical Theory and Computation, 12 (3), 1342-1350.</i> <a href="https://doi.org/10.1021/acs.jctc.5b01053"target="_blank"> DOI: 10.1021/acs.jctc.5b01053</a>
dc.relation.haspart<b>Artikkeli II:</b> 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. <i>ACS Nano, 11 (12), 11872-11879.</i> <a href="https://doi.org/10.1021/acsnano.7b07787"target="_blank"> DOI: 10.1021/acsnano.7b07787</a>
dc.relation.haspart<b>Artikkeli III:</b> Pohjolainen, E., Malola, S., Groenhof, G., & Häkkinen, H. (2017). Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. <i>Bioconjugate Chemistry, 28 (9), 2327-2339.</i> <a href="https://doi.org/10.1021/acs.bioconjchem.7b00367"target="_blank"> DOI: 10.1021/acs.bioconjchem.7b00367</a>
dc.titleAtomistic Simulation View on Gold Nanocluster Functionalities via Ligand Shell Dynamics
dc.identifier.urnURN:ISBN:978-951-39-7781-8


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