dc.contributor.author | Pohjolainen, Emmi | |
dc.date.accessioned | 2019-05-28T13:55:52Z | |
dc.date.available | 2019-05-28T13:55:52Z | |
dc.date.issued | 2019 | |
dc.identifier.isbn | 978-951-39-7781-8 | |
dc.identifier.uri | https://jyx.jyu.fi/handle/123456789/64255 | |
dc.description.abstract | 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 | en |
dc.format.mimetype | application/pdf | |
dc.language.iso | eng | |
dc.publisher | Jyväskylän yliopisto | |
dc.relation.ispartofseries | JYU 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.rights | In Copyright | |
dc.title | Atomistic Simulation View on Gold Nanocluster Functionalities via Ligand Shell Dynamics | |
dc.type | Diss. | |
dc.identifier.urn | URN:ISBN:978-951-39-7781-8 | |
dc.contributor.yliopisto | University of Jyväskylä | en |
dc.contributor.yliopisto | Jyväskylän yliopisto | fi |
dc.relation.issn | 2489-9003 | |
dc.rights.copyright | © The Author & University of Jyväskylä | |
dc.rights.accesslevel | openAccess | |
dc.type.publication | doctoralThesis | |
dc.format.content | fulltext | |
dc.rights.url | https://rightsstatements.org/page/InC/1.0/ | |