POSTMODERN ALCHEMY

Simulations and experiments meet: Machine learning predicts the structures of gold nanoclusters

University of Jyväskylä - Jyväskylän yliopisto

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Atomistic snapshots describing how two thiolate-protected gold nanoclusters of 144 gold atoms each coalesce producing a single larger cluster matching a size that previously has been synthesized. 

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Credit: Maryam Sabooni Asre Hazer, University of Jyväskylä.

Researchers at University of Jyväskylä (Finland) advance understanding of gold nanocluster behavior at elevated temperatures using machine learning-based simulations. This information is crucial in the design of nanomaterials so that their properties can be modified for use in catalysis and other technological applications.

Thiolate protected gold nanoclusters are hybrid nanomaterials with promising applications in nanomedicine, bioimaging and catalysis. However, understanding how these nanoclusters behave under elevated temperatures, which is critical for their use, has remained largely unexplored due to the prohibitive computational cost of traditional simulation methods. 

Record-long simulations of gold nanoclusters

Researchers at the University of Jyväskylä have successfully employed machine learning-driven simulations to investigate the thermal dynamics of Au₁₄₄(SR)₆₀, one of the most well-studied gold nanoclusters. Using a recently developed atomic cluster expansion (ACE) potential trained on extensive density functional theory data, the researchers conducted molecular dynamics simulations extending up to 0.12 microseconds. This is approximately five orders of magnitude longer than what is feasible with conventional quantum chemical methods.

"This work opens new possibilities for understanding how ligand-protected metal nanoclusters behave under realistic operating conditions," says lead author Dr. Maryam Sabooni Asre Hazer. "Through this work, we can observe in atomistic detail how these clusters transform, fragment, and even merge at elevated temperatures over timescales that are relevant for experimental conditions."

Layer-by-layer thermal transformations revealed

The study revealed that thermal effects induce structural changes in a layer-by-layer fashion, starting from the outermost gold-thiolate protective shell. At temperatures between 300 and 550 K, the researchers observed the spontaneous formation of polymer-like chains and ring structures of gold-thiolate units, which can dynamically detach and reattach to the cluster surface. The remaining cluster compositions closely matched those observed in experimental studies, demonstrating the accuracy of the machine learning potential.

"What's particularly exciting is that we can now see how gold atoms migrate between different layers of the cluster and how the surface restructures under thermal stress," explains Dr. Sabooni Asre Hazer. "These processes are directly relevant to understanding why thermally treated gold nanoclusters become effective catalysts."

Gold clusters joined together in the simulation

In an even more remarkable finding, the researchers successfully simulated the complete coalescence of two Au₁₄₄(SR)₆₀ clusters at 550 K. The fusion process produced a larger cluster with composition Au₂₃₉(SR)₆₉, strikingly similar to a gold nanocluster previously synthesized experimentally. 

"The merged cluster exhibited a twinned face-centered cubic metal core structure, matching the symmetry determined from experimental X-ray diffraction data," says Dr. Sabooni Asre Hazer.

Opening new avenues for nanomaterials research

The methodology enables detailed atomistic studies of processes that were previously inaccessible to computational investigation, including cluster-cluster interactions, catalytic activation mechanisms, thermal stability, and inter-particle reactions.

"Our results provide fundamental insights into how ligand-protected nanoclusters behave as they transition toward larger nanoparticles," explains Professor Hannu Häkkinen, who supervised the research. "This knowledge is instrumental for the rational design of nanomaterials with tailored functionalities for catalysis and other applications.", he continues. 

The research was published in Nature Communications. The publication was recognized as an Editors' Highlight in the Inorganic and Physical Chemistry section of Nature Communications.

The work was supported by the Research Council of Finland and the European Research Council (ERC) through the Advanced Grant project DYNANOINT. Computational resources on supercomputers Puhti and Mahti were provided by the Finnish national supercomputing center CSC. 

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Journal

Nature Communications

DOI

10.1038/s41467-025-67700-w 

Method of Research

Imaging analysis

Subject of Research

Not applicable

Article Title

Thermal dynamics and coalescence of Au144(SR)60 clusters from a machine-learned potential

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XXI CENTURY ALCHEMY

'Trojan horse' may deliver toxic dose of copper to bacterial colonies, including drug-resistant MRSA infections

University of Arizona

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A research team at the University of Arizona College of Medicine – Tucson is developing a drug that works in combination with copper to kill bacteria, including those that cause MRSA, a type of staph infection that is resistant to usual treatments. They published their results last month in mSphere.

MRSA is caused by methicillin-resistant Staphylococcus aureus, which is classified as a serious threat by the Centers for Disease Control and Prevention and a high-priority pathogen by the World Health Organization.

"It likes to live on our skin – about 30% of people are colonized with it. It becomes a problem when it gets in a wound, where it can wreak havoc," said Michael D. L. Johnson, an associate professor of immunobiology and senior author of the paper.

While MRSA can be treated with other antibiotics, bacteria's ability to evolve drug resistance means finding novel treatments is crucial.

"History has shown us that bacteria have an exquisite ability to adapt to their surroundings," Johnson said. "The more tools we have in our toolkit, the better prepared we will be to fight the next threat."

MRSA can be spread by skin-to-skin contact and appear as a painful boil. It can also occur in a hospital setting, where it might colonize a surgical wound or be introduced to the body through tubing, such as a catheter, or an implant, such as an artificial joint.

"People who are diabetic are very susceptible to staph infections, specifically in wounds they may develop," Johnson said. "It also binds to plastic really well. Can you guess where there's a lot of plastic? In a hospital. We've become quite reliant on plastic, which creates a niche for that microbe."

The team also looked at a cousin of MSRA, Staphylococcus epidermidis, which is usually harmless but can cause infections in hospitals due to its affinity for plastic. Both MSRA and S. epidermidis adhere to plastic by producing a "glue" called biofilm.

"That stuff you feel on your teeth when you wake up in the morning – that's biofilm," Johnson said. "Bacteria make biofilm to hold on to host cells or surfaces, and that biofilm is a protective shield from the bacteria's environment – such as antibiotics or antimicrobial peptides our bodies make."

Supported by funding from Tech Launch Arizona, the Johnson Lab designed the platform for a molecule called BMDC, short for N-benzyl-N-methyldithiocarbamate, to work with copper, based on a similar molecule they studied previously. TLA provided the funds through its Asset Development Program, which provides support to move potentially impactful innovations closer to readiness for commercialization and real-world impact.

"This one actually worked better than our original compound, DMDC, which killed different Streptococcusspecies – but not staph," Johnson said.

He says BMDC works by disguising itself as iron, a nutrient that hungry bacteria scavenge from their surroundings. But instead of iron, the compound contains a toxic dose of copper.

"Our compound mimics specialized molecules that carry iron. The staph bacteria are like, 'Oh, sweet, iron! This is my lucky day!' They unlock the compound, and, oops, it's copper," he explained. "Our compound is a Trojan horse, intoxicating bacteria with copper, killing them within the biofilm. The bacteria don't learn from their mistakes, and they do it over and over again."

Working with TLA, Johnson has filed a patent application on the technology, and they are searching for a company to license the product to develop it further. Their plan is to take it to clinical trials in humans, which they hope will lead to FDA approval to treat MRSA and other infections.

In the meantime, the Johnson Lab is preparing to launch a collaboration with the Department of Surgery's Division Chief of Pediatric Surgery Kenneth W. Liechty, to conduct additional laboratory experiments to see if their compound helps with wound infections and healing.

"How amazing would it be if someday, we could put some of our stuff on an open wound with a bad infection, and the infection got better?" said Johnson, who is also a member of the BIO5 Institute. "We're very interested in the translation of our discoveries to the clinic, and you don't do that unless you're partnered with amazing people here at U of A to do those experiments."

Johnson says the possibility that his work in the lab could someday benefit humanity is profoundly inspiring.

"Those are the things basic science and translational researchers dream about," he said. "It makes the science more exciting when you can see the application at the end of the road."

This research is supported in part by the National Institute of General Medical Sciences, a division of the National Institutes of Health, under award No. 2R35128653.

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Journal

mSphere

DOI

10.1128/msphere.00691-25