Category: Chemistry

by Macquarie University

A new review of the research on cell-penetrating peptide (CPP) clusters by scientists from Macquarie University and Oxford University will provide a roadmap for biomedical scientists to develop the next generation of treatments for cancer and neurodegenerative diseases.

Biological barriers such as the blood-brain barrier and the plasma membrane, which protects neurons, prevent toxins from attacking the central nervous system, but they also stop potentially lifesaving treatments from reaching their intracellular targets.

More than half of the structures in the body that could potentially be affected by medicines are found inside the cells, making it vital to find ways of carrying large molecules like antibodies and genetic treatments across these biological barriers.

CPPs were first discovered three decades ago as a potential answer to the problem. They are cheap to produce, have a long history in research, and are easy to integrate into biologic drugs, but issues with their efficacy have meant that no therapies using them have yet been approved by the world’s regulatory bodies.

A breakthrough came two years ago, in the form of CPP clusters that could be created to carry cargos of antibodies, proteins, enzymes, and peptides across biological barriers.

Oxford University researchers created the first tricyclic CPP cluster, which was also the first in the world to transport functional antibodies into cells at low concentrations. At the same time, another research team from Nanyang Technological University in Singapore made a conceptually similar discovery, using a different agent to transport mRNA into cells.

Dr. Ole Tietz, one of the Oxford team, is now a Senior Research Fellow at the Macquarie University Dementia Research Centre (DRC). He says this breakthrough marked a fundamental shift in the understanding of how CPPs could be used.

“The key to successful CPP cluster carriers lies in arranging them in a specific configuration, so they can act as a key to the barrier’s lock,” he says. “These clusters are molecular Trojan horses, fooling the blood-brain barrier into allowing the molecules they’re carrying to cross over.

“Until now, many therapies have had to be administered in very high doses for a small amount to get through, and this can cause cytotoxicity, which can have very serious effects. There is a small therapeutic window with these treatments, after which you reach a concentration that is toxic and starts killing the cells instead.

“These new generation CPPs have the potential to allow us to deliver the minimum needed for treatment, which could improve patient outcomes dramatically.”

To help other biomedical scientists navigate the development and use of CPPs, Dr. Tietz’s team has written a systematic review, published in the latest edition of Trends in Chemistry, that collects all the research findings on this new class of CPP, effectively creating a roadmap to using the new paradigm.

Lead author, Joseph Reeman, a Master of Research student at Macquarie Medical School, says one of the key aspects of the paper is its provision of a set of design criteria.

“These guidelines will assist researchers in developing the next generation of intracellular therapeutics, with a focus on translation into clinical practice,” he says.

“We cover how to use existing CPP clusters with cargos and how to create new clusters, the outstanding questions of what needs to happen in the field, as well as some of what we are currently addressing through our research program.”

The team is currently developing a CPP cluster that they hope could be used as a “plug and play” carrier for various types of intracellular treatments, including antibodies and gene therapies. Animal testing has already shown it can penetrate the brain, and they are now investigating whether it can transport an antibody across the blood-brain barrier and into a neuron.

If successful, it could be used to target the pathogenic build-ups of the brain proteins TDP-43 and tau that are associated with neurodegenerative diseases including Alzheimer’s disease, frontotemporal dementia and motor neuron disease, which are a key research focus for DRC scientists.

More information: Joseph Reeman et al, Strength in numbers: cell penetrating peptide clusters to build next-generation therapeutics, Trends in Chemistry (2024). DOI: 10.1016/j.trechm.2024.09.003

Journal information: Trends in Chemistry 

Provided by Macquarie University 

by American Chemical Society

Today, people increasingly seek non-alcoholic versions of beer or wine. Despite boasting different flavors, these two drinks share many aromas, which makes it difficult to produce alcohol-free versions that mimic the real thing. Researchers in the Journal of Agricultural and Food Chemistry report on a literature analysis and experiment to characterize the chemical compounds that give beer and wine their unique fragrances. They say their findings could aid the development of flavorful, non-alcoholic substitutes.

Food and beverage researchers are working to recreate the enjoyable aromas and flavors of beer and wine in alcohol-free substitutes. However, because both beer and wine are fermented, they have similar fragrances, and little is known about which scents evoke the unique character of each drink. So, Xingije Wang, Stephanie Frank and Martin Steinhaus set out to identify the key ingredients that distinguish the aroma of beer from that of wine.

First, the team conducted a literature review and identified the average proportions of 29 compounds from beer and 32 from wine that make up the drinks’ aromas. The researchers used these proportions like recipes to concoct standard beverages that smelled like either beer or wine.

From there, they tweaked these standards, swapping levels of select fragrances in the beer-like beverage to match those in the wine-like beverage, or vice versa, to test which ingredients influenced the perception of each drink. Trained taste-testers smelled each tweaked sample and evaluated it on a scale of beer-like to wine-like.

The researchers report that the taste-testers found that stronger fruity aromas made drinks smell more like wine. The team also swapped the entire profile of scented compounds from one standard into the opposite drink’s base liquid. They discovered that the scented compounds, rather than the base liquid, made the biggest difference in beer- versus wine-like aroma to the testers. The researchers say their results could be used to develop drinks that better mimic beer or wine while meeting consumers’ preferences for non-alcoholic options.

More information: Xingjie Wang et al, Molecular Insights into the Aroma Difference between Beer and Wine: A Meta-Analysis-Based Sensory Study Using Concentration Leveling Tests, Journal of Agricultural and Food Chemistry (2024). DOI: 10.1021/acs.jafc.4c06838

Journal information: Journal of Agricultural and Food Chemistry 

by University of Sheffield

Researchers have made a significant breakthrough in understanding how certain pathogens defend themselves against the host’s immune system.

This collaborative study, led by scientists from the University of Sheffield, as well as other British, Dutch and Chinese institutions focuses on the role of a group of enzymes known as zinc-dependent macrodomains (Zn-Macros) in reversing ADP-ribosylation, a vital cellular process.

This discovery could lead to innovative treatments to combat antimicrobial resistance, a growing global health threat. The work is published in the Journal of Biological Chemistry.

ADP-ribosylation is a reversible modification of proteins and DNA that regulates important cellular responses to stress. While this signaling mechanism is well-studied in higher eukaryotes, where it regulates responses to DNA damage, reactive oxygen species and infection, the importance of its role in microorganisms is also becoming increasingly evident, which includes the regulation of the host immune response, microbial immune evasion and adaptation to specific hosts.

The research team used a combination of phylogenetic, biochemical, and structural approaches to investigate the function of Zn-Macros. These enzymes are found in some pathogenic microbes and are essential for removing ADP-ribosyl modifications, thereby helping the pathogens survive oxidative stress.

The study revealed that the catalytic activity of Zn-Macros is strictly dependent on a zinc ion within the active site of these enzymes. The researchers also identified structural features that contribute to substrate selectivity within different types of Zn-Macro enzymes, which may be exploited for the development of future therapies.

The findings have significant implications for the fight against bacterial and fungal infections that pose an increasing risk to human health, a problem that is exacerbated by the development of antimicrobial resistance and the emergence of multidrug-resistant strains. The World Health Organization has published lists of priority pathogens that pose the greatest risk, emphasizing the need for new antimicrobial strategies.

Addressing antimicrobial resistance will require a multifaceted strategy, including the discovery and characterization of new antimicrobial targets, along with assessing their potential for therapeutic use in innovative (co-)treatment approaches.

The authors of the study suggest that targeting the Zn-Macro pathway could reduce the virulence of major human pathogens, including Staphylococcus aureus and Streptococcus pyogenes. These pathogens rely on the crosstalk between lipoic acid metabolism and ADP-ribosylation signaling for their defense mechanisms. Disrupting this pathway could enhance the effectiveness of existing treatments and provide new therapeutic options.

The study’s findings represent a significant step forward in the fight against antimicrobial resistance and highlight the potential of Zn-Macros as therapeutic targets.

“Our findings uncover the evolutionary and molecular mechanisms behind ADP-ribosylation reversal by zinc-dependent macrodomains. By understanding this regulatory process, we can explore new avenues for drug development in diseases where ADP-ribosylation plays a critical role.

“I believe that further investigation into the physiological role of Zn-Macros could lead to the development of new antimicrobial therapies as these enzymes are primarily found in pathogenic microorganisms and have structurally distinct features that make them suitable for drug development,” says Dr. Antonio Ariza, university teaching associate.

More information: Antonio Ariza et al, Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains, Journal of Biological Chemistry (2024). DOI: 10.1016/j.jbc.2024.107770

Journal information: Journal of Biological Chemistry 

by Meike Drießen, Ruhr-Universitaet-Bochum

Using state-of-the-art microscopy and simulation techniques, an international research team has systematically observed how iron atoms alter the structure of grain boundaries in titanium. Their findings were published in the journal Science on October 25, 2024.

They were in for a surprise: “Iron atoms not only segregate to the interface, but they form entirely unexpected cage-like structures,” explains Prof. Dr. Christian Liebscher from the Research Center Future Energy Materials and Systems of the University Alliance Ruhr. The researchers did not expect such a behavior.

A new type of segregation behavior

Most technological materials have a polycrystalline structure: They are composed of different crystals, where atoms are arranged in a regular lattice. These crystals do not have the same orientation everywhere and the interfaces separating them are known as grain boundaries.

“These grain boundaries have an enormous influence on the durability and overall performance of a material,” says Dr. Vivek Devulapalli, who performed the microscopy work in the study. “But we have very limited understanding of what happens when elements segregate to grain boundaries and how they influence the properties of a material.”

The key to success was to observe and model the structures at atomic resolution. The researchers correlated their results from atomic-resolution scanning transmission electron microscopy with advanced computer simulations. A new grain boundary structure prediction algorithm was able to generate the experimentally observed structures and enabled study of their structure.

“Our simulations show that for different iron contents, we always find the cage structures as the underlying building blocks of different grain boundary phases. As the iron level increases at the grain boundary, more icosahedral units appear and eventually agglomerate,” explains Dr. Enze Chen from Stanford University. An icosahedron is a geometric object with 12 corners or vertices, in this case occupied by atoms, and 20 planes.

“We have identified more than five distinct structures or grain boundary phases of the same boundary, all composed of different arrangements of the same icosahedral cage units,” adds Dr. Timofey Frolov, who led the computational work of the study.

Quasicrystalline-like grain boundary phases

A closer inspection of the cage structures revealed that the atoms adopt an icosahedral arrangement with iron atoms being located at the center of the icosahedron and titanium atoms occupying its vertices. “The icosahedral cages enable a dense packing of iron atoms and since they can form aperiodic clusters, more than two to three times the amount of iron can be accommodated at the grain boundary,” explains Devulapalli.

“It appears as if iron is trapped inside of quasicrystalline-like grain boundary phases,” adds Chen.

“This is attributed to the properties of the icosahedral cages,” says Liebscher, “and we now need to find ways to study how they influence the interface properties and this material behavior.”

New pathways for materials design

Understanding and controlling the formation of icosahedral grain boundary phases with different structures and properties can potentially be used to tailor the properties of materials.

The researchers now want to systematically investigate how these novel grain boundary states can be used to tune material behavior, adjust a certain material functionality and to make materials more resilient against degradation processes.

More information: Vivek Devulapalli et al, Topological grain boundary segregation transitions, Science (2024). DOI: 10.1126/science.adq4147

Journal information: Science 

Provided by Ruhr-Universitaet-Bochum 

by Food Packaging Forum Foundation

Plastics contain a vast number of chemicals, some of which greatly impact the environment and human health. However, information on the presence of individual substances in plastic products is oftentimes not publicly available.

In a study, published on 29 October 2024, in Environmental Science and Technology Letters, a new publicly accessible database on chemicals measured in plastics is presented—LitChemPlast. The database contains over 3,500 substances measured in over 47,000 samples of plastic products across 372 studies.

The database shows that, due to inadequate control measures, mechanical recycling of plastics often leads to contamination with hazardous substances. For example, brominated flame retardants have frequently been detected in toys.

LitChemPlast is a significant step forward for better understanding of chemicals’ movement through different life stages of plastics. The database provides real-world chemical data, including on concentrations in products, that is useful for improving models estimating human and environmental exposure to plastic chemicals.

Moreover, LitChemPlast enables researchers, regulators and practitioners to identify chemicals that are of interest for regulation, to find safer materials for recycling, and to trace plastic pollution back to its source. It may also assist in identifying hazardous chemicals that are non-intentionally added to plastics (so called NIAS).

LitChemPlast also highlights research gaps, such as limited regional coverage in low- and middle-income countries, a lack of nontargeted measurements for non-food packaging categories, and a narrow focus on well-known hazardous chemicals.

Future concerted efforts in these understudied areas are essential to support the transition toward a safe and sustainable circular plastics economy, including achieving full transparency of chemicals in plastics.

The open database can serve as a starting point for guiding future research on identifying and quantifying chemicals in plastics, develop policy measures for ensuring safer material cycles, and support researchers, regulators and practitioners in better understanding the flow of chemicals throughout plastic products’ life cycles.

Finally, the authors encourage the scientific and regulatory communities to continue developing and using the database which is part of the larger PlastChem database that was published earlier in 2024.

Helene Wiesinger, Ph.D., currently scientific officer at the Food Packaging Forum and corresponding author of the study said, “Many scientific efforts focus only on whether plastics comply with current regulations, rather than whether they are actually safe. This is worrying because there are many chemicals in plastics that are not yet adequately regulated, meaning that potential risks could slip through the cracks.”

Zhanyun Wang, Ph.D., Scientist at Empa—Swiss Federal Laboratories for Materials Science and Technology and corresponding author of the study said, “Transparency of chemicals in plastics is crucial for ensuring safer material cycles, protecting human and environmental health, and fostering a sustainable circular economy.

“LitChemPlast marks a significant step in this direction, and we encourage widespread collaboration to further expand and refine this valuable resource.”

More information: LitChemPlast: An open database of chemicals measured in plastics, Environmental Science & Technology Letters (2024). DOI: 10.1021/acs.estlett.4c00355

Journal information: Environmental Science & Technology Letters 

by Pennsylvania State University

A newly discovered protein naturally houses an unusual binding site that can differentiate between rare earth elements, and researchers at Penn State have made it even better. Rare earth elements are key components used in everything from modern tech to gasoline production. The protein, called LanD, enriches neodymium and praseodymium over other similar rare earth elements (REEs) and has the potential to revolutionize industrial mining, researchers said.

Scientists at Penn State, led by professor of chemistry Joseph Cotruvo, Jr., recently published their LanD discovery in the Proceedings of the National Academy of Sciences.

“Each rare earth element has specific properties that make it useful for different applications, yet they are notoriously difficult to separate from each other,” said Cotruvo, who has filed a patent application related to the work. “Current industrial methods are inefficient and require heavy use of toxic chemicals, so a protein-based method for rare earth mining could make this process more efficient, greener, and less expensive.”

Close to 80% of the United States’ REE supply is imported, according to the United States International Trade Commission. Cotruvo explained that there is plenty of domestic raw material—including recycling old tech and industrial byproducts—to source REEs, but not all REEs are of equal value and application.

A more effective separation approach could help secure a national supply of REEs. The 17 REEs, including 15 metals called “lanthanides,” are commonly divided into “light” and “heavy” groups, with the light REEs being far more abundant. Unfortunately, however, the most common light REEs, lanthanum and cerium, have little value, whereas the other light REEs, praseodymium and (in particular) neodymium, are much more valuable.

Neodymium is a critical component of permanent magnets used in smartphones and renewable energy machinery like wind turbines, and praseodymium is often combined with neodymium for these applications.

Cotruvo’s lab previously identified another protein, LanM, that binds to all REEs with high specificity over any other metal. It does this in a fashion similar to a lock and key mechanism, with the protein being the lock and the REE a key. When the protein binds a REE, it undergoes a change in shape analogous to the key turning in the lock. The LanM proteins studied to date are very good at differentiating between heavy REEs, but they do not do well separating the light REEs, akin to a keyhole that fits a few different keys.

The newly discovered LanD protein, however, has improved separation abilities among the light REEs that are as good as, if not better than, current industry practices, Cotruvo said. With a unique, never-before-seen binding site—where the metal “key” can lock into the protein—LanD’s natural REE separation abilities can be engineered to be even more efficient, offering new hope for a greener rare earth element mining industry, he said.

“Current efforts are concentrated towards optimizing REE separation to make it less labor and material intensive,” Cotruvo said. “But this organism, Methylobacterium extorquens, a bacterium found abundantly in nature, makes proteins that seem to have already solved the problem.”

Methylobacterium extorquens is a species of bacteria known for its ability to grow on one-carbon compounds like methanol, and prefers to use specific REEs, mostly lanthanum and cerium, to support that growth.

When Cotruvo discovered LanM as the first high-affinity, high-specificity REE-binding protein six years ago, it was not clear why LanM needed to bind REEs so tightly in the cell. The discovery of LanD suggested an answer to that question: the two proteins work in tandem, with LanD binding to the lanthanides that the bacterium takes up but doesn’t need and delivering them to LanM, where they are sequestered. Those lanthanides, while not important to the bacteria, are the ones that are most important to tech production, Cotruvo said.

“The bacterium can take up a broader group of lanthanides than the small subset that it prefers to use, so it needs a way to prevent those undesirable lanthanides from interfering with the functions of the desirable lanthanides in the cell,” Cotruvo said. “LanD and LanM appear to work together to do this sorting, which explains why the previously identified LanM protein is good at lanthanide separations in general.”

He added that LanD, with its unique binding site, is much better for the light REEs specifically.

“LanD conveniently binds best to neodymium, which is by far the most valuable of the light REEs,” Cotruvo said. “While the naturally occurring LanD protein exhibits a preference for neodymium, we re-engineered it to more effectively be able to extract neodymium from a mixed solution of light REEs, disfavoring the other REEs that are of lesser value.”

The researchers found that engineering the LanD binding site allows separations yielding the desired neodymium and praseodymium to become much more effective. In future applications, the researchers said they hope to be able to whittle down the protein size and increase the preference of this binding site even more—and implement it in a larger-scale separation. The site can serve as the starting point for chemists and engineers to develop highly specific proteins to perfect sorting of other tricky-to-separate elements, Cotruvo said.

Furthermore, because LanD and LanM specialize in separation of different REEs, they could be used together in a process to separate complex REE sources like ores.

“The LanD protein is a promising way to improve REE separation practices,” he said. “And we’re working on making it even better, to pave a path toward more effective, greener rare earth mining.”

Paper co-authors include Wyatt Larrinaga and Jonathan Jung, graduate students in chemistry; Chi-Yun Lin, postdoctoral researcher in chemistry; and Amie Boal, professor of chemistry and of biochemistry and molecular biology.

More information: Wyatt B. Larrinaga et al, Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2410926121

Journal information: Proceedings of the National Academy of Sciences 

Provided by Pennsylvania State University 

by Hillary Sanctuary, Ecole Polytechnique Federale de Lausanne

Motivated to turn greenhouse gases like carbon dioxide into high value chemicals like methanol, EPFL chemical engineers have developed a new method to make catalysts. Catalysts are major tools in the chemical industry and are largely made to make petrochemicals.

In this method, they have developed a way to build—with near atomic precision—metal clusters on solid supports that have the potential to improve catalytic activity. The results are published in Nature Catalysis.

“You want to produce as much product per time per catalyst as possible, and we’ve found that when a catalyst is prepared with near atomic precision, you get a more active material,” says Jeremy Luterbacher, professor at EPFL’s Laboratory of Sustainable and Catalytic Processing. “This technique is particularly interesting for difficult reactions like that of carbon dioxide with hydrogen gas for producing renewable methanol.”

A bit about catalysts

Though they are ubiquitous in industry, we most commonly interact with solid catalysts in the tailpipe of our car. There, a catalytic converter takes the exhaust from fuel combustion and helps to reduce the amount of toxic pollutants released into the air.

The engine of a car notably produces carbon monoxide (CO), an odorless and colorless toxic gas that, in high concentrations, can cause illness and death if inhaled. Inside the chamber is a catalyst, usually made of small platinum or palladium particles on a cheaper solid. This metal binds air and pollutants like carbon monoxide, and helps them react to produce the less toxic carbon dioxide (CO₂) gas into the air.

“A reaction can happen without a catalyst at high temperature. For instance, burning carbon monoxide in a flame makes it possible for the carbon monoxide and oxygen to crash together to form carbon dioxide because they’re hot enough for the collision to be sufficiently powerful,” explains Luterbacher.

“With a catalyst, the carbon monoxide and the oxygen are bound to a metal surface and they can react despite colliding at a lower temperature. It’s like they’re ice-skating on the surface of the catalyzer and the surface helps the transformation between the pollutant and the reactant along.”

The catalysts of the future need to be able to turn carbon dioxide, a greenhouse gas that’s the largest source of renewable carbon on our planet, into high value gases like methanol. This process takes place in a chemical reaction referred to as a hydrogenation, a difficult reaction since it can produce many things other than methanol. Making a catalyst that is active enough to transform carbon dioxide fast enough to methanol without making other products is a significant challenge.

Precision layering of the catalyst

To make a solid catalyst, a metal particle is deposited on top of a material with high surface area like a porous powder, to maximize contact with the reactant.

Luterbacher and his team wondered if they could control and speed up reactions by precisely controlling the catalyst composition, notably by choosing just the right amount of material to tune how tightly reactants would bind to the catalyst.

They had discovered in previous research that they could deposit islands of metals with near atomic precision on solid supports, a method called liquid-phase atomic layer deposition (ALD), perfect for creating precise catalyst active sites for enabling a reaction.

Indeed, depositing these small islands or clusters of several metals with near atomic precision allowed the EPFL team to hydrogenate carbon dioxide at rates that were more than 10 times higher than with a catalyst of the same composition but built without this control.

They used magnesium oxide as the support, which usually binds carbon dioxide too tightly to be reactive, and they deposited small zirconia islands, which is a material that usually binds carbon dioxide too lightly. Then, they added copper to bind the hydrogen. When placed together in just the right proportions, they seemed to have the right mix to make a lot of methanol quickly and little of anything else.

“Magnesium oxide is widely recognized as a stable material for CO₂ capture, but its strong affinity for CO₂ has limited its use as a catalyst support. We turned this limitation into an opportunity by teaming it up with zirconia.

“Finding the optimal balance for CO₂ affinity by combining MgO and ZrO₂ with differing properties was only achievable through the powerful tool of liquid-phase atomic layer deposition,” says Seongmin Jin, former postdoctoral researcher at LPDC and lead author of the study.

“If we compare the amount of catalyst material to its copper content, then our catalyzer is more active than even commercial catalysts. Our activity per active site is also superior. It’s worth noting that our activity per weight of catalyst material is still inferior to commercial equivalents because we need to figure out how to make many more of these clusters on the surface.

“But we’ve shown that it’s possible to achieve very high control even at the atomic level, and this control appears to be very important. This opens the avenues to explore many combinations of metals or possibilities,” concludes Luterbacher.

More information: Seongmin Jin et al, Atom-by-atom design of Cu/ZrOx clusters on MgO for CO2 hydrogenation using liquid-phase atomic layer deposition, Nature Catalysis (2024). DOI: 10.1038/s41929-024-01236-y

Journal information: Nature Catalysis 

Provided by Ecole Polytechnique Federale de Lausanne 

by Pacific Northwest National Laboratory

A recent collaboration among researchers from HUN-REN Wigner Research Center for Physics in Hungary and the Department of Energy’s Pacific Northwest National Laboratory, along with industry collaborators SandboxAQ and NVIDIA, has achieved unprecedented speed and performance in efforts to model complex metal-containing molecules.

The collaboration resulted in 2.5 times the performance improvement over previous NVIDIA graphics processing unit (GPU) calculations and 80 times the acceleration compared to similar calculations using central processing unit (CPU) methods. The research study, recently published in the Journal of Chemical Theory and Computation, sets a new benchmark for electronic structure calculations.

Accelerating molecular modeling

The research team’s efforts have enabled unprecedented calculations for complex biochemical systems, which include transition metal metalloenzymes. Such metal-containing catalysts are crucial in numerous industrial and biological processes, playing an essential role in facilitating chemical reactions.

These powerhouses of energy conversion are vital for many industries, including medicine, energy and consumer products. They accelerate chemical reactions, lowering the energy required and making processes more efficient and sustainable. Understanding and optimizing these catalysts is essential for addressing global challenges, such as clean energy production and environmental sustainability.

“When you have one or more metals in your system, then you have a lot of electronic states that are very close in energy, but behave differently, and that’s why it’s really important to make sure that you describe them accurately,” said Sotiris Xantheas, a PNNL Lab Fellow, a co-author of the research study, and a chemical physicist who leads the Center for Scalable and Predictive methods for Excitation and Correlated phenomena (SPEC), as well as the Computational and Theoretical Chemistry Institute at PNNL.

Highly correlated quantum chemistry calculations

The recent advances have been made possible by bringing together academic and industry experts with expertise in the development of tensor network state algorithms and high performance computing, led by Örs Legeza, a co-PI of the SPEC project, and his group at the HUN-REN Wigner Research Center for Physics, in Hungary, working with SandboxAQ’s team of scientists, led by co-author Martin Ganahl, to perform quantum chemistry calculations on NVIDIA GPUs.

The diverse team contributions underscore the importance of collaboration and point to an exciting future for the field powered by GPUs. For instance, this work implemented the ab initio Density Matrix Renormalization Group method, which describes physical properties of large, complex electronic structures on all GPUs within a single node for the first time.

The goal of the research was to achieve efficient and accurate solutions to the many-body Schrödinger equation. These algorithms are crucial for understanding the electronic structures of molecules and materials and require computational power only available on a few computing systems worldwide.

The group’s collective expertise and shared resources have helped push the boundaries of quantum chemistry, allowing for rapid iteration and refinement in the study of highly correlated complex chemical systems. The project illustrates the potential of large-scale calculations to revolutionize how scientists approach challenging quantum chemistry problems.

“With advancing computational hardware and the extension to multi-GPU, multi-node architectures are expected to enable even more comprehensive calculations beyond the current capabilities,” said Legeza, who also holds an appointment as a research fellow at the Institute for Advanced Study at the Technical University of Munich.

“The ongoing collaboration aims to adopt large-scale GPU-accelerated calculations, further enhancing the efficiency and accuracy of quantum chemistry computations, utilizing even more recent hardware developments.”

As noted in the published study, chemists today largely rely on their intuition because rapid, highly accurate calculations are often unattainable. The ability to quickly iterate on different choices of large active spaces enables a more systematic search. Today’s GPU computing frameworks, combined with AI-guided physics and new methods for generating training data for large quantitative machine learning models, are expected to contribute to applications in energy, sustainability and health.

“The combination of NVIDIA’s state-of-the-art hardware with cutting-edge simulation techniques like tensor network algorithms for quantum chemistry has the potential to unlock an entirely new field of discovery,” said Ganahl.

More information: Andor Menczer et al, Parallel Implementation of the Density Matrix Renormalization Group Method Achieving a Quarter petaFLOPS Performance on a Single DGX-H100 GPU Node, Journal of Chemical Theory and Computation (2024). DOI: 10.1021/acs.jctc.4c00903

Provided by Pacific Northwest National Laboratory 

by Chiba University

There have been many attempts to create monochromatic metallic materials, but few materials change luster color in response to external stimuli. In a recent breakthrough, researchers from Chiba University have prepared a diacetylene derivative-based metallic luster material that changes from silver to gold under UV irradiation.

These findings are expected to find applications in decorative items, printing inks, photomask patterning, UV laser lithography, and cosmetics.

Societies of the past and present have given high regard to precious metals like gold and silver. Both metals remind us of nobility and luxury. However, they are quite expensive, which restricts their applications. Therefore, materials with attractive but artificial gold- and silver-like metallic lusters are popular, finding use in jewelry, reflective materials, inks, and cosmetics.

Unfortunately, typical metallic luster materials cause environmental harm, rendering them unsustainable. Thus, scientists are actively searching for metal-free alternatives, examining organics such as thiophene, pyrrole, porphyrin, azobenzene, and stilbene derivatives. They have found some success in creating materials whose colors can be tuned by external stimuli while maintaining the metallic luster. However, the task still remains challenging.

Recently, a group of researchers from Chiba University, led by Professor Michinari Kohri and Kyoka Tachibana from the Graduate School of Engineering, in collaboration with scientists from Mitsubishi Pencil Co., Ltd., Tokyo University of Science, Keio University, and Yamagata University, has demonstrated the preparation of a metallic luster material that changes color from silver to gold under UV irradiation.

Their findings were published in ACS Applied Materials & Interfaces on September 14, 2024.

Highlighting the motivation behind this study, Prof. Kohri says, “Expanding on our earlier findings on biomimetic metallic luster materials, we conducted a targeted search for molecular structures capable of transitioning between silver and gold. This effort resulted in the identification of a novel material with desirable properties.”

In this study, researchers developed diacetylene (DA) derivative-based luster materials incorporating stilbenes via linkers at both ends, denoted as DS-DAn (where n represents the linker carbon number, ranging from 1 to 6). Varying n yielded diverse metallic luster and color change behaviors.

After several innovative experimental trials, the researchers observed that the stacked structure of platelet crystals comprising DS-DA1, the derivative with the shortest linker carbon chain, had a silver look. Its luster notably turned to gold upon UV irradiation, a remarkable external stimulus-based behavior.

The team attributed this to the unique crystal structure of DS-DA1 with two coexisting assembled states, revealing that partial topochemical polymerization (a polymerization method performed by monomers that are aligned in the crystal state) of DA within the structure modified its color tone from silver to gold.

The silver luster material developed in this study can express a golden luster selectively in specific areas using only light irradiation. It is also possible to add gradation colors of gold and silver. Thus, it has the potential to be useful in a variety of applications, such as decorative items, printing inks, and cosmetics.

“By eliminating metal components, our innovative material minimizes environmental footprint and weight. Moreover, its suitability for UV laser-based drawing techniques opens up new possibilities for high-end decorative printing. Further exploration of molecular structures may make it possible to express a wider variety of glossy colors,” concludes Prof. Kohri.

This work advances the fundamental science of DA polymerization and unlocks new opportunities for metallic luster materials with desirable properties in photomask patterning and UV laser lithography.

More information: Kyoka Tachibana et al, Silver to Gold Metallic Luster Changes in Stimuli-Responsive Diacetylene Derivatives Uniquely Arranged within Crystals, ACS Applied Materials & Interfaces (2024). DOI: 10.1021/acsami.4c14218

Journal information: ACS Applied Materials and Interfaces 

by Public Library of Science

A new study of human skeletal remains from the wreck of the 16th century English warship “Mary Rose” suggests that whether a person is right- versus left-handed may influence how their clavicle bone chemistry changes as they age. Dr. Sheona Shankland of Lancaster University, U.K., and colleagues present these findings in the open-access journal PLOS ONE on October 30, 2024.

The Mary Rose was part of the Tudor navy during Henry VIII’s reign. On July 19, 1545, it sank while engaging French ships in the Battle of the Solent. Excavated in the late 20th century, the ship’s artifacts and the crew’s skeletal remains were notably well preserved, allowing for extensive research into the belongings, appearance, and health of the crew members.

Now, Dr. Shankland and colleagues contribute new insights into the biology of 12 men aged 13 to 40 who sank with the ship. This work explored how the chemistry of bone might adjust in response to physical activity and aging, so a person’s bone chemistry may hold clues about their lifestyle.

In this case, the researchers analyzed human clavicles (collarbones) from the wreck using a non-destructive laser technique called Raman spectroscopy to reveal bone chemistry.

The analysis focused on organic proteins and inorganic minerals, as they are the two main components of bone. It revealed that, among the 12 men, mineral content increased with age, while protein content decreased, albeit to a lesser degree.

These age-related changes were more pronounced in right clavicles than in left clavicles. A higher proportion of people are naturally right- than left-handed, and at the time when the Mary Rose sank, left-handedness was associated with witchcraft and therefore strongly discouraged.

So, assuming right-handed preference among the crew, this finding suggests that handedness may have affected their clavicle chemistry, perhaps through putting more stress on their right side during repeated ship-related activities.

The authors note that more research on the Mary Rose clavicles will be needed to better understand these findings. Nonetheless, this study could contribute to ongoing understanding of handedness and age-related changes in bone chemistry, with potential implications for risk of fracture, osteoarthritis, and other bone conditions.

Dr. Sheona Shankland adds, “Having grown up fascinated by the Mary Rose, it has been amazing to have the opportunity to work with these remains. The preservation of the bones and the non-destructive nature of the technique allows us to learn more about the lives of these sailors, but also furthers our understanding of the human skeleton, relevant to the modern world.”

Dr. Jemma Kerns adds, “It has been a privilege to work with these unique and precious human remains to learn more about life for sailors in the 16th century while finding out more about changes to bone composition as we age, which is relevant to today’s health, has been fascinating.”

Prof. Adam Taylor adds, “This study sheds new light on what we know about the clavicle and its mineralization. The bone plays a critical role in attaching your upper limb to the body and is one of the most commonly fractured bones.”

Dr. Alex Hildred adds, “Our museum is dedicated to the men who lost their lives defending their country. The hull is surrounded on three sides by galleries containing their possessions, and we continue to explore their lives through active research. The non-destructive nature of Raman spectroscopy makes it an ideal research tool for investigating human remains.

“We are delighted that the current research undertaken by Lancaster Medical School not only provides us with more information about the lives of our crew, but also demonstrates the versatility of Raman. The fact that this research has tangible benefits today, nearly 500 years after the ship sank, is both remarkable and humbling.”

More information: Shining light on the Mary Rose: Identifying chemical differences in human aging and handedness in the clavicles of sailors using Raman spectroscopy, PLOS ONE (2024). DOI: 10.1371/journal.pone.0311717

Journal information: PLoS ONE 

Provided by Public Library of Science