Tag: Tokyo University of Science

Dendritic structures that emerge during the growth of thin films are a major obstacle in large-area fabrication, a key step towards commercialization. However, current methods of studying dendrites involve crude visual inspection and subjective analysis. Moreover, growth optimization methods for controlling dendrite formation require extensive trial and error. Now, researchers have developed a new AI model that incorporates topology analysis and free energy to reveal the specific conditions and mechanisms that drive dendrite branching.

Thin film devices, composed of layers of materials a few nanometers thick, play an important role in various technologies, from semiconductors to communication technologies. For instance, graphene and hexagonal-boron nitride (h-BN) multilayer thin films, deposited on copper substrates, are promising materials for next-generation high-speed communications systems. Thin films are grown by depositing tiny layers of materials onto a substrate. The growth process conditions significantly influence the microstructure of these films, which in turn influences their function and performance.

Dendritic structures, or tree-like branching patterns that emerge during growth, pose a major challenge to large-area fabrication of thin-film devices, a key step toward commercial application. They are commonly observed in materials like copper, graphene, and borophene, particularly in the early growth stage and multilayer films. Since the microstructure directly impacts device performance, reducing dendritic formation is, therefore, critical. However, methods for studying dendrites have largely relied on crude visual analysis and subjective interpretation. Understanding the conditions that drive dendritic branching is essential for optimizing the thin-film growth process, but existing approaches often require considerable trial and error.

To address these challenges, a research team, led by Professor Masato Kotsugi from the Department of Material Science and Technology at Tokyo University of Science (TUS), Japan, developed an innovative explainable artificial intelligence (AI) model for analyzing dendritic structures. The team included Misato Tone, also from TUS, and Ippei Obayashi from Okayama University. The team developed a novel method that bridges structure and process in dendritic growth by integrating persistent homology and machine learning with energy analysis. “Our approach provides new insights into growth mechanisms and offers a powerful, data-driven pathway for optimizing thin-film fabrication,” explains Prof. Kotsugi. Their study was published online in Science and Technology of Advanced Materials: Methods on March 7, 2025.

To analyze the morphology of dendrite structures, the team used a cutting-edge topology method called persistent homology (PH). PH enables multiscale analysis of holes and connections within geometric structures, capturing the complex topological features of the tree-like dendrite microstructures that conventional image processing techniques often overlook.

The researchers combined PH with principal component analysis (PCA), a machine learning technique. Through PCA, the essential features of the dendrite morphology extracted via PH were reduced to a two-dimensional space. This enabled the team to quantify structural changes in dendrites and establish a relationship between these changes and Gibbs free energy, or the energy available in a material that influences how dendrites form during crystal growth. By analyzing this relationship, they uncovered the specific conditions and hidden growth mechanisms that influence dendritic branching. Prof. Kotsugi explains, “Our framework quantitatively maps dendritic morphology to Gibbs free energy variations, revealing energy gradients that drive branching behavior.”

To validate their approach, the researchers studied dendrite growth in a hexagonal copper substrate and compared their results with data from phase-field simulations.

“By integrating topology and free energy, our method offers a versatile approach to material analysis. Through this integration, we can establish a hierarchical connection between atomic-scale microstructures and macroscopic functionalities across a wide range of materials, paving the way for future advancements in material science,” remarks Prof. Kotsugi. “Importantly, our method could lead to the development of high-quality thin-film devices leading to high-speed communication beyond 5G.”

This study’s framework could pave the way for breakthroughs in sensor technology, nonequilibrium physics, and high-performance materials by uncovering hidden structure-function relationships and advancing complex system analysis.

Overuse of chemical pesticides has driven resistance in agricultural pests, including the adaptable two-spotted spider mite. Researchers from Japan have discovered novel elicitor proteins, Tet3 and Tet4, in mite saliva that could enhance sustainable pest control. They found that these proteins play a crucial role in modulating plant defense responses by acting as key players in the complex interactions between parasite and host, paving the way for new mite countermeasures.

As global food demand continues to increase, effective pest control remains one of agriculture’s most pressing challenges. Worldwide, farmers apply nearly 4 million tons of chemical pesticides annually to protect their crops, representing a $60 billion industry. While these compounds have significantly boosted agricultural productivity, their widespread use has raised concerns regarding environmental impact, health risks, and the long-term sustainability of modern farming.

The two-spotted spider mite, Tetranychus urticae, exemplifies the limitations of conventional pesticide-based pest management in agriculture and horticulture. These microscopic arachnids infest a wide range of crops and fruit trees and can reproduce extremely quickly. More importantly, unlike many other pests, they rapidly develop resistance to chemical pesticides, making control efforts increasingly challenging. With pesticide resistance on the rise, farmers worldwide are urgently seeking alternative, sustainable pest control strategies.

A research team led by Professor Gen-ichiro Arimura from the Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Japan, closely examined the fine molecular interplay that occurs between T. urticae mites and their host plants. Their study was published online in The Plant Journal on March 4, 2025. The team focused on specific substances called elicitors, secreted by T. urticae, and examined their biological effects on various crops.

“An elicitor is a molecule that plants or pests possess that can enhance the defense response of plants,” explains Prof. Arimura. “In our previous research, we identified two tetranins, labeled Tet1 and Tet2, as elicitors in the salivary glands of two-spotted spider mites; these substances induce defense responses in the common bean and other commercially important crops.”

The research team investigated the effects of an additional 18 salivary gland proteins on the resistance of common bean leaves to T. urticae. According to this initial screening, they identified two new tetranins—Tet3 and Tet4—that appear to reduce the reproduction of spider mites on the plants.

After a series of experiments involving genetic engineering and advanced molecular and biochemical methods, the team uncovered the roles of Tet3 and Tet4 in the complex interactions between T. urticae and its host plants. Interestingly, they found that the expression of Tet3 and Tet4 varies greatly depending on which plant the mites fed on. Mites feeding on common beans, their preferred host, had significantly higher levels of Tet3 and Tet4 expression than those on cucumbers, a less preferred option.

Notably, plants exposed to mites with higher expression of Tet3 and Tet4 exhibited stronger defense responses, including increased calcium-ion influx, higher generation of reactive oxygen species, and elevated expression of a defensive gene named PR1. The individual application of Tet3 and Tet4 to plants had different effects on plant defense responses, highlighting the specificity of each elicitor’s role. “Taken together, our findings show that these tetranins respond to variable host cues that may optimize herbivore fitness by altering the anti-mite response of the host plant,” remarks Prof. Arimura.

The implications of these findings are twofold. First, understanding the molecular mechanisms that underlie interactions between organisms leads to a better understanding of evolution, ecosystems, and biodiversity. Elicitors such as tetranins act as crucial links in these complex systems, making their detailed study essential for uncovering broader biological insights. From an agricultural perspective, tetranins and similar elicitors offer potential for crop improvement, as insights into the elicitor-sensing system can aid in breeding more sensitive and resilient crops. “Elicitors may be useful as biostimulants that can increase the potential pest resistance of plants,” highlights Prof. Arimura. “The development of such organic farming techniques is extremely meaningful in today’s world, as the environmental and ecological impact of heavy pesticide use grows more severe. Hopefully, identifying elicitors secreted by pests and elucidating their functions will lead to unprecedented spider mite countermeasures.”

With continued research, this fascinating topic could contribute to more sustainable agriculture and enhanced food safety.

Irritable bowel syndrome (IBS) is a common digestive disorder with unclear causes, affecting about 10% of the global population. Researchers from Japan have now discovered that opioid delta-receptor agonists may alleviate IBS symptoms by acting directly on the central nervous system. Using a novel stress-induced mouse model, they found these drugs reduce abdominal pain and regulate bowel movements. This research suggests a promising approach to treating IBS by targeting stress as a contributing factor.

Irritable bowel syndrome (IBS) is a common digestive disorder that affects the intestine, causing symptoms such as abdominal pain, bloating, gas, and changes in bowel habits, including diarrhea, constipation, or both. Although this condition affects about a tenth of the global population, the underlying causes and mechanisms of IBS remain unclear. Consequently, treatments for IBS primarily focus on managing symptoms rather than addressing the root cause of the disorder.

At Tokyo University of Science (TUS), Japan, Professor Akiyoshi Saitoh and his research group have spent the past decade exploring this topic. This study published online in the British Journal of Pharmacology on December 25, 2024, discovered that a class of drugs called opioid delta-receptor (DOP) agonists may help alleviate IBS symptoms by targeting the central nervous system rather than acting directly on the intestine. This study was co-authored by Toshinori Yoshioka, a third-year PhD student at TUS.

One of the main motivations for this study was the growing evidence linking IBS closely to psychological stress. Saitoh’s group aimed to address this potential root cause by focusing on finding a novel animal model for this condition. In a study published in 2022, they developed a mice model repeatedly exposed to psychological stress—using a method called chronic vicarious social defeat stress (cVSDS)—which developed symptoms similar to a type of IBS called IBS-D. These symptoms included overly active intestines and heightened sensitivity to abdominal pain, even though their organs showed no physical damage. The cVSDS animal model involved having the subject mouse repeatedly witness a territorial, aggressive mouse defeating a cage mate, inducing indirect chronic stress.

Using the cVSDS model, the researchers sought to determine whether DOP in the brain, which is closely linked to pain and mood regulation, could serve as promising drug targets for treating stress-induced IBS. To achieve this, they performed a series of detailed experiments to observe the effects of DOP agonists on IBS symptoms and chemical signaling in the brain. Some experiments involved measuring the speed of a charcoal meal through the intestine to assess gastrointestinal motility and evaluate the impact of stress or treatments on bowel movement speed, along with directly measuring neurotransmitter concentrations using in vivo brain microdialysis. This revealed that re-exposure to VSDS increased glutamate levels in the insular cortex, but these elevated levels were normalized with DOP agonists.

According to the results, the administration of DOP agonists helped relieve abdominal pain and regulated bowel movements in cVSDS mice. Interestingly, applying the DOP agonists directly to a specific brain region called the insular cortex had similar effects on IBS symptoms as systemic treatment. “Our findings demonstrated that DOP agonists acted directly on the central nervous system to improve diarrhea-predominant IBS symptoms in mice, and suggest that the mechanism of action involves the regulation of glutamate neurotransmission in the insular cortex,” highlights Saitoh.

Taken together, the continued research by Saitoh’s group on this topic could pave the way for effective treatments for IBS. “DOP agonists could represent a groundbreaking new IBS treatment that not only improves IBS-like symptoms but also provides anti-stress and emotional regulation effects. In the future, we would like to conduct clinical developments with the goal of expanding the indication of DOP agonists for IBS, in addition to depression,” remarks Saitoh.

Compared to currently available IBS treatments, such as laxatives, antidiarrheals, analgesics, and antispasmodics, targeting the underlying stress with DOP agonists may offer a more definitive solution with minimal adverse effects. Further clarification of the roles of stress and brain chemistry in the development of IBS will be essential in achieving this much-needed medical breakthrough. With promising prospects, future studies will translate Saitoh’s group’s findings to humans, bringing great relief to those affected by IBS.

Ising machines are specialized computing systems designed to solve complex optimization problems by arranging “spins” to minimize system energy. However, their fully connected architecture leads to a large circuit footprint, limiting scalability. In a recent study, researchers from Japan developed a method to halve the required spin–spin interactions using a novel matrix-folding technique. Their findings will pave the way for highly scalable Ising machines, making them more practical for real-world applications.

Computers are essential for solving complex problems in fields, like scheduling, logistics,
and route planning, but traditional computers struggle with large-scale combinatorial optimization, as they can’t efficiently process vast numbers of possibilities. To address this, researchers have explored specialized systems.

One such system is the Hopfield network, a significant artificial intelligence breakthrough from 1982, proven in 1985 to solve combinatorial optimization by representing solutions as energy levels and naturally finding the lowest energy, or optimal, solution. Building on similar ideas, Ising machines use the principles of magnetic spin to find efficient solutions by minimizing system energy through a process akin to annealing. However, a major challenge with Ising machines is their large circuit footprint, especially in fully connected
systems where every spin interacts with others, complicating their scalability.

Fortunately, a research team from the Tokyo University of Science, Japan, has been working towards finding solutions to this problem related to Ising machines. In a recent study led by Professor Takayuki Kawahara, they reported an innovative method that can halve the number of interactions that need to be physically implemented. Their findings were published in the journal IEEE Access on October 01, 2024.

The proposed method focuses on visualizing the interactions between spins as a two-dimensional matrix, where each element represents the interaction between two specific spins. Since these interactions are ‘symmetric’ (i.e., the interaction between Spin 1 and Spin 2 is the same as that between Spin 2 and Spin 1), half of the interaction matrix is redundant and can be omitted—this concept has been around for several years. In 2020, Prof. Kawahara and colleagues presented a method to fold and rearrange the remaining half of the interaction matrix into a rectangle shape to minimize the circuit footprint.
While this led to efficient parallel computations, the wiring required to read the interactions and update the spin values became more complex and harder to scale up.

In this study, the researchers proposed a different way of halving the interaction matrix that leads to better scalability in circuitry. They divided the matrix into four sections and halved each of these sections individually, alternatively preserving either the ‘top’ or ‘bottom’ halves of each submatrix. Then, they folded and rearranged the remaining elements into a rectangular shape, unlike the previous approach, which retained the regularity of its arrangement.

Leveraging this crucial detail, the researchers implemented a fully coupled Ising machine based on this technique on their previously developed custom circuit containing 16 field-programmable gate arrays (FPGAs). “Using the proposed approach, we were able to implement 384 spins on only eight FPGA chips. In other words, two independent and fully connected Ising machines could be implemented on the same board,” remarks Prof. Kawahara, “Using these machines, two classic combinatorial optimization problems were solved simultaneously—namely, the max-cut problem and four-color problem.” 

The performance of the circuit developed for this demo was astounding, especially when compared to how slow a conventional computer would be in the same situation. “We found that the performance ratio of two independent 384-spin fully coupled Ising machines was about 400 times better than simulating one Ising machine on a regular Core i7-4790 CPU to solve the two problems sequentially,” reports Kawahara, excited about the results.

In the future, these cutting-edge developments will pave the way to scalable Ising machines suitable for real-world applications such as faster molecular simulations to accelerate drug and materials discovery. Moreover, improving the efficiency of data centers and the electrical power grid is also feasible to use cases, which align well with global sustainability goals of reducing the carbon footprint of emerging technologies like electric vehicles and 5G/6G telecommunications. As innovations continue to unfold, scalable Ising
machines may soon become invaluable tools across industries, transforming how we tackle some of the world’s most complex optimization challenges.

Scientists from Tokyo University of Science uncover a pivotal enzyme, XccOpgD, and its critical role in synthesizing CβG16α, a key compound used by Xanthomonas pathogens to enhance their virulence against plants. This breakthrough opens new avenues for developing targeted pesticides that combat plant diseases without harming beneficial organisms. Insights into XccOpgD’s enzymatic mechanism and optimal conditions offer promising prospects for sustainable agriculture, bolstering crop resilience and global food security while minimizing environmental impact.

Plant diseases pose significant challenges to agricultural productivity, presenting formidable hurdles that require urgent attention. Left unchecked, these diseases can spread rapidly, inflicting widespread damage on crops and leading to reduced yields and substantial economic losses. Therefore, accurately identifying the pathogens responsible for these diseases is crucial. This identification allows for targeted interventions that minimize risks and effectively mitigate the agricultural impacts.

Xanthomonas species are notorious plant pathogens that affect a broad spectrum of hosts, including key crops like rice, wheat, and tomatoes. These pathogens augment their pathogenicity by utilizing α-1,6-cyclized β-1,2-glucohexadecaose (CβG16α) to suppress essential plant defense mechanisms, such as the expression of pathogenesis-related proteins and the accumulation of callose.

In a recent breakthrough published on June 19, 2024, in the Journal of the American Chemical Society, a team of researchers led by Associate Professor Masahiro Nakajima from Tokyo University of Science unveiled a significant discovery. They identified XccOpgD, a glycoside hydrolase (GH186) found in X. campestris pv campestris which plays a pivotal role in the biosynthesis of CβG16α. The research team also included Mr. Sei Motouchi from Tokyo University of Science, Principal Scientist Shiro Komba from the Institute of Food Research, NARO, and Hiroyuki Nakai from Niigata University.

“Glycan structures are intricate and multifaceted and fulfill diverse crucial roles in nature and organisms. Enzymes synthesize and degrade glycans, exhibiting diverse structures and functions that correspond to the glycan diversity. However, our understanding of these enzymes is still limited, which drives the search for new enzymes with varied new potentials,” explains Prof. Nakajima, elaborating on the study’s rationale.

The team conducted biochemical analysis to elucidate the role of XccOpgD in CβG16α biosynthesis. Advanced techniques such as X-ray crystallography were employed as structural analysis to unravel the enzyme’s catalytic mechanism and substrate specificity.

These efforts have yielded profound insights. XccOpgD belongs to the GH186 family, essential for regulating bacterial cell wall components. Unlike the first identified GH186 enzymes, XccOpgD exhibits an unprecedented enzymatic mechanism known as anomer-inverting transglycosylation.

“Reactions of typical GH enzymes are classified into four types by combination of retaining or inverting, and reaction with water (hydrolysis) or sugar (transglycosylation) theoretically. However, one classification is missing somehow in a long history of researches on carbohydrate associated enzymes and we discovered the missing classification. This breakthrough was made possible by unique structural environment, opening new possibilities for enzyme-based glycosylation,” explains Prof. Nakajima. Moreover, the sugar chains synthesized through this mechanism are not merely minor components but rather essential structures utilized by various Gram-negative bacteria in nature for pathogenic purposes.

Detailed studies revealed that linear β-1,2-glucan was converted to cyclic compound and the compound was identified as CβG16α using nuclear magnetic resonance. Structural analysis of the Michaelis complex identified crucial substrate binding residues, further elucidating specific interactions along the glucan chain. Notably, XccOpgD utilizes an anomer-inverting transglycosylation mechanism, with D379 and D291 playing pivotal roles as catalysts.

These findings deepen our understanding and open avenues for developing targeted strategies against Xanthomonas-induced plant diseases. “We are expecting a pesticide concept targeting this enzyme homolog in the future. Unlike fungicides that promote the emergence of drug-resistant bacteria in soil, targeting this enzyme could potentially inhibit pathogenicity without causing sterilization. Enzyme homologs identified in this study may serve as promising structure-based drug targets, offering a potential solution to the issue of drug-resistant bacteria,” says a hopeful Prof. Nakajima.

The discovery of XccOpgD and its role in CβG16α biosynthesis marks a major breakthrough in agriculture. It promises enhanced resilience and food security while mitigating environmental impacts linked to conventional pesticides. Overall, this advancement offers sustainable solutions to global agricultural challenges, promoting environmental stewardship and economic viability for farmers worldwide.

In a recent breakthrough, researchers at Tokyo University of Science have successfully developed an efficient method to synthesize eutyscoparol A and violaceoid C, two naturally occurring compounds with promising antimalarial and antibacterial properties. The new approach involves the synthesis of these compounds using readily available dinitriles. This method requires fewer steps and produces the bioactive compounds in higher yields compared to previous approaches, opening up new avenues for drug development.

The natural world is rich in chemical compounds with remarkable medicinal properties. A notable example is penicillin, discovered by chance from the Penicillium mold. This discovery revolutionized the treatment of bacterial infections and highlighted the potential of natural compounds in medicine. Since then, the identification, isolation, and synthesis of novel bioactive compounds from plants, fungi, and bacteria have become fundamental to drug development.

Recently, two groups of naturally occurring bioactive compounds have garnered significant attention: violaceoids A–F from the fungus Aspergillus violaceofuscus and eutyscoparols A-G from the fungus Eutypella scoparia. These compounds share similar structures, featuring a 2,3-alkylated quinol moiety and a hydroxymethyl group, and are believed to possess antimalarial and antibacterial properties. Following their initial discovery in 2014 and 2020, scientists have been working to produce these compounds in larger quantities for further study.

In a recent study, researchers from Tokyo University of Science (TUS), led by Associate Professor Takatsugu Murata and Professor Isamu Shiina from the Department of Applied Chemistry, Faculty of Science, have made significant progress by developing an efficient method to synthesize eutyscoparol A and violaceoid C. Their work, featured on the cover of Volume 13, Issue 7 of the Asian Journal of Organic Chemistry, and published on 25 April 2024, could lead to new treatments or drugs.

“Eutyscoparol is a group of compounds whose pharmacological activity had not been thoroughly explored. Our goal was to make this possible through artificial synthesis and support the development of new drugs,” says Dr. Murata.

The researchers used a retrosynthetic analysis to simplify the production process. This approach breaks down complex molecules into simpler, more accessible materials. They used this method to synthesize eutyscoparol A (4) and violaceoid C (3) starting from commercially available dinitriles (6) through violaceoid A (1) intermediates. Dinitriles were chosen because they are easy to obtain and can be converted into aldehydes (5), which are precursors to violaceoid A intermediates. To make the aldehyde (5), dinitrile (6) was first converted into diester. Then, the hydroxy groups in diester were protected with a tert-butyldiphenylsilyl (TBDPS) group to form protected ether. This ether was reduced to form a symmetric diol. One hydroxy group in diol was then selectively protected to create desymmetrized tetrahydropyranyl (THP)-ether, which was oxidized to produce the aldehyde.

With the aldehyde prepared, the researchers proceeded to synthesize violaceoid A (1) and rac-violaceoid B (2) intermediates through a series of reactions. To prepare violaceoid A (1), the aldehyde was first alkylated to form an intermediate, which was then converted to olefin using mesylation or the Julia–Kocienski reagent. The THP-protecting group in olefin was removed with isopropyl alcohol to produce alcohol. Finally, two TBDPS groups were removed from the alcohol to get violaceoid A (1). Rac-violaceoid B (2) was synthesized using similar methods.

These improvements made the process much more efficient. The researchers synthesized violaceoid A (1) in 8 steps with a 33% yield, compared to the previous 10-step process that had only an 11% yield. Similarly, they prepared rac-violaceoid B (rac-2) in 8 steps with a 35% yield, improving on the earlier 9-step process with a 15% yield.

After successfully synthesizing the intermediates, the researchers moved on to produce violaceoid C (3) and eutyscoparol A (4). The synthesis of violaceoid C (3) was relatively straightforward, involving the hydrogenation of the double bond in violaceoid A (1) to yield violaceoid C (3) with high efficiency. For eutyscoparol A (4), the researchers selectively methylated two of the three hydroxy groups in violaceoid A (1) by refluxing the reaction mixture with potassium carbonate and iodomethane. Overall, violaceoid C (3) was synthesized in nine steps with a 30% yield, and eutyscoparol A (4) in nine steps with a 28% yield.

With improved yields and simpler synthesis steps, the proposed approach makes it easier to produce these compounds on a larger scale and could lead to further research into their potential therapeutic properties. “The synthesis of violaceoid A and eutyscoparol C on a subgram scale will help us study their pharmacological effects, which we expect to include cytotoxic, antibacterial, and antimalarial activities,” concludes Prof. Shiina.

The photoisomerization of E-to-Z alkenes has many applications in diverse fields, including organic chemistry, polymer chemistry, and medicinal chemistry. In a new study, researchers from Japan developed a new closed-loop method for photoisomerization of E-to-Z alkenes using a recycling photoreactor. This innovative method utilizes the high-performance liquid chromatography method to recycle the samples, thereby improving efficiency. This eco-friendly method can lead to the sustainable development of various chemicals, including pharmaceuticals.

Z-alkenes are organic compounds with a double bond between two carbon atoms and two substituents attached to the carbon atoms on the same side of the double bond. They are ubiquitous structural components of organic compounds in chemistry and biology. It is well known that many of the Z-alkenes cannot be prepared through conventional methods involving thermodynamic methods while photoisomerization can offer good yields. Photoisomerization is a process in which the structural arrangement of an isomer of a molecule is changed to another isomer by absorption of light. The photoisomerization of E-alkenes to produce Z-alkenes has many applications in the fields of organic chemistry, polymer chemistry, and medicinal chemistry.

Many studies have explored different methods for photoisomerization of E-to-Z alkenes. A notable approach involved a continuous-flow system, in which the photosensitizer was immobilized in an ionic liquid and continuously recycled via a simple phase separation process. Photosensitizers are materials that enhance the rate of photoisomerization reactions by absorbing light energy and transferring it to the reactant molecule. However, current methods based on the use of ionic liquids are time-consuming and difficult to apply to recycling high-performance liquid chromatography (HPLC) technology, which enables the recycling of samples and therefore can enhance the efficiency of photoisomerization.

Inspired by these findings, in a new study, a team of researchers from Japan, led by Professor Hideyo Takahashi from the Faculty of Pharmaceutical Sciences at Tokyo University of Science, explored the photoisomerization of E-cinnamamides to Z-cinnamamides using a recycling photoreactor coupled with an HPLC system. The study, published online in The Journal of Organic Chemistry on June 05, 2024, included contributions from Ms. Mayuko Suga, Ms. Saki Fukushima, and Assistant Professor Dr. Kayo Nakamura, also from Tokyo University of Science.

The team had previously developed a recycling photoreactor based on the deracemization concept. Prof. Takahashi explains, “Our closed-loop recycling photoreactor was initially used to convert a racemate, a mixture of left and right-handed enantiomers of a chiral molecule, into the pure desired enantiomer. It consists of a photocatalyst immobilized on a resin, which converts an undesired enantiomer into a racemate, and an HPLC column which separates the desired enantiomer. In this study, we adapted this method to convert E-cinnamamides to their Z-isomers.”
To employ this method for E-to-Z photoisomerization of alkenes, a photosensitizer that promotes rapid photoisomerization is required. To this end, the researchers screened several commercially available photosensitizers and identified thioxanthone as the best candidate. Next, they investigated its immobilization. Thioxanthone, with functional amide groups as linkages, was immobilized on a modified silica gel. This immobilization not only prevented the leakage of photosensitizer in the solid phase but also enhanced the catalytic activity compared to the parent soluble thioxanthone. This enhancement was particularly interesting, as solid-phase reactions are typically slower than liquid-phase reactions.

This superior catalytic activity was attributed to the introduction of suitable functional groups. The researchers, therefore, evaluated the catalytic activity of various photosensitizers with different functional groups by comparing the total amount of light required for promoting photoisomerization. With the optimal photosensitizer identified, they conducted the photoisomerization reactions in the recycling photoreactor, yielding the desired Z-alkenes in good yields after 4–10 cycles.

“This recycling photoreactor shows promise as an efficient alternative system to produce Z-alkenes,” remarks Prof. Takahashi. “Due to the continuous closed-loop recycling of the samples, it represents an environmentally friendly and sustainable method.”

This innovative method can lead to more eco-friendly development of Z-alkenes, and therefore pharmaceuticals, paving the way towards a sustainable future.

The anti-Michael addition reaction, which involves nucleophilic addition reactions to the α-position of α,β-unsaturated carbonyl compounds, has been difficult to achieve so far. In a new study, researchers from Japan have developed a new method for successful anti-Michael addition reaction of α-unsaturated carbonyl compounds, which are commonly used in pharmaceuticals. This reaction is expected to be used as a one-step synthesis method with 100% atomic efficiency for α-unsaturated carbonyl compounds.

In 1887, chemist Sir Arthur Michael reported a nucleophilic addition reaction to the β-position of α,β- unsaturated carbonyl compounds. These reactions, named Michael addition reactions, have been extensively studied to date. In contrast, the anti-Michael addition reaction, referring to the nucleophilic addition reaction to the α-position, has been difficult to achieve. This is due to the higher electrophilicity of the β-position compared to the α-position. Previous attempts to overcome these difficulties have involved two main methods. The first is restricting the addition position via intramolecular reactions, while the second method involves introducing a strong-electron withdrawing group at the β-position. However, these methods are not ideal for synthesizing complex molecules via the anti-Michael reaction.

In a new study, a global team of researchers, led by Professor Takanori Matsuda and including Mr. Ryota Moro, both from the Department of Applied Chemistry at Tokyo University of Science, Japan, as well as including Assistant Professor Hirotsugu Suzuki from the Tenure-Track Program for Innovative Research at the University of Fukui, Japan, successfully achieved palladium-catalyzed anti-Michael addition reaction of acrylamides. This represents the first example of an anti-Michael-type addition reaction. “We found that the presence of a catalytic amount of palladium(II) trifluoroacetate Pd(TFA)2 is capable of facilitating the anti-Michael addition of indole to acrylamide with an aminoquinoline group as a directing group, producing the addition product in high-yield,” explains Prof. Matsuda.

Their study was made available online on May 14, 2024, and published in Volume 146, Issue 20 of the Journal of the American Chemical Society on May 22, 2024.

The team reasoned introducing a directing group into an α,β-unsaturated carbonyl compound could facilitate an anti-Michael type addition reaction by stabilizing the reaction intermediate. To test this, the researchers first used an acrylamide having an aminoquinoline-directing group, and a nucleophile, 1-methylindole, as model substrates to investigate the anti-Michael type addition reaction in the presence of the palladium catalyst. This reaction produced the desired product with a 90% yield. At a reaction scale of two millimoles, there was no yield loss, signifying the practicality of the reaction.

This reaction was also carried out with β-substituted cinnamamide derivatives and crotonamide derivatives with an alkyl group. Moreover, the reaction proceeded smoothly with a wide range of nucleophiles, including many indoles, heterocyclic compounds such as pyrroles and thiophenes, and electron-rich aromatic compounds. Additionally, the aminoquinoline-directing group used in this reaction can be converted to carboxylic acids and other amides, signifying the usefulness of the reaction.

The researchers also investigated the mechanism for this reaction through labeling experiments. They found that initially, the acrylamide coordinates to Pd(TFA)2 to form a five-membered ring palladacyle intermediate. The reaction then proceeds with the nucleophilic attack by indole on the intermediate, producing alkylpalladium species. Finally, an acid removes palladium and regenerates Pd(TFA)2, producing the desired α-substituted carbonyl compound.

Highlighting the potential applications of this study, Dr. Suzuki says, “The anti-Michael type addition is expected to become an ideal one-step reaction with 100% atomic efficiency for the synthesis of α-substituted carbonyl compounds, which are often used in pharmaceuticals. Our method will enable the widespread application of this reaction.”

Overall, this novel method can lead to efficient and sustainable synthesis of α-substituted carbonyl compounds and consequently pharmaceuticals, among other organic compounds.

Doxepin is an antihistaminic, antidepressant, and sleeping aid that has two geometric isomers—molecules with equal chemical formulas but different 3D arrangements. While its Z-isomer is known to be more effective than its E-isomer, the precise nature of its binding to the histamine H1 receptor remained elusive. Now, in a recent study, researchers from Japan thoroughly addressed this knowledge gap through an innovative experimental protocol, paving the way to next-generation antihistamines with fewer side effects.

Even if two molecules have the exact same chemical formula and the same number and types of bonds, their three-dimensional arrangements can still be different. While some people might mistakenly disregard this as a minor detail, even simple changes in the position or orientation of a functional group can dramatically affect the biological properties of a molecule, sometimes rendering an otherwise benign substance into a highly toxic one. Thus, the study of such possible molecular variants, called ‘geometric isomers,’ is essential in the field of drug development.

Doxepin stands out as a notable example of a drug that is commercialized as a mixture of two geometric isomers, namely the E- and Z-isomers. Both doxepin isomers bind to histamine H1 receptor (H1R), which is expressed throughout the central nervous system, smooth muscle cells, and vascular endothelial cells. Besides its use as an antihistaminic drug, doxepin is also typically used as an antidepressant and sleeping aid. While biological tests in animals have shown that the Z-isomer is more effective than the E-isomer, the differences in affinity to H1R between the E- and Z-isomers are unknown. Moreover, the specifics of how these compounds actually bind to H1R remain elusive.

Against this backdrop, a research team from Tokyo University of Science, Japan, set out to clarify the finer details of the interactions between doxepin isomers and H1R. Their latest paper, which was published on June 25, 2024, in the Journal of Molecular Recognition, was co-authored by Professor Mitsunori Shiroishi, Mr. Hiroto Kaneko, and Associate Professor Tadashi Ando, among others. This study is a follow-up to past work done by Prof. Shiroishi and colleagues. “We previously revealed the crystal structure of the complex formed by H1R and doxepin, but we were unable to determine which isomer was bound,” he explains, “We then came up with a method to determine the binding affinity of the isomers, and thus carried out this study.”

To achieve this challenging goal, the researchers first produced a customized yeast expression vector by strategically inserting the H1R gene into it. This vector was used to modify yeast cultures so that they produce H1R. After retrieving the membranes from these cells, they applied a solution containing commercial doxepin, producing H1R-doxepin complexes. Following extraction and purification of these complexes, they removed any excess (unbound) doxepin. Finally, by denaturing the H1R receptors, they could free the bound doxepin molecules and measure their numbers in a high-performance liquid chromatography setup.

Using this protocol, the researchers could accurately quantify the amount of each isomer that was bound to the extracted receptors, which is directly tied to their relative binding affinity. They found that the affinity to H1R of the Z-isomer was over five times higher than that of the E-isomer.

The team then delved deeper into the nature of how doxepin isomers bind to H1R. Through experiments on a mutant variant of H1R coupled with molecular dynamics simulations, they revealed that the Thr112 side chain in the ligand-binding pocket of H1R creates a chemical environment that enhances selectivity for the Z-isomer.

Taken together, the findings of this study shed light on how a widely used small molecule drug interacts with an important cellular receptor. “Our efforts could serve as the basis for designing next-generation antihistamines that are more effective and have fewer side effects,” highlights Prof. Shiroishi, “Worth noting, this newfound knowledge will be useful for designing compounds that bind not only to H1R, but also other disease-relevant target proteins.”

The rational design of future drugs, aided and validated by computational techniques like molecular dynamics simulations, could usher in a new era in medicine. More specifically, by understanding the binding properties of isomers in detail, many small-molecule drugs could be made more effective, safer, and better suited for targeted therapies.

Let us hope this vision of the future becomes a reality soon!

Solid oxide fuel cells (SOFCs) are a promising avenue to meet global demands for clean energy. They can produce electricity through environmentally friendly electrochemical reactions. However, existing SOFCs operate at high temperatures, which lowers their efficiency. Now, researchers from Japan have developed a novel perovskite-based anode material for SOFCs that exhibits mixed hole–proton conduction at medium-range temperatures. Their findings will help establish more efficient energy technologies, leading the way to more sustainable societies.

Amidst the ongoing energy and climate crises, the stakes have never been higher. We are pressed for time to find better ways of producing clean energy to replace fossil fuels. Thus far, fuel cells appear to be one of the most promising research directions. These electrochemical devices can produce electricity directly from chemical reactions, which can be tailored to be environmentally friendly in terms of their reactants and outputs.

Various types of fuel cells exist, but solid oxide fuel cells (SOFCs) have attracted special attention from researchers. By operating without the need for a liquid electrolyte, they offer higher safety and are often easier to manufacture. Unfortunately, one of their main drawbacks is their high operating temperature. Conventional SOFCs need to be at over 700 °C to work properly, which limits their applicability, reduces their efficiency and power output, and often compromises their durability. Thus, proton-conducting SOFCs (PC-SOFCs), which can operate within a lower temperature range, are being investigated as a promising alternative.

Against this backdrop, a research team including Professor Tohru Higuchi from Tokyo University of Science has achieved a breakthrough in PC-SOFCs by developing a novel hole–proton mixed-conductor material. Their findings, which have been published in the Journal of the Physical Society of Japan on June 18, 2024, could pave the way for important technological advancements in energy technologies.

The material in question is a perovskite-type oxide ceramic with the formula BaCe0.4Pr0.4Y0.2O3−δ (BCPY). These particular dopants, namely Pr and Y ions, were selected based on previous works by members of the research team. They observed that BaCe0.9Y0.1O3−δ and BaPrO3−δ exhibited proton and hole (a type of positive charge carrier) conduction, respectively. Thus, they theorized that co-doping with both Pr and Y might lead to high proton–hole mixed conductivity.

Such a material could be used in the anode electrode of PC-SOFCs, as Prof. Higuchi explains: “The Pt metal electrode used in other fuel cells has issues, such as a large drop in power output because electrochemical reactions occur only at the three-phase interface where the fuel gas/electrode/electrolyte intersect. To solve this issue, a dense membrane with mixed conduction could be useful for improving the performance of PC-SOFC by expanding the electrochemical reaction area.”

Using a sputtering technique, the researchers produced thin films of BCPY and carefully analyzed its conduction properties, seeking to find evidence of mixed proton–hole conduction. To this end, they established a quantitative evaluation method to determine oxygen vacancies using X-ray absorption spectroscopy and defect chemistry analysis. Through these and several additional experiments, including synchrotron radiation photoelectron spectroscopy for electronic band structure analysis, they found substantial evidence that mixed hole–proton conductivity can occur on the surface of the proposed electrode material.

Notably, BCPY electrodes exhibited a high conductivity of over 10−2 S.K/cm at 300 °C, which outlines a bright future not only for PC-SOFCs, but for other technologies as well. “If we can further confirm that BCPY thin films do enable hole–proton mixed conductivity, BCPY may become a novel oxide material for not only PC-SOFC anode electrode membranes but also electric-double-layer-transistors,” highlights Prof. Higuchi. To clarify, this transistor technology can address the scalability and miniaturization problems of conventional transistors, which will be crucial to developing artificial intelligence systems and increasing the computational capacity of personal electronic devices.

In any case, this study sheds some much-needed light on new electrode materials for PC-SOFCs. With further advances in this exciting field, electrochemical energy generation could eventually enable us to power up our homes and cars with cleaner electricity, paving the way to more sustainable societies.