Developing novel conducting polymer-hydrogel interpenetrating networks for neural interfacing

by Li Yuan, Chinese Academy of Sciences

Novel conducting polymer-hydrogel interpenetrating networks developed for neural interfacing
Graphical abstract. Credit: ACS Applied Materials & Interfaces (2023). DOI: 10.1021/acsami.3c07189

A research group led by Prof. Lu Yi from the Shenzhen Institute of Advanced Technology (SIAT) of the Chinese Academy of Sciences (CAS) has proposed three-dimensional (3D) conductive polymer-hydrogel interpenetrating networks for high-performance chronic electrode/neural interfacing. The study was published in ACS Applied Materials & Interfaces.

Long-term, reliable detection of electrophysiological signals is pivotal for comprehending mechanisms that underlie brain disorders and for advancing effective treatments. Nonetheless, maintaining stability and biocompatibility of neural electrode interface for necessary extended periods remains challenging.

Poly (3,4-ethylenedioxythiophene), or PEDOT, is known for its excellent biocompatibility and low electrochemical impedance, making it a commonly used modified conductive polymer material in neural-electrode interfaces. However, PEDOT films often exhibit cracks or delaminations due to their limited electrochemical and mechanical stability, posing a significant challenge to the long-term viability of neural electrodes.

To address this issue, the researchers proposed a novel interface modification strategy in their work. They prepared a polystyrene sulfonate/polyvinyl alcohol (PSS/PVA) hydrogel film and applied it as a pre-coating on the surfaces of a microelectrode array, forming a 3D scaffold rich in counter ions.

Subsequently, they electropolymerized the 3, 4-ethylene dioxythiophene monomer within the PSS/PVA scaffold to create an interpenetrating conducting polymer network (ICPN). The resultant ICPN exhibited 3D highly porous microstructure, with pore sizes ranging from 0.1 to 1.0 μm.

This 3D porous structure plays a significant role in dissipating mechanical energy, enhancing adhesion, and ensuring the long-term stability of the conducting hydrogel coatings. Additionally, the ICPN film possesses a low Young’s modulus (191 kPa) and remarkable stretchability (72%).

The research team also discovered that this ICPN film featured low electrochemical impedance, high capacitance, and outstanding biocompatibility, meeting the requirements for neural interfaces in a wide range of in-vivo applications.

Furthermore, the researchers conducted a comparative analysis of the electrophysiological signal quality between ICPN and PEDOT/PSS film-modified neural electrode arrays after 12 weeks of implantation into the mouse hippocampus.

Their findings indicated that ICPN-modified interfaces significantly enhanced the quality of signals during chronic electrophysiological recordings.

The study holds potential to expand applications of neural implants and provides new insights into diagnosis and treatment of neuropsychiatric disorders in the future.

More information: Mengying Yan et al, Conducting Polymer-Hydrogel Interpenetrating Networks for Improving the Electrode–Neural Interface, ACS Applied Materials & Interfaces (2023). DOI: 10.1021/acsami.3c07189

Journal information: ACS Applied Materials and Interfaces 

Provided by Chinese Academy of Sciences 

New double z-scheme photocatalyst for selective removal of sulfamethoxazole in water

by Chinese Society for Environmental Sciences

New double z-scheme photocatalyst for selective removal of sulfamethoxazole in water
Graphical abstract. Credit: Environmental Science and Ecotechnology (2023). DOI: 10.1016/j.ese.2023.100308

In a new study published in Environmental Science and Ecotechnology, researchers from Harbin Institute of Technology, have developed a novel double Z-scheme photocatalyst, called the molecularly imprinted TiO2@Fe2O3@g-C3N4 (MFTC) composite, that selectively removes SMX from water.

Traditional photocatalytic methods have faced challenges with selectivity, often causing the indiscriminate degradation of organic pollutants and coexisting contaminants at high concentrations. However, the MFTC composite was purposefully designed to overcome this limitation by incorporating molecularly imprinted sites on its surface.

These specialized sites exhibit a unique ability to recognize and enhance the adsorption of sulfamethoxazole (SMX), making the MFTC highly effective in selectively targeting SMX in the presence of other pollutants like sulfadiazine (SDZ), ibuprofen (IBU), and bisphenol A (BPA). In simulated wastewater conditions, the MFTC composite impressively demonstrated a selective degradation efficiency rate of 96.8% for SMX, nearly twice as effective as competing catalysts for other pollutants.

The “lock and key” mechanism of the molecularly imprinted sites played a pivotal role in selectively capturing SMX, resulting in superior performance. The degradation process of SMX by the MFTC photocatalytic system involved the generation of •OH and •O2 free radicals, which facilitated the removal of SMX through a newly proposed double Z-scheme mechanism. This mechanism enhanced charge carrier transfer and separation, leading to significantly improved photocatalytic activity.

Moreover, the MFTC composite showcased remarkable stability and recyclability over multiple cycles, making it a promising and practical solution for water treatment applications. The exceptional performance and selectivity of the MFTC composite offer exciting prospects for the advancement of efficient and selective photocatalysts, contributing to the development of eco-friendly and cost-effective solutions for water purification and environmental remediation.

New double z-scheme photocatalyst for selective removal of sulfamethoxazole in water
A, The fabrication process of MFTC. b–d, SEM images of MFT (b), NFT (c), MFTC (d). e–f, TEM images of MFTC. g, SEM element mapping images for C, Fe, Ti, and N of MFTC. Credit: Environmental Science and Ecotechnology (2023). DOI: 10.1016/j.ese.2023.100308

This research not only provides valuable insights into the selective removal of sulfamethoxazole (SMX) but also opens the door for further exploration of molecularly imprinted nanocomposite materials in selectively eliminating other pharmaceutical residues and organic pollutants.

More information: Jing-Yan Zhang et al, Selective removal of sulfamethoxazole by a novel double Z-scheme photocatalyst: Preferential recognition and degradation mechanism, Environmental Science and Ecotechnology (2023). DOI: 10.1016/j.ese.2023.100308

Provided by Chinese Society for Environmental Sciences

Electron transfer kineties of CdS/Zn(impim) dots-on-rods designed for efficient visible-light reduced C-X bond

by Liu Jia, Chinese Academy of Sciences

Electron transfer kineties of CdS/Zn(impim) dots-on-rods designed for efficient visible-light reduced C-X bond
Graphical abstract . Credit: ACS Applied Materials & Interfaces (2023). DOI: 10.1021/acsami.3c07110

Using solar energy to drive the cleavage of C-X bonds in halogenated organic compounds to form C-H bonds can not only control environmental pollution but also achieve important organic conversion reactions.

In a study published in ACS Applied Materials & Interfaces, a research group led by Prof. Cao Rong from Fujian Institute of Research on the Structure of Matter of the Chinese Academy of Sciences reported a CdS/Zn(impim) coupled system in which the electron transfer kinetics of photocatalytic reduction of C-X bond for CdS/Zn(impim) composites has been explored.

The researchers synthesized CdS/Zn(impim) (MOF) dots-on-rods composite photocatalyst under mild conditions, and characterized the structure and morphology by powder X-ray diffraction (PXRD), scanning electron microscope (SEM) and transmission electron microscope (TEM).

They found that CdS nanoparticles are uniformly loaded on the surface of rod-shaped Zn(impim) MOF, promoting the separation of electron-hole pairs.

To prove the direction of electron transfer from CdS to Zn(impim), the researchers measured the surface work functions by the Kelvin probe force microscope (KPFM). The fluorescence lifetime of CdS/Zn(impim) was significantly reduced compared to CdS. The related electron transfers kinetic was specified in detail by fluorescence spectrum and femtosecond transient absorption spectroscopy (fs-TAS).

In order to demonstrate the photocatalytic performance of CdS/Zn(impim), the researchers selected α-bromoacetophenone, bromobenzonitrile, and their derivatives as model reactions.

They revealed that the photocatalytic dehalogenation activity of CdS/Zn(impim) composite is much higher than that of CdS or Zn(impim) alone. The catalyst enjoyed good stability, and the morphology and structure of the catalyst did not change obviously after five consecutive cycles.

In the dehalogenation reaction of α-bromoacetophenone, the researchers detected the intermediate of acetophenone radical by electron paramagnetic resonance (EPR), proving the intermediate process of the reaction.

Under visible light irradiation, the electrons in CdS are excited and transferred to Zn(impim), and holes are retained in CdS, resulting in charge separation, thereby slowing down the charge recombination process and ultimately improving the efficiency of photocatalytic dehalogenation.

This study provides a further understanding of the electron transfer mechanism in semiconductor/MOF composites and the process of photocatalytic halide dehalogenation, and a feasible idea to design higher-performance photocatalytic materials.

More information: Yanan Feng et al, Rational Design of Electron Transfer Kineties of CdS/Zn(impim) Dots-on-Rods for Efficient Visible-Light Reduced C-X Bond, ACS Applied Materials & Interfaces (2023). DOI: 10.1021/acsami.3c07110

Journal information: ACS Applied Materials and Interfaces 

Provided by Chinese Academy of Sciences 

‘Crappier-than-crap’ molecule exposed in overhaul of carbon-nitrogen-hydrogen chemistry

by Liz Switzer, Skolkovo Institute of Science and Technology

'Crappier-than-crap' molecule exposed in overhaul of carbon-nitrogen-hydrogen chemistry
Stability map of molecules with the formula CmN1Hk, where the amount of carbon and hydrogen in the compound varies from zero to 12 atoms. The m and k axes stand for carbon and hydrogen, respectively, and the amount of nitrogen is limited to one atom per molecule. Each bar stands for one compound, its height denotes stability, and the symbols on top refer to the medium, if any, where that compound has been experimentally observed to date. Among the most stable, or “magic,” compounds is a close relative of the crap molecule skatole. Credit: The Journal of Physical Chemistry Letters (2023). DOI: 10.1021/acs.jpclett.3c01753

Russian researchers have explained why scientists studying crude oil and celestial chemistry—as well as certain down-to-earth matters—frequently come across some molecules incorporating carbon, nitrogen, and hydrogen but not other combinations of these three elements. The discovery transforms what used to be a jumble of haphazard rules of organic chemistry into a neat self-contained logical system based on the current fundamental understanding of quantum physics.

Published in The Journal of Physical Chemistry Letters, the study is not only sure to please many a perfectionist out there, but will actually guide astrophysicists toward new “chemical species” in outer space—yes, that’s really what they’re called.

“If you think about how organic chemistry is often taught, it’s a bit like trying to memorize the yellow pages,” said Skoltech Professor Artem R. Oganov, the principal investigator of the study. “Some molecules are stable and therefore common, others not so much. Some react readily, others not. But why? There are rules to this that sort of work, but it’s not a neat system built from the ground up—more like a disorganized collection of observations.”

“Our study remedies this situation and shows how to explain and predict these things from first principles for the system of carbon, nitrogen, and hydrogen,” he went on. “Now there’s one small chart that explains whatever we’ve seen so far in space or in crude oil, and then some, as far as the combinations of these three atoms are concerned.” The underlying principle was borrowed from nuclear physics and nanoscience, and identifies “magic” molecules—those that have lower energy than the molecules of nearest compositions.

The laws of physics say that matter tends to assume the lowest energy state available. That means the pretty, highly organized systems, which someone has put a lot of energy into, tend to degrade when left to their own devices (sorry, parents). Food is a good example: Before too long, a juicy apple packed with tasty energy loses it either to the environment by decaying or, hopefully, to someone who can appreciate it.

Stripped of its energy, the compounds in the apple transform into the familiar reaction products, with the most noticeable molecule among them—think smell—being skatole, named after the Ancient Greek word for poo. So, technically, what makes a molecule crappy is just how low the energy of the molecule that came before was prepared to fall in the course of the reaction.

Skatole (C9NH9) is close to being a “magic” molecule (and another molecule with the same composition and a slightly different arrangement of atoms proved to be magic). Ironically, the malodorous skatole is used in ice-cream and perfume, but in very tiny quantities—guess what for? For its aroma.

While the lead author of the paper, Skoltech master’s student Elizaveta Vaneeva from Oganov’s Material Discovery Laboratory, was reluctant to delve into the whole skatole aspect of the study, she generously commented on where the new compound stability map might actually be used in science and industry. “The predictions of our model agree well with the list of molecules found in crude oil and outer space.

“But while oil has been thoroughly investigated, when it comes to the interstellar medium and planetary atmospheres, we might be able to give astrochemists some hints about what to look for, and it’s much faster and easier to discover new molecules when you have a list of candidates at hand.”

“As for the technological applications, one could imagine organic chemists trying to synthesize an industrially useful compound that belongs to the class we were looking at,” Vaneeva added. “This could be an organic dye, for example, a blue pigment. And instead of tediously doing experiments to figure out which compound would be stable, they could use our method, which relies on fundamental quantum chemical calculations, to predict the likely candidates. The method has no analogs, is quite fast, and now its predictions have been tested against the published astro- and petrochemistry data.”

In the future, the researchers intend to expand their approach to encompass other organic systems, such as amino acids—the building blocks of DNA and RNA—and proteins.

More information: Elizaveta E. Vaneeva et al, Prediction and Rationalization of Abundant C–N–H Molecules in Different Environments, The Journal of Physical Chemistry Letters (2023). DOI: 10.1021/acs.jpclett.3c01753

Journal information: Journal of Physical Chemistry Letters 

Provided by Skolkovo Institute of Science and Technology 

Atomic Ru coordinated by channel ammonia in V-doped tungsten bronze for highly efficient hydrogen-evolution reaction

by Chinese Academy of Sciences

Atomic Ru coordinated by channel ammonia in V-doped tungsten bronze as HER electrocatalyst
The atomically dispersed Ru is achieved in the hexagonal crystal channels of vanadium-doped tungsten bronze support via the precise coordination with channel ammonia, which exhibited highly efficient performance for hydrogen evolution reaction with remarkable mass activity in wide pH range. Credit: Chinese Journal of Catalysis

The utilization of hydrogen produced through electrochemical water splitting is widely regarded as an optimal pathway towards achieving the imminent objective of carbon neutrality.

Therefore, the development of materials for hydrogen evolution reaction (HER) under the wide range of pH conditions has become highly desirable in the field of electrocatalysis over the past decade. Due to their exceptional intrinsic activity, Pt-group metals (PGM) have been recognized for their immense potential and subsequently utilized in the fabrication of commercial HER.

The synthesis of atomically dispersed PGM electrocatalysts has been acknowledged as a prominent strategy for significantly enhancing the utilization of PGM, based on the premise of preserving exceptional intrinsic activity. The highly dispersed PGM atoms generally need a support characterized by an electron-rich coordination environment, which is typically provided by metallic compounds with abundant vacancies or heteroatom-doped carbon.

However, the formation of vacancies and the doping in materials are always random at atomic scale, which consequently give rise to the bad controlling on the distribution of PGM atoms. Thus, despite the fact that coordination configurations can be characterized by X-ray absorption measurements, effectively manipulating the spatial distribution of PGM atoms remains a crucial and formidable challenge in the development of atomically dispersed PGM electrocatalysts.

Recently, a research team led by Prof. Weilin Xu from Changchun Institute of Applied Chemistry, Chinese Academy Sciences, and University of Science and Technology of China, reported atomic Ru with a regulated spatial distribution and electronic structure owing to its unique coordination with the ammonia species in the hexagonal channels of vanadium-doped tungsten bronze (V-NHWO).

The unique integration of atomic Ru can not only promote the tight interaction between Ru atoms and V-NHWO, but also enhance the Ru utilization. When applied as the electrocatalyst for HER, it exhibits remarkable HER performance with multiply increasing mass activity to the Pt/C in a wide pH range.

Theoretical calculations revealed that the multi-channel vertically integrated atomic Ru sites in V-doped channels, as well as the coexisted Ru sites without the multi-channel or V doped effect, behave the improved free energy of water dissociation and hydrogen sorption, which ultimately promoting the HER activity. The results were published in Chinese Journal of Catalysis.

More information: Ce Han et al, Atomic Ru coordinated by channel ammonia in V-doped tungsten bronze for highly efficient hydrogen-evolution reaction, Chinese Journal of Catalysis (2023). DOI: 10.1016/S1872-2067(23)64489-4

Provided by Chinese Academy of Sciences 

Scientists uncover mystery of important material for semiconductors at the surface

by Scott Gibson, Oak Ridge National Laboratory

Scientists uncovered mystery of important material for semiconductors at the surface
Using the ultrahigh-vacuum atomic force microscope at DOE’s Center for Nanophase Materials Sciences at ORNL, researchers found unique environmentally induced ferroelectric phase transitions in hafnium zirconium oxide, a material important in developing advanced semiconductors. Credit: Arthur Baddorf/ORNL, Dept. of Energy

A team of scientists with the Department of Energy’s Oak Ridge National Laboratory has investigated the behavior of hafnium oxide, or hafnia, because of its potential for use in novel semiconductor applications.

Materials such as hafnia exhibit ferroelectricity, which means that they are capable of extended data storage even when power is disconnected and that they might be used in the development of new, so-called nonvolatile memory technologies. Innovative nonvolatile memory applications will pave the way for the creation of bigger and faster computer systems by alleviating the heat generated from the continual transfer of data to short-term memory.

The scientists explored whether the atmosphere plays a role in hafnia’s ability to change its internal electric charge arrangement when an external electric field is applied. The goal was to explain the range of unusual phenomena that have been obtained in hafnia research. The team’s findings were recently published in Nature Materials. The title of the paper is “Ferroelectricity in hafnia controlled via surface electrochemical state.”

“We have conclusively proven that the ferroelectric behavior in these systems is coupled to the surface and is tunable by changing the surrounding atmosphere. Previously, the workings of these systems were speculation, a hypothesis based on a large number of observations both by our group and by multiple groups worldwide,” said ORNL’s Kyle Kelley, a researcher with the Center for Nanophase Materials Sciences. CNMS is a DOE Office of Science user facility.

Kelley performed the experiments and envisioned the project in collaboration with Sergei Kalinin of the University of Tennessee, Knoxville.

Materials commonly used for memory applications have a surface, or dead, layer that interferes with the material’s ability to store information. As materials are scaled down to only several nanometers thick, the effect of the dead layer becomes extreme enough to completely stop the functional properties. By changing the atmosphere, the scientists were able to tune the surface layer’s behavior, which in hafnia, transitioned the material from the antiferroelectric to the ferroelectric state.

“Ultimately, these findings provide a pathway for predictive modeling and device engineering of hafnia, which is urgently needed, given the importance of this material in the semiconductor industry,” Kelley said.

Predictive modeling enables scientists to use previous research to estimate the properties and behavior of an unknown system. The study that Kelley and Kalinin led focused on hafnia alloyed, or blended, with zirconia, a ceramic material. But future research could apply the findings to anticipate how hafnia may behave when alloyed with other elements.

The research relied on atomic force microscopy both inside a glovebox and in ambient conditions, as well as ultrahigh-vacuum atomic force microscopy, methods available at the CNMS.

“Leveraging the unique CNMS capabilities enabled us to do this type of work,” Kelley said. “We basically changed the environment all the way from ambient atmosphere to ultrahigh vacuum. In other words, we removed all gases in the atmosphere to negligible levels and measured these responses, which is extremely hard to do.”

Team members from the Materials Characterization Facility at Carnegie Mellon University played a key role in the research by providing electron microscopy characterization, and collaborators from the University of Virginia led the materials development and optimization.

ORNL’s Yongtao Liu, a researcher with CNMS, performed ambient piezoresponse force microscopy measurements.

The model theory that underpinned this research project was the result of a long research partnership between Kalinin and Anna Morozovska at the Institute of Physics, National Academy of Sciences of Ukraine.

“I have worked with my colleagues in Kiev on physics and chemistry of ferroelectrics for almost 20 years now,” Kalinin said. “They did a lot for this paper while almost on the front line of the war in that country. These people keep doing science in conditions that most of us cannot imagine.”

The team hopes that what they have discovered will stimulate new research specific to exploring the role of controlled surface and interface electrochemistries—the relationship between electricity and chemical reactions—in a computing device’s performance.

“Future studies can extend this knowledge to other systems to help us understand how the interface affects the device properties, which, hopefully, will be in a good way,” Kelley said. “Typically, the interface kills your ferroelectric properties when scaled to these thicknesses. In this case, it showed us a transition from one material state to another.”

Kalinin added, “Traditionally, we explored surfaces at the atomic level to understand phenomena such as chemical reactivity and catalysis, or the modification of the rate of a chemical reaction. Simultaneously, in traditional semiconductor technology, our goal was only to keep surfaces clean from contaminants. Our studies show that in fact, these two areas—the surface and the electrochemistry—are connected. We can use surfaces of these materials to tune their bulk functional properties.”

More information: Kyle P. Kelley et al, Ferroelectricity in hafnia controlled via surface electrochemical state, Nature Materials (2023). DOI: 10.1038/s41563-023-01619-9

Journal information: Nature Materials 

Provided by Oak Ridge National Laboratory 

Reducing the carbon footprint of methane by converting it into methanol with a new enzyme

by Nagoya University

Reducing the carbon footprint of methane by converting it into methanol with a new enzyme
New technology converts a component of natural gas, methane (left), to methanol (right), using the P450BM3 enzyme (middle, gray) with a decoy molecule (middle, colored). This method can be a cheap and effective mean of reducing the carbon footprint of natural gas. Credit: Ariyasu Shinya

A team led by Professor Osami Shoji at Nagoya University in Japan has developed a technology to convert methane, the principal component of natural gas, into methanol at room temperature in water. They used an enzyme that can be easily mass-produced, offering the possibility of a cheap and effective means to reduce the carbon footprint of natural gas. They published the results in ACS Catalysis.

Methane is the key component of natural gas and an abundant natural resource. However, it is chemically stable, requiring huge amounts of energy before it undergoes chemical conversion. One solution is to convert methane to methanol.

Methane can be converted to methanol, which is cleaner than other fossil fuels and can be easily stored and transported. Converting methane to methanol can be done using the methane monooxygenase enzyme. However, the enzyme has a complex structure, making it difficult to handle and unsuitable for mass production.

Enzymes are usually very specific, often compared to a key for a particular lock. Converting methane to methanol using enzymes other than methane monooxygenase was thought to be impossible.

However, the research group turned to their previous work on the addition of chemically synthesized molecules to an enzyme to change the characteristics of the enzyme itself. This enables the chemical conversion of compounds that would not normally be accepted, a process called a substrate misrecognition system.

“In this system, artificial molecules called decoy molecules are designed and synthesized to resemble the compounds, called substrates, that the target enzyme usually accepts,” said Shoji.

“When added to the enzyme, the enzyme mistakenly takes in the ‘decoy molecules’ as the original target compound, and the enzyme is activated. If a molecule, in this case methane, that is normally unreactive, is added to the enzyme, the enzyme will mistake the decoy molecule for the original target compound and take it in. The activated enzyme then converts the methane to another molecule by ‘mistake.'”

The research group used chemical enzyme control technology on the enzyme P450BM3. It hydroxylates long-chain fatty acid molecules and has been used to convert similar substances such as benzene, ethane, and propane. However, as these substances are more reactive and larger than methane, methane conversion presented a greater challenge.

The group next searched for decoy molecules with an optimal structure to anchor the smallest methane molecule in the reaction pocket of P450BM3. The researchers investigated about 40 molecules that had been found to be effective in ethane hydroxylation from a library of about 600 decoy molecules. In a breakthrough, Shoji confirmed that the most efficient decoy molecule could convert methane to methanol in water at room temperature.

“When we tested it, we successfully converted methane to methanol using P450BM3,” said Shoji. “This was an exciting breakthrough as P450BM3 is derived from the bacterium Priestia megaterium (formerly Bacillus megaterium), making it is easy to handle and produce in large quantities using E. coli. This makes it an attractive new option for the effective utilization of methane gas.”

One day, decoy molecules could enable the conversion of compounds less difficult than methane. “We expect that the technology can be developed into a low-energy, environmentally friendly conversion technology for many other hydrocarbons besides methane,” said Shoji.

“Therefore, it is expected to contribute to the promotion of the use of enzymes in the discovery of low environmental impact substance conversion technologies in Japan. We expect this achievement to have a significant impact on the fields of catalytic and enzymatic chemistry.”

Japan may prove to be an ideal test site for their technology because of discoveries of large amounts of methane buried as methane hydrate in the surrounding seas. Shoji is optimistic about the potential for using this untapped resource.

“Developing effective methods of methane utilization is an important issue for both solving environmental problems and increasing the efficiency of resource use. We hope that our research can help to solve the problem of limited natural resources in Japan,” he said.

More information: Shinya Ariyasu et al, Catalytic Oxidation of Methane by Wild-Type Cytochrome P450BM3 with Chemically Evolved Decoy Molecules, ACS Catalysis (2023). DOI: 10.1021/acscatal.3c01158

Journal information: ACS Catalysis 

Provided by Nagoya University 

Team develops technique for building DNA-based programmable gate arrays

by Bob Yirka , Phys.org

Team develops technique for building DNA-based programmable gate arrays
Schematic workflow of DPGA programming. A complex task circuit beyond the capability of a single DPGA was divided into subcircuits, for which molecular instructions were generated. Involved computing units of each subcircuit, as shown by the logical arrangement in the scheme, were called by their logical address and the function was implemented via intra-DPGA routing with molecular instructions. The transmission of intermediate output between subcircuits was realized via DNA origami register-mediated inter-DPGA routing. Credit: Nature (2023). DOI: 10.1038/s41586-023-06484-9

A team of chemists and chemical engineers at Shanghai Jiao Tong University, working with a colleague from the Chinese Academy of Sciences, both in China, has built a DNA-based programmable gate array for use in general-purpose DNA computing. In their study, reported in the journal Nature, the group overcame obstacles that had hindered the development of multipurpose DNA-based circuits and created circuits using their new process.

In 1994, Leonard Adleman won the Turing award for his proposed use of DNA base-pairing to create a biocomputing device. Since that time, many such devices have been created. But until now, any given device could do only one thing. In this new effort, the team in China has overcome problems faced by other researchers working on making such devices more universal by developing a technique for creating a field-programmable gate array using DNA, which they describe as a DNA-based programmable gate array (DPGA).

The work involved adding strands of DNA to a tube containing a buffer fluid. They then induced chemical reactions that forced the strands together in desired ways, creating longer strands that together made up a DPGA. The team then added fluorescence markers to allow for viewing and keeping track of circuit formation. Testing showed that a single DPGA could be designed in a way that allowed for the creation of 100 billion unique circuits simply by adding specific amounts of short molecules to the DNA strands.

In testing their DPGAs, the researchers found that by connecting just three of them together, they were able to build a circuit capable of solving quadratic equations or square roots. They note that numbers could be added for computing such formulas by adding molecules of a specific shape. Output from the DPGAs was done by studying the molecules that were produced by the final reaction using the fluorescent markers.

The team found that they could also use their DPGAs as a classification tool for small RNA molecules, which allowed for isolating certain types—such as those that were markers for certain types of cancer cells.

More information: Hui Lv et al, DNA-based programmable gate arrays for general-purpose DNA computing, Nature (2023). DOI: 10.1038/s41586-023-06484-9

Journal information: Nature 

© 2023 Science X Network

Scientists probe the source of key hydrocarbons on Earth—and in space

by US Department of Energy

Scientists probe the source of key hydrocarbons on Earth—and in space
The formation of naphthalene—the simplest polycyclic aromatic hydrocarbon—from two resonantly stabilized free radicals, propargyl and benzyl. Credit: Ralf I. Kaiser, University of Hawai’i at Manoa

Polycyclic aromatic hydrocarbons (PAHs) are a type of organic molecule that carry fused rings made of the chemical benzene. Scientists believe that PAHs are responsible for chemical processes that eventually lead to soot and other carbonaceous nanoparticles on Earth and around and between the stars in deep space. On Earth, PAHs form in part because of the incomplete combustion of coal, oil, and other substances and are detrimental to human health.

Across the universe, PAHs account for as much as 30% of all carbon, whether around stars, interstellar clouds, or planets. However, scientists do not fully understand the role of reactions involving two free radicals in how PAHs form in extreme environments. Free radicals are molecules with an unpaired electron, which is delocalized over at least three atoms. In a study published in the journal Chemical Science, researchers conducted experiments to uncover how the prototype PAH—naphthalene—can form from reactions that take place in the gas phase of matter.

The results provide fundamental knowledge on the processes that can form the simplest representative of PAHs naphthalene—a key ingredient in mothballs. The researchers found that this reaction can occur in the gas phase via the reaction of radicals that are found in combustion flames and in the space around carbon-rich stars. This provides new foundational knowledge of the chemistry and carbon balance of our galaxy.

Polycyclic aromatic hydrocarbons (PAHs) and their descendant soot particles represent unwanted byproducts in combustion processes of fossil fuel, but scientists do not have a complete understanding of the fundamental mechanisms of their formation. An isomer selective product detection reveals that the reaction of the resonantly stabilized benzyl (C7H7) and the propargyl (C3H3) radicals synthesizes the simplest representative of PAHs—the 10p Hückel aromatic naphthalene (C10H8) molecule.

The gas-phase preparation of naphthalene affords a radical new concept of the reaction of combustion relevant propargyl radicals with aromatic radicals carrying the radical center at the methylene moiety (aromatic-CH2•), which have been previously overlooked as a source of aromatics in high temperature environments.

This facile Propargyl Addition—BenzAnnulation (PABA) mechanism of propargyl radicals with other aromatic-CH2• radicals beyond benzyl could lead to higher order PAHs like anthracene and phenanthrene. This finding is a fundamental shift in the perception that PAHs are predominantly formed via the Hydrogen-Abstraction—Acetylene Addition (HACA) and Phenyl Addition DehydroCyclization (PAC) pathways in high temperature combustion settings.

This PABA mechanism offers versatile and diverse routes to three key classes of aromatic hydrocarbons: acenes (PAHs consisting of linearly fused benzene rings), phenacenes (PAHs carrying zig-zag structured benzene rings), and helicenes (ortho-condensed PAHs in which benzene rings are angularly annulated yielding helically shaped chiral molecules), thus bringing scientists closer to an understanding of the aromatic universe we live in.

More information: Chao He et al, Unconventional gas-phase preparation of the prototype polycyclic aromatic hydrocarbon naphthalene (C10H8) via the reaction of benzyl (C7H7) and propargyl (C3H3) radicals coupled with hydrogen-atom assisted isomerization, Chemical Science (2023). DOI: 10.1039/D3SC00911D

Journal information: Chemical Science 

Provided by US Department of Energy 

Selective removal of aging cells opens new possibilities for treating age-related diseases

by JooHyeon Heo, Ulsan National Institute of Science and Technology

Selective removal of aging cells opens new possibilities for treating age-related diseases
A schematic diagram, illustrating a groundbreaking study that specifically targets mitochondria within aging cells. Credit: Journal of the American Chemical Society (2023). DOI: 10.1021/jacs.3c06898

A research team, led by Professor Ja Hyoung Ryu from the Department of Chemistry at UNIST, in collaboration with Professor Hyewon Chung from Konkuk University, has achieved a significant breakthrough in the treatment of age-related diseases. Their cutting-edge technology offers a promising new approach by selectively removing aging cells, without harming normal healthy cells. This groundbreaking development is poised to redefine the future of health care and usher in a new era of targeted therapeutic interventions.

Aging cells, known as senescent cells, contribute to various inflammatory conditions and age-related ailments as humans age. To address this issue, the research team focused on developing a technology that could precisely target and eliminate aging cells, while sparing normal healthy cells.

In their study, the team designed organic molecules that selectively target receptors overexpressed in the membranes of aging cells. By leveraging the higher levels of reactive oxygen species (ROS) found in aging cells, these molecules promote the formation of disulfide bonds and create oligomers that bind together. The research is published in the Journal of the American Chemical Society.

Selective removal of aging cells opens new possibilities for treating age-related diseases
Peptide oligomerization and self-assembly into α-helical structures. Credit: Journal of the American Chemical Society (2023). DOI: 10.1021/jacs.3c06898

Through self-assembly of these oligomers, the researchers successfully created artificial proteins with a stable α-helix secondary structure. These protein-like nanoassemblies exhibited strong binding affinity to the mitochondrial membranes of aging cells, leading to membrane disruption and subsequent cell self-destruction.

“The selective removal of aging cells by targeting the mitochondria and inducing dysfunction has been successfully demonstrated in our experiments,” stated Professor Ryu. “This approach represents a new paradigm for treating age-related diseases.”

This innovative technology offers several advantages, including minimal toxicity concerns and a wide therapeutic window by specifically targeting organelles within cells. It opens up exciting possibilities for designing preclinical and clinical trials in the future.

More information: Sangpil Kim et al, Supramolecular Senolytics via Intracellular Oligomerization of Peptides in Response to Elevated Reactive Oxygen Species Levels in Aging Cells, Journal of the American Chemical Society (2023). DOI: 10.1021/jacs.3c06898

Journal information: Journal of the American Chemical Society 

Provided by Ulsan National Institute of Science and Technology