Chemistry news and discussions

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New study confirms 'rippled sheet' protein structure predicted in 1953
https://phys.org/news/2022-09-rippled-s ... otein.html
by University of California - Santa Cruz

An unusual protein structure known as a "rippled beta sheet," first predicted in 1953, has now been created in the laboratory and characterized in detail using X-ray crystallography.

The new findings, published in July in Chemical Science, may enable the rational design of unique materials based on the rippled sheet architecture.

"Our study establishes the rippled beta sheet layer configuration as a motif with general features and opens the road to structure-based design of unique molecular architectures, with potential for materials development and biomedical applications," said Jevgenij Raskatov, associate professor of chemistry and biochemistry at UC Santa Cruz and corresponding author of the paper.

Proteins come in an enormous range of shapes and sizes to carry out their myriad structural and functional roles in living cells. Certain common structural motifs, such as the alpha helix, are found in many protein structures.

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Researchers explore enzymes that use a cation, not oxygen-addition, to drive reactions
https://phys.org/news/2022-09-explore-e ... tions.html
by Tracey Peake, North Carolina State University

Researchers from North Carolina State University and the University of Texas at Austin have defined the structure of a substrate-bound iron 2-oxoglutarate (Fe/2OG) enzyme to explore whether these enzymes could be used to create a wide array of molecules. They probed the enzyme's active site to determine its ability to bind with different substrates. Additionally, rather than oxygen-addition, they saw that Fe/2OG enzymes likely utilize cations—highly reactive species—to drive desaturation during catalysis. The work, published in Nature Communications, could lead to the use of Fe/2OG enzymes in making a wide array of valuable molecules.

Enzymes in the Fe/2OG family are naturally occurring—they are found in everything from bacteria to plants and animals. As such, these enzymes have the potential to be used as a greener, more efficient platform for creating molecules such as vinyl isonitriles, which have antibiotic properties. However, the pathways by which Fe/2OG enzymes create these molecules are poorly understood.

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New phases of water detected
https://phys.org/news/2022-09-phases.html
by University of Cambridge

Scientists at the University of Cambridge have discovered that water in a one-molecule layer acts like neither a liquid nor a solid, and that it becomes highly conductive at high pressures.

Much is known about how "bulk water" behaves: it expands when it freezes, and it has a high boiling point. But when water is compressed to the nanoscale, its properties change dramatically.

By developing a new way to predict this unusual behavior with unprecedented accuracy, the researchers have detected several new phases of water at the molecular level.

Water trapped between membranes or in tiny nanoscale cavities is common—it can be found in everything from membranes in our bodies to geological formations. But this nanoconfined water behaves very differently from the water we drink.

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Scientist discovers new oxidation state of rhodium
https://phys.org/news/2022-09-scientist ... odium.html
by University of Freiburg

Mayara da Silva Santos, doctoral candidate at the University of Freiburg's Institute of Physics, has discovered a new oxidation state of rhodium. This chemical element is one of the most catalytically important platinum-group metals and is used, for example, in catalytic converters for automobiles.

Rhodium is actually already well studied. What helped Silva Santos make the rare discovery of a surprisingly high oxidation state was a new approach: As part of her doctoral dissertation, she is studying unusual transition metal oxides. Her discovery of so-called rhodium(VII) has just been published in Angewandte Chemie International Edition.

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Researchers find new sugar substitutes in citrus that could change food and beverage industry
https://phys.org/news/2022-09-sugar-sub ... erage.html
by University of Florida

Americans' love affair with sugar can be a deadly attraction that sometimes leads to major health problems, including obesity and type 2 diabetes.

Finding natural, non-caloric sugar substitutes is desirable but challenging. However, researchers at the University of Florida Institute of Food and Agricultural Sciences have made a breakthrough—discovering new, natural sweeteners in citrus for the first time.

This finding opens opportunities for the food industry to produce food and beverages with lower sugar content and lower calories while maintaining sweetness and taste using natural products.

Yu Wang, associate professor of food science at UF/IFAS, managed the multi-year project that found eight new sweetener or sweetness-enhancing compounds in 11 citrus cultivars.

"We were able to identify a natural source for an artificial sweetener, oxime V, that had never been identified from any natural source previously," said Wang, a faculty member at the UF/IFAS Citrus Research and Education Center in Lake Alfred, Florida. "This creates expanded opportunities for citrus growers and for breeding cultivars to be selected to obtain high yields of sweetener compounds."

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Automated carbohydrate synthesizer produces polysaccharides of record-breaking length
https://phys.org/news/2022-09-automated ... ength.html
by Bob Yirka , Phys.org

A team of researchers with members from Peking University and WuXi AppTec (Tianjin) Co., Ltd., has designed and built an automated carbohydrate synthesizer that produced polysaccharides of record-breaking length. In their paper published in the journal Nature Synthesis the group describes how they built their device and its possible uses. Hanchao Cheng and Peng George Wang with the Southern University of Science and Technology, in China, have published a News & Views piece in the same journal issue outlining the work by the team in China.

As Cheng and Wang note, carbohydrates play a very important role in biology—they are a biochemical source of energy. And as they also note, naturally occurring carbohydrates tend to be structurally undefined, which means they are made up of mixtures of molecules, making them quite complex.

For this reason, well-defined carbohydrates are prized. Unfortunately, synthesizing them has proven to be difficult, most particularly as they grow larger. In this new effort, the researchers have created a means for speeding up the process—an automated synthesizer, one that overcomes problems associated with other machines meant to do the same.

The synthesizer created by the team has three parts: a synthesizing system, a system for monitoring progress and software that is used to control the hardware. The synthesizer involves a stirrer and heat controls, and a lamp that is used to incite light induced reactions.

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Developing an eco-friendly ammonia catalyst
https://phys.org/news/2022-10-eco-frien ... alyst.html
by Daegu Gyeongbuk Institute of Science and Technology

A DGIST research team led by Professor Sangaraju Shanmugam, Department of Energy Engineering, developed a catalyst that converts nitric oxide (NO) to ammonia (NH3). This electrochemical technology offers high Faradaic efficiency and low overpotential and produces NH3 in an eco-friendly manner.

NH3 is an important chemical raw material in the fertilizer, textile, and pharmaceutical industries, and it is considered a carbon-free hydrogen carrier with a high energy density. Typically, NH3 is produced using the Haber–Bosch process; however, this process is responsible for approximately 1–2% of global CO2 emissions.

The electrochemical conversion of NO to NH3, an alternative to the Haber–Bosch process, has received considerable attention. This eco-friendly method consumes the air pollutant NO gas to produce NH3. Therefore, this promising approach can replace conventional methods without affecting the environment or emitting CO2.

However, owing to the corrosive nature of NO gas, the morphology of the metal-nanoparticle electrocatalyst degrades during electrosynthesis. Therefore, it is necessary to obtain a catalyst material with high stability that facilitates long-term electrochemical NH3 synthesis.

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Developing stable water-splitting catalysts that don't require expensive iridium
https://phys.org/news/2022-10-stable-wa ... quire.html
by Mike Williams, Rice University

Creating a hydrogen economy is no small task, but Rice University engineers have discovered a method that could make oxygen evolution catalysis in acids, one of the most challenging topics in water electrolysis for producing clean hydrogen fuels, more economical and practical.

The lab of chemical and biomolecular engineer Haotian Wang at Rice's George R. Brown School of Engineering has replaced rare and expensive iridium with ruthenium, a far more abundant precious metal, as the positive-electrode catalyst in a reactor that splits water into hydrogen and oxygen.

The lab's successful addition of nickel to ruthenium dioxide (RuO2) resulted in a robust anode catalyst that produced hydrogen from water electrolysis for thousands of hours under ambient conditions.

"There's huge industry interest in clean hydrogen," Wang said. "It's an important energy carrier and also important for chemical fabrication, but its current production contributes a significant portion of carbon emissions in the chemical manufacturing sector globally. We want to produce it in a more sustainable way, and water-splitting using clean electricity is widely recognized as the most promising option."

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A first-of-its-kind framework to characterize hydrogels for biomedical scientists and engineers

by National University of Ireland, Galway
https://phys.org/news/2022-11-first-of- ... dical.html

Researchers at CÚRAM have this week published an interdisciplinary framework that enables the development of extracellular matrix-inspired hydrogels for biomedical applications.

An extracellular matrix (ECM) is a three-dimensional cementing material that gives structural support to our cells. Hydrogels mimicking this extracellular matrix (ECM) have become increasingly attractive in biomedical science research due to their tunability and biocompatibility. However, hydrogel development and characterization require an interdisciplinary approach that is seldom fully achieved as it needs an extraordinary degree of researcher skill.

This review is a first-of-its-kind approach that will provide information on available tools for properly characterizing ECM-based hydrogels and interpreting the resulting data. It also provides an accurate roadmap that can be used by biomedical researchers when attempting to bridge the gap between material science and biomedicine.

The review paper was published by Matter.

Lead author and Director of CÚRAM Professor Abhay Pandit says that "with this proposed review, we aim to combine the knowledge of chemistry, material science, and biology by critically discussing the available tools to properly characterize ECM-based hydrogels and interpreting the resulting data, leading to an accurate roadmap to be applied in this exciting field."

ECM hydrogel development and characterization involve a wide array of interdisciplinary tools; this review will appeal to chemists, material scientists, engineers, and biologists working in the field. This review provides a concise, complete, and easy-to-follow guide for advanced undergraduates, early postgraduate researchers, industry (MedTech, Pharmaceutical, and BioTech), and experts in this interdisciplinary field.

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Charged porphyrins: The key to investigating the properties of stacked ion pairs
https://phys.org/news/2022-11-porphyrin ... d-ion.html
by Ritsumeikan University

Ions are created when an atom or molecule either loses or gains electrons, thus gaining a charge. When two oppositely charged ions are combined, it can lead to the creation of an ion pair. The influence of different ion pairs on the physical properties of the material they are present in has been widely studied as it can lead to the creation of new functional electronic materials.

Of particular interest is the study of π-electronic ion pairs for their ability to employ intermolecular interactions to produce dimension-controlled assemblies. These are useful for creating new electronic materials.

These interactions (known as "iπ−iπ interactions") cause the stacking of ions into π-stacked ion pairs (π-sips). Controlling the electronic state of these π-sips can create π-stacked radical pairs (π-srps). Both of these have attractive properties for the creation of electronic materials, but have not been studied much owing to the difficulties in preparation and structure determination.

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Chemists create quantum dots at room temperature using lab-designed protein
https://phys.org/news/2022-12-chemists- ... ature.html
by Wendy Plump, Princeton University

Nature uses 20 canonical amino acids as building blocks to make proteins, combining their sequences to create complex molecules that perform biological functions.

But what happens with the sequences not selected by nature? And what possibilities lie in constructing entirely new sequences to make novel (de novo) proteins bearing little resemblance to anything in nature?

That's the terrain where Michael Hecht, professor of chemistry, works with his research group. Recently, their curiosity for designing their own sequences paid off.

They discovered the first known de novo (newly created) protein that catalyzes (drives) the synthesis of quantum dots. Quantum dots are fluorescent nanocrystals used in electronic applications from LED screens to solar panels.

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3D printing of single atom catalysts pioneered
https://phys.org/news/2023-01-3d-atom-catalysts.html
by Susan Bogle, Australian Nuclear Science and Technology Organisation (ANSTO)

A large international collaboration led by Prof Shizhang Qiao, an Australian Laureate Fellow at the University of Adelaide has developed a straightforward and cost-effective synthesizing approach using a 3D printing technique to produce single-atom catalysts (SACs)—potentially paving the way for large-scale commercial production with broad industrial applications.

The research has been published in Nature Synthesis.

The team mailed in samples to the Australian Synchrotron during the COVID lockdown for materials characterization using the X-ray absorption spectroscopy (XAS) beamline.

A catalyst is a substance that is designed to drive a specific chemical reaction to convert chemicals to other, less harmful, valuable industrial products. The efficiency at which a given catalyst aids the reaction is often found to be determined by its surface area.

For example, a bulk metallic cobalt foil may aid in chemical reductions, but the same number of cobalt atoms in the form of nanoparticles would be significantly more efficient given the greater surface area available for the reaction to take place.

Taken to its extreme, single-atom catalysts (SACs) refer to individual metal atoms, not bonding to metal but often dispersed uniformly on a fixed substrate (such as carbon), offering the highest possible value of atom economy.

The ideal atom economy, known as 100% atom economy, for a chemical reaction is a process in which all reactant atoms are found in the desired product.

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Scientists created a weird new type of ice that is almost exactly as dense as water
By Stephanie Pappas
https://www.livescience.com/new-medium- ... rphous-ice
Part of the experimental setup for making medium-density amorphous ice.

Using ultracold temperatures and some steel ball bearings, scientists have created a brand-new, bizarre form of ice that has the same density of liquid water.

The ice, known as medium-density amorphous ice, fits into a gap in the annals of frozen water that scientists weren't sure would ever be filled. Unlike the crystalline ice that forms naturally on Earth, the newly created ice doesn't have an organized molecular structure. Instead, its molecules are in a chaotic mismatch, more like glass — a state known as amorphous. Other types of amorphous ice have been made before, but they've been either much less dense or far denser than liquid water. This new Goldilocks version of amorphous ice is right in the middle, almost exactly matching liquid water's density, researchers explained in a new study published in the journal Science today (Feb. 2).

"It's something completely new," said study senior author Christoph Salzmann (opens in new tab), a professor of physical and materials chemistry at University College London.

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How a record-breaking copper catalyst converts carbon dioxide into liquid fuels

by Theresa Duque, Lawrence Berkeley National Laboratory
https://phys.org/news/2023-02-record-br ... oxide.html

Since the 1970s, scientists have known that copper has a special ability to transform carbon dioxide into valuable chemicals and fuels. But for many years, scientists have struggled to understand how this common metal works as an electrocatalyst, a mechanism that uses energy from electrons to chemically transform molecules into different products.

Now, a research team led by Lawrence Berkeley National Laboratory (Berkeley Lab) has gained new insight by capturing real-time movies of copper nanoparticles (copper particles engineered at the scale of a billionth of a meter) as they convert CO2 and water into renewable fuels and chemicals: ethylene, ethanol, and propanol, among others. The work was reported in the journal Nature last week.

"This is very exciting. After decades of work, we're finally able to show—with undeniable proof—how copper electrocatalysts excel in CO2 reduction," said Peidong Yang, a senior faculty scientist in Berkeley Lab's Materials Sciences and Chemical Sciences Divisions who led the study. Yang is also a professor of chemistry and materials science and engineering at UC Berkeley.

"Knowing how copper is such an excellent electrocatalyst brings us steps closer to turning CO2 into new, renewable solar fuels through artificial photosynthesis."

The work was made possible by combining a new imaging technique called operando 4D electrochemical liquid-cell STEM (scanning transmission electron microscopy) with a soft X-ray probe to investigate the same sample environment: copper nanoparticles in liquid. First author Yao Yang, a UC Berkeley Miller postdoctoral fellow, conceived the groundbreaking approach under the guidance of Peidong Yang while working toward his Ph.D. in chemistry at Cornell University.

Scientists who study artificial photosynthesis materials and reactions have wanted to combine the power of an electron probe with X-rays, but the two techniques typically can't be performed by the same instrument.

Electron microscopes (such as STEM or TEM) use beams of electrons and excel at characterizing the atomic structure in parts of a material. In recent years, 4D STEM (or "2D raster of 2D diffraction patterns using scanning transmission electron microscopy") instruments, such as those at Berkeley Lab's Molecular Foundry, have pushed the boundaries of electron microscopy even further, enabling scientists to map out atomic or molecular regions in a variety of materials, from hard metallic glass to soft, flexible films.

On the other hand, soft (or lower-energy) X-rays are useful for identifying and tracking chemical reactions in real time in an operando, or real-world, environment.

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Newly discovered form of salty ice could exist on surface of extraterrestrial moons
https://phys.org/news/2023-02-newly-sal ... trial.html
by University of Washington

The red streaks crisscrossing the surface of Europa, one of Jupiter's moons, are striking. Scientists suspect it is a frozen mixture of water and salts, but its chemical signature is mysterious because it matches no known substance on Earth.

A team led by the University of Washington may have solved the puzzle with the discovery of a new type of solid crystal that forms when water and table salt combine in cold and high-pressure conditions. Researchers believe the new substance created in a lab on Earth could form at the surface and bottom of these worlds' deep oceans.

The study, published Feb. 20 in the Proceedings of the National Academy of Sciences, announces a new combination for two of Earth's most common substances: water and sodium chloride, or table salt.

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Researchers describe promising method to optimize and scale up the production of fuel cell input
https://phys.org/news/2023-03-method-op ... -fuel.html
by Ricardo Muniz, FAPESP

A novel process described in an article published in the journal Electrochemistry Communications converts nitrogen and hydrogen to ammonia (NH3) at ambient temperature and pressure with high energy efficiency. Ammonia, a gas composed of nitrogen and hydrogen, is the world's most synthesized molecule and is used in agriculture as well as many production processes.

It does not emit CO2 when burned and is expected to become a next-generation fuel as it contains properties ideally suited for the hydrogen economy. Annual output of ammonia amounts to about 1.2 million metric tons.

In response to growing interest in decarbonization routes, researchers have recently turned their attention to the use of ammonia in fuel cells—electrochemical or galvanic cells that generate electricity from specific chemical reactions, such as the nitrogen reduction reaction (NRR).

NRR electrochemistry is studied with two main goals: production of a key industrial input and potential future fuel; and storing hydrogen in a molecule—ammonia—that can easily be diluted in water and transported more safely and cheaply than hydrogen alone. If ammonia fuel cell research initiatives are successful, global demand for ammonia will grow even more strongly.

The group used an electrochemical reactor to outperform the Haber-Bosch process, which releases large amounts of heat into the environment. Haber-Bosch is the primary industrial method of producing ammonia from nitrogen and hydrogen.

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Observing what happens in the first picosecond when a proton detaches from a dye after exposure to light
https://phys.org/news/2023-04-picosecon ... osure.html
by Ruhr-Universitaet-Bochum

In certain molecules, the so-called photoacids, a proton can be released locally by excitation with light. There is a sudden change in the pH value in the solution—a kind of fast switch that is important for many chemical and biological processes. Until now, however, it was still unclear what happens at the moment of proton release. This is exactly what researchers in the Cluster of Excellence Ruhr Explores Solvation RESOLV at Ruhr University Bochum, Germany, have now been able to observe in an experiment using new technology.

They observed a beating between solute and solvent initiating a tiny quake, lasting only three to five picoseconds, before the proton starts to detach. They report on this in the journal Chemical Sciences.
So far, the focus has been on dye or base

One of the most studied so-called photoacids is pyranine, the fluorescent dye used, for instance, in yellow highlighters. "Despite a wealth of experimental studies, the process that is at the very beginning of proton detachment still remained the subject of controversial debate," reports Professor Martina Havenith, spokesperson for RESOLV. However, the entire detachment process also happens on a time scale of only 90 picoseconds. A picosecond corresponds to a millionth of a millionth of a second.

While previous studies focused mainly on the change of the dye after light excitation, the team was able to observe the change of the solvent, in this case water, during this process for the first time. This was achieved with the help of a newly developed technique, "Optical Pump THz Probe Spectroscopy."

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Birch reduction simplified to a one-minute mechanochemical process
https://phys.org/news/2023-04-birch-red ... mical.html
by Hokkaido University

The traditionally cumbersome yet widely-used Birch reduction can now be carried out in a mere minute in air using an optimized mechanochemical approach.

The Birch reduction is a reaction commonly used to make medicines and bioactive compounds, but the laborious process typically requires that chemists handle liquid ammonia, use cryogenic temperatures, and carry out time-consuming steps.

Researchers at the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) in Hokkaido University have developed a simplified method for performing the Birch reduction that avoids the use of ammonia, can be done at room temperature and in ambient air, and is 20–150 times faster than conventional methods. Their findings are published in the journal Angewandte Chemie International Edition.

A number of lithium-based methods for performing the Birch reduction in solution have been previously developed, but since lithium reacts with both air and water, these processes still required complicated reaction setups with an inert atmosphere or dehydrated conditions. Researchers in this study saw an opportunity to avoid these issues by switching from a solution-based method to a solvent-less method using a ball mill, in which reactants are shaken rapidly in a small metal jar along with a metal ball that smashes the solid reactants together.

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Catalyst cleans up CO2 better with different preparation
https://phys.org/news/2023-05-catalyst-co2.html
by Utrecht University

An international research team led by Bert Weckhuysen (Utrecht University) and Sara Bals (University of Antwerp) has shown that a promising catalyst for clearing CO2 becomes significantly more active and selective if its pretreatment is modified. The scientists have visualized the mechanism underlying this concept with unparalleled precision. The results of the study are published in Science on May 11. Matteo Monai, Kellie Jenkinson and Angela Melcherts are the first authors.

Cleaning up carbon dioxide or converting it into something useful is becoming increasingly common, for example in the energy and transportation sectors, where huge amounts of the greenhouse gas are emitted. Catalysts are necessary for such a cleanup process to proceed properly and quickly. In the case of CO2 hydrogenation, which is a widely used chemical reaction to clean up CO2, a nickel-supported titanium dioxide catalyst is used.

In this study, the scientists show that the catalyst's performance is highly dependent on the temperature at which it is prepared. The selectivity and activity of the catalyst were much better during CO2 hydrogenation at a pretreatment temperature of 600°C than at 400°C. Better selectivity is desirable because the catalyst provides fewer unwanted by-products. Improved activity results in a faster progression of the catalytic reaction. The researchers expect the same principle to apply to catalysts with metal oxides other than titanium oxide.

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When crystals flow: Semicrystalline polymer shown to flow at temperatures below its melting point
https://phys.org/news/2023-05-crystals- ... tures.html
by Thamarasee Jeewandara , Phys.org

Semicrystalline polymers are solids that are assumed to flow only above their melting temperature. In a new study published in Science Advances, Chien-Hua Tu and a research team at the Max Planck Institute for Polymer Research in Germany and the University of Ioannina Greece confined crystals within nanoscopic cylindrical pores to show the flowing nature of semicrystalline polymers below their melting point, alongside an intermediate state of viscosity to the melt and crystal states.

The capillary process was strong during the phenomenon and dragged the polymer chains into the pores without melting the crystal. The unexpected improvement in flow facilitated polymer processing conditions applicable to low temperatures, suited for use in organic electronics.