Author: chemistadmin

The Stach Group in Penn Engineering has led a collaborative team identifying how chemical catalysts drive the creation of liquid fuels from sunlight, paving the way for more efficient removal of greenhouse gases from the atmosphere.

“Imagine standing in a desert under a clear, starlit sky,” says Eric Stach, Robert D. Bent Professor of Engineering at the University of Pennsylvania. “With just your naked eye, you might spot the shimmering band of the Milky Way or the fuzzy glow of Andromeda. But without a telescope and other sophisticated tools, it’s nearly impossible to distinguish individual stars or truly understand their arrangement in the cosmos.”

Stach likens this experience to the challenge the team faced in trying to visualize molecular catalysts, the microscopic structures key to chemical reactions like converting carbon dioxide (CO₂) into usable fuels, on surfaces of semiconductor materials.

These catalysts, which contain heavy metal atoms, are scattered across surfaces in ways that are crucial to their performance, yet, like stars in the night sky, “their precise placement and clustering are difficult to discern with conventional techniques,” Stach says.

To that end, Stach and his collaborators at the University of North Carolina at Chapel Hill (UNC) and Yale University—working together as part of the Center for Hybrid Approaches in Solar Energy to Liquid Fuels— combined atomic-resolution imaging with machine learning analysis to better characterize the distribution of molecular catalysts.

The team published their findings on the determination of the conditions, behaviors, and qualities of different catalysts in the journal Matter.

“The project brought together researchers with complementary expertise in imaging, molecular synthesis, catalysis, and surface chemistry,” says Jillian L. Dempsey of UNC. “The collaboration was essential for visualizing how individual catalysts are distributed across semiconductor photoelectrodes.”

By providing a new understanding of how molecular catalysts behave on semiconductor surfaces, the team’s findings pave the way for more efficient catalytic systems. Advances could accelerate developments in renewable energy technologies, such as CO₂ conversion and hydrogen production, and offer insights applicable to a wide range of industrial processes.

“The elegance of our approach really lies in a simple yet powerful idea,” says Sungho Jeon, a postdoctoral researcher in the Stach Group and co-first author of the paper. “If you want to correlate variables, like how molecular coverage and distribution influence catalyst performance, you first have to measure them accurately.

“Our work shows how to precisely and robustly measure surface coverage, quantify distributions, and see how changing conditions, like the type of molecule or functionalization process, alters those properties.”

Making an atomic map

The team used High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF-STEM) carried out at the Singh Center for Nanotechnology at Penn. This generates images with atomic-level resolution by highlighting the contrast between heavy atoms, such as rhenium or platinum, and their lighter surroundings. While techniques like HAADF-STEM provide extraordinary detail, they only capture small regions at a time and give researchers massive datasets that can be tricky to analyze manually.

“Enter Sungho’s convolutional neural networks (CNNs),” Stach says. “It’s a type of machine learning that excels at pattern recognition. Sungho trained CNNs to detect individual atoms in HAADF-STEM images, which let us see them to systematically map the surface coverage and distribution of catalysts across their supports.”

This allowed the researchers to not only quantify the number of immobilized molecules but also understand whether they were clustered, evenly spaced, or randomly scattered—insights critical for optimizing catalytic performance.

Why does this matter? The spatial arrangement of catalysts can dramatically influence their efficiency and selectivity. Molecules that are too densely packed might interfere with each other, reducing their effectiveness. Conversely, evenly dispersed catalysts can increase reaction rates and improve outcomes.

“Understanding these details is a game-changer,” says Stach. “It’s the first step toward designing catalytic systems with precision, tailoring their structure to enhance their function.”

Do not destroy

The team also overcame major practical hurdles, like the fragility of molecular catalysts under the intense electron beams used for imaging. They developed sample preparation methods and stabilization techniques to protect the molecules, ensuring the images accurately reflected real-world conditions.

Stach explains that there was an initial concern that the high-energy electrons would “destroy everything” upon impact, potentially “knocking atoms around like pinballs,” rendering the images unreliable and making it impossible to accurately determine their true arrangement. So, the researchers employed new sample preparation techniques, including backfilling the surface with stabilizing molecules to minimize electron beam damage.

“We had to convince ourselves—and reviewers—that what we were imaging was real and not an artifact of the imaging process,” says Stach. He notes that this ensured that the molecular catalysts’ true distribution was captured without distortion. Through this approach, the researchers uncovered distinct patterns in how catalysts interacted with their surfaces.

The researchers observed that some molecules, like the CO₂-reducing Re-Phen, tended to cluster, while others, such as the hydrogen-evolving Pt-Porph, exhibited more dispersed arrangements. These differences, they found, were influenced by variables such as the choice of attachment group and the functionalization process used to bond the molecules to the surface.

“This work would not have been possible without the combined expertise of researchers across institutions,” says Nilay Hazari of Yale. “Each team brought unique skills that enabled us to perform these imaging experiments. The superb instrumentation at Penn, in particular, was crucial to our success.”

The clustering of catalysts like Re-Phen was found to potentially hinder catalytic efficiency due to interactions between neighboring molecules, while dispersed arrangements optimized performance.

Looking ahead, the team is already exploring how this methodology can be adapted to study catalysts on more complex surfaces, such as “porous materials that offer greater surface area but pose additional imaging challenges,” Stach says. “We would’ve never bothered with something this tricky a couple of years ago, but the information we got from this paper’s already paying tremendous dividends in the preliminary data.”

Hydrogen sulfide, a colorless gas that smells like rotten eggs, is produced naturally from decaying matter. This gas is lethal to breathe in, and hydrogen sulfide present in high concentrations can cause death very rapidly.

Its relative density is also greater than air, causing it to accumulate at lower altitudes and posing an enormous threat to workers at sites, such as manholes, sewage systems and mining operations.

Why is hydrogen sulfide so dangerous? It binds strongly to the heme-containing cytochrome c oxidase (CcO) enzyme and blocks the cellular process of aerobic (oxygen-dependent) respiration.

What is even more concerning is that, as of now, there is no identified antidote that can treat hydrogen sulfide poisoning. Hence, there is an urgent need to develop therapeutic agents that can be stored for long durations and are effective against hydrogen sulfide poisoning immediately.

A study led by Professor Hiroaki Kitagishi at Doshisha University and published online on December 10, 2024, in Scientific Reports has proposed a novel antidote for hydrogen sulfide poisoning.

Atsuki Nakagami, Ph.D. students in the Department of Applied Chemistry at the Graduate School of Doshisha University, Dr. Qiyue Mao, Specially Appointed Assistant Professor at Doshisha University, Associate Professor Masaki Horitani at the Faculty of Agriculture, Saga University, and Professor Masahito Kodera at the Faculty of Science and Engineering, Doshisha University, also contributed to the results of this study.

They decided to tackle this problem by using artificial heme-model compounds that would have a higher affinity towards hydrogen sulfide than the native hemes present in our bodies.

Providing more context to their approach, Prof. Kitagishi explains, “We have developed and studied synthetic heme-model compounds (hemoCDs) over the last two decades. The series of hemoCDs, which consist of porphyrin and cyclodextrins, is our original heme-model system that realizes the biological functions of hemes (like hemoglobin) while using completely synthetic materials.”

Previously, Prof. Kitagishi and his collaborators used two novel hemoCDs dubbed “hemoCD-Twins”—met-hemoCD-P and met-hemoCD-I—to successfully treat carbon monoxide and hydrogen cyanide poisoning in mice.

In this study, they decided to test if these two complexes had the potential to “scavenge” hydrogen sulfide in an aqueous medium. Interestingly, they found that met-hemoCD-I in particular had a very high affinity for hydrogen sulfide under normal physiological conditions—almost 10 times higher than that of human met-hemoglobin.

Met-hemoCD-I was able to convert toxic hydrogen sulfide into nontoxic sulfite and sulfate ions, indicating that it could be used to treat hydrogen sulfide poisoning.

To test this antidote, they injected hydrogen sulfide-treated mice with met-hemoCD-I. The results were very promising—mice injected with met-hemoCD-I showed improved survival rates compared to mice that were not given the antidote. Additionally, CcO activity in the brain and heart tissues (which had decreased because of poisoning) recovered and returned to normal.

Another aspect of met-hemoCD-I that makes it a very promising antidote is its demonstrated safety—it was found that injected met-hemoCD-I was excreted in the urine of the rats without undergoing any chemical decomposition in their body.

The results of this study show that hemoCD-Twins could be used as a powerful antidote to treat carbon monoxide, hydrogen cyanide, and now hydrogen sulfide poisoning without the risk of any side effects.

Explaining their vision for this treatment, Prof. Kitagishi says, “Using hemoCD-Twins, we can provide one powerful solution for multiple gas poisoning, even if the cause of poisoning is unknown. Worldwide, we still do not have an actual solution for accidentally occurring gas poisoning—we would like to supply hemoCD to fulfill this unmet medical need.”

In the future, they hope to bring this rapid and effective treatment to clinics and other medical settings. “We will proceed with non-clinical and clinical trials in cooperation with medical doctors in order to implement this compound as a therapeutic agent actually used in the world,” adds Prof. Kitagishi.

We are confident that this antidote will prove invaluable for improving the safety of workers and rescue personnel around the world.