First atomic-level video of catalytic reaction reveals hidden pathways

A Northwestern University-led international team of scientists has, for the first time, directly observed catalysis in-action at the atomic level.

In mesmerizing new videos, single atoms move and shake during a chemical reaction that removes hydrogen atoms from an alcohol molecule. By viewing the process in real time, the researchers discovered several short-lived intermediate molecules involved in the reaction as well as a previously hidden reaction pathway.

The observations were made possible by single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), a powerful instrument that enables researchers to watch individual molecules react in real time.

Observing reactions in this manner helps scientists understand how catalysts work. These new insights could potentially lead to designs for more efficient and sustainable chemical processes.

The study, “Atomic-resolution imaging as a mechanistic tool for studying single-site heterogeneous catalysis,” is published in the journal Chem.

“By visualizing this process and following the reaction mechanisms, we can understand exactly what’s happening in the finest detail,” said Northwestern’s Yosi Kratish, the study’s first and co-corresponding author.

“In the past, we haven’t been able to see how atoms move. Now we can. When I realized what we accomplished, I had to close my laptop and take a break for a few hours. Nobody has done this before in catalysis, so I was stunned.”

“Catalysts make modern life possible,” said Northwestern’s Tobin J. Marks, the study’s senior author. “They are used to make everything from fuel and fertilizers to plastics and medicines. To make chemical processes more efficient and environmentally friendly, we need to understand exactly how catalysts work at the atomic level. Our study is a big step toward achieving that.”

An expert in catalysis, Marks is the Charles E. and Emma H. Morrison Professor of Chemistry and Vladimir N. Ipatieff Professor of Catalytic Chemistry at Northwestern’s Weinberg College of Arts and Sciences and a professor of chemical and biological engineering at Northwestern’s McCormick School of Engineering.

Kratish is a research assistant professor of chemistry in Marks’ group. Marks and Kratish co-led the study with Michael Bedzyk, professor of materials science and engineering at McCormick, and George C. Schatz, the Charles E. and Emma H. Morrison Professor of Chemistry at Weinberg, as well as the University of Tokyo’s Professor Eiichi Nakamura, who invented SMART-EM, and Assistant Professor Takayki Nakamuro.

Catching fleeting molecules with ‘cinematic chemistry’

Researchers have long sought to observe live catalytic events at the atomic level. Chemical reactions are like a journey between starting materials and the final product. Along the journey, transient—and sometimes unexpected—molecules form and then abruptly transform into other molecules. Because these so-called “intermediate” molecules are unpredictable and fleeting, they are difficult to detect.

By directly watching the reaction unfold, however, scientists can determine the exact sequence of events to reveal the complete reaction pathway—and view those elusive intermediates. But, until recently, it was impossible to observe these covert dynamics.

While traditional electron microscopes can image atoms, their beams are too strong to image the soft, organic matter used in catalysis. The high-energy electrons easily break down carbon-based structures, destroying them before scientists can gather the data.

“Most conventional transmission electron microscopy techniques operate at conditions that easily damage organic molecules,” Kratish said. “This makes it extremely challenging to directly observe sensitive catalysts or organic matter during a reaction using traditional TEM methods.”

To overcome this challenge, the team turned to SMART-EM, a novel technique that can capture images of delicate organic molecules. Unveiled by Nakamura and his team in 2018, SMART-EM uses a much lower electron dose, minimizing the amount of energy—and damage—transferred to the sample. By capturing rapid sequences of images, SMART-EM generates videos of dynamic processes, which Nakamura calls “cinematic chemistry.”

“Since 2007, physicists have been able to realize a dream over 200 years old—the ability to see an individual atom,” Nakamura said in a 2019 statement. “But it didn’t end there. Our research group has reached beyond this dream to create videos of molecules to see chemical reactions in unprecedented detail.”

From messy to measurable

When applying SMART-EM to catalysis for the first time, the Northwestern team chose a simple chemical reaction: removing hydrogen atoms from an alcohol molecule. But first they needed to select the right catalyst. About 85% of industrial catalysts are heterogeneous, meaning they are solid materials that react with liquids and gases.

Although heterogeneous catalysts are stable and efficient, they are also messy, with many different surface sites where reactions might occur.

“Heterogeneous catalysts have many advantages,” Kratish said. “But there’s a major disadvantage: in many cases, they are a black box. They have an unknown number of sites where reactions can occur. So, we don’t fully understand where and how reactions take place. That means we cannot exactly figure out what part of the catalyst is most effective.”

To make the catalyst easier to study, the Northwestern team designed a single-site heterogeneous catalyst with a well-defined active site. The single-site catalyst comprised molybdenum oxide particles anchored to a cone-shaped carbon nanotube. Then, the team used SMART-EM to investigate how their catalyst facilitated the conversion of ethanol into hydrogen gas, a clean alternative to fossil fuels.

“Having a single site is a lot more convenient,” Kratish said. “We can pick a good site to monitor and really zoom into it.”

Unveiling a hidden pathway

Before the study, scientists posited that alcohol went straight to the catalyst, where it became hydrogen gas and aldehyde (a molecule that forms when an alcohol molecule oxidizes). From there, the aldehyde, which is a gas at room temperature, escaped into the air. But watching the process unfold revealed a different story.

Using SMART-EM, the researchers discovered the aldehyde doesn’t float away but instead sticks to the catalyst. They also found the aldehydes linked together to form short-chain polymers—a previously unknown step that appeared to drive the overall reaction. In another surprise, the researchers discovered the aldehyde also reacts with alcohol to form hemiacetal, an intermediate molecule that is then converted into other products.

To confirm these findings, the team used various microscopy techniques, X-ray analysis, theoretical models and computer simulations. All matched the SMART-EM data.

“This is a big breakthrough,” Kratish said. “SMART-EM is changing the way we look at chemistry. Eventually, we want to isolate those intermediates, control the amount of energy we put into the system and study the kinetics of a live organic catalytic transformation. That will be phenomenal. This is just the beginning.”