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Understanding Mechanisms Behind Chemical Reactions Using Supercomputers

On occasion when experimental scientists get to work on a supercomputer, it can alter the course of their professions and pave way for new questions for exploration.

Dr. Abdurrahman Ateşin, UTRGV lecturer II, chemistry, and his wife, Dr. Tülay Ateşin, UTRGV assistant professor of chemistry, photographed on Friday, July 26, 2018, on the UTRGV Edinburg Campus. (UTRGV Photo by Paul Chouy)

This was the scenario with Abdurrahman and Tülay Ateşin, husband and wife chemists, collaborators and professors at the University of Texas Rio Grande Valley. Experimentalists by training, when they relocated to Texas in 2013, a colleague informed them that through the University of Texas Research Cyberinfrastructure initiative they had free access to some of the world’s advanced computing systems at the Texas Advanced Computing Center (TACC).

We weren't planning on doing intensive computational studies, but once we were introduced to resources at TACC it opened our research horizons to collaborate with other groups within UT system and other parts of the country. It has been extremely helpful for both of our research groups and our research productivity. Having TACC resources helped us a great amount in continuing our research.

Tülay Ateşin

In the last five years, the Ateşins have employed TACC supercomputers - at first Longhorn, Lonestar, and Stampede, then Lonestar5 and now Stampede2 - to examine organometallic compounds: chemical compounds that have bonds between a carbon atom of an organic molecule and a metal.

Organometallic compounds are extensively used in industrial applications and act as catalysts for the manufacture of pharmaceuticals, polymers, and many other types of practical products. However, it is not the final products that concern the Ateşins as much as the process molecules undergo to get there.

Their most recent research involves with the element, palladium, and its role in synthesizing cyclopentenones - five-membered rings which play a role in varied compounds like the scent of jasmine and prostaglandins, a lipid that triggers hormone-like effects in animals.

In July 2018, the Ateşins, working with UTRGV collaborators Oscar Rodriguez, Diego Rivera, and Lohany Garcia, published the results of a research in Computational and Theoretical Chemistry investigating the structure of a palladium catalyst so as to understand the excellent selectivity seen in palladium-catalyzed reactions.

The results confirmed their hypothesis that the molecule’s most stable form is chair-shaped and that repulsion between this conformation and the substrate (the substance on which the molecule acts) commands which ultimate end-product forms.

To reach this inference, the scientists performed molecular mechanical calculations to produce 53 unique structures that could potentially signify phosphoramidites—a group of versatile molecules with a variety of applications for catalysis. They then used quantum mechanical calculations on the Stampede supercomputer at TACC to further examine these structures and establish which had the lowest energy (and therefore were the most probable to occur in nature) and to measure the forces at play when they reacted.

The study findings can be used to comprehend the observed selectivity in a number of impactful palladium-catalyzed reactions and to guide the synthesis of new and enhanced variants of this vital catalyst group.

In a separate study reported in Organometallics in September 2017, they elucidated the mechanism of a reaction which a number of scientists thought was a "Nazarov" reaction since the reactants and the products of the reaction are the same as a classical "Nazarov" reaction.

"Everyone in the field thought that palladium(0) does not function as a Lewis acid, but its role was not clear," Tülay Ateşin said. In 2012, when the reaction was first stated, "the mechanism was unknown. So, we studied what the mechanism could be."

What they discovered was the first identified instance of the use of an "asymmetric allylic alkylation reaction" for the synthesis of a chiral cyclopentenone. (Chirality is a molecule’s feature meaning that it cannot be superimposed on its mirror image.)

To reveal the mechanism, they used a computational technique called density functional theory (DFT), according to Abdurrahman.

"With DFT, we input a beginning structure and a final structure that we've determined experimentally, and we try different routes and approaches to see how you can connect those," he said. "This requires some chemical intuition into what the metal can do and some luck as well."

DFT simulations on Stampede revealed the proton transfer and ring formation processes, as well as the energy levels and geometry variations of the constituent molecules. They also performed simulations with and without palladium - basically running blank experiments that are difficult to do in the lab. The scientists then envisioned these simulations to comprehend what was taking place to the molecules at all of the in-between stages.

"It's difficult to isolate reaction intermediates and transition states in the lab, because they're so short-lived," Tülay said. However, computer simulations can illustrate each probable step of the process, including intermediates, which helps researchers come up with new hypotheses and theories about how the reaction takes place.

"We never thought we'd have discovered these intermediates," Tülay said. "We weren't looking for an allylic alkylation reaction. We were asking, ‘What if the metal is here? What if it's there?' And that led us to see what other possibilities were out there in terms of the mechanisms."

They discovered that the most central advantage of the process is that it is 100% efficient and forms a complex without the incorporation of other substances. Research in this line may allow chemists to synthesize materials one day—especially natural compounds and other bioactive molecules with all-carbon-atom centers—that are presently hard to create. It may even pave the way to totally new types of chemical reactions that are not presently known or applied.

Mechanistic studies using TACC resources offer the Ateşins a competitive edge in their research, Tülay said. "It takes our research to a higher level than just working on experimental research. It also impacts how we design our next set of experiments."

Teaching Critical Thinking through Computation

While the Ateşins are pleased with their research development, they are likewise satisfied by their role as teachers.

"Understanding the mechanisms of chemical reactions is very difficult, but it's important for our students to learn in order for them to be critical thinkers and not just doers," Tülay said.

Students, including high school students taking part in summer programs, have the chance to interpret the Ateşins' computational studies and learn how advanced computing can be used in chemistry.

"They're getting the opportunity to expand their critical thinking skills with state-of-the-art computational resources," she said. "It challenges them and the way that they think changes. I enjoy seeing their growth."

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