Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Supercomputing the 'how' of chemical reactions

31.07.2018

Researchers from the University of Texas Rio Grande Valley use systems at the Texas Advanced Computing Center to uncover the mechanisms behind chemical reactions

Sometimes, when experimental scientists get their hands on a supercomputer, it can change the course of their careers and open up new questions for exploration.


This is an animation showing the lowest energy transition state for the formation of cyclopentenones, which are found in a large number of natural products, including jasmin oils, aflatoxins, and several prostaglandins.

Credit: Tülay Atesin, Gabriela Martinez, and David Flores

This was the case with Abdurrahman and Tülay Atesin, husband and wife chemists, collaborators and professors at the University of Texas Rio Grande Valley. Experimentalists by training, when they moved to Texas in 2013, a colleague told them that through the University of Texas Research Cyberinfrastructure initiative they had free access to some of the advanced computing systems in the world 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," said Tülay. "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."

Over the past five years, the Atesins have used TACC supercomputers - initially Longhorn, Lonestar and Stampede, then Lonestar5 and now Stampede2 - to study organometallic compounds: chemical compounds that contain bonds between a carbon atom of an organic molecule and a metal.

Organometallic compounds are widely used in industrial applications and serve as catalysts for the production of polymers, pharmaceuticals, and many other types of practical products. However, it isn't the end products that interest the Atesins as much as the process molecules go through to get there.

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

In July 2018, the Atesins, working with UTRGV collaborators Oscar Rodriguez, Diego Rivera, and Lohany Garcia, published the results of a study in Computational and Theoretical Chemistry exploring the structure of a palladium catalyst in order to understand the exceptional selectivity observed in palladium-catalyzed reactions.

The results supported their hypothesis that the most stable form of the molecule is chair-shaped and that repulsion between this conformation and the substrate (the substance on which the molecule acts) dictates which ultimate final product forms.

To arrive at this conclusion, the researchers performed molecular mechanical calculations to generate 53 unique structures that could potentially represent phosphoramidites -- a class of versatile molecules with a range of applications for catalysis. They then used quantum mechanical calculations on the Stampede supercomputer at TACC to further analyze these structures and determine which had the lowest energy (and therefore were the most likely to occur in nature) and to assess the forces at work when they reacted.

The research findings can be used to understand the observed selectivity in many impactful palladium-catalyzed reactions and to guide the synthesis of new and improved variants of this important catalyst family.

In separate research reported in Organometallics in September 2017, they explained the mechanism of a reaction that many 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 Atesin said. In 2012, when the reaction was first reported, "the mechanism was unknown. So, we studied what the mechanism could be."

What they discovered was the first known example of the use of an "asymmetric allylic alkylation reaction" for the synthesis of a chiral cyclopentenone. (Chirality is a characteristic of a molecule that means it cannot be superimposed on its mirror image.)

To uncover the mechanism, they used a computational method known as density functional theory, or 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 changes of the constituent molecules. They also performed simulations with and without palladium - essentially running blank experiments that are impossible to perform in the lab. The researchers then visualized these simulations to understand what was happening to the molecules at all of the intermediate 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 show each potential step of the process, including intermediates, which helps scientists generate new hypotheses and theories about how the reaction occurs.

"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."

The most important advantage of the process they unearthed is that it is 100 percent efficient and forms a complex without the addition of other substances. Research in this vein may one day allow chemists to synthesize materials - in particular natural compounds and other bioactive molecules with all-carbon-atom centers -- that are currently difficult to create. It may even lead to entirely new types of chemical reactions that are not currently known or used.

Mechanistic studies using TACC resources give the Atesins a competitive edge in their work, 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."

Media Contact

Aaron Dubrow
aarondubrow@tacc.utexas.edu
512-471-8217

 @TACC

http://www.tacc.utexas.edu/ 

Aaron Dubrow | EurekAlert!
Further information:
https://www.tacc.utexas.edu/-/supercomputing-the-how-of-chemical-reactions
http://dx.doi.org/10.1016/j.comptc.2018.07.007

Further reports about: Advanced Computing Supercomputing TACC chemical reactions

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: High-pressure scientists in Bayreuth discover promising material for information technology

Researchers at the University of Bayreuth have discovered an unusual material: When cooled down to two degrees Celsius, its crystal structure and electronic properties change abruptly and significantly. In this new state, the distances between iron atoms can be tailored with the help of light beams. This opens up intriguing possibilities for application in the field of information technology. The scientists have presented their discovery in the journal "Angewandte Chemie - International Edition". The new findings are the result of close cooperation with partnering facilities in Augsburg, Dresden, Hamburg, and Moscow.

The material is an unusual form of iron oxide with the formula Fe₅O₆. The researchers produced it at a pressure of 15 gigapascals in a high-pressure laboratory...

Im Focus: From China to the South Pole: Joining forces to solve the neutrino mass puzzle

Study by Mainz physicists indicates that the next generation of neutrino experiments may well find the answer to one of the most pressing issues in neutrino physics

Among the most exciting challenges in modern physics is the identification of the neutrino mass ordering. Physicists from the Cluster of Excellence PRISMA+ at...

Im Focus: Therapies without drugs

Fraunhofer researchers are investigating the potential of microimplants to stimulate nerve cells and treat chronic conditions like asthma, diabetes, or Parkinson’s disease. Find out what makes this form of treatment so appealing and which challenges the researchers still have to master.

A study by the Robert Koch Institute has found that one in four women will suffer from weak bladders at some point in their lives. Treatments of this condition...

Im Focus: A step towards controlling spin-dependent petahertz electronics by material defects

The operational speed of semiconductors in various electronic and optoelectronic devices is limited to several gigahertz (a billion oscillations per second). This constrains the upper limit of the operational speed of computing. Now researchers from the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg, Germany, and the Indian Institute of Technology in Bombay have explained how these processes can be sped up through the use of light waves and defected solid materials.

Light waves perform several hundred trillion oscillations per second. Hence, it is natural to envision employing light oscillations to drive the electronic...

Im Focus: Freiburg researcher investigate the origins of surface texture

Most natural and artificial surfaces are rough: metals and even glasses that appear smooth to the naked eye can look like jagged mountain ranges under the microscope. There is currently no uniform theory about the origin of this roughness despite it being observed on all scales, from the atomic to the tectonic. Scientists suspect that the rough surface is formed by irreversible plastic deformation that occurs in many processes of mechanical machining of components such as milling.

Prof. Dr. Lars Pastewka from the Simulation group at the Department of Microsystems Engineering at the University of Freiburg and his team have simulated such...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

70th Lindau Nobel Laureate Meeting: Around 70 Laureates set to meet with young scientists from approx. 100 countries

12.02.2020 | Event News

11th Advanced Battery Power Conference, March 24-25, 2020 in Münster/Germany

16.01.2020 | Event News

Laser Colloquium Hydrogen LKH2: fast and reliable fuel cell manufacturing

15.01.2020 | Event News

 
Latest News

New molten metal hybrid filters from TU Freiberg will make components even safer and more resistant in the future

28.02.2020 | Materials Sciences

Polymers get caught up in love-hate chemistry of oil and water

28.02.2020 | Life Sciences

Two NE tree species can be used in new sustainable building material

28.02.2020 | Architecture and Construction

VideoLinks
Science & Research
Overview of more VideoLinks >>>