Joel Bowman's view from the top of theoretical chemistry

"Imagine how sensational it would be if we could predict where and when a cloud will form," says Joel Bowman. Photo by Bryan Meltz, Emory Photo/Video.

By Carol Clark

As Joel Bowman flew across the country recently, on his way to collect the Herschbach Prize for theoretical chemistry, his attention turned to the clouds outside the jet’s window. What’s happening at the molecular level, he wondered, in a cloud at 30,000 feet?

“As we all know, clouds are essentially water in the gaseous state,” says Bowman, Samuel Candler Dobbs Professor of Theoretical Chemistry at Emory. “And, of course, it’s really cold at that altitude. So why do you find clouds at sub-zero temperatures? It’s an obvious but interesting question. The answer certainly has something to do with energy the cloud has absorbed from the sun and with potential energy surfaces: The delicate, attractive forces holding little water molecules together.”

Bowman’s work on developing potential energy surfaces is just one example of why he received the Herschbach Prize for Theory, presented in July at the Dynamics of Molecular Collisions 2013 Conference. The prize is named for Nobel Prize winning chemist Dudley Herschbach, who describes the award’s criteria as “bold and architectural work” that “addresses fundamental, challenging, frontier questions … and typically excites evangelical fervor that recruits many followers.”

The two-sided medal for the Herschbach Prize represents both theoretical (left) and experimental (right) molecular collision dynamics. The designer chose an angel for theory to symbolize “our yearning to attain an exalted, exhilarating comprehension."

Bowman was also recently elected to the International Academy of Quantum Molecular Sciences, and is lauded in the August 15 issue of the Journal of Physical Chemistry, the leading journal in its field. The cover art shows results from two of Bowman’s recent collaborations with experimentalists: One, concerning the dynamics of clusters of water molecules and another involving the complex kinetics of the chemicals in a comet. This special “Festschrift Issue” includes a tribute article to Bowman.

“These are all great honors to me,” says Bowman, who turned 65 this year and has no plans to retire. “Right now, I’m at the top of my game, the sweet spot of my career,” he says, citing four major research grants currently funding his group’s work.

Theoretical chemists do not work with chemicals: They write equations, analyze data and develop simulation models for molecular behaviors. It tends to be “a mature field,” Bowman says, where researchers hit their stride after years of experience, patience and perseverance.

Bowman is considered “one of the founding fathers of theoretical reaction dynamics,” the tribute authors write. (Click here to read the whole article, and more highlights from his career.) More recently, they add, he has made exceptional contributions to modeling potential energy surfaces, or PESs: “Without the PESs emerging from Joel’s group, many theorists would be unable to apply powerful methods of modern quantum dynamics to some of the most challenging problems of great current interest.”

Those problems include the molecular dynamics of water, a puzzle that particularly intrigues Bowman these days. During that cross-country plane flight, while most other passengers were probably trying not to think about things like turbulence and a stormy sky, Bowman took out his iPhone to make a video of lightning shooting through dark clouds (see below).



“What’s going on inside a cloud is extremely complicated, involving chemistry, physics, fluid dynamics and heat transfer, among other things,” Bowman says. “Clouds are full of energy, but parts of them can be cold while other parts are warming up. That’s a recipe for turbulence. Suddenly you can get a violent storm and boom! And all the action is taking place in what seems like just a simple little cloud. It’s mostly water.”

Currently, weather forecasting depends greatly on receiving continuous data from satellites and observing approaching fronts and other activity. “We can measure wind direction, high-and-low pressure, and use that information to create models, but that’s not nearly the level of data my research focuses on,” Bowman says.

Potential energy surfaces describe how water molecules bind together, and how much energy it takes to break them up into individual molecules.

“Imagine how sensational it would be if we could predict where and when a cloud will form,” Bowman says. “We’re getting closer to that ability, but we’re not there yet.”

Solving these kinds of puzzles could not only improve the accuracy of 10-day weather forecasts, it could help us predict long-term climate change, he says. “We don’t currently have the knowledge or the theoretical tools to fully understand what our climate will be like 20 to 30 years from now.”

Bowman is also exploring molecular mysteries underlying questions such as why we need water to live. “We know that we are made up of 70 to 80 percent water, and that without water, you cannot have life,” Bowman says. “And yet, from a chemical standpoint, we don’t really understand how water molecules interact with biological systems.”

"When I look at clouds, all kinds of questions come to my mind," Bowman says. Photo by Bryan Meltz, Emory Photo/Video.

Bowman joined Emory in 1986, during a time of rapid growth for the chemistry department. He has served as department chair, and helped establish Emory’s Emerson Center for Scientific Computation, becoming its acting director from 1991 to 1993. The center’s supercomputers are crucial to the Bowman Group’s work.

“Computer power has changed the field enormously,” Bowman says. “We can address problems and think about complicated chemical reactions in ways that people couldn’t dream of 20 years ago. Today, the computer winds up being almost like a laboratory where you can go in and do experiments.”

One challenge is to formulate the right question and get it onto the computer in a reasonable way, Bowman says. “Once you find the right question, and pose it correctly, getting the answer is often fairly straight-forward. Of course, then you have to interpret and understand the result that the computer spits out.”

While many of Bowman’s high-impact publications are collaborations with experimentalists, the theoretical work often begins with three or four members of his group sitting at a round table in his office, discussing a problem. “For me, the biggest joy is bouncing ideas around with my students and post-docs, questioning what’s known,” Bowman says. “And, of course, the discovery of things is a thrill. I get so excited they have to calm me down sometimes.”

Theoretical chemistry “is such a complex subject, involving math, physics, chemistry and computer science,” Bowman says. “Rather than intense focus on one thing, it involves carrying around a lot of data in your brain and thinking about many different things at the same time. That’s why when I look at clouds, all kinds of questions come to my mind and I start scratching my head.”

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Chemists map cascade of reactions for producing atmosphere's 'detergent'

"Our detailed data proves a much sharper view of the actual dynamics of the troposphere," says theoretical chemist Joel Bowman. In this NASA photo of the space shuttle Endeavor, silhouetted against Earth's atmosphere, the troposphere is the orange layer. The white layer is the stratosphere and the blue is the mesosphere.

By Carol Clark

Chemists have identified a cascade of reactions for how mysterious molecules known as Criegee intermediates generate hydroxyl radicals – an oxidant that helps remove pollutants from the lower atmosphere.

Nature Chemistry is publishing the findings, a collaboration of Emory University and the University of Pennsylvania.

“We’ve solved another piece of the puzzle in the formation of hydroxyl radicals, by zooming in to see all the steps of the reaction in much finer detail than ever before,” says co-author Joel Bowman, a theoretical chemist at Emory. “This kind of detailed data is important to atmospheric chemists trying to make predictive models for how the atmosphere will respond to climate change.”

The Bowman group collaborated with the lab of experimental chemist Marsha Lester at the University of Pennsylvania.

The theoretical work revealed that a Criegee intermediate first produces highly energized vinyl hydroperoxide, or VHP, then rapidly decomposes to hydroxyl radicals, along with vinoxy byproducts.

In 2014, Lester’s lab was the first to observe the creation of a hydroxyl radical by a Criegee intermediate in a laboratory setting. Many questions remained about the process, however, since it occurs so rapidly in the lab, as well as in the troposphere.

The turbulent troposphere, the lowest layer of Earth’s atmosphere, is where the weather happens. It’s like a giant washing machine filled with molecules – hydrogen, oxygen and nitrogen and all the other chemical byproducts of plant, animal and human activity that float up and mix with solar energy.

Hydroxyl radicals are sometimes called the detergent in this mix because they are extremely reactive to many common pollutants and greenhouse gases. When a hydroxyl radical encounters a molecule of sulfur dioxide, for instance, it steals its electrons and oxidizes it. Both the hydroxyl radical and the sulfur dioxide vanish, turning into an innocuous aerosol.

The troposphere, the lowest layer of Earth's atmosphere, is where the weather happens.

Most hydroxyl radicals are produced during the daytime as sunlight breaks down ozone, releasing oxygen atoms that react with water vapor and become hydroxyl radicals. About a third of the troposphere’s hydroxyl radicals, however, are produced through a more mysterious process that can even occur at night.

German scientist Rudolf Criegee proposed a hypothesis in 1949 for this process. He predicted the existence of another radical, known as the Criegee intermediate, as a step in the chain of reactions needed to produce hydroxyl radicals from ozone, without daytime solar energy.

“Alkene ozonolysis is a fancy term to describe the process Criegee proposed,” Bowman says. “The Criegee intermediate, or carbonyl oxide, is one of the stepping stones in the process, but it has a lot of energy so it breaks up right after it forms. The Criegee intermediate was certainly possible – it followed the rules governing how bonds form and rearrange – but for decades it remained hypothetical.”

It was not until 2012 that researchers managed to create a Criegee intermediate in a laboratory setting. That discovery was followed by the Lester lab’s 2014 work: Actually tracking a Criegee intermediate through the reaction that results in a hydroxyl radical, using a technique known as infrared action spectroscopy.

For the current Nature Chemistry paper, the Lester lab teamed with the Bowman group to combine its experiments with theoretical modeling.

As theorists, the chemists in the Bowman group can slow down time, in a sense, to study and measure a reaction in more detail. “We have developed sophisticated algorithms and software codes that allow us to study chemical reactions at the ultimate level of detail,” Bowman says. “Running the calculations for a reaction that occurs in picoseconds requires days of computer time, and we have to run it over and over again. The result is a mind-boggling data set, made up of billions of pieces, that we then have to analyze.”

The theoretical results both extended the experimental work and were validated by them, giving an unprecedented insight into the multi-step cascade of reactions.

“What actually happens in the wild is so much more complicated than in a controlled laboratory setting,” Bowman says. “Our detailed data provides a much sharper view of the actual dynamics of the troposphere.”

Sophisticated experimental techniques, high-powered computers and powerful new algorithms are driving advances faster than ever before, he adds.

“A lot of science done prior to 50 years ago, before computers, involved brilliant people, like Rudolf Criegee, doing hypothetical work that they could not prove,” Bowman says. “They would be bowled over by our capability now to actually settle many of these questions.”

Additional authors on the paper include Emory chemist Xiaohong Wang and University of Pennsylvania chemists Nathanael Kidwell and Hongwei Li.

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Chemists crack complete quantum nature of water

"Now that we have a good template for understanding how water molecules interact among themselves, we have a basis to deepen our understanding of the role of water in biochemical processes essential to life," says Joel Bowman,  Emory professor of theoretical chemistry.

Chemists have produced the first full quantum mechanical model of water — one of the key ingredients of life. The Journal of Physical Chemistry Letters published the breakthrough, which used machine learning to develop a model that gives a detailed, accurate description for how large groups of water molecules interact with one another. 

“We believe we have found the missing piece to a complete, microscopic understanding of water,” says Joel Bowman, professor of theoretical chemistry at Emory University and senior author of the study. “It appears that we now have all that we need to know to describe water molecules under any conditions, including ice, liquid or vapor over a range of temperature and pressure.” 

The researchers developed free, open-source software for the model, which they dubbed “q-AQUA.” The q-AQUA software provides a universal tool for studying water. 

“We anticipate researchers using it for everything from predicting whether an exoplanet may have water to deepening our understanding of the role of water in cellular function,” Bowman says. 

Read more about the discovery here. 

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Joel Bowman's view from the top of theoretical chemistry

Behaviors of tiniest water droplets revealed

Chemists modify rules for reaction rates

By Carol Clark

Theoretical chemists at Emory University have solved an important mystery about the rates of chemical reactions and the so-called Polanyi rules.

The findings, published in the journal Science, reveal why a reaction involving methane does not conform to the known rules, a problem that has baffled physical chemists in recent years.

“We showed that a pre-reactive, long-range force can align the reaction of a chorine atom with methane, or natural gas, in a way that actually inhibits the reaction,” says Joel Bowman, a professor of theoretical chemistry at Emory and the Cherry L. Emerson Center for Computational Chemistry. “We believe that the theoretical work that we did has extended and modified the Polanyi rules.”

Bowman published the results with Gabor Czako, a post-doctoral fellow in theoretical chemistry who performed most of the complex computational and mathematical analyses that uncovered the results.

Long-range, their findings could play a role in the development of cleaner, more efficient fuels.

The reactive properties of methane are of particular interest, since it is an important fuel. Photo by Carol Clark.

Understanding the dynamics of chemical reactions is key to driving reactions efficiently, whether in a laboratory experiment or in an industrial application. In 1986, John Polanyi shared the Nobel Prize in chemistry, in part by providing general rules for how different forms of energy affect the rates of reactions.

“The Polanyi rules tell you the best way to deposit energy in a simple molecule to make a chemical reaction occur,” Bowman says. “It’s a bit like knowing in advance how to invest $1,000 to maximize the return on investment.”

Polanyi developed the framework based on studies of simple reactions of chlorine and fluorine atoms with hydrogen gas. As technology has advanced in recent years, some chemists began testing the Polanyi rules for more complicated reactions, and the rules appeared to break down. Most notably, sophisticated molecular beam experiments by Kopin Liu at the Institute of Atomic and Molecular Sciences in Taiwan showed that the reaction of halogen atoms with methane did not conform to the rules.

“Suddenly, the rules appeared to have changed, and no one could explain why,” Bowman says. “We decided to roll up our sleeves and attack the problem theoretically.”

Bowman and Czako drew from the computational power of the Emerson Center, specialized software and analytical techniques. They first created theoretical-computational simulations of the experiments done by Liu and others, and then described the results mathematically.

“Our calculations showed essentially an exact agreement with the experimental results,” Bowman says. “When theory and experiment agree you’re happy, but you still want to know why.”

Determining why the reactions did not conform to the Polanyi rules was another complicated task, involving quantum mechanics and forces that govern the reaction down to the atomic level.

“As theoreticians, we’re able to zoom in and look at the results of our calculations in a way that’s virtually impossible in an experiment,” Bowman says.

They identified a subtle interplay between the Polanyi rules and a pre-reactive long-range force of methane with chlorine. If you follow the Polanyi rules, this long-range force, or steric control, will misalign the reactants, preventing them from docking correctly and inhibiting a reaction. But if you apportion the energy in the opposite way to the rules, the misalignment is wiped out and the reaction occurs.

“This long-range force was playing a bigger role than was previously realized,” Bowman says. “It can actually trump the Polanyi rules, at least in the reactions that Liu and we looked at. The Polanyi rules are certainly not all wrong, they just appear to be too simple to apply to more complex reactions.”

The research was funded by the National Science Foundation and the U.S. Department of Energy.

The reactive properties of natural gas are of particular interest since it is an important fuel. Bowman and Czako are now applying their techniques to study the combustion of methane and oxygen, which produces carbon dioxide. “It’s important to understand the dynamics of this reaction, because it might lead to more efficient ways to produce fuel, and a reduction in the levels of pollution emitted,” Bowman says.

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Behaviors of tiniest water droplets revealed

Water mediates all biological processes, but we still don't fully understand its behavior.

From Science Daily:

“A new study by researchers at the University of California, San Diego, and Emory University has uncovered fundamental details about the hexamer structures that make up the tiniest droplets of water, the key component of life – and one that scientists still don't fully understand.

“The research, recently published in the Journal of the American Chemical Society, provides a new interpretation for experimental measurements as well as a vital test for future studies of our most precious resource. Moreover, understanding the properties of water at the molecular level can ultimately have an impact on many areas of science, including the development of new drugs or advances in climate change research.

A 3-D model of the prism structure of the water hexamer, the smallest drop of water. "Ours are the first simulations that use an accurate, full-dimensional representation of the molecular interactions and exact inclusion of nuclear quantum effects through state-of-the-art computational approaches," says study co-author Joel Bowman, a theoretical chemist at Emory University. "These allow ws to accurately determine the stability of the different isomers over a wide range of temperatures."

‘"About 60% of our bodies are made of water that effectively mediates all biological processes,’ said Francesco Paesani, a study co-author and a biochemist at UC San Diego. ‘Without water, proteins don't work and life as we know it wouldn't exist. Understanding the molecular properties of the hydrogen bond network of water is the key to understanding everything else that happens in water. And we still don't have a precise picture of the molecular structure of liquid water in different environments.’

“As described in the JACS paper, researchers have determined the relative populations of the different isomers of the water hexamer as they assemble into various configurations called 'cage', 'prism', and 'book'.

A 3-D model of the cage structure of the water hexamer. The mesh contours represent the actual quantum-mechanical densities of the oxygen (red) and hygrogen (white) atoms. The small yellow spheres represent the hydrogen bonds between the six water molecules. Model images courtesy of UC San Diego.

“The water hexamer is considered the smallest drop of water because it is the smallest water cluster that is three dimensional, i.e., a cluster where the oxygen atoms of the molecules do not lie on the same plane. As such, it is the prototypical system for understanding the properties of the hydrogen bond dynamics in the condensed phases because of its direct connection with ice, as well as with the structural arrangements that occur in liquid water.

“This system also allows scientists to better understand the structure and dynamics of water in its liquid state, which plays a central role in many phenomena of relevance to different areas of science, including physics, chemistry, biology, geology, and climate research. For example, the hydration structure around proteins affects their stability and function, water in the active sites of enzymes affects their catalytic power, and the behavior of water adsorbed on atmospheric particles drives the formation of clouds.”

Read the whole article in Science Daily.

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Top photo by iStockphoto.com.