How simulations could help get PFAS out of soil

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There are many ways PFAS can enter the environment, all of which increase the odds of finding these chemicals in our food or water. Credit: Michigan Department of Environment, Great Lakes and Energy

Michigan State University chemists are discovering new information to help remediate “forever chemicals” by showing for the first time how they interact with soil at the molecular level.

The researchers, Narasimhan Loganathan and Angela K. Wilson in the College of Natural Science, published their findings online in the journal Environmental Science & Technology.

“Forever chemicals”—more formally known as PFAS or perfluoroalkyl and polyfluoroalkyl substances—earned the label because they don’t break down naturally. When PFAS pollute soil and water, they can enter the food system through plants, livestock and drinking water.

A Centers for Disease Control and Prevention report from 2015 estimated that PFAS is in the blood of 97% of Americans. Other, more recent studies have put that number closer to 99%.

What makes PFAS so ubiquitous is a combination of persistence and utility. More than 9,000 chemicals qualify as PFAS and they’re found in a wide range of applications, including food packaging, nonstick cookware, firefighting foams and many more. While time and nature can degrade certain components of these products—and of the waste generated in producing them—the PFAS lingers, accumulating in the environment.

Removing PFAS from soil and water, then, is important for reducing exposure to these chemicals and the harm they can cause, including thyroid disease and increased risk of some cancers.

“When you start looking at , you see a lot about removing PFAS from water, but there’s very little about PFAS in soil,” said Loganathan, a senior research associate in MSU’s Department of Chemistry.

“And some of the studies are ‘molecule blind,'” said Wilson, John A. Hannah Distinguished Professor of chemistry and a scientist with the MSU Center for PFAS Research. “That is, they’re not paying attention to the chemistry.”

Wilson and Loganathan decided to help change that by performing the first molecular-level simulations of interactions between PFAS with a soil component, kaolinite.

For the study, the duo focused on some of the most prevalent and problematic PFAS chemicals. They chose kaolinite on the soil side because it is a common soil mineral, especially in Michigan.

PFAS are a concern everywhere, but they present a unique challenge in Michigan. Michigan has an abundance of PFAS, with more than 200 known PFAS-contaminated sites. On top of that, agriculture and the Great Lakes are foundational to the state’s identity. Protecting Michigan’s land and water is a shared goal of many of the state’s communities, legislators and companies.

“Even before this work, we were going to huge meetings and talking about PFAS with people from different municipalities, farms, and more,” Wilson said. “A lot of people are looking for solutions.”

The study was inspired by a Michigan engineering firm that asked Wilson about how PFAS might spread in soil and how best to remediate the chemicals. She didn’t have the answers, but she knew Loganathan could help her start finding some.

She recruited him to join this project, supported by the National Science Foundation. The duo also had access to provided by the National Energy Research Scientific Computing Center and MSU’s Institute for Cyber-Enabled Research, or iCER.

The results of the simulations did provide some reasons for optimism with regard to remediation. For example, some of the PFAS the researchers studied that had longer carbon chains serving as their backbones congregated on the kaolinite.

“Ideally, this is what you’d want. You’d like all PFAS just to sit in a clump so you can grab it and filter it out,” Wilson said. The flipside is that the shorter-chained PFAS were less likely to clump, remaining more mobile in soil.

“The take-home message is that not all PFAS behave similarly,” Wilson said. “And not all soils behave the same with regard to PFAS.”

“The components in the soil play a big role,” Loganathan said. “The soil composition around any contaminated site is going to be critical for how far PFAS make it into the subsurface, where they can then reach groundwater.”

Although the idea of examining the myriad combinations of PFAS and soil components is imposing, the researchers have shown their computational approach is well-suited to tackling the diversity of problems inherent to PFAS pollution.

“The beauty of computational chemistry is that you can study so many different systems,” said Wilson, whose research team is also examining interactions of PFAS with proteins in the body. Her team is also studying PFAS in different fish species with support from Great Lakes Fisheries Trust and the Strategic Environmental Research and Development Program, which are state and federal organizations, respectively, that fund environmental projects. The goal, in the and biology projects, is to reveal interactions that could help protect more people from PFAS exposure.

“Such insights are going to be incredibly important for any remediation strategy,” Loganathan said.

More information:
Narasimhan Loganathan et al, Adsorption, Structure, and Dynamics of Short- and Long-Chain PFAS Molecules in Kaolinite: Molecular-Level Insights, Environmental Science & Technology (2022). DOI: 10.1021/acs.est.2c01054

How simulations could help get PFAS out of soi

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Hexbyte Glen Cove Simulations show using novel wheat genotypes coupled with deep sowing can increase yields

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Credit: CC0 Public Domain

A quartet of researchers with CSIRO Agriculture & Food in Australia has found via simulations that planting novel wheat genotypes using deep sowing could increase yields. In their paper published in the journal Nature Climate Change, Zhigan Zhao, Enli Wang, John Kirkegaard and Greg Rebetzke, describe how they used data from a variety of sources to create a simulation to show how wheat yields in Australia might be increased as conditions grow warmer and drier.

Most large-scale wheat farming operations, including those in Australia, are based on semi-dwarf varietals that were developed decades ago to increase yields. Such varieties increased yields because they were less prone to damage from wind and because they took less time to mature and were more responsive to fertilizer. But they have an Achilles heel—short coleoptiles.

Coleoptiles are sheathings that protect young shoots. The shortness means they need moist soil near the surface to survive. But as progresses, soil near the surface grows warmer and drier. And because of that, scientists in Australia are worried that the semi-dwarf varieties will not grow under the increasingly hot sun found in Australia’s wheat fields. The researchers with this new effort suggest the solution is clear—Australian wheat farmers need to switch to newer varieties of wheat—ones that have longer coleoptiles allowing them to reach down deeper into the soil where it is wetter. They also need to plant their crops earlier to allow them to mature before the hottest summer weather arrives.

To come to these conclusions, the researchers developed a framework that allowed for integrating the physiological effects of gibberellic-acid-sensitive dwarfing genes on coleoptile growth and the vigor they might show in the real world. They then added data from both the real world and the framework into an agricultural production system simulator that took into account the conditions that are likely to exist in the parts of Australia used for growing wheat as the planet warms.

The simulations showed that switching to such novel wheat genotypes and also using deeper and earlier sowing could increase yields by 18 to 20%, under current conditions. They claim their simulations suggest that such changes could also help to prevent crop loss due to warming temperatures. And they further suggest that the same approach could also be used to prevent yield decreases in other parts of the world in the coming years.

More information:
Zhigan Zhao et al, Novel wheat varieties facilitate deep sowing to beat the heat of changing climates, Nature Climate Change (2022). DOI: 10.1038/s41558-022-01305-9

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Simulations show using novel wheat genotypes coupled with deep sowing can increase yields (2022, March 9)
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Hexbyte Glen Cove Simulations show iron catalyzes corrosion in ‘inert’ carbon dioxide

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Iron (blue) can react with trace amounts of water to produce corrosive chemicals despite being bathed in “inert” supercritical fluids of carbon dioxide. Atomistic simulations carried out at Rice University show how this reaction happens. Credit: Evgeni Penev/Rice University

Iron that rusts in water theoretically shouldn’t corrode in contact with an “inert” supercritical fluid of carbon dioxide. But it does.

The reason has eluded to now, but a team at Rice University has a theory that could contribute to new strategies to protect iron from the environment.

Materials theorist Boris Yakobson and his colleagues at Rice’s George R. Brown School of Engineering found through atom-level simulations that iron itself plays a role in its own corrosion when exposed to supercritical CO2 (sCO2) and trace amounts of water by promoting the formation of reactive species in the fluid that come back to attack it.

In their research, published in the Cell Press journal Matter, they conclude that thin hydrophobic layers of 2D materials like graphene or could be employed as a barrier between and the reactive elements of sCO2.

Rice graduate student Qin-Kun Li and research scientist Alex Kutana are co-lead authors of the paper. Rice assistant research professor Evgeni Penev is a co-author.

Supercritical fluids are materials at a temperature and pressure that keeps them roughly between phases—say, not all liquid, but not yet all gas. The properties of sCO2 make it an ideal working fluid because, according to the researchers, it is “essentially inert,” noncorrosive and low-cost.

“Eliminating corrosion is a constant challenge, and it’s on a lot of people’s minds right now as the government prepares to invest heavily in infrastructure,” said Yakobson, the Karl F. Hasselmann Professor of Materials Science and NanoEngineering and a professor of chemistry. “Iron is a pillar of infrastructure from ancient times, but only now are we able to get an atomistic understanding of how it corrodes.”

The Rice lab’s simulations reveal the devil’s in the details. Previous studies have attributed corrosion to the presence of bulk water and other contaminants in the superfluid, but that isn’t necessarily the case, Yakobson said.

“Water, as the primary impurity in sCO2, provides a hydrogen bond network to trigger interfacial reactions with CO2 and other impurities like and to form corrosive acid detrimental to iron,” Li said.

The simulations also showed that the iron itself acts as a catalyst, lowering the reaction energy barriers at the interface between iron and sCO2, ultimately leading to the formation of a host of corrosive species: oxygen, hydroxide, carboxylic acid and nitrous acid.

To the researchers, the study illustrates the power of theoretical modeling to solve complicated chemistry problems, in this case predicting thermodynamic reactions and estimates of corrosion rates at the interface between and sCO2. They also showed all bets are off if there’s more than a trace of water in the superfluid, accelerating corrosion.

More information:
Qin-Kun Li et al, Iron corrosion in the “inert” supercritical CO2, ab initio dynamics insights: How impurities matter, Matter (2022). DOI: 10.1016/j.matt.2021.12.019

Simulations show iron catalyzes corrosion in ‘inert’ carbon dioxide (2022, January 21)
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Hexbyte Glen Cove Do simulations represent the real world at the atomic scale? thumbnail

Hexbyte Glen Cove Do simulations represent the real world at the atomic scale?

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Pictorial representation of joint experimental and computational study of materials. The study utilized the Advanced Photon Source (upper panel) and Argonne Leadership Computing Facility (lower panel). The team addressed the atomistic structure of interfaces, which are ubiquitous in materials. Credit: Emmanuel Gygi, University of California, San Diego

Computer simulations hold tremendous promise to accelerate the molecular engineering of green energy technologies, such as new systems for electrical energy storage and solar energy usage, as well as carbon dioxide capture from the environment. However, the predictive power of these simulations depends on having a means to confirm that they do indeed describe the real world.

Such confirmation is no simple task. Many assumptions enter the setup of these simulations. As a result, the simulations must be carefully checked by using an appropriate “validation protocol” involving experimental measurements.

“We focused on a solid/liquid interface because interfaces are ubiquitous in materials, and those between oxides and water are key in many energy applications.”—Giulia Galli, theorist with a joint appointment at Argonne and the University of Chicago

To address this challenge, a team of scientists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory, the University of Chicago and the University of California, Davis, developed a groundbreaking validation protocol for simulations of the atomic structure of the interface between a solid (a metal oxide) and . The team was led by Giulia Galli, a theorist with a joint appointment at Argonne and the University of Chicago, and Paul Fenter, an Argonne experimentalist.

“We focused on a solid/liquid interface because interfaces are ubiquitous in materials, and those between oxides and water are key in many energy applications,” said Galli.

“To date, most validation protocols have been designed for bulk materials, ignoring interfaces,” added Fenter. “We felt that the atomic-scale structure of surfaces and interfaces in realistic environments would present a particularly sensitive, and therefore challenging, validation approach.”

The validation procedure they designed uses high-resolution X-ray reflectivity (XR) measurements as the experimental pillar of the protocol. The team compared XR measurements for an aluminum oxide/water interface, conducted at beamline 33-ID-D at Argonne’s Advanced Photon Source (APS), with results obtained by running high-performance at the Argonne Leadership Computing Facility (ALCF). Both the APS and ALCF are DOE Office of Science User Facilities.

“These measurements detect the reflection of very high energy X-ray beams from an oxide/water interface,” said Zhan Zhang, a physicist in Argonne’s X-ray Science division. At the beam energies generated at the APS, the X-ray wavelengths are similar to interatomic distances. This allows the researchers to directly probe the molecular-scale structure of the .

“This makes XR an ideal probe to obtain experimental results directly comparable to simulations,” added Katherine Harmon, a graduate student at Northwestern University, an Argonne visiting student and the first author of the paper. The team ran the simulations at the ALCF using the Qbox code, which is designed to study finite temperature properties of materials and molecules using simulations based on quantum mechanics.

“We were able to test several approximations of the theory,” said Francois Gygi from the University of California, Davis, part of the team and lead developer of the Qbox code. The team compared measured XR intensities with those calculated from several simulated structures. They also investigated how X-rays scattered from the electrons in different parts of the sample would interfere to produce the experimentally observed signal.

The endeavor of the team turned out to be more challenging than anticipated. “Admittedly, it was a bit of a trial and error at the beginning when we were trying to understand the right geometry to adopt and the right theory that would give us accurate results,” said Maria Chan, a co-author of the study and scientist at Argonne’s Center for Nanoscale Materials, a DOE Office of Science User Facility. “However, our back and forth between theory and experiment paid off, and we were able to set up a robust validation protocol that can now be deployed for other interfaces as well.”

“The validation protocol helped quantify the strengths and weaknesses of the simulations, providing a pathway toward building more accurate models of solid/liquid interfaces in the future,” said Kendra Letchworth-Weaver. An assistant professor at James Madison University, she developed software to predict XR signals from simulations during a postdoctoral fellowship at Argonne.

The simulations also shed new insight on the XR measurements themselves. In particular, they showed that the data are sensitive not only to the atomic positions, but also to the electron distribution surrounding each atom in subtle and complex ways. These insights will prove beneficial to future experiments on oxide/liquid interfaces.

The interdisciplinary team is part of the Midwest Integrated Center for Computational Materials, headquartered at Argonne, a computational materials science center supported by DOE. The work is presented in an article titled “Validating first-principles molecular dynamics calculations of oxide/water interfaces with X-ray reflectivity data,” which appeared in the November 2020 issue of Physical Review Materials.

More information:
Katherine J. Harmon et al, Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data, Physical Review Materials (2020). DOI: 10.1103/PhysRevMaterials.4.113805

Do simulations represent the real world at the atomic scale? (2021, January 20)
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