Tag Archives: polycyclic aromatic hydrocarbons (PAHs)

New approach to detecting soil contaminants

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This new approach doesn’t require test samples!?! A May 9, 2925 news item on ScienceDaily explains how that is possible,

A team of researchers at Rice University and Baylor College of Medicine has developed a new strategy for identifying hazardous pollutants in soil, even ones that have never been isolated or studied in a lab.

The new approach, described in a study published in Proceedings of the National Academy of Sciences [PNAS], uses light-based imaging, theoretical predictions of compounds’ light signatures and machine learning (ML) algorithms to detect toxic compounds like polycyclic aromatic hydrocarbons (PAHs) and their derivative compounds (PACs) in soil. A common by-product of combustion, PAHs and PACs have been linked to cancer, developmental issues and other serious health problems.

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A May 9, 2025 Rice University news release (also on EurekAlert), which originated the news item, goes on to give details, Note: Links have been removed,

Identifying pollutants in soil usually requires advanced laboratories and standard physical reference samples of the suspected contaminants. However, for many environmental pollutants that pose a public health risk, there is no experimental data available that can be used to detect them.

“This method makes it possible to identify chemicals that have not yet been isolated experimentally,” said Naomi Halas, University Professor and the Stanley C. Moore Professor of Electrical and Computer Engineering at Rice.

The new method uses a light-based imaging technique known as surface-enhanced Raman spectroscopy, which analyzes how light interacts with molecules, tracking the unique patterns, or spectra, they emit. Spectra serve as “chemical fingerprints” for each compound. The technique is refined through the use of signature nanoshells designed to enhance relevant traits in the spectra.

Using density functional theory ⎯ a computational modeling technique that can predict how atoms and electrons behave in a molecule ⎯ the researchers calculated what the spectra of a whole range of PAHs and PACs look like based on the compounds’ molecular structure. This allowed them to generate a virtual library of “fingerprints” for PAHs and PACs.

Two complementary ML algorithms ⎯ characteristic peak extraction and characteristic peak similarity ⎯ were used to parse relevant spectral traits in real-world soil samples and match them to compounds mapped out in the virtual library of spectra.

“We are using PAHs in soil to illustrate this very important new strategy,” Halas said. “There are tens of thousands of PAH-derived chemicals and this approach ⎯ calculating their spectra and using machine learning to connect the theoretically calculated spectra to those observed in a sample ⎯ allows us to identify chemicals that we may not, or do not, have any experimental data for.”

The method addresses a critical gap in environmental monitoring, opening the door to identifying a much broader range of hazardous compounds ⎯ including those that have changed over time. This is especially important given that soil is a dynamic environment where chemicals are subject to transformations that can render them harder to detect.

Thomas Senftle, Rice’s William Marsh Rice Trustee Associate Professor of Chemical and Biomolecular Engineering, compared the process to using facial recognition in order to find an individual in a crowd.

“You can imagine we have a picture of a person when they’re a teenager, but now they’re in their 30s,” Senftle said. “In my group what we do is, on the theory side, we can predict what the picture will look like.”

The researchers tested the method on soil from a restored watershed and natural area using both artificially contaminated samples and a control sample. Results showed the new approach reliably picked out even minute traces of PAHs using a simpler and faster process than conventional techniques.

“This method can identify lesser-known and largely unstudied PAH and PAC pollutant molecules,” said Oara Neumann, a Rice research scientist who is a co-author on the study.

In the future, the method could enable on-site field testing by integrating the ML algorithms and theoretical spectral library with portable Raman devices into a mobile system, making it easier for farmers, communities and environmental agencies to test soil for hazardous compounds without needing to send samples to specialized labs and wait days for results.

Ankit Patel, assistant professor of electrical and computer engineering at Rice and assistant professor of neuroscience at BCM, is a corresponding author on the study alongside Halas.

Other Rice co-authors include computer science doctoral alum Yilong Ju; doctoral students Sarah Denison, Peixuan Jin and Andres Sanchez-Alvarado; Peter Nordlander, the Wiess Chair in Physics and Astronomy and professor of electrical and computer engineering and materials science and nanoengineering; and Pedro Alvarez, the George R. Brown Professor of Civil and Environmental Engineering.

The research was supported by the National Institutes of Health (P42ES027725-01), the Welch Foundation (C-1220, C-1222) and the Carl and Lillian Illig Fellowship (Smalley-Curl Institute, H20398-239440). The content herein is solely the responsibility of the authors and does not necessarily represent the official views of the funding organizations and institutions.

Here’s a link to and a citation for the paper,

In silico machine learning–enabled detection of polycyclic aromatic hydrocarbons from contaminated soil by Yilong Ju, Oara Neumann, Sara B. Denison, Peixuan Jin, Andres B. Sanchez-Alvarado, Peter Nordlander, Thomas P. Senftle, Pedro J. J. Alvarez, Ankit Patel, and Naomi J. Halas. PNAS [Proceedings of the National Academy of Sciences] 122 (19) e2427069122 May 13, 2025 DOI: https://doi.org/10.1073/pnas.2427069122 PUblished online: May 8, 2025

This paper is behind a paywall.

Probing the physical limits of plasmons in organic molecules with fewer than 50 atoms

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A Sept. 5, 2018  news item on ScienceDaily introduces the work,

Rice University [Texas, US] researchers are probing the physical limits of excited electronic states called plasmons by studying them in organic molecules with fewer than 50 atoms.

A Sept. 4, 2018 Rice University news release (also on EurekAlert published on Sept. 5, 2018), which originated the news item, explains what plasmons are and why this research is being undertaken,

Plasmons are oscillations in the plasma of free electrons that constantly swirl across the surface of conductive materials like metals. In some nanomaterials, a specific color of light can resonate with the plasma and cause the electrons inside it to lose their individual identities and move as one, in rhythmic waves. Rice’s Laboratory for Nanophotonics (LANP) has pioneered a growing list of plasmonic technologies for applications as diverse as color-changing glass, molecular sensing, cancer diagnosis and treatment, optoelectronics, solar energy collection and photocatalysis.

Reporting online in the Proceedings of the National Academy of Sciences, LANP scientists detailed the results of a two-year experimental and theoretical study of plasmons in three different polycyclic aromatic hydrocarbons (PAHs). Unlike the plasmons in relatively large metal nanoparticles, which can typically be described with classical electromagnetic theory like Maxwell’s [James Clerk Maxwell] equations, the paucity of atoms in the PAHs produces plasmons that can only be understood in terms of quantum mechanics, said study co-author and co-designer Naomi Halas, the director of LANP and the lead researcher on the project.

“These PAHs are essentially scraps of graphene that contain five or six fused benzene rings surrounded by a perimeter of hydrogen atoms,” Halas said. “There are so few atoms in each that adding or removing even a single electron dramatically changes their electronic behavior.”

Halas’ team had experimentally verified the existence of molecular plasmons in several previous studies. But an investigation that combined side by side theoretical and experimental perspectives was needed, said study co-author Luca Bursi, a postdoctoral research associate and theoretical physicist in the research group of study co-designer and co-author Peter Nordlander.

“Molecular excitations are a ubiquity in nature and very well studied, especially for neutral PAHs, which have been considered as the standard of non-plasmonic excitations in the past,” Bursi said. “Given how much is already known about PAHs, they were an ideal choice for further investigation of the properties of plasmonic excitations in systems as small as actual molecules, which represent a frontier of plasmonics.”

Lead co-author Kyle Chapkin, a Ph.D. student in applied physics in the Halas research group, said, “Molecular plasmonics is a new area at the interface between plasmonics and molecular chemistry, which is rapidly evolving. When plasmonics reach the molecular scale, we lose any sharp distinction of what constitutes a plasmon and what doesn’t. We need to find a new rationale to explain this regime, which was one of the main motivations for this study.”

In their native state, the PAHs that were studied — anthanthrene, benzo[ghi]perylene and perylene — are charge-neutral and cannot be excited into a plasmonic state by the visible wavelengths of light used in Chapkin’s experiments. In their anionic form, the molecules contain an additional electron, which alters their “ground state” and makes them plasmonically active in the visible spectrum. By exciting both the native and anionic forms of the molecules and comparing precisely how they behaved as they relaxed back to their ground states, Chapkin and Bursi built a solid case that the anionic forms do support molecular plasmons in the visible spectrum.

The key, Chapkin said, was identifying a number of similarities between the behavior of known plasmonic particles and the anionic PAHs. By matching both the timescales and modes for relaxation behaviors, the LANP team built up a picture of a characteristic dynamics of low-energy plasmonic excitations in the anionic PAHs.

“In molecules, all excitations are molecular excitations, but select excited states show some characteristics that allow us to draw a parallel with the well-established plasmonic excitations in metal nanostructures,” Bursi said.

“This study offers a window on the sometimes surprising behavior of collective excitations in few-atom quantum systems,” Halas said. “What we’ve learned here will aid our lab and others in developing quantum-plasmonic approaches for ultrafast color-changing glass, molecular-scale optoelectronics and nonlinear plasmon-mediated optics.”

Here’s a link to and a citation for the paper,

Lifetime dynamics of plasmons in the few-atom limit by Kyle D. Chapkin, Luca Bursi, Grant J. Stec, Adam Lauchner, Nathaniel J. Hogan, Yao Cui, Peter Nordlander, and Naomi J. Halas. PNAS September 11, 2018 115 (37) 9134-9139; published ahead of print August 27, 2018 DOI: https://doi.org/10.1073/pnas.1805357115

This paper is behind a paywall.

Multicolor, electrochromic glass

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Electrochromic (changes color to block light and heat) glass could prove to be a significant market by 2020 according to a March 8, 2017 news item on phys.org,

Rice University’s latest nanophotonics research could expand the color palette for companies in the fast-growing market for glass windows that change color at the flick of an electric switch.

In a new paper in the American Chemical Society journal ACS Nano, researchers from the laboratory of Rice plasmonics pioneer Naomi Halas report using a readily available, inexpensive hydrocarbon molecule called perylene to create glass that can turn two different colors at low voltages.

“When we put charges on the molecules or remove charges from them, they go from clear to a vivid color,” said Halas, director of the Laboratory for Nanophotonics (LANP), lead scientist on the new study and the director of Rice’s Smalley-Curl Institute. “We sandwiched these molecules between glass, and we’re able to make something that looks like a window, but the window changes to different types of color depending on how we apply a very low voltage.”

Adam Lauchner, an applied physics graduate student at Rice and co-lead author of the study, said LANP’s color-changing glass has polarity-dependent colors, which means that a positive voltage produces one color and a negative voltage produces a different color.

“That’s pretty novel,” Lauchner said. “Most color-changing glass has just one color, and the multicolor varieties we’re aware of require significant voltage.”

Glass that changes color with an applied voltage is known as “electrochromic,” and there’s a growing demand for the light- and heat-blocking properties of such glass. The projected annual market for electrochromic glass in 2020 has been estimated at more $2.5 billion.

A March 8, 2017 Rice University news release (also on EurekAlert), which originated the news item, provides more detail about the research,

Lauchner said the glass project took almost two years to complete, and he credited co-lead author Grant Stec, a Rice undergraduate researcher, with designing the perylene-containing nonwater-based conductive gel that’s sandwiched between glass layers.

“Perylene is part of a family of molecules known as polycyclic aromatic hydrocarbons,” Stec said. “They’re a fairly common byproduct of the petrochemical industry, and for the most part they are low-value byproducts, which means they’re inexpensive.”

Grant Stec and Adam Lauchner

Grant Stec and Adam Lauchner of Rice University’s Laboratory for Nanophotonics have used an inexpensive hydrocarbon molecule called perylene to create a low-voltage, multicolor, electrochromic glass. (Photo by Jeff Fitlow/Rice University)

There are dozens of polycyclic aromatic hydrocarbons (PAHs), but each contains rings of carbon atoms that are decorated with hydrogen atoms. In many PAHs, carbon rings have six sides, just like the rings in graphene, the much-celebrated subject of the 2010 Nobel Prize in physics.

“This is a really cool application of what started as fundamental science in plasmonics,” Lauchner said.

A plasmon is [a] wave of energy, a rhythmic sloshing in the sea of electrons that constantly flow across the surface of conductive nanoparticles. Depending upon the frequency of a plasmon’s sloshing, it can interact with and harvest the energy from passing light. In dozens of studies over the past two decades, Halas, Rice physicist Peter Nordlander and colleagues have explored both the basic physics of plasmons and potential applications as diverse as cancer treatment, solar-energy collection, electronic displays and optical computing.

The quintessential plasmonic nanoparticle is metallic, often made of gold or silver, and precisely shaped. For example, gold nanoshells, which Halas invented at Rice in the 1990s, consist of a nonconducting core that’s covered by a thin shell of gold.

Grant Stec, Naomi Halas and Adam Lauchner

Student researchers Grant Stec (left) and Adam Lauchner (right) with Rice plasmonics pioneer Naomi Halas, director of Rice University’s Laboratory for Nanophotonics. (Photo by Jeff Fitlow/Rice University)

“Our group studies many kinds of metallic nanoparticles, but graphene is also conductive, and we’ve explored its plasmonic properties for several years,” Halas said.

She noted that large sheets of atomically thin graphene have been found to support plasmons, but they emit infrared light that’s invisible to the human eye.

“Studies have shown that if you make graphene smaller and smaller, as you go down to nanoribbons, nanodots and these little things called nanoislands, you can actually get graphene’s plasmon closer and closer to the edge of the visible regime,” Lauchner said.

In 2013, then-Rice physicist Alejandro Manjavacas, a postdoctoral researcher in Nordlander’s lab, showed that the smallest versions of graphene — PAHs with just a few carbon rings — should produce visible plasmons. Moreover, Manjavacas calculated the exact colors that would be emitted by different types of PAHs.

“One of the most interesting things was that unlike plasmons in metals, the plasmons in these PAH molecules were very sensitive to charge, which suggested that a very small electrical charge would produce dramatic colors,” Halas said.

Electrochromic glass that glass that turns from clear to black

Rice University researchers demonstrated a new type of glass that turns from clear to black when a low voltage is applied. The glass uses a combination of molecules that block almost all visible light when they each gain a single electron. (Photo by Jeff Fitlow/Rice University)

Lauchner said the project really took off after Stec joined the research team in 2015 and created a perylene formulation that could be sandwiched between sheets of conductive glass.

In their experiments, the researchers found that applying just 4 volts was enough to turn the clear window greenish-yellow and applying negative 3.5 volts turned it blue. It took several minutes for the windows to fully change color, but Halas said the transition time could easily be improved with additional engineering.

Stec said the team’s other window, which turns from clear to black, was produced later in the project.

“Dr. Halas learned that one of the major hurdles in the electrochromic device industry was making a window that could be clear in one state and completely black in another,” Stec said. “We set out to do that and found a combination of PAHs that captured no visible light at zero volts and almost all visible light at low voltage.”

Here’s a link to and a citation for the paper,

Multicolor Electrochromic Devices Based on Molecular Plasmonics by Grant J. Stec, Adam Lauchner, Yao Cui, Peter Nordlander, and Naomi J. Halas. ACS Nano, Article ASAP DOI: 10.1021/acsnano.7b00364 Publication Date (Web): February 22, 2017

Copyright © 2017 American Chemical Society

This paper is behind a paywall.