Chemical Physics

JILA Researcher Megan Bentley Named Arnold O. Beckman Postdoctoral Fellow

Steven Burrows — Thu, 02 Apr 2026 17:55:00 +0000

JILA Researcher Megan Bentley Named Arnold O. Beckman Postdoctoral Fellow Steven Burrows Thu, 04/02/2026 - 11:55

Steven Burrows / JILA Science Communications Manager

JILA postdoctoral researcher Dr. Megan Bentley, a member of Heather Lewandowski’s research group, has been awarded a 2026 Arnold O. Beckman Postdoctoral Fellowship from the Arnold and Mabel Beckman Foundation. The prestigious national fellowship recognizes outstanding early career scientists pursuing innovative research in the chemical sciences.

Bentley was selected as one of 18 fellows nationwide in the 2026 cohort following a highly competitive, multi stage review process led by a panel of scientific experts. Fellows are chosen for both the originality of their research and their potential to transition from mentored postdoctoral work to independent scientific leadership.

In the Lewandowski group at JILA, Bentley’s research focuses on experimental atomic, molecular, and optical physics, with close connections to fundamental chemical physics. Her work aligns with the Beckman Foundation’s mission to support foundational scientific research that advances experimental methods and deepens understanding of the physical world.

The Arnold O. Beckman Postdoctoral Fellowship supports advanced research in core areas of chemistry, including chemical physics and related instrumentation. The award provides multi year funding for salary and research expenses and is designed to accelerate the professional development of exceptional postdoctoral researchers.

Bentley’s selection highlights both her individual research accomplishments and JILA’s strength as a home for interdisciplinary, early career science at the interface of physics and chemistry.

JILA postdoctoral researcher Dr. Megan Bentley, a member of Heather Lewandowski’s research group, has been named a 2026 Arnold O. Beckman Postdoctoral Fellow. The prestigious national award recognizes Bentley’s innovative research and supports outstanding early‑career scientists in the chemical sciences as they transition toward independent research careers.

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JILA Researchers Overturn 25-Year-Old Explanation of Benzene Formation in Space

Steven Burrows — Fri, 09 Jan 2026 18:21:00 +0000

JILA Researchers Overturn 25-Year-Old Explanation of Benzene Formation in Space Steven Burrows Fri, 01/09/2026 - 11:21

Bailey Bedford / Freelance Science Communicator

Interstellar formation of PAHs terminates at C6H5+. Image credit: Steven Burrows / JILA

Space is famously empty. The cold vacuum of space—or more specifically, the interstellar medium—lacks much of anything, including the air needed to conduct sound. But it isn’t quite completely empty. While it’s vacant compared to what we experience in daily life, there are occasional atoms and molecules spread throughout it.

Those atoms and molecules mean that there is chemistry in space, although it doesn’t always resemble the dense, warm reactions that routinely occur in a chemist’s test tubes. One aspect of chemistry in space that researchers are interested in is the formation of polycyclic aromatic hydrocarbons (PAHs), which are molecules of carbon and hydrogen that make a broad array of chemicals on earth and in the void of space. Researchers have seen signs of light interacting with a variety of these molecules in space and being absorbed—leaving a distinctive fingerprint in the remaining light that reaches Earth. These molecules are estimated to contain somewhere between a tenth and a quarter of the carbon spread across the interstellar medium, and the molecules’ foundational building blocks are benzene (C₆H₆)—a ring of six carbon atoms, each holding a hydrogen atom.

Since 1999, researchers have had a model that they thought explained how benzene formed from smaller molecules. However, the challenges of performing experiments at the low temperatures and densities involved in mimicking the conditions in the interstellar medium have meant that researchers have relied on their theoretical understanding of the process and haven’t thoroughly tested it in experiments.

Now, JILA Fellow and University of Colorado Boulder Physics Professor Heather Lewandowski and members of her lab have used tools developed in physics laboratories to recreate the necessary conditions and have investigated how the chemistry plays out. The team described their experiment in an article published in the journal Nature Astronomy in May 2025. When they tested the process, the first steps played out as expected, but then they were surprised to find that the benzene failed to form at the final step. Their results give scientists a new window into how chemistry occurs in the interstellar medium and reopens the question of how carbon gets caught up in PAHs throughout space.

The key to recreating the chemistry occurring in the interstellar medium was creating a vacuum in a chamber and using lasers to cool molecules and hold them in place in the vacated space. This required the researchers to look at just a small number of molecules and to set aside the beakers and test tubes that are stereotypical of chemistry and instead rely on large metal chambers, air pumps, laser beams and many mirrors and lenses.

“It's a laboratory full of lasers, and vacuum chambers, and optics,” Lewandowski says. “It fills up half a room to be able to cool down these hundred little molecules.”

Selecting the right color of laser and aligning the beams correctly allows the researchers to suspend—trap—particles in a vacuum chamber as well as cool them down through a process called laser cooling. Laser cooling relies on the fact that light can give atoms and molecules a shove to slow them down and that the interaction can be tailored to depend on how the particles are moving. Carefully applied, laser cooling can get molecules down to temperatures just above absolute zero.

“Laser cooling and trapping has really been in the domain of physicists,” Lewandowski says. “The nice thing about JILA is we have physicists and chemists working together. In my own group, we have both backgrounds, and so we have the tools now that can answer these questions that really chemists didn't have the technology to tackle and physicists didn't know it was an interesting question to answer.”

These techniques allow them to focus on a small number of molecules and get a close look at the interactions that normally are obscured in a chaos of many reactions occurring rapidly and simultaneously.

With the equipment creating the needed conditions, the group started following the proposed recipe for creating benzene in the interstellar medium. The recipe’s main ingredient is a molecule of two carbon atoms and two hydrogen atoms, called acetylene (C₂H₂). The first step is mixing acetylene with molecules containing two nitrogen atoms and one hydrogen atom (N₂H⁺). The nitrogen atoms can provide their hydrogen atom to create new molecules with two carbon and three hydrogen atoms. That opens the door to two more steps of interactions with acetylene molecules to produce a molecule with six carbon atoms and five hydrogen atoms (C₆H₅⁺)—just one hydrogen short of the target benzene ring. The exact behavior of this molecule is not thoroughly understood, but the established recipe proposed that it could form benzene by capturing a molecule made from a pair of hydrogens and then letting the excess atoms go.

The team supplied just enough of the needed ingredients in the chamber so that it was improbable that more than two molecules would be reacting at a time. Using laser cooling, they cooled the molecules in the chamber down to just a few degrees Kelvin. This setup let them recreate what happens when two lonely molecules finally come together in space and get the chance to interact.

The group repeatedly ran the experiment, stopping after different amounts of time to eject the cloud of molecules and check which molecules had been formed. They saw the mixture progress through the expected steps of the recipe. They observed increases of various molecules as they were created and then decreases as they were consumed in the construction of even larger molecules. But as they waited progressively longer and longer, they never caught sight of any benzene rings. The mixture in the chamber eventually just reached a steady amount of C₆H₅⁺, and the final step of the recipe failed to occur.

“Initially we were very confused—and a little irritated—because we could never get the final reaction to happen,” says JILA postdoctoral researcher G. Stephen Kocheril, the lead author of the paper.

After performing several runs of the experiment and analyzing the data, the team concluded that the expected chain of events wasn’t happening and there must be something else occurring to produce all the benzene in space.

“None of the models now actually predict what's out there,” Lewandowski says. “If you look at observations of how many of these molecules we have out there, no model works. So we sort of said, ‘this model isn't it.’ We don't have a new model yet; that's what we're working on now. So it was kind of big for the community because it changed how larger and larger carbon-containing molecules are formed in space.”

Moving beyond the old explanation gives chemists insights into how they should think about the formation of these molecules and provides astronomers with new clues about which molecules they should be keeping an eye out for if they want to understand the chemistry happening out in the interstellar medium.

JILA Fellow and University of Colorado Boulder Physics Professor Heather Lewandowski and members of her lab have shattered a 25-year-old theory about how benzene forms in the interstellar medium, revealing that the long-accepted chemical recipe doesn’t work under space-like conditions. Their groundbreaking laser-cooling experiments open a new chapter in understanding the origins of complex carbon molecules in the cosmos.

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JILA’s Mathias Weber Named Fellow of the American Physical Society

Steven Burrows — Fri, 10 Oct 2025 15:42:26 +0000

JILA’s Mathias Weber Named Fellow of the American Physical Society Steven Burrows Fri, 10/10/2025 - 09:42

Steven Burrows / JILA Science Communications Manager

Mathias Weber.

JILA and the University of Colorado Boulder are proud to announce that Professor J. Mathias Weber has been elected a Fellow of the American Physical Society (APS), one of the highest honors in the physics community. This prestigious recognition is awarded to no more than 0.5% of APS members annually and celebrates exceptional contributions to the field of physics.

The APS citation highlights Weber’s “fundamental contributions to our understanding of molecular interactions and solvation effects in complex systems, obtained via elegant vibrational/electronic laser photodissociation spectroscopy of molecular and cluster ions in the gas phase.”

As a Fellow of JILA and a professor in ��Ҵ�ý�ƽ�� Department of Chemistry, Weber has long been at the forefront of chemical physics research. His work explores how molecules interact and behave in isolated environments, using advanced spectroscopic techniques to probe the structure and dynamics of ions and clusters. These insights have broad implications, from understanding atmospheric chemistry to designing novel materials.

Weber’s lab specializes in cryogenic ion spectroscopy, a technique that allows scientists to study molecular systems at extremely low temperatures, revealing subtle interactions that are often masked at room temperature. His recent work has shed light on how water molecules interact with aromatic systems, and how ion-receptor complexes behave in biologically relevant environments.

Originally from Germany, Weber earned his doctorate from the University of Kaiserslautern and completed postdoctoral research at Yale University before joining ��Ҵ�ý�ƽ��.

The APS Fellowship adds to a growing list of accolades for Weber, including the NSF CAREER Award and the Emmy-Noether Award from the German Research Foundation.

JILA congratulates Professor Weber on this well-deserved honor and celebrates the continued impact of his research on science and society.

JILA and the University of Colorado Boulder are proud to announce that Professor J. Mathias Weber has been elected a Fellow of the American Physical Society (APS), for fundamental contributions to our understanding of molecular interactions and solvation effects in complex systems, obtained via elegant vibrational/electronic laser photodissociation spectroscopy of molecular and cluster ions in the gas phase.

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Dr. Surya Pratap Deopa Wins 2025 BioFrontiers Outstanding Contribution Award

Steven Burrows — Sat, 30 Aug 2025 01:07:56 +0000

Dr. Surya Pratap Deopa Wins 2025 BioFrontiers Outstanding Contribution Award Steven Burrows Fri, 08/29/2025 - 19:07

Steven Burrows / JILA Science Communications Manager

Dr. Surya Pratap Deopa

JILA is proud to announce that Dr. Surya Pratap Deopa, Postdoctoral Fellow in the lab of JILA Fellow and MCDB Professor Tom Perkins, has been honored with the 2025 BioFrontiers Outstanding Contribution Award. This prestigious recognition celebrates Dr. Deopa’s impactful research contributions within the BioFrontiers community.

Dr. Deopa was recognized for his innovative technical advances that revitalized a previously stalled research project, significantly enhancing both the data quality and throughput of cutting-edge atomic force microscopy (AFM) experiments. His work has not only pushed the boundaries of experimental precision but also established molecular dynamics simulations as a powerful computational companion to AFM measurement interpretation.

Beyond his technical achievements, Dr. Deopa has distinguished himself as a generous and collaborative colleague, contributing meaningfully through both formal partnerships and informal scientific exchanges. His dedication to fostering a supportive and productive research environment exemplifies the values of the BioFrontiers Institute.

As part of the award, Dr. Deopa receives a certificate of appreciation and a $1,000 prize in recognition of his outstanding contributions.

Dr. Surya Pratap Deopa, Postdoctoral Fellow in the lab of JILA Fellow and MCDB Professor Tom Perkins, has been honored with the 2025 BioFrontiers Outstanding Contribution Award.

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Molecular Lock and Key: Decoding the Secrets of Ion Binding

Steven Burrows — Wed, 09 Apr 2025 18:25:48 +0000

Molecular Lock and Key: Decoding the Secrets of Ion Binding Steven Burrows Wed, 04/09/2025 - 12:25

Kenna Hughes-Castleberry / JILA Science Communicator

Understanding how molecules interact with ions is a cornerstone of chemistry, with applications from pollution detection and cleanup to drug delivery. In a series of new studies led by JILA Fellow and University of Colorado Boulder chemistry professor Mathias Weber, researchers explored how a specific ion receptor called octamethyl calix[4]pyrrole (omC4P) binds to different anions, such as fluoride or nitrate. These findings, published in The Journal of the American Chemical Society, The Journal of Physical Chemistry Letters, and The Journal of Physical Chemistry B, provide fundamental insights about molecular binding that could help advance fields such as environmental science and synthetic chemistry.

“The main issue with understanding these interactions is that there is a competition between an ion binding to a certain receptor and that same ion wanting to be surrounded by solvent molecules,” Weber explains. “This competition impacts how effective and specific an ion receptor can be, and we currently don’t understand it sufficiently well to design better ion receptors for applications. This has been a problem for decades, and we can now try to solve it by taking a different perspective.”

Looking at Ion Receptors

The test molecule in question, omC4P, is a prototypical anion receptor that has received much interest for nearly 30 years, a macrocyclic molecule with a cup-like structure designed to capture negatively charged ions (anions). Its rigid yet adaptable cavity contains four NH groups that form hydrogen bonds with incoming ions, making it an ideal system for investigating how different anions interact with molecular hosts.

What makes omC4P especially interesting is its specificity. Because its binding pocket has a particular size and shape, simple anions like fluoride or chloride fit quite snugly. However, when larger or more complex anions enter, like nitrate or formate, their shapes can disrupt the pocket structure, and the ions stick out into the surrounding solvent . At the same time, some ions bind strongly to omC4P even though they are relatively large, because they bind tightly to the NH groups.

Understanding these variations in binding is crucial for designing selective receptors. If a receptor can differentiate between closely related anions, it could help significantly in advancing applications such as water purification, medical diagnostics, or industrial sensing.

“These studies help us figure out what makes a receptor highly selective,” elaborates JILA graduate student Lane Terry, the papers’ first author. “If we can fine-tune its structure, we can create targeted ion sensors for real-world applications.”

The many different molecules trying to fill the binding site of octamethyl calix[4]pyrrole (omC4P). Image credit: Steven Burrows / JILA

First Step: Simple Halides

The team’s first study, published in The Journal of the American Chemical Society, focused on halide ions—fluoride, chloride, and bromide—with simple spherical shapes.

“We started with halides because they are the simplest—they act as just a single point charge,” Terry explains.

To analyze how these anions interacted with omC4P, researchers used cryogenic ion vibrational spectroscopy (CIVS) to take a molecular “snapshot” showing the interactions happening in the sample. CIVS is a technique that investigates ionized molecules cooled to low temperatures, which reduces their movement and isolates their vibrations. Ions are then bombarded with infrared photons, causing the ions to absorb specific wavelengths based on how their atoms are arranged and how they vibrate. This, in combination with quantum chemical calculations, allows researchers to measure how the receptor interacts with different ions without interference from external factors like solvent molecules.

After multiple CIVS measurements, the team verified their measurements with those predicted by Density Functional Theory (DFT), a computational method that calculates the molecular structure of complexes to predict how they interact.

“DFT helps us compare our experimental data with theoretical models,” Terry explains, “so we can confirm what we’re seeing and refine our understanding of ion binding.”

Through this process, the team discovered that fluoride formed the strongest hydrogen bonds, remaining tightly bound even in solution, whereas chloride and bromide showed weaker ion-receptor interactions due to weaker proton affinities and thus, more susceptible to solvent interaction.

“This is important because most of these ion receptors are used in aqueous environments,” Terry notes. “Meaning that fluoride’s binding will be more stable with these ion receptors than the other halides.”

Adding Complexity: Nitrate’s Unique Binding

Building on this foundation, the team then explored the nitrate anion binding to omC4P, detailed in The Journal of Physical Chemistry Letters. Unlike halides, nitrate is polyatomic, meaning it has multiple atoms, in this case, arranged in a Y-shape.

Using the CIVS plus DFT method, the researchers found that nitrate prefers a binding mode where only one of its three oxygen atoms interacts with the omC4P’s NH groups. This was a surprising result, as one might expect two oxygen atoms to bind symmetrically.

“Even though nitrate has multiple possible configurations, it strongly favors just one,” Terry says. “The ion shape and charge distribution make a big difference, especially when in an aqueous environment.”

The Most Complex Case: Formate and Isomerism

The final study, published in The Journal of Physical Chemistry B, tackled the most intricate binding behavior yet—formate (HCOO⁻), a small but more asymmetric anion binding to the omC4P. Unlike nitrate, formate was observed to have multiple binding configurations—a process known as isomerism—to the ion receptor.

"Formate actually isomerizes at a low enough energy that we detect multiple isomers, even at cryogenic temperatures,” Terry explains.

The researchers observed that the formate shifted between different configurations, unlike nitrate, which settled into one stable structure. Interestingly, the most stable formate configuration was not symmetrical at all, defying conventional expectations. While highly symmetrical structures often allow for predictable, in contrast, asymmetry can lead to unexpected behaviors that influence selectivity and stability in ion receptors.

After analyzing these findings, the team is now investigating modified omC4P with added structural “walls” to deepen the binding cavity and alter ion interactions, which will add further complexity to their experiment.

Beyond Fundamentals:

While these studies focus on fundamental chemistry, their implications extend far beyond the lab. Environmental monitoring, drug delivery, and chemical sensing all rely on understanding ion interactions at the molecular level.
Terry says, “We work closely with organic chemists who design these molecules. Our findings help them build better ion receptors with improved selectivity.”

Whether detecting contaminants in water or designing better drug carriers, their discoveries bring us one step closer to harnessing chemistry for the greater good.

This research was supported by the National Science Foundation, the JILA Physics Frontier Center, the University of Colorado Boulder, and Colorado State University.

Understanding how molecules interact with ions is a cornerstone of chemistry, with applications from pollution detection and cleanup to drug delivery. In a series of new studies led by JILA Fellow and University of Colorado Boulder chemistry professor Mathias Weber, researchers explored how a specific ion receptor called octamethyl calix[4]pyrrole (omC4P) binds to different anions, such as fluoride or nitrate. These findings provide fundamental insights about molecular binding that could help advance fields such as environmental science and synthetic chemistry.

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JILA and University of Colorado Boulder Physics Alum Dr. Olivia Krohn is Awarded the 2025 APS Global Summit Thesis Prize

Steven Burrows — Mon, 24 Mar 2025 16:12:23 +0000

JILA and University of Colorado Boulder Physics Alum Dr. Olivia Krohn is Awarded the 2025 APS Global Summit Thesis Prize Steven Burrows Mon, 03/24/2025 - 10:12

Kenna Hughes-Castleberry / JILA Science Communicator

JILA and ��Ҵ�ý�ƽ�� Physics alum Dr. Olivia Krohn has been awarded the Thesis Prize at the 2025 APS Global Summit. Image credit: Olivia Krohn

Dr. Olivia Krohn, a former JILA graduate student and now a postdoctoral researcher at Sandia National Laboratories, has been awarded the prestigious Justin Jankunas dissertation award, given out by the American Physical Society (APS) division of chemical physics at the APS Global Summit conference. This award recognizes exceptional doctoral research that advances the frontiers of physics. Krohn’s award highlights her dissertation research, which bridges the legacy of JILA’s origins in astrophysics with its current role as a global leader in atomic, molecular, and optical (AMO) physics.

Krohn’s thesis, completed under the mentorship of JILA Fellow and University of Colorado Boulder physics professor Heather Lewandowski, investigates the ion-neutral gas-phase chemical reactions of interstellar relevance using cold arrays of trapped ions known as “coulomb crystals”. Her work explores the fundamental processes that govern the chemistry of space—particularly focusing on the elusive ion CCl⁺—within the controlled conditions of the laboratory.

“While ‘JILA’ once stood for the ‘Joint Institute for Laboratory Astrophysics,’ the name is now an acronym-less moniker signifying a research center that pushes the frontier of AMO physics,” says Krohn. “My dissertation is a great example that these two identities of JILA are still sometimes entangled.”

To trap and cool the cold ensembles into Coulumb crystals, an ultra-high vacuum (UHV) environment is needed to make the crystal. However, having the ions in UHV is not the only influence in creating Coulomb crystals. By doing this, Krohn could simulate key reactions of the interstellar medium. Her research not only provided insight into chemical networks that may help explain why CCl⁺ has yet to be detected in space but also advanced the understanding of how chemical reactions behave at temperatures close to absolute zero—where quantum mechanics begins to dominate.

A major component of her work also involved developing methods to pair a traveling wave Stark decelerator with the ion trap, an innovation that allows precise tuning of the collision energy between ions and neutral molecules.

“At the colder end of this spectrum, at collision energies equivalent to a few Kelvin,” she explains, “we can venture into regimes where quantum mechanics plays a more direct role on the chemical dynamics and push the frontier of studying fundamental chemical transformation to colder and more controlled systems.”

Dr. Lewandowski praised Krohn’s scientific leadership and creativity throughout her graduate career.

“This is a well-deserved recognition of the outstanding work Olivia completed for her Ph.D. dissertation,” Lewandowski says. “She was a true leader in these studies, which have important implications for chemistry in the interstellar medium. I was incredibly fortunate to have the opportunity to work with her during her time at JILA.”

Reflecting on the award, Krohn expressed gratitude for the community that supported her research.

“I was extremely humbled and grateful to receive this award,” she notes. “I am thankful for the amazing guidance of Heather and for the incredible teammates I worked beside in my Ph.D. I am indebted to support from my friends and family. And of course, I learned so much from our amazing JILA shop, support staff, and colleagues. It was a privilege to conduct my dissertation research at JILA.”

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Cold Coulomb Crystals, Cosmic Clues: Unraveling the Mysteries of Space Chemistry

Steven Burrows — Tue, 16 Apr 2024 17:18:29 +0000

Cold Coulomb Crystals, Cosmic Clues: Unraveling the Mysteries of Space Chemistry Steven Burrows Tue, 04/16/2024 - 11:18

Kenna Hughes-Castleberry / JILA Science Communicator

Coulomb crystals are surrounded by molecules used in the Lewandowski laboratory to study astrochemical reactions. Image credit: Steven Burrows / JILA

Now, in the recently published cover article of the Journal of Physical Chemistry A, JILA Fellow and University of Colorado Boulder Physics Professor Heather Lewandowski and former JILA graduate student Olivia Krohn highlight their work to mimic ISM conditions by using Coulomb crystals, a cold pseudo-crystalline structure, to watch ions and neutral molecules interact with each other.

From their experiments, the researchers resolved chemical dynamics in ion-neutral reactions by using precise laser cooling and mass spectrometry to control quantum states, thereby allowing them to emulate ISM chemical reactions successfully. Their work brings scientists closer to answering some of the most profound questions about the chemical development of the cosmos.

Filtering Via Energy

“The field has long been thinking about which chemical reactions are going to be the most important to tell us about the makeup of the interstellar medium,” explains Krohn, the paper’s first author. “A really important group of those is the ion-neutral molecule reactions. That's exactly what this experimental apparatus in the Lewandowski group is suited for, to study not just ion-neutral chemical reactions but also at relatively cold temperatures.”

To begin the experiment, Krohn and other members of the Lewandowski group loaded an ion trap in an ultra-high vacuum chamber with various ions. Neutral molecules were introduced separately. While they knew the reactants going into the ISM-type chemical experiment, the researchers weren’t always certain what products would be created. Depending on their test, the researchers used different types of ions and neutral molecules similar to those in the ISM. This included CCl+ ions fragmented from tetrachloroethylene.

“CCl+ has been predicted to be in different regions of space. But nobody's been able to effectively test its reactivity with experiments on Earth because it's so difficult to make,” Krohn adds. “You have to break it down from tetrachloroethylene using UV lasers. This creates all kinds of ion fragments, not just CCl+, which can complicate things.”

Whether using calcium or CCl+ ions, the experimental setup allowed the researchers to filter out unwanted ions using resonant excitation, leaving the desired chemical reactants behind.
“You can shake the trap at a frequency resonant with a particular ion’s mass-to-charge ratio, and this ejects them from the trap,” says Krohn.

Cooling via Laser to Create Coulomb Crystals

After filtering, the researchers cooled their ions using a process known as Doppler cooling. This technique uses laser light to reduce the motion of atoms or ions, effectively cooling them by exploiting the Doppler effect to preferentially slow particles moving toward the cooling laser. As the Doppler cooling lowered the particles’ temperatures to millikelvin levels, the ions arranged themselves into a pseudo-crystalline structure, the Coulomb crystal, held in place by the electric fields within the vacuum chamber. The resulting Coulomb crystal was an ellipsoid shape with heavier molecules sitting in a shell outside the calcium ions, pushed out of the trap's center by the lighter particles due to the differences in their mass-to-charge ratios.

Thanks to the deep trap that contains the ions, the Coulomb crystals can remain trapped for hours, and Krohn and the team can image them in this trap. In analyzing the images, the researchers could identify and monitor the reaction in real time, seeing the ions organize themselves based on mass-to-charge ratios.

The team also determined the quantum-state dependence of the reaction of calcium ions with nitric oxide by fine-tuning the cooling lasers, which helped produce certain relative populations of quantum states of the trapped calcium ions.

“What's fun about that is it leverages one of these more specific atomic physics techniques to look at quantum resolved reactions, which is a little bit more, I think, of the physics essence of the three fields, chemistry, astronomy, and physics, even though all three are still involved,” adds Krohn.

Timing is Everything

Besides trap filtration and Doppler cooling, the researchers' third experimental technique helped them emulate the ISM reactions: their time-of-flight mass spectrometry (TOF-MS) setup. In this part of the experiment, a high-voltage pulse accelerated the ions down a flight tube, where they collided with a microchannel plate detector. The researchers could determine which particles were present in the trap based on the time it took for the ions to hit the plate and their imaging techniques.

“Because of this, we've been able to do a couple of different studies where we can resolve neighboring masses of our reactant and product ions,” adds Krohn.

This third arm of the ISM-chemistry experimental apparatus improved the resolution even further as the researchers now had multiple ways to determine which products were created in the ISM-type reactions and their respective masses.

Calculating the mass of the potential products was especially important as the team could then switch out their initial reactants with isotopologues with different masses and see what happened.

As Krohn elaborates, “That allows us to play cool tricks like substituting hydrogens with deuterium atoms or substituting different atoms with heavier isotopes. When we do that, we can see from the time-of-flight mass spectrometry how our products have changed, which gives us more confidence in our knowledge of how to assign what those products are.”

As astrochemists have observed more deuterium-containing molecules in the ISM than is expected from the observed atomic deuterium-to-hydrogen ratio, swapping isotopes in experiments like this allows researchers to get one step closer to determining why this may be.

“I think, in this case, it allows us to have good detection of what we're seeing,” Krohn says. “And that opens more doors.”

This work was supported by the National Science Foundation and the Air Force Office of Scientific Research.

While it may not look like it, the interstellar space between stars is far from empty. Atoms, ions, molecules, and more reside in this ethereal environment known as the Interstellar Medium (ISM). The ISM has fascinated scientists for decades, as at least 200 unique molecules form in its cold, low-pressure environment. It’s a subject that ties together the fields of chemistry, physics, and astronomy, as scientists from each field work to determine what types of chemical reactions happen there.

Now, in the recently published cover article of the Journal of Physical Chemistry A, JILA Fellow and University of Colorado Boulder Physics Professor Heather Lewandowski and former JILA graduate student Olivia Krohn highlight their work to mimic ISM conditions by using Coulomb crystals, a cold pseudo-crystalline structure, to watch ions and neutral molecules interact with each other.

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JILA Postdoctoral Researcher Vít Svoboda is Awarded a 2023 JUNIOR STAR project by the Czech Science Foundation

Steven Burrows — Mon, 06 Nov 2023 22:08:50 +0000

JILA Postdoctoral Researcher Vít Svoboda is Awarded a 2023 JUNIOR STAR project by the Czech Science Foundation Steven Burrows Mon, 11/06/2023 - 15:08

Catherine Klauss / JILA Science Communicator

JILA postdoctoral researcher Vit Svoboda

Every year, the Czech Science Foundation (GCAR) funds several JUNIOR STAR projects focused on new research areas and building powerful collaborative teams. These projects are awarded to early-career scientists coming to the Czech Republic from other countries or with significant international experience. Each project is awarded CZK 25 million over the following five years.

This year, JILA postdoctoral researcher Vít Svoboda is one of the 17 awardees in the 2023 JUNIOR STAR cohort. The title of his JUNIOR STAR project: “Probing Chiral Dynamics on Femtosecond Timescales,” will dive into using time-resolved photoelectron spectroscopy to study the physics of chiral molecules during chemical transformations. Congratulations!

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Remembering JILA Fellow W. Carl Lineberger

Steven Burrows — Wed, 18 Oct 2023 21:24:30 +0000

Remembering JILA Fellow W. Carl Lineberger Steven Burrows Wed, 10/18/2023 - 15:24

Kenna Hughes-Castleberry / JILA Science Communicator

Collage of JILA Fellow William Carl Lineberger

William Carl Lineberger, 83, loving husband, died on October 17, 2023, in Boulder, Colorado. Born in 1939, in Hamlet, North Carolina, Carl was the only child of Evelyn Pilot Cooper and Caleb Henry Lineberger. He is survived by his wife, Kitty Edwards, and his beloved dog, Jude.

Carl received his B.S., M.S., and Ph.D. at the Georgia Institute of Technology and served in the Army Ordnance Corps during the Vietnam War. He was a teacher, mentor, and research scientist in the Department of Chemistry, University of Colorado, for 52 years. He was appointed by President Obama to the National Science Board in 2010 and served in that capacity until 2022. The American Chemical Society and the American Physical Society, both of which he was a member, granted him their top awards. In 1983, he was elected to the National Academy of Sciences; in 2015, he received their NAS Award in the Chemical Sciences, given for both scientific achievement and benefit to humanity.

Carl Lineberger’s incredibly productive approach to scientific research derived from his unusual combination of expertise in chemistry and physics, together with his mastery of engineering. These complementary skills allowed him to attack new classes of chemical problems with his signature blend of elegance and precision. His unique perspective also enabled him to see connections in nature that could be overlooked by his contemporaries. Carl’s colleagues knew to listen especially carefully when he shared a seeming child-like view regarding some aspect of science, as it was then in fact that they might gain the deepest insights into nature’s inner workings.

Carl Lineberger’s enduring impact on the scientific community is broader than the important paradigms he contributed from his laboratory. He was described by a colleague as having been instrumental in creating the “magic” of JILA, a joint institute between the National Institute of Science and Technology and the University of Colorado devoted to research into the frontier interface between chemistry and physics. He molded a style of collaborative research starting in the 1970s that continues today.

Carl was not only brilliant, but kind. It was known that, however close he was to a proposal or other deadline, if a troubled student, staff member, or colleague knocked on his door, he would drop everything to listen and try to help.

His sense of humor was present to the end. In his final days he was asked if he had any regrets. He smiled and quipped, “Maybe I should have spent more time hang gliding.”

Carl will be remembered not just for the heights of his science, but for the depth of his humanity.
A Celebration of Life for Carl Lineberger will be held on January 6, 2024 in Boulder, Colorado. For information, contact Krista Beck kristab@jila.colorado.edu

If you wish to honor Carl, you may make a donation to the University of Colorado Foundation and designate it for JILA at https://giving.cu.edu/fund/jila-fund

Please contribute any memories or photos of Carl to this memorial page.

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Looking at a Cellular Switch

Steven Burrows — Tue, 23 May 2023 17:56:28 +0000

Looking at a Cellular Switch Steven Burrows Tue, 05/23/2023 - 11:56

Kenna Hughes-Castleberry / JILA Science Communicator

An artistic rendering of the bacterium's riboswitch and its interactions with three different potential ligands. Image credit: Steven Burrows / JILA

Although one might think it would be simple, the genetics of bacteria can be rather complicated. A bacterium’s genes use a set of regulatory proteins and other molecules to monitor and change genetic expressions within the organism. One such mechanism is the riboswitch, a small piece of RNA that can turn a gene “on” or “off.” In order to “flip” this genetic switch, a riboswitch must bind to a specific ion or molecule, called a ligand, at a special riboswitch site called the aptamer. The ligand either activates the riboswitch (allowing it to regulate gene expression) or inactivates it until the ligand unbinds and leaves the aptamer. Understanding the relationship between ligands and aptamers can have big implications for many fields, including healthcare. “Understanding riboswitches and gene expression can help us develop better antimicrobial drugs,” explained JILA graduate student Andrea Marton Menendez. “The more we know about how to attack bacteria, the better, and if we can just target one small interaction that prevents or abets a gene from being translated or transcribed, we may have an easier way to treat bacterial infections.”

To better understand the dynamics of aptamer and ligand binding, Marton Menendez, along with JILA and NIST Fellow David Nesbitt, looked at the lysine (an amino acid) riboswitch in Bacillus subtilis, a common type of bacterium present in environments ranging from cow stomachs to deep sea hydrothermal vents. With this model organism, the researchers studied how different secondary ligands, like, potassium, cesium, and sodium, affect riboswitch activation, or its physical folding. The results have been published in the Journal of Physical Chemistry B.

Pairing Up Molecules

“We know that cells are complicated; living systems are really complicated,” Marton Menendez stated. “There's a lot going on in them. But when we're trying to study complicated processes, such as how exactly does DNA or RNA fold? we tend to simplify a lot. So, we usually end up reducing the system down to the simplest DNA/RNA structure we want to study and a few necessary salts.” With this idea in mind, Marton Menendez and Nesbitt analyzed their bacterial system using single molecule FRET (fluorescence resonance energy transfer) microscopy. This type of microscopy uses pairs of fluorescent dye molecules to tag specific nucleic acid positions, for this study in particular, a larger RNA riboswitch, allowing researchers to study binding, folding, and unfolding in real time

For this particular riboswitch to work, lysine first binds to the aptamer, which causes the aptamer to fold around lysine. However, in the x-ray crystallography images of the riboswitch, a potassium ion was also bound in the aptamer. According to Marton Menendez: “You can take crystal structures of these pieces of RNA and analyze their content. If the something shows up in the crystal structure, like the potassium ion, it is likely to have been very tightly bound in the riboswitch, because it means that it stayed there a long time. This tells us that potassium can play a ligand-like role for our riboswitch.”

Besides studying potassium as a potential ligand, the researchers also found that when potassium was bound to the riboswitch, it changed how the riboswitch interacted with lysine, the primary ligand. “We looked at how the riboswitch functions with respect to lysine and potassium because they affect each other,” Marton Menendez said, “mainly potassium can tweak some of the lysine’s binding abilities. That's interesting because we think of riboswitches as extremely specific and working only with one specific target molecule.” Instead, in the B. subtilis system, this riboswitch interacts with both lysine and potassium, cooperatively, with the presence of one species enhancing the impact of the other.

A Complex Bacterial Evolution

The idea of RNA regulating its own gene expression suggests that the history of bacterial genetic evolution is more complicated than expected. “If you are an early bacterium, how do you regulate your own genes?” Marton Menendez explained. “"There is a hypothesis that the ancient world had only RNA, no proteins or DNA. So RNA alone was responsible for gene storage and regulation. Riboswitches are an example of how RNA can perform these regulatory functions without protein assistance.” As proteins and more complicated organisms emerged, it is easy to expect these genetic systems to evolve to being more complicated, with a larger number of genes and corresponding regulatory proteins. However, results like Marton Menendez’s and Nesbitt’s suggest that there is more in the bacteria’s genes than meets the eye.

With a more complicated relationship between ligands and aptamers, Marton and Nesbitt were interested to see if this relationship could be found in other bacteria, not just B. subtilis. “There's also a version of a lysine riboswitch that exists in bacteria that live in habitats that are at 80 degrees Celsius, near hydrothermal vents on the sea floor,” elaborated Marton Menendez. “We are preparing a paper comparing how regulation by the lysine riboswitches differs between the two bacteria.”

More Complicated and Cooperative Ligand Relationships

Curious about the flexibility in ligand binding to their aptamer, Marton Menendez and Nesbitt decided to see just how versatile the aptamer could be. “We were also interested to see if potassium ion could then be swapped out for something similar,” Marton Menendez added. “The reason the riboswitch goes for lysine might have something to do with the fact that you've got potassium in the system. But, if you have something that's bigger or smaller than potassium, the riboswitch may have higher or lower binding affinity to lysine.” This experiment suggested an additional project looking at how closely connected the potassium and lysine were as ligands, and also to see if the aptamer would bind to other potential ligand-cation combinations of different sizes. Cations are small positive molecules that organic systems use to regulate different molecular processes.

As Marton Menendez said: “We studied the size effects of ions binding to the riboswitch. The riboswitch typically binds lysine with potassium, so we tested cesium and sodium ions [common molecules within the bacterium] instead of potassium. However, it seems that cesium might be too big and sodium too small to allow lysine to bind properly.” Analyzing the data, the researchers found that the aptamer was quite specific with respect to choice of cation preferentially binding to potassium and lysine as the “perfect Goldilocks combination of sizes.” Most importantly, this finding suggests that riboswitch activity can be regulated with vastly more flexibility by responding cooperatively to more than a single ligand species concentration at a time. This cooperativity is a trick that Nature has long exploited for increasing functionality of proteins (e.g., oxygen bonding to hemoglobin in red blood cells), so it would seem an entirely plausible strategy for nucleic acids as well.

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