Tag Archives: chemistry

Quantum mechanical calculations reveal the hidden states of enzyme active sites (Nature Chemistry)

[2Fe–2S] cluster in front of a leaf. (Image by C. Todd Reichart)

Researchers at Princeton University have reported the first direct observation of the electronic states of iron-sulfur clusters, common to many enzyme active sites. Iron-sulfur cluster in front of a leaf. (Image by C. Todd Reichart)

By Tien Nguyen, Department of Chemistry

Enzymes carry out fundamental biological processes such as photosynthesis, nitrogen fixation and respiration, with the help of clusters of metal atoms as “active” sites. But scientists lack basic information about their function because the states thought to be critical to their chemical abilities cannot be experimentally observed.

Now, researchers at Princeton University have reported the first direct observation of the electronic states of iron-sulfur clusters, common to many enzyme active sites. Published on August 31 in the journal Nature Chemistry, the states were revealed by computing the complicated quantum mechanical behavior of the electrons in the clusters.

“These complexes were thought of as impossible to model, due to the complexity of the quantum mechanics,” said Garnet Chan, the A. Barton Hepburn Professor of Chemistry and corresponding author on the paper.

Iron-sulfur clusters

Caption: (a) [2Fe–2S] clusters (b) [4Fe–4S] (c) Area-law entanglement of the physical states can be used to reduce the complexity of quantum calculations (d) Wavefunctions with area-law entanglement can be written compactly as a tensor network where each tensor (represented here by a circle) denotes an active space orbital and the bonds between adjacent orbitals introduce local entanglement between them. (Source: Garnet Chan)

In these systems, the electrons interact strongly with each other, their movements resembling a complicated dance. To reduce the complexity, the researchers drew on a new understanding, gained from fundamental work in quantum information theory, that the motion of the electrons had a special pattern.

“At first glance, the electrons appear to move in a complicated way, but eventually you realize that they only care about what their immediate neighbors are doing, similar to being in a crowded room. This restriction on their behavior leads to important simplifications: the calculations become very difficult rather than impossible — it’s just on the edge of what can be done,” Chan said.

Using their new method, Chan and coworkers found that iron-sulfur clusters possess an order of magnitude more accessible electronic states than previously reported. The researchers suggested that this unusual richness might explain their ubiquity in biological processes.

This finding, that there are many more available electronic states than previously thought, presents many different chemical possibilities. What if these clusters simultaneously used a combination of mechanisms, instead of the accepted chemical idea that there is one distinct electronic pathway, Chan wondered. To test that idea and learn more about the clusters’ behavior, the researchers plan to extend their calculations to observe a chemical transformation in action.

“If you want to understand why iron-sulfur clusters are a ubiquitous biological motif and how we can create even better synthetic analogs, then you need to know what the electrons are doing,” Chan said. “Now we’ve caught a first glimpse as to what they are getting up to.”

Read the abstract.

Sharma, S.; Sivalingam, K.; Neese, F.; Chan, K.-L. G. “Low-energy spectrum of iron sulfur clusters directly from many-particle quantum mechanics.Nat. Chem. 2014, 6, 927.

This work was supported by the US National Science Foundation (CHE-1265277) and used software developed with the support of OCI-1265278. F.N. and K.S acknowledge financial support from the Max Planck Society, the University of Bonn and the SFB 813 “Chemistry at Spin Centers.”

 

 

Unstoppable magnetoresistance (Nature)

Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichert.

Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichart.

by Tien Nguyen, Department of Chemistry

Mazhar Ali, a fifth-year graduate student in the laboratory of Robert Cava, the Russell Wellman Moore Professor of Chemistry at Princeton University, has spent his academic career discovering new superconductors, materials coveted for their ability to let electrons flow without resistance. While testing his latest candidate, the semimetal tungsten ditelluride (WTe2), he noticed a peculiar result.

Ali applied a magnetic field to a sample of WTe2, one way to kill superconductivity if present, and saw that its resistance doubled. Intrigued, Ali worked with Jun Xiong, a student in the laboratory of Nai Phuan Ong, the Eugene Higgins Professor of Physics at Princeton, to re-measure the material’s magnetoresistance, which is the change in resistance as a material is exposed to stronger magnetic fields.

“He noticed the magnetoresistance kept going up and up and up—that never happens.” said Cava. The researchers then exposed WTe2 to a 60-tesla magnetic field, close to the strongest magnetic field mankind can create, and observed a magnetoresistance of 13 million percent. The material’s magnetoresistance displayed unlimited growth, making it the only known material without a saturation point. The results were published online on September 14 in the journal Nature.

Crystal structure of WTe2 (Source: Nature)

Crystal structure of WTe2 (Source: Nature)

Electronic information storage is dependent on the use of magnetic fields to switch between distinct resistivity values that correlate to either a one or a zero. The larger the magnetoresistance, the smaller the magnetic field needed to change from one state to another, Ali said. Today’s devices use layered materials with so-called “giant magnetoresistance,” with changes in resistance of 20,000 to 30,000 percent when a magnetic field is applied. “Colossal magnetoresistance” is close to 100,000 percent, so for a magnetoresistance percentage in the millions, the researchers hoped to coin a new term.

Their original choice was “ludicrous” magnetoresistance, which was inspired by “ludicrous speed,” the fictional form of fast-travel used in the comedy “Spaceballs.” They even included an acknowledgement to director Mel Brooks. After other lab members vetoed “ludicrous,” the researchers considered “titanic” before Nature editors ultimately steered them towards the term “large magnetoresistance.”

Terminology aside, the fact remained that the magnetoresistance values were extraordinarily high, a phenomenon that might be understood through the structure of WTe2. To look at the structure with an electron microscope, the research team turned to Jing Tao, a researcher at Brookhaven National Laboratory.

“Jing is a great microscopist. They have unique capabilities at Brookhaven,” Cava said. “One is that they can measure diffraction at 10 Kelvin (-441 °F). Not too many people on Earth can do that, but Jing can.”

Electron microscopy experiments revealed the presence of tungsten dimers, paired tungsten atoms, arranged in chains responsible for the key distortion from the classic octahedral structure type. The research team proposed that WTe2 owes its lack of saturation to the nearly perfect balance of electrons and electron holes, which are empty docks for traveling electrons. Because of its structure, WTe2 only exhibits magnetoresistance when the magnetic field is applied in a certain direction. This could be very useful in scanners, where multiple WTe2 devices could be used to detect the position of magnetic fields, Ali said.

“Aside from making devices from WTe2, the question to ask yourself as a scientist is: How can it be perfectly balanced, is there something more profound,” Cava said.

Read the abstract.

Ali, M. N.; Xiong, J.; Flynn, S.; Tao, J.; Gibson, Q. D.; Schoop, L. M.; Haldolaarachchige, N.; Hirschberger, M.; Ong, N. P.; Cava, R. J. “Large, non-saturating magnetoresistance in WTe2.” Nature. Published online September 14. 514, 205–208 (09 October 2014).

This research was supported by the Army Research Office, grants W911NF-12-1-0461 and W911NF-11-1-0379, and the NSF MRSEC Program Grant DMR-0819860. This work was supported by the US Department of Energy’s Basic Energy Sciences (DOE BES) project “Science at 100 Tesla.” The electron microscopy study at Brookhaven National Laboratory was supported by the DOE BES, by the Materials Sciences and Engineering Division under contract DE-AC02-98CH10886, and through the use of the Center for Functional Nanomaterials.

Longstanding bottleneck in crystal structure prediction solved (Science)

By Tien Nguyen, Department of Chemistry

benzene crystal

Orthographic projections of a cluster cut from the benzene crystal along the two directions (Image courtesy of Science/AAAS)

Two years after its release, the HIV-1 drug Ritonavir was pulled from the market. Scientists discovered that the drug had crystallized into a slightly different form—called a polymorph—that was less soluble and made it ineffective as a treatment.

The various patterns that atoms of a solid material can adopt, called crystal structures, can have a huge impact on its properties. Being able to accurately predict the most stable crystal structure for a material has been a longstanding challenge for scientists.

“The holy grail of this particular problem is to say, I’ve written down this chemical formula for a material, and then just from the formula be able to predict its structure—a goal since the dawn of chemistry,” said Garnet K. L. Chan, the A. Barton Hepburn Professor of Theoretical Chemistry at Princeton University. One major bottleneck towards achieving this goal has been to compute the lattice energy—the energy associated with a structure—to sufficient accuracy to distinguish between several competing polymorphs.

Chan’s group has now accomplished this task, publishing their results in the journal Science on August 8. The research team demonstrated that new techniques could be used to calculate the lattice energy of benzene, a simple yet important molecule in pharmaceutical and energy research, to sub-kilojoule per mole accuracy—a level of certainty that allows polymorphism to be resolved.

Chan credited this success to the combined application of advances in the field of quantum mechanics over the last 15 years. “Some of these advances allow you to resolve the behavior of electrons more finely, do computations on more atoms more quickly, and allow you to consider more electrons at the same time,” Chan said. “It’s a triumph of the modern field of quantum chemistry that we can now determine the behavior of Nature to this level of precision.”

The group’s next goal is to shorten the time it takes to run the desired calculations. These initial calculations consumed several months of computer time, Chan said, but with some practical modifications, future predictions should take only a few hours.

Chan’s colleagues on the work included first author Jun Yang, an electronic structure theory specialist and lecturer in chemistry, and graduate student Weifeng Hu at Princeton University. Additional collaborators were Denis Usvyat and Martin Schutz of the University of Regensburg and Devin Matthews of the University of Texas at Austin.

The work was supported by the U.S. Department of Energy under grant no. DE-SC0008624, with secondary support from grant no. DE-SC0010530. Additional funding was received from the National Science Foundation under grant no. OCI-1265278 and CHE-1265277. D.M. was supported by the U.S. Department of Energy through a Computational Science Graduate Fellowship, funded by grant no. DE-FG02-97ER25308.

Read the abstract.

Yang J., Hu, W., Usvyat, D., Matthews, D., Schutz, M., Chan, G. K. L. Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mol accuracy. Science 2014, 345, 640.

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Solar panels light the way from carbon dioxide to fuel (Journal of CO2 Utilization)

By Tien Nguyen, Department of Chemistry

Research to curb global warming caused by rising levels of atmospheric greenhouse gases, such as carbon dioxide, usually involves three areas: Developing alternative energy sources, capturing and storing greenhouse gases, and repurposing excess greenhouse gases. Drawing on two of these approaches, researchers in the laboratory of Andrew Bocarsly, a Princeton professor of chemistry, collaborated with researchers at start-up company Liquid Light Inc. of Monmouth Junction, New Jersey, to devise an efficient method for harnessing sunlight to convert carbon dioxide into a potential alternative fuel known as formic acid. The study was published June 13 in the Journal of CO2 Utilization.

Pictured with the photovoltaic-electrochemical cell system from left to right: Graduate student James White (Princeton), Professor Andrew Bocarsly (Princeton and Liquid Light) and principal engineer Paul Majsztrik (Liquid Light). (Photo by Frank Wojciechowski)

Pictured with the photovoltaic-electrochemical cell system from left to right: Graduate student James White (Princeton), Professor Andrew Bocarsly (Princeton and Liquid Light) and principal engineer Paul Majsztrik (Liquid Light). (Photo by Frank Wojciechowski)

The transformation from carbon dioxide and water to formic acid was powered by a commercial solar panel provided by the energy company PSE&G that can be found atop electric poles across New Jersey. The process takes place inside an electrochemical cell, which consists of metal plates the size of rectangular lunch-boxes that enclose liquid-carrying channels.

To maximize the efficiency of the system, the amount of power produced by the solar panel must match the amount of power the electrochemical cell can handle, said Bocarsly. This optimization process is called impedance matching. By stacking three electrochemical cells together, the research team was able to reach almost 2 percent energy efficiency, which is twice the efficiency of natural photosynthesis. It is also the best energy efficiency reported to date using a man-made device.

A number of energy companies are interested in storing solar energy as formic acid in fuel cells. Additionally, formate salt—readily made from formic acid—is the preferred de-icing agent on airplane runways because it is less corrosive to planes and safer for the environment than chloride salts. With increased availability, formate salts could supplant more harmful salts in widespread use.

Using waste carbon dioxide and easily obtained machined parts, this approach offers a promising route to a renewable fuel, Bocarsly said.

This work was financially supported by Liquid Light, Inc., which was cofounded by Bocarsly, and the National Science Foundation under grant no. CHE-0911114.

Read the abstract.

White, J. L.; Herb, J. T.; Kaczur, J. J.; Majsztrik, P. W.; Bocarsly, A. B. Photons to formate: Efficient electrochemical solar energy conversion via reduction of carbon dioxide. Journal of CO2 Utilization. Available online June 13, 2014.

Unlocking the potential of bacterial gene clusters to discover new antibiotics (Proc. Natl. Acad. Sci.)

High-throughput screening for the discovery of small molecules that activate silent bacterial gene clusters

High-throughput screening for the discovery of small molecules that activate silent bacterial gene clusters. Image courtesy of Mohammad Seyedsayamdost.

by Tien Nguyen, Department of Chemistry

Resistance to antibiotics has been steadily rising and poses a serious threat to the stronghold of existing treatments. Now, a method from Mohammad Seyedsayamdost, an assistant professor of chemistry at Princeton University, may open the door to the discovery of a host of potential drug candidates.

The vast majority of anti-infectives on the market today are bacterial natural products, made by biosynthetic gene clusters. Genome sequencing of bacteria has revealed that these active gene clusters are outnumbered approximately ten times by so-called silent gene clusters.

“Turning these clusters on would really expand our available chemical space to search for new antibiotic or otherwise therapeutically useful molecules,” Seyedsayamdost said.

In an article published last week in the journal Proceedings of the National Academy of Sciences, Seyedsayamdost reported a strategy to quickly screen whole libraries of compounds to find elicitors, small molecules that can turn on a specific gene cluster. He used a genetic reporter that fluoresces or generates a color when the gene cluster is activated to easily identify positive hits. Using this method, two silent gene clusters were successfully activated and a new metabolite was discovered.

Application of this work promises to uncover new bacterial natural products and provide insights into the regulatory networks that control silent gene clusters.

Read the abstract.

Seyedsayamdost, M. R. “High-throughput platform for the discovery of elicitors of silent bacterial gene clusters.” Proc. Natl. Acad. Sci. 2014, Early edition.

Now in 3D: Video of virus-sized particle trying to enter cell (Nature Nanotechnology)

Video of virus trying to enter cell

3D movie (below) of virus-like nanoparticle trying to gain entry to a cell

By Catherine Zandonella, Office of the Dean for Research

Tiny and swift, viruses are hard to capture on video. Now researchers at Princeton University have achieved an unprecedented look at a virus-like particle as it tries to break into and infect a cell. The technique they developed could help scientists learn more about how to deliver drugs via nanoparticles — which are about the same size as viruses — as well as how to prevent viral infection from occurring.

The video reveals a virus-like particle zipping around in a rapid, erratic manner until it encounters a cell, bounces and skids along the surface, and either lifts off again or, in much less time than it takes to blink an eye, slips into the cell’s interior. The work was published in Nature Nanotechnology.

Video caption: ‘Kiss and run’ on the cell surface. This 3D movie shows actual footage of a virus-like particle (red dot) approaching a cell (green with reddish brown nucleus), as captured by Princeton University researchers Kevin Welcher and Haw Yang. The color of the particle represents its speed, with red indicating rapid movement and blue indicating slower movement. The virus-like particle lands on the surface of the cell, appears to try to enter it, then takes off again. Source: Nature Nanotechnology.

“The challenge in imaging these events is that viruses and nanoparticles are small and fast, while cells are relatively large and immobile,” said Kevin Welsher, a postdoctoral researcher in Princeton’s Department of Chemistry and first author on the study. “That has made it very hard to capture these interactions.”

The problem can be compared to shooting video of a hummingbird as it roams around a vast garden, said Haw Yang, associate professor of chemistry and Welsher’s adviser. Focus the camera on the fast-moving hummingbird, and the background will be blurred. Focus on the background, and the bird will be blurred.

The researchers solved the problem by using two cameras, one that locked onto the virus-like nanoparticle and followed it faithfully, and another that filmed the cell and surrounding environment.

Putting the two images together yielded a level of detail about the movement of nano-sized particles that has never before been achieved, Yang said. Prior to this work, he said, the only way to see small objects at a similar resolution was to use a technique called electron microscopy, which requires killing the cell.

“What Kevin has done that is really different is that he can capture a three-dimensional view of a virus-sized particle attacking a living cell, whereas electron microscopy is in two-dimensions and on dead cells,” Yang said. “This gives us a completely new level of understanding.”

In addition to simply viewing the particle’s antics, the researchers can use the technique to map the contours of the cell surface, which is bumpy with proteins that push up from beneath the surface. By following the particle’s movement along the surface of the cell, the researchers were able to map the protrusions, just as a blind person might use his or her fingers to construct an image of a person’s face.

“Following the motion of the particle allowed us to trace very fine structures with a precision of about 10 nanometers, which typically is only available with an electron microscope,” Welsher said. (A nanometer is one billionth of a meter and roughly 1000 times smaller than the width of a human hair.) He added that measuring changes in the speed of the particle allowed the researchers to infer the viscosity of the extracellular environment just above the cell surface.

The technology has potential benefits for both drug discovery and basic scientific discovery, Yang said.  “We believe this will impact the study of how nanoparticles can deliver medicines to cells, potentially leading to some new lines of defense in antiviral therapies,” he said. “For basic research, there are a number of questions that can now be explored, such as how a cell surface receptor interacts with a viral particle or with a drug.”

Welsher added that such basic research could lead to new strategies for keeping viruses from entering cells in the first place.

“If we understand what is happening to the virus before it gets to your cells,” said Welsher, “then we can think about ways to prevent infection altogether. It is like deflecting missiles before they get there rather than trying to control the damage once you’ve been hit.”

To create the virus-like particle, the researchers coated a miniscule polystyrene ball with quantum dots, which are semiconductor bits that emit light and allow the camera to find the particle. Next, the particle was studded with protein segments known as Tat peptides, derived from the HIV-1 virus, which help the particle find the cell. The width of the final particle was about 100 nanometers.

The researchers then let loose the particles into a dish containing skin cells known as fibroblasts. One camera followed the particle while a second imaging system took pictures of the cell using a technique called laser scanning microscopy, which involves taking multiple images, each in a slightly different focal plane, and combining them to make a three-dimensional picture.

The research was supported by the US Department of Energy (DE-SC0006838) and by Princeton University.

Read the abstract.

Kevin Welsher and Haw Yang. 2014. Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles. Nature nanotechnology. Published online: 23 February 2014 | DOI: 10.1038/NNANO.2014.12

When scaling the quantum slopes, veer for the straight path (Physical Review A)

Research image

Princeton University researchers found that the “landscape” for quantum control (above) — a representation of quantum mechanics that allows the dynamics of atoms and molecules to be manipulated — can be unexpectedly simple, which could help scientists realize the next generation of technology by harnessing atoms and molecules to create small but incredibly powerful devices. Scientists achieve quantum control by finding the ideal radiation field (top of the graphic) that leads to the desired response from the system. Like a mountain hiker, a scientist can take a difficult, twisting path that requires frequent stops to evaluate the next step (right path). Or, they can opt for a straighter trail that cuts directly to the summit (left path). The researchers provide in their paper an algorithm that scientists can use to identify the starting point of the straight path to their desired quantum field. (Image courtesy of Arun Nanduri)

By Morgan Kelly, Office of Communications

Like any task, there is an easy and a hard way to control atoms and molecules as quantum systems, which are driven by tailored radiation fields. More efficient methods for manipulating quantum systems could help scientists realize the next generation of technology by harnessing atoms and molecules to create small but incredibly powerful devices such as molecular electronics or quantum computers.

Of course, controlling quantum systems is as painstaking as it sounds, and requires scientists to discover the ideal radiation field that leads to the desired response from the system. Scientists know that reaching that state of quantum nirvana can be a long and expensive slog, but Princeton University researchers have found that the process might be more straightforward than previously thought.

The researchers report in the journal Physical Review A that quantum-control “landscapes” — the path of a system’s response from the initial field to the final desired field — appears to be unexpectedly simple. Although still a mountain of a task, finding a good control radiation field turns out to be very much like climbing a mountain, and scientists need only choose the right path. Like a hiker, a scientist can take a difficult, twisting path that requires frequent stops to evaluate which step to take next. Or, as the Princeton researchers show, they can opt for a straighter trail that cuts directly to the summit.

The researchers observe in their paper that these fast tracks toward the desired control field actually exist, and are scattered all over the landscape. They provide an algorithm that scientists can use to identify the starting point of the straight path to their desired quantum field.

The existence of nearly straight paths to reach the best quantum control was surprising because the landscapes were assumed to be serpentine, explained first author Arun Nanduri, who received his bachelor’s degree in physics from Princeton in 2013 and is working in the laboratory of Herschel Rabitz, Princeton’s Charles Phelps Smyth ’16 *17 Professor of Chemistry.

“We found that not only can you always climb to the top, but you can climb along a simple path to the top,” Nanduri said. “If we could consistently identify where these paths are located, a scientist could efficiently climb the landscape. Looking around for the next good step along an unknown path takes great effort. However, starting along a straight path requires you to look around once, and you can keep walking forward with your eyes closed, as it were.”

Following a straighter path could be a far more efficient way of achieving control of atoms and molecules for a host of applications, including manipulating chemical reactions and operating quantum computers, Nanduri said. The source of much scientific excitement, quantum computers would use “qubits” that can be entangled to potentially give them enormous storage and computational capacities far beyond the capabilities of today’s digital computers.

If the Princeton research helps scientists quickly and easily find the control fields they need, it could also allow them to carry out improved measurements of quantum systems and design new ones, Nanduri said.

“We don’t know if our discovery will directly lead to futuristic quantum devices, but this finding should spur renewed research,” Nanduri said. “If straight paths to good quantum control solutions can be routinely found, it would be remarkable.”

Read the abstract.

Nanduri, Arun, Ashley Donovan, Tak-San Ho, Herschel Rabitz. 2013. Exploring quantum control landscape structure. Physical Review A. Article published: Sept. 30, 2013. DOI: 10.1103/PhysRevA.88.033425

The work was funded by the Program in Plasma Science and Technology at Princeton University, the Army Research Office, and the U.S. Department of Energy.