Fringe benefits: new technique makes x-rays more laser-like

Detecting a chemical change is often easy: colors may change, heat may be released, or something may smell different. Seeing reactions at the molecular level is not quite so easy, but knowing exactly when and how chemical bonds form or atoms move around is crucial to understanding chemical processes.

animated gif showing atomic-level structural changes taking place during the chemical reaction
X-ray pulses allow researchers to create real-time movies of chemical reactions at the molecular scale (click on image to see animation)

In a new study published March 15 in Proceedings of the National Academy of Sciences, University of Wisconsin–Madison physics professor Uwe Bergmann and his collaborators have turned ultrafast x-ray pulses into something more akin to an optical laser, with cleaner, directional pulses. Their work may lead to visualizing chemical reactions faster than ever at the atomic scale.

“This work is the first step to do with x-rays the same kind of [techniques] which you do with regular lasers,” says Bergmann, the study’s senior author. “We have opened a time window for looking at chemical processes with attosecond [one billionth of one billionth of a second] precision. It’s a new frontier.”

Profile picture of Uwe Bergmann
Uwe Bergmann

Around a decade ago, researchers began using powerful x-ray free-electron lasers, which allow them to make ultrafast movies of molecular changes in real time on the femtosecond scale (one thousand times slower than an attosecond). Compared to visible lasers, which provide clean, single-wavelength beams of light, x-ray lasers are somewhat dirty: they contain multiple wavelengths of light of randomly varying intensity.

“What all scientists have done, and are still doing, is that you just adapt to what you get and then you design your experiments around them,” Bergmann says. “That also means that certain experiments, which in the optical laser regime are now standard, have not been possible.”

Bergmann and his colleagues somewhat accidentally discovered a way to make x-rays more like an optical laser. In their experimental setup, they shine intense but dirty x-ray pulses at a manganese sample. When these pulses hit a manganese atom, a lower-level electron is ejected and the hole it leaves is rapidly filled by a higher-level electron. The energy difference is emitted as a photon of a characteristic color. Very intense pulses can create enough of these holes. An emitted photon can effectively stimulate the emission of another one, leading to an avalanche of stimulated X-ray emission, mostly in the forward direction towards their detector.

Every so often, the detector that captures these stimulated emissions showed something they were not expecting: strong fringes, the characteristic pattern that results from constructively and destructively interfering signals. The fringes suggested that they had observed two x-ray emission pulses, separated by only a few femtoseconds.

“We were confused,” Bergmann says. “How did such a pair of x-ray pulses come about?”

After many discussions, calculations, and simulations, the team ruled out many possible explanations, until they finally realized what had happened: occasionally, two of the many spikes in the dirty pulses were much stronger than the rest of them. When these strong spikes occurred a few femtoseconds apart, and each had enough intensity, a clean pair of stimulated x-ray emission pulses emerged.

depiction of the experiment: a pulse of x-rays is shown as jagged white peaks. that pulse travels through the sample, represented as a thin square, where the signals are stimulated into larger, unidirectional peaks, shown as a red and yellow taller peaks. those peaks are streched out length-wise by the monochromator such that they now overlap. The result is a rainbow-colored splotch representing intensity of the measured signal. The splotch looks like a comb, which are the fringes.
Two strong x-ray pulses hit the manganese sample, are stretched through the monochromator, and overlap, leading to the characteristic fringes.

Before these two pulses reach the detector, they first travel through a monochromator — essentially a prism that stretches light, much like how white light passing through a clear prism is stretched into a rainbow. These stretched pulses then overlap timewise, and those frequencies that are in phase with each other can add up to become more intense or cancel each other out into dark troughs. Hence, the fringes.

“At times, each signal is rather clean and of similar strength, and one obtains very strong interference fringes,” Bergmann says. “We know that the fringe spacings are directly related to the time difference of the two pulses, and because we can measure them very precisely, we can obtain their time difference with extreme, attosecond precision.”

Currently, these pulse pairs are generated very rarely, Bergmann and his collaborators will work with the accelerator scientists to find ways to manipulate the ‘dirty’ pulses and enhance the chance of producing the pairs. They are optimistic that their work opens the door to new applications of such x-ray pulse pairs — the types of techniques that are used commonly with visible laser light.

“We’re trying to move nonlinear laser optics into the x-ray regime,” Bergmann says. “In the x-ray regime, you can probe certain phenomena that you just cannot optically access. X-ray wavelengths are comparable to the distances between atoms, and we can knock out lower-level electrons to get element specificity with them.”

Bergmann’s contribution to this research was funded in part by the U.S. Department of Energy, Laboratory Directed Research and Development program at SLAC National Accelerator Laboratory (DE-AC02-76SF00515). Other authors were supported by various funding as described in the study.

Bucket brigades and proton gates: Researchers shed new light on water’s role in photosynthesis

This story is adapted from one originally published by SLAC by Ali Sundermier

Photosystem II is a protein in plants, algae and cyanobacteria that uses sunlight to break water down into its atomic components, unlocking hydrogen and oxygen. A longstanding question about this process is how water molecules are funneled into the center of Photosystem II, where water is split to produce the oxygen we breathe. A better understanding of this process could inform the next generation of artificial photosynthetic systems that produce clean and renewable energy from sunlight and water.

In a paper published last week in Nature Communications, an international collaboration between scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (LBNL), SLAC National Accelerator Laboratory and several other institutions uncovers how the protein takes in water and how hydrogen is removed in order to release the oxygen molecules.

Profile picture of Uwe Bergmann
Uwe Bergmann

“Plants use the energy from sunlight to split two water molecules and produce the oxygen we breath. The study shows for the first time atomic-resolution snapshots of the likely channel and gate, where the water molecules arrive to the catalytic center to be split apart, and the channel where the protons are shuttled out during the splitting,” says Uwe Bergmann, the Martin L. Perl professor in ultrafast x-ray science at UW–Madison. “This information will help our understanding of one of the most fundamental reactions on earth, and how we might use sunlight in the future to create fuels.”

At SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, the team illuminated samples from cyanobacteria with ultrafast pulses of X-rays to collect both X-ray crystallography and spectroscopy data to simultaneously map the protein structure and how electrons flow in the protein. Through this technique, they are able to test competing theories of how Photosystem II splits water into oxygen. Over the past few years, the team has used this method to observe various steps of this water-splitting cycle at the temperature at which it occurs in nature. 

Scientists at UW–Madison have been instrumental to developing these and related x-ray imaging methods over the last decade.

The center of the protein acts as a catalyst, which drives certain chemical reactions to happen in a highly efficient manner. This research seeks to unlock how nature has optimized this catalytic process over millions of years of evolution. A cluster of four manganese atoms and one calcium atom are connected by oxygen atoms, and surrounded by water and the outer layers of the protein. In the step the scientists looked at, water flows through a pathway into the center of the protein, where one water molecule ultimately forms a bridge between a manganese atom and a calcium atom. The researchers showed that this water molecule likely provides one of the oxygen atoms in the oxygen molecule produced at the end of the cycle.

a schematic of the proposed mechanism is shown
The proposed proton gate around D1-E65, D2-E312, and D1-R334 in the open and closed state. | In Nature Communications, https://doi.org/10.1038/s41467-021-26781-z

Last year, the researchers discovered that Photosystem II ferries water into the center as if through a bucket brigade: Water molecules move in many small steps from one end of the pathway to the other. They also showed that the calcium atom within the center could be involved in shuttling the water in. In this most recent study, the researchers pinpoint, for the first time, the exact pathway where this process unfolds.

“This might prevent water from interacting with the center prematurely, resulting in unwanted intermediates such as peroxide that can cause damage to the enzyme,” said Jan Kern, staff scientist at LBNL and one of the corresponding authors.

The researchers also showed that there is another pathway dedicated to removing hydrogen protons generated during the water-splitting reaction. In the proton pathway, they discovered the existence of a “proton gate,” which blocks the proton from coming back to the center.

“These results show where and how the water molecules enter the catalytic site, and where the protons are released, advancing our understanding of how two waters may come together to form the oxygen we breathe,” said Junko Yano, senior scientist at LBNL and one of the corresponding authors. “It demonstrates that it is just not enough to determine the structure of the main catalytic center, but it is also important to understand how the entire protein carries out the reaction.”

In addition to SLAC and LBNL, the collaboration includes researchers from Uppsala University in Sweden; Humboldt University of Berlin; and the University of Wisconsin-Madison.

LCLS is a DOE Office of Science user facility. This research was supported by the Office of Science.