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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2017-06-22 13:05:15
  • Article ID: 676925

A Single Electron's Tiny Leap Sets Off 'Molecular Sunscreen' Response

A new X-ray laser technique will help scientists study a wide range of organic molecules that respond to light, from DNA building blocks to plastic products and receptors in your eyes.

  • Credit: Greg Stewart/SLAC National Accelerator Laboratory

    Thymine – the molecule illustrated in the foreground – is one of the four basic building blocks that make up the double helix of DNA. It’s such a strong absorber of ultraviolet light that the UV in sunlight should deactivate it, yet this does not happen. Researchers used an X-ray laser at SLAC National Accelerator Laboratory to observe the infinitesimal leap of a single electron that sets off a protective response in thymine molecules, allowing them to shake off UV damage.

In experiments at the Department of Energy’s SLAC National Accelerator Laboratory, scientists were able to see the first step of a process that protects a DNA building block called thymine from sun damage: When it’s hit with ultraviolet light, a single electron jumps into a slightly higher orbit around the nucleus of a single oxygen atom.

This infinitesimal leap sets off a response that stretches one of thymine’s chemical bonds and snaps it back into place, creating vibrations that harmlessly dissipate the energy of incoming ultraviolet light so it doesn’t cause mutations.

The technique used to observe this tiny switch-flip at SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser can be applied to almost any organic molecule that responds to light – whether that light is a good thing, as in photosynthesis or human vision, or a bad thing, as in skin cancer, the scientists said. They described the study in Nature Communications today.

“All of these light-sensitive organic molecules tend to absorb light in the ultraviolet. That’s not only why you get sunburn, but it’s also why your plastic eyeglass lenses offer some UV protection,” said Phil Bucksbaum, a professor at SLAC and Stanford University and director of the Stanford PULSE Institute at SLAC. “You can even see these effects in plastic lawn furniture – after a couple of seasons it can become brittle and discolored simply due to the fact that the plastic was absorbing ultraviolet light all the time, and the way it absorbs sun results in damage to its chemical bonds.”

Catching Electrons in Action

Thymine and the other three DNA building blocks also strongly absorb ultraviolet light, which can trigger mutations and skin cancer, yet these molecules seem to get by with minimal damage. In 2014, a team led by Markus Guehr – then a SLAC senior staff scientist and now on the faculty of the University of Potsdam in Germany – reported that they had found the answer: The stretch-snap of a single bond and resulting energy-dissipating vibrations, which took place within 200 femtoseconds, or millionths of a billionth of a second after UV light exposure.

But what made the bond stretch? The team knew the answer had to involve electrons, which are responsible for forming, changing and breaking bonds between atoms. So they devised an ingenious way to catch the specific electron movements that trigger the protective response.

It relied on the fact that electrons don’t orbit an atom’s nucleus in neat concentric circles, like planets orbiting a sun, but rather in fuzzy clouds that take a different shape depending on how far they are from the nucleus. Some of these orbitals are in fact like a fuzzy sphere; others look a little like barbells or the start of a balloon animal. You can see examples here.

Strong Signal Could Solve Long-Standing Debate

For this new experiment, the scientists hit thymine molecules with a pulse of UV laser light and tuned the energy of the LCLS X-ray laser pulses so they would home in on the response of the oxygen atom that’s at one end of the stretching, snapping bond.

The energy from the UV light excited one of the atom’s electrons to jump into a higher orbital. This left the atom in a sort of tippy state where just a little more energy would boost a second electron into a higher orbital; and that second jump is what sets off the protective response, changing the shape of the molecule just enough to stretch the bond.

The first jump, which was previously known to happen, is difficult to detect because the electron winds up in a rather diffuse orbital cloud, Guehr said. But the second, which had never been observed before, was much easier to spot because that electron ended up in an orbital with a distinctive shape that gave off a big signal.

“Although this was a very tiny electron movement, the signal kind of jumped out at us in the experiment,” Guehr said. “I always had a feeling this would be a strong transition, just intuitively, but when we saw this come in it was a special moment, one of the best moments an experimentalist can have.”

Settling a Longstanding Debate

Study lead author Thomas Wolf, an associate staff scientist at SLAC, said the results should settle a longstanding debate about how long after UV exposure the protective response kicks in: It happens 60 femtoseconds after UV light hits. This time span is important, he said, because the longer the atom spends in the tippy state between the first jump and the second, the more likely it is to undergo some sort of reaction that could damage the molecule.

Henrik Koch, a theorist at NTNU in Norway who was a guest professor at Stanford at the time, led the study with Guehr. He led the effort to model, understand and interpret what happened in the experiment, and he participated in it to an unusual extent, Guehr said.

“He is extremely experienced in applying theory to methodology development, and he had this curiosity to bring this to our experiment,” Guehr said. “He was so fascinated by this research that he did something completely untypical of a theorist – he came to LCLS, into the control room, and he wanted to see the data coming in. I found that completely amazing and very motivating. It turned out that some of my previous thinking was completely right but other aspects were completely wrong, and Henrik did the right theory at the right level so we could learn from it.”

LCLS is a DOE Office of Science User Facility. Other institutions involved in the study were Norwegian University of Science and Technology; University of Trieste and Elettra synchrotron in Trieste, Italy; Aarhus University in Denmark; University of Gothenburg and Uppsala University in Sweden; University of Connecticut; the DOE’s Argonne National Laboratory; Northwestern University; Ecole Polytechnique Federal de Lausanne in Switzerland; and the RIKEN Laser Technology Laboratory in Japan. The DOE Office of Science funded the research.


SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, Calif., SLAC is operated by Stanford University for the U.S. Department of Energy's Office of Science.

SLAC National Accelerator Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

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Coupling Experiments to Theory to Build a Better Battery

A Berkeley Lab-led team of researchers has reported that a new lithium-sulfur battery component allows a doubling in capacity compared to a conventional lithium-sulfur battery, even after more than 100 charge cycles.

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A Shortcut to Modeling Sickle Cell Disease

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Conservation Mind Game

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X-Rays Reveal 'Handedness' in Swirling Electric Vortices

Scientists used spiraling X-rays at Berkeley Lab to observe, for the first time, a property that gives left- or right-handedness to swirling electric patterns - dubbed polar vortices - in a layered material called a superlattice.

Breaking Bad Metals with Neutrons

By combining the latest developments in neutron scattering and theory, researchers are close to predicting phenomena like superconductivity and magnetism in strongly correlated electron systems. It is likely that the next advances in superconductivity and magnetism will come from such systems, but they might also be used in completely new ways such as quantum computing.

ORNL Researchers Use Titan to Accelerate Design, Training of Deep Learning Networks

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Dark Energy Survey Publicly Releases First Three Years of Data

At a special session held during the American Astronomical Society meeting in Washington, D.C., scientists on the Dark Energy Survey (DES) announced today the public release of their first three years of data. This first major release of data from the Survey includes information on about 400 million astronomical objects, including distant galaxies billions of light-years away as well as stars in our own galaxy.

Ingredients for Life Revealed in Meteorites That Fell to Earth

A detailed study of blue salt crystals found in two meteorites that crashed to Earth - which included X-ray experiments at Berkeley Lab - found that they contain both liquid water and a mix of complex organic compounds including hydrocarbons and amino acids.


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Superconducting X-Ray Laser Takes Shape in Silicon Valley

An area known for high-tech gadgets and innovation will soon be home to an advanced superconducting X-ray laser that stretches 3 miles in length, built by a collaboration of national laboratories. On January 19, the first section of the machine's new accelerator arrived by truck at SLAC National Accelerator Laboratory in Menlo Park after a cross-country journey that began in Batavia, Illinois, at Fermi National Accelerator Laboratory.

Kelsey Stoerzinger Earns Young Investigator Lectureship

Kelsey Stoerzinger, Pauling Fellow at Pacific Northwest National Laboratory, is one of the 2018 Caltech Young Investigator Lecturers in Engineering and Applied Physics.

North Dakota State University Joins Two National Distributed Computing Groups

The NDSU Center for Computationally Assisted Science and Technology (CCAST) joins OSG (Open Science Grid) and XSEDE (Extreme Science and Engineering Discovery Environment).

DOE Announces Funding for New HPC4Manufacturing Industry Projects

The Department of Energy's Advanced Manufacturing Office (AMO) today announced the funding of $1.87 million for seven new industry projects under an ongoing initiative designed to utilize DOE's high-performance computing (HPC) resources and expertise to advance U.S. manufacturing and clean energy technologies.

DOE Announces First Awardees for New HPC4Materials for Severe Environments Program

The Department of Energy's Office of Fossil Energy (FE) today announced the funding of $450,000 for the first two private-public partnerships under a brand-new initiative aimed at discovering, designing and scaling up production of novel materials for severe environments.

Two Argonne Scientists Recognized for a Decade of Breakthroughs

Two scientists with the U.S. Department of Energy's (DOE) Argonne National Laboratory have been named to the Web of Science's Highly Cited List of 2017, ranking in the top 1 percent of their peers by citations and subject area. Materials Scientist Khalil Amine and Energy and Environmental Policy Scientist David Streets say they are thrilled to see their work -- and the laboratory -- recognized in such a way.

Argonne Welcomes Department of Energy Secretary Perry

U.S. Department of Energy Secretary Rick Perry visited Argonne National Laboratory yesterday, getting a first-hand view of the multifaceted and interdisciplinary research program laboratory of the Department.

Argonne names John Quintana Deputy Laboratory Director for Operations and COO

John Quintana has been named Deputy Laboratory Director for Operations and Chief Operations Officer (COO) of the U.S. Department of Energy's (DOE) Argonne National Laboratory.

Developing Next-Generation Sensing Technologies

Recently, the Advanced Research Projects Agency-Energy (ARPA-E) announced $20 million in funding for 15 projects that will develop a new class of sensor systems to enable significant energy savings via reduced demand for heating and cooling in residential and commercial buildings.

Supporting the Development of Offshore Wind Power Plants

Offshore wind is becoming a reality in the United States, especially in the northeast states. To support this development, the Center for Future Energy System (CFES) at Rensselaer Polytechnic Institute will present a webinar titled "Turbine and Transmission System Technologies for Offshore Wind (OSW) Power Plants." The program will be held on Wednesday, Dec. 20, from 2 to 4 p.m. Advance registration is required.


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Exploring Past, Present, and Future Water Availability Regionally, Globally

New open-source software simulates river and runoff resources.

Arctic Photosynthetic Capacity and Carbon Dioxide Assimilation Underestimated by Terrestrial Biosphere Models

New measurements offer data vital to projecting plant response to environmental changes.

DRIFTing to Fast, Precise Data

Non-destructive technique identifies key variations in Alaskan soils, quickly providing insights into carbon levels.

Superconducting Tokamaks Are Standing Tall

Plasma physicists significantly improve the vertical stability of a Korean fusion device.

Graphene Flexes Its Muscle

Crumpling reduces rigidity in an otherwise stiff material, making it less prone to catastrophic failure.

Remotely Predicting Leaf Age in Tropical Forests

New approach offers data across species, sites, and canopies, providing insights into carbon uptake by forests.

What's the Noise Eating Quantum Bits?

The magnetic noise caused by adsorbed oxygen molecules is "eating at" the phase stability of quantum bits, mitigating the noise is vital for future quantum computers.

Rewritable Wires Could Mean No More Obsolete Circuitry

An electric field switches the conductivity on and off in atomic-scale channels, which could allow for upgrades at will.

Filtering Water Better than Nature

Water passes through human-made straws faster than the "gold standard" protein, allowing us to filter seawater.

Machine Learning Provides a Bridge to the Texture of the Quantum World

Machine learning and neural networks are the foundation of artificial intelligence and image recognition, but now they offer a bridge to see and recognize exotic insulating phases in quantum materials.


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