Scientists capture molecular energy redistribution atom-by-atom using X-ray pulses

A team of researchers has achieved something that seemed impossible just years ago: watching a single molecule convert light energy into motion, atom by atom, as it happens. The breakthrough came from an unlikely partnership between a small ring-shaped molecule called 3-fluoropyridine and one of the world's most powerful X-ray machines, the European XFEL facility.

Here's what they observed. When ultraviolet light strikes the molecule, something dramatic unfolds in mere picoseconds—trillionths of a second. The molecule absorbs that energy and its electrons jump into an excited state, causing the entire structure to twist and contort out of its normal flat shape. Then comes the crucial moment: the molecule passes through what physicists call a conical intersection, a fleeting but pivotal crossing point where the movement of electrons and the motion of atomic nuclei become locked together. After that threshold, the molecule settles back down to its resting state, but something has changed. The energy that was purely electronic—bound up in excited electrons—has been converted into vibrations, the atoms now jiggling and oscillating in place.

What makes this discovery remarkable is not just that the team could see this happen, but that they could see it happening differently at different atoms. Using a technique called time-resolved X-ray photoelectron spectroscopy at the Small Quantum Systems instrument, they fired an ultraviolet laser at the molecules first, then followed up with precisely timed soft X-ray pulses that knocked deeply bound electrons loose from either the nitrogen or fluorine atoms. By measuring the energy of those ejected electrons at many different moments in time, the researchers could reconstruct how the chemical environment around each atom evolved over those few picoseconds. The fluorine atom, it turned out, acted as a clean signal of vibrational relaxation—a straightforward readout of how the molecule was shaking. The nitrogen atom told a more complex story, one tangled up in both electron redistribution and the structural rearrangement happening simultaneously.

Antonio Picón, a co-author from the Instituto de Ciencia de Materiales de Madrid, captured the insight plainly: different atoms in the same molecule report on different aspects of what's happening. Some reveal where electrical charge is moving. Others show how the whole structure vibrates. It's as if each atom is a different kind of sensor, each tuned to a different frequency of the molecular drama.

The team's work required more than just experimental skill. They built advanced computer simulations to interpret what the X-ray data was actually showing, creating models that could translate the raw measurements into a coherent picture of molecular motion. Daniel Rivas, a guest scientist at the facility, described the achievement in terms of capability: European XFEL was built precisely for this kind of work—to watch chemical change unfold at the atomic scale and on the timescale where it naturally occurs. By combining the ability to sense multiple atomic sites with femtosecond time resolution, they've opened a new window onto the microscopic mechanisms that drive photochemistry.

The implications extend far beyond this one molecule. The same approach could be applied to understand how light triggers structural change in far more complex systems: functional organic molecules used in electronics, the building blocks of biological molecules, materials designed to capture and convert solar energy. For the first time, researchers have a tool that can follow the atomic choreography of photochemistry in real time, watching not just what happens, but where and when it happens, one atom at a time.