New Haven, Conn. — The movement of protons through electrically charged water is one of the most fundamental processes in chemistry. It is evident in everything from eyesight to energy storage to rocket fuel — and scientists have known about it for more than 200 years.

But no one has ever seen it happen. Or precisely measured it on a microscopic scale.

Now, the Mark Johnson lab at Yale has — for the first time — set benchmarks for how long it takes protons to move through six charged water molecules. The discovery, made possible with a highly customized mass spectrometer that has taken years to refine, could have far-reaching applications for researchers in years to come.

“We show what happens in a tiny molecular system where there is no place for the protons to hide,” said Johnson, the Arthur T. Kemp Professor of Chemistry in Yale’s Faculty of Arts and Sciences, and senior author of a new study in the journal Science. “We’re able to provide parameters that will give theorists a well-defined target for their chemical simulations, which are ubiquitous but have been unchallenged by experimental benchmarks.”

Johnson has spent decades developing new tools to analyze chemical reactions, such as the deformation of networks of interconnected water molecules in the presence of electrical charge — a key property of water. But water’s ability to transport positive charge, via protons, has proven elusive — due, in part, to the intrinsically quantum mechanical nature of protons.

“They aren’t polite enough to stay in one place long enough to let us observe them easily,” Johnson said. “They are thought to conduct the charge through an atomic-scale relay mechanism, in which protons jump from molecule to molecule.”

For the study, Johnson and his team studied the proton transfer that occurs when six molecules are attached to 4-aminobenzoic acid carrying an extra proton, a small, positively charged molecule ideally suited for studying water-mediated proton movement.

“To monitor the movement of the charge, you need a special type of organic molecule that can attach a proton in two different locations that are easily differentiated by the color of light they absorb,” said Payten Harville, a Ph.D. student in chemistry in the Yale School of Graduate Studies and co-lead author of the new study, along with fellow Ph.D. student Abhijit Rana. “It’s designed so that the only way for protons to get from one docking site to the other is to hitch a ride on a water network ‘taxi.’”

Johnson’s team runs these molecules through their paces with a specialized mass spectrometer that they’ve adapted to enable multiple interactions with carefully timed pulses of laser light. Located in Yale’s Sterling Chemistry Laboratory, the 30-foot-long device consists of carefully orchestrated piping, electronics, lasers, and a “refrigerator” that chills the molecules down to nearly absolute zero. The tiny assembly of water around the molecule is synthesized, triggered to react, and destructively analyzed for formation of products ten times a second.

“It took years to get the instrument to this point,” Rana said. “And we have finally succeeded in measuring the rate of a chemical reaction that occurs within a finite system.”

Even so, the reaction is so difficult to pin down that the researchers are only able to set parameters for its beginning and end.

“We can’t see it in the intermediate, but we know where the proton started and where it ended up,” Johnson said. “And now we know how long it takes to get there.”

Thien Khuu, a graduate of the Johnson lab who is now a postdoctoral fellow at the University of Southern California, is co-author of the study.

Funding for the research came from the U.S. Department of Energy, the U.S. Air Force Office of Scientific Research, a John C. Tully Graduate Research grant, and the National Institutes of Health.