Physicists track biochemical reactions in Darwin’s ‘warm little ponds’

07 Aug 2023 Isabelle Dumé

Two neighbouring urea molecules in an aqueous solution exchange protons. (Courtesy: DESY, Ludger Inhester)

When life first appeared on Earth four billion years ago, it may have got its start in what the 19th-century naturalist Charles Darwin called “warm little ponds”: volcanically heated pools containing a soup of initially lifeless organic molecules. In a recent study, researchers in Switzerland and Germany shed further light on this topic by examining how one such molecule, urea, responds to pulses of ionizing radiation. The results of their work, which used ultrafast X-ray absorption spectroscopy to follow chemical reactions in real time, could advance our understanding of the biochemical origins of life.

When urea is exposed to ionizing radiation, it forms malonic acid. This acid then reacts with un-ionized urea to form several nucleobases, which are the fundamental components of RNA and DNA. Such processes could well have occurred when the “warm little ponds” were exposed to the Sun’s ultraviolet radiation and may have played a role in the emergence of early lifeforms.

Two pulses

In their experiment, researchers led by Jean-Pierre Wolf of the University of Geneva and Hans Jakob Wörner at ETH Zurich, Switzerland, applied a laser pulse to a highly concentrated solution of urea, causing some of the urea molecules to lose electrons and become ionized. Immediately afterwards, they sent in an ultrashort pulse of soft-X-rays. This second pulse reveals how the urea molecule responds to the loss of an electron.

The researchers repeated the experiment several times, varying the time interval between the ionizing laser pulse and the soft-X-ray pulses. This technique, known as time-resolved X-ray absorption spectroscopy (XAS), is routinely employed in the optical regime to study specific particles within materials, but this work extends it into the X-ray part of the electromagnetic spectrum.

“We also wanted to recreate experimental conditions as close as possible to the ‘real world’ and thus needed to perform our measurements in the liquid phase,” explains study lead author Zhong Yin, a former member of the ETH Zurich team who is now at Tohoku University in Japan. “For this, we developed a liquid flat sheet with sub-micron thickness, which is required for artefact-free XAS because of the very short attenuation length of the system.”

Another key element in the experiment, Yin adds, is that their light source could deliver ultrashort pulses over a range of energies broad enough to cover the absorption edges of carbon and nitrogen in the urea molecule. “This meant we could identify that the absorption signal comes exclusively from urea, since liquid water has no carbon and nitrogen in it,” he tells Physics World.

Femtosecond scale resolution

Using this technique, the team was able to reconstruct the sequence of events on the scale of a few femtoseconds (10-15 s), meaning the researchers could follow the chemical reactions in real time and observe how the system evolves. Even with a new technique and the right tools, however, it wasn’t easy. “Interpreting the spectra proved to be particularly challenging, and required detailed computer simulations which we developed here at DESY over many years,” explains Ludger Inhester, who is a theoretical physicist in the CFEL at DESY in Hamburg.READ MORE

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The researchers observed that when a urea molecule is ionized (that is, becomes positive as it loses an electron), it pushes a proton (a hydrogen nucleus) over to a nearby neutral, non-ionized, urea molecule in an effort to lose this positive charge. “This femtosecond-rate proton transfer creates a urea radical along with a positively charged urea ion,” says Inhester. “Both are chemically reactive and could have led to the formation of RNA molecules – essential building blocks of early life – billions of years ago.”

The new experiment is the first to observe such extremely fast processes in a molecule in an aqueous environment, he adds. Previous experiments were performed in the gas phase, but observing the behaviour of molecules suspended in water is important, especially when it comes to understanding biological processes.

Members of the Hamburg-Geneva-Zurich team would now like to further investigate the initial step of the ionization dynamics. “Such an experiment will require an even higher temporal resolution and will take some time to set up,” Yin says. “I am positive, though, that we will observe something new and exciting when we do this.”

Their present study is detailed in Nature.

Isabelle Dumé is a contributing editor to Physics World

FROM PHYSICSWORLD.COM  8/8/2023