F Rosa Rubicondior: Abiogenesis News - Urea May Have Been The Precursor to Life.

Thursday 29 June 2023

Abiogenesis News - Urea May Have Been The Precursor to Life.

Why urea may have been the gateway to life | ETH Zurich
Artist's impression of the pre-biotic Earth.

A new technique for observing chemical reactions with an extremely high temporal resolution has enabled Swiss scientists working at Eidgenössische Technische Hochschule, Zürich (ETH Zürich) and Geneva University to see what happens when urea in water is subject to ionizing radiation - the conditions that would have existed on pre-biotic Earth, billions of years ago.

The dominant theory explaining abiogenesis is that it took place around deep ocean hydrothermal vents, or black smokers, but a rival theory, which harks back to Darwin's 'warm little pond', is that it could have occurred in shallow pools subjected to ionizing radiation from the sun. The team's observation of how urea reacts lends support to the latter theory.

Urea is a highly reactive molecule that exists in concentrated solutions as a dimer (two molecules chemically bonded). The researchers observed that ionizing radiation causes a hydrogen ion (i.e., a proton, which carries a positive charge) to move from one molecule in the dimer to the other, creating a negatively charged urea- radical from one molecule and a protonated urea+ molecule from the other. The former is highly reactive and can then form malonic acid - believed to be the first step in creating larger molecules such as RNA. This happens so fast (in about 1 femtosecond, or 150 billionths of a second) that it effectively monopolizes the dimer and prevents other chemical reactions from occurring, so favouring the formation of malonic acid.

The details are given in the ETH Zürich press release:
In brief
  • Researchers can now observe chemical reactions taking place in liquids at high temporal resolution.
  • Using their new method, the researchers studied a chemical reaction that may have led to the emergence of life on Earth.
  • The method is relevant not only in biochemistry but also for important industrial synthesis reactions.
Researchers from ETH Zurich and the University of Geneva have developed a new method that allows them to observe chemical reactions taking place in liquids at extremely high temporal resolution. This means they can examine how molecules change within just a few femtoseconds – in other words, within a few quadrillionths of a second. The method is based on earlier work done by the same group of researchers led by Hans Jakob Wörner, Professor of Physical Chemistry at ETH Zurich. That work yielded similar results for reactions that take place in gas environments.

To expand their X-ray spectroscopy observations to liquids, the researchers had to design an apparatus capable of producing a liquid jet with a diameter of less than one micrometre in a vacuum. This was essential because if the jet were any wider, it would absorb some of the X-rays used to measure it.

Molecular pioneer in biochemistry

Using the new method, the researchers were able to gain insights into the processes that led to the emergence of life on Earth. Many scientists assume that urea played a pivotal role here. It is one of the simplest molecules containing both carbon and nitrogen. What’s more, it’s highly likely that urea was present even when the Earth was very young, something that was also suggested by a famous experiment done in the 1950s: American scientist Stanley Miller concocted a mixture of those gases believed to have made up the planet’s primordial atmosphere and exposed it to the conditions of a thunderstorm. This produced a series of molecules, one of which was urea.

According to current theories, the urea could have become enriched in warm puddles – commonly called primordial soup – on the then lifeless Earth. As the water in this soup evaporated, the concentration of urea increased. Through exposure to ionising radiation such as cosmic rays, it’s possible that this concentrated urea produced malonic acid over multiple synthesis steps. In turn, this may have created the building blocks of RNA and DNA.

Why this exact reaction tool place

Using their new method, the researchers from ETH Zurich and the University of Geneva investigated the first step in this long series of chemical reactions to find out how a concentrated urea solution behaves when exposed to ionising radiation.

A whole host of important chemical and biochemical reactions take place in liquids, both in the human body and in industrial synthesis.

Hans Jakob Wörner, co-corresponding author
Laboratory of Physical Chemistry,
ETH Zürich, Zurich, Switzerland.
It’s important to know that the urea molecules in a concentrated urea solution group themselves into pairs, or what are known as dimers. As the researchers have now been able to show, ionising radiation causes a hydrogen atom within each of these dimers to move from one urea molecule to the other. This turns one urea molecule into a protonated urea molecule, and the other into a urea radical. The latter is highly chemically reactive – so reactive, in fact, that it’s very likely to react with other molecules, thereby also forming malonic acid.

That’s so fast that this reaction preempts all other reactions that might theoretically also take place. This explains why concentrated urea solutions produce urea radicals rather than hosting other reactions that would produce other molecules.

Hans Jakob Wörner.

A whole host of important chemical reactions take place in liquids – not just all biochemical processes in the human body, but also a great many chemical syntheses relevant to industry. This is why it’s so important that we have now expanded the scope of X-ray spectroscopy at high temporal resolution to include reactions in liquids.

Hans Jakob Wörner.
The researchers also managed to show that this transfer of a hydrogen atom happens extremely quickly, taking only around 150 femtoseconds, or 150 quadrillionths of a second.

Reactions in liquids are highly relevant

In the future, Wörner and his colleagues want to examine the next steps that lead to the formation of malonic acid. They hope this will help them to understand the origins of life on Earth.

As for their new method, it can also generally be used to examine the precise sequence of chemical reactions in liquids.

The researchers from ETH Zurich and the University of Geneva were assisted in this work by colleagues from Deutsches Elektronen-Synchrotron DESY in Hamburg, who performed calculations required to interpret measurement data.
The team's findings are published, open access, in Nature:
Fig. 1: Overview of the experimental setup and the pumped and unpumped spectra.
a, Schematic depiction of the experimental setup. b, Schematic molecular-orbital diagram illustrating ionization by a pump pulse, followed by probing of the system with a SXR pulse. c, XAS spectrum of a 10 M urea solution covering the carbon and nitrogen K edges with and without pump, and the time-averaged ΔOD signal.

Proton transfer is one of the most fundamental events in aqueous-phase chemistry and an emblematic case of coupled ultrafast electronic and structural dynamics1,2. Disentangling electronic and nuclear dynamics on the femtosecond timescales remains a formidable challenge, especially in the liquid phase, the natural environment of biochemical processes. Here we exploit the unique features of table-top water-window X-ray absorption spectroscopy3,4,5,6 to reveal femtosecond proton-transfer dynamics in ionized urea dimers in aqueous solution. Harnessing the element specificity and the site selectivity of X-ray absorption spectroscopy with the aid of ab initio quantum-mechanical and molecular-mechanics calculations, we show how, in addition to the proton transfer, the subsequent rearrangement of the urea dimer and the associated change of the electronic structure can be identified with site selectivity. These results establish the considerable potential of flat-jet, table-top X-ray absorption spectroscopy7,8 in elucidating solution-phase ultrafast dynamics in biomolecular systems.

Whatever the truth about abiogenesis turns out to be, we can be sure that, when that gap closes, like all other gaps closed by science, the answer will conform entirely to the laws of chemistry and physics. There will be no place for magic gods in the explanation and nothing that requires the laws of chemistry and physics to be suspended or over-ruled.

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