The synthesis of one of the most abundant organic lipids elucidates its structure


Crenarchaeol is a large, closed-loop lipid that is found in the membranes of archaea oxidizing ammonium, a single-celled life form that ubiquitously exists in the oceans. In comparison with other Archean membrane lipids, crenarchaeol is very complex, and so far attempts to confirm its structure by synthesizing the entire molecule have been unsuccessful. Organic chemists at the University of Groningen took up this challenge and found that the proposed structure for the molecule was largely, but not entirely, correct.

Crenarchaeol contains 86 carbon atoms and is a “macrocycle, a large closed loop.” No less than 22 positions in the molecule are chiral. The molecule can be present in two forms which are mirror images of each other, such as a left hand and a right hand. In the crenarcheol molecule, the 22 chiral centers have their own specific “workability”. In addition, crenarchaeol contains a very rare cyclohexane group.


This complex molecule was first isolated in 2002 by Jaap Sinninghe Damsté and his colleagues at the Royal Netherlands Institute for Sea Research, NIOZ. They identified its structure using spectroscopic techniques but their result has never been confirmed. This is surprising because ammonium-oxidizing archaea play a key role in the ocean nitrogen cycle, and the fossil crenarchaeol and its companion lipids are widely used by molecular paleontologists to replenish past sea temperatures. “The structure of crenarchaeol is a formidable challenge for synthetic organic chemistry,” says Adri Minnaard, professor of organic chemistry at the University of Groningen. “And we decided to take it up. “

First, 3 milligrams of the natural compound were isolated and purified with NIOZ, which took about three months. There are only tiny amounts of crenarchaeol in each cell, only 0.000000001 gram, but because there are so many of these cells in the oceans of the world and the molecule is very stable and has accumulated in sediment for millions of years, it is believed to be one of the most abundant organic molecules in marine sediments.

Mount Everest

There are several problems with the synthesis of crenarchaeol; getting all the chiral centers in the correct orientation is one of them. “And the molecule contains a lot of carbon-to-carbon bonds, which are difficult to build.” But it is a challenge that a synthetic organic chemist cannot resist, just as an ambitious climber cannot resist Mount Everest. Minnaard showed the structure to her doctoral student Mira Holzheimer, who worked on synthetic reactions catalyzed by palladium. “His literal response was, ‘I want to climb this mountain.’ They devised a plan of attack on paper, which involved breaking down the molecule into building blocks that could be synthesized. This produced a provisional route to the synthesis of complete molecules of crenarchaeol, which Holzheimer explored.

Similar to climbing a mountain for the first time, the synthetic course they originally designed sometimes led to a dead end. It meant going back over those steps and trying a new approach. “You start with several grams of the basic compounds. But in each of the more than 65 intermediate stages, you lose material, sometimes up to 50%. And if you run out of middlemen, you have to go back, ”says Minnaard.


After three years of hard work, Holzheimer had produced much of the molecule, about half of the macrocycle. Minnaard: “At this point, we decided to compare it to the corresponding part of natural crenarcheol. This was done using gas chromatography coupled with mass spectrometry. The comparison was made with NIOZ and the results were a shock: “We synthesized the right carbon skeleton, but the chromatographic behavior was not the same as that of natural crenarchaeol. Something was wrong, ”recalls Minnaard.

After two days of verification, Minnaard and Holzheimer concluded that they had really achieved the proposed structure. And since it did not completely match the natural crenarcheol, that could only mean one thing: the proposed structure was not quite correct. The results pointed to one of the chiral centers in the unusual group of cyclohexane. “Our NIOZ staff assigned only one chiral center out of 22.” The structural correction was supported by calculations on the spectra of natural and prepared crenarchaeols, which were performed by Prof. Remco Havenith and Dr Ana Da Cunha. Minnaard: “This shows the value of synthetic chemistry: the construction of a proposed structure is the gold standard for validation. “


Such a complex construction as with crenarchaeol brings additional advantages: “We had to develop new synthesis tools, which are now added to the organic synthesis toolbox. In addition, having the right structure is relevant for scientists studying Archean membranes. This is usually done by simulating molecular dynamics, Minnaard explains, and the fully correct structure is now available. However, this gain is not the greatest motivation for Minnaard to undertake these projects: “He does not always need to have a goal. For me, building molecules can be an art.

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