Obscure Molecules In Familiar Smells

At both the macroscopic and micro levels, not all organisms get equal attention. Because of their sheer numbers, there are still undiscovered species of plants and roundworms at the feet of botanists and zoologists, respectively. Other specimens have been named but little is known about them. At the astronomical level we come across two factors: an overwhelming number of stars and bodies, compounded by a detection limit.

The latter is rarely a problem for molecules, but there are so many combinations of atoms possible, especially when both their sequence and arrangement in three dimensional space has such a marked effect on chemical properties. Just the single association of carbon, hydrogen and oxygen in a ratio of 6:12:1hexanal (C6H12O) has produced almost 300 versions(isomers), and only one, hexanal, gives off the scent of freshly cut grass. Here are fairly well-studied molecules of the same three elements but in different ratios. Not having found their way into too many scientific magazines or websites, they are obscure molecules in familiar smells that should be part of the popular imagination.

1. Geosmin and its Unsaturated Version

Fertile soil is actually a blend of living and nonliving material, so it’s not surprising that the characteristic smell of freshly plowed earth is due to a  compound released by bacteria. Almost 50 years ago, a mixture of compounds from a smelly strain of Streptomyces griseoluteus was obtained. Some species of Streptomyces decompose leaves and organic matter in soil and are known to produce antibiotics. The investigators tried to purify the mixture through ether-extraction and by using activated charcoal and chloroform. Although they did not reduce it to a single compound, the mixture retained its earthy odor even after it was diluted by a factor of a billion!

Two years later, after using methylene chloride-extraction and gas chromatography, another group realized that the smell did not come from what was previously believed to be a blend of esters, acids, alcohols, aldehydes and ammonia. It was mainly due  to a molecule which they dubbed geosmin. gesominWhen it’s too concentrated, geosmin smells like manure. But when a concentration of 0.7 micrograms per kilogram (the human nose’s threshold) is not too amplified, the molecule’s interaction with nasal receptors is a pleasant experience for most people. It also gives rise to the smell of soil after rainfall. When some animals are drawn to the odor of geosmin they place their snouts into the ground and help distribute bacterial spores.

More recently, geosmin has also been found to be released by some cyanoba


cteria, and the perfume industry have found geosmin in three species of cacti flowers.  Discovered about 15 years ago, the unsaturated version of geosmin, dehydrogeosmin, has a musty, earthy odor and is found in over 50 members of the cactus family. It’s ironic that desert plants are producing a smell that we associate with damp places.  But the smell plays a role in the pollination of the endangered Mexican species Turbinicarpus pseudomacrochele, which produces dehydrogeosmin in a high concentration along with trace amounts of geosmin.

2.   Filbertones and A Related Ketone
Filbertone is a liquid isolated from hazelnuts. The nut contains almost equal amounts of the two mirror image-versions of the molecule known as enantiomers. Prior to their 1989 discovery,  chemists were already familiar with how enantiomers can have different properties. Limonene, for instance, smells like oranges, while its mirror image has harsh lemon notes which can even be mistaken for turpentine.  Similarly, with filbertone, we are less sensitive to the odor of one enantiomer: it is more buttery and chocolate-like. The other has a stronger and more fatty smell. There are, however, dozens of other compounds that account for the symphony of hazelnut aroma.
Filbertone’s ketone group and part of its methylated skeleton is reminiscent of butanedione, a cheesy-smelling compound partly responsible for the flavor of butter. butanedione
The enantiomer ratio of filbertones is fairly constant and independent of the hazelnut’s geographical area. nocciolaWhat inspired that particular investigation is the fact that hazelnut oil is often used as an adulterant in more expensive olive oil.

After laboriously handpicking over a thousand nuts from their socket-like receptacles and drying them for weeks in the Avellino sun, I once tried to smuggle them through the Montreal airport. They were confiscated. I hope the custom officers at least cracked their shells, bit into the kernels and released their filbertones.


One Man’s Weed Is Another Man’s Science

When I was a teenager, my father would sooner believe that I was an incompetent lawn mower than even entertain the possibility that I was motivated to preserve what he considered weeds, those suburban symbols of lassitude and irresponsibility.


If I’d see a patch of flowering clover or the tiny star-like flowers of stitchwort (Stellaria),I felt compelled to mow around them, come back to the patches with lawn clippers to cut protruding blades of grass and try to make the weeds as inconspicuous as possible, hoping to sneak my conservation effort past my father’s critical eye.  But it never worked. Even though I tried to point out that stitchwort was rich in vitamin C, in his eyes there was a place for everything, and only grass should be grown in lawns.

I discovered that one of my father’s many kindred spirits lives on my street. A few nights ago while walking my dog, I noticed he was destroying an attractive patch of black medic from his lawn that bordered the sidewalk.

With the friendliest tone I could manage, I asked him, “Did you know that plant is a member of the legume family, and it makes its own fertilizer?”

“Yes, but it’s not nice,”  he replied.

I sensed it was hopeless, but my compulsion to explain science obliged me to continue. “The nitrogen from the air gets converted to useful ammonium by a helpful bacterium in that plant’s roots,” I said.

“Yes, but it’s not nice,”  he repeated, still friendly.

For the sake of neighborly relations, now seemed like a good time to let go, so I smiled and concluded, “Oh well…it’s your property.”

black medic

So, alas, unable to spark a street discussion of the intricacies of black medic, I turn once again to the laptop keyboard. Medicago lupilina, is a member of the pea family (Leguminosae or Fabaceae). A close look at the cluster of yellow flowers reveals a set of miniature pea-like flowers. The bases, sepals and stamens are fused together into a cup-like structure, and you have to lift the cup and have exceptional closeup eyesight to see its reproductive parts.

A key ecological feature of this family is the nitrogen-fixing ability shared by most of its 18 to 20 thousand members. It happens through a symbiotic association with Rhizobium, which infect legume roots and form nodules, where in exchange for sugars, the bacteria use an anaerobic reaction to convert diatomic nitrogen into ammonium ion (NH4+). In the reaction, the nitrogen is “fixed”, because plants cannot convert relatively inert N2 into needed amino acids, but ammonium will do the trick. But free nitrogen gas has an oxidation number of zero, and it gets converted into  NH4+ , whose nitrogen atom has an oxidation number of (-3). This reduction process would not occur if the common oxidizer in air, oxygen, would come into contact with the nitrogen-fixing enzymes.

root nodules of black medic

But the problem is that the natural form of nitrogen fixation has something in common with the industrial version (Haber Process): it is an energy-demanding reaction,and what better way is there to release energy from sugars than through cellular respiration, which needs oxygen?

The bacteria get around this dilemma by making use of leghemoglobin(LEG), a pigment similar in structure to our hemoglobin but with a higher affinity for oxygen. In the diagram, notice that the pigment is actually in the nodule, outside of the bacterial cell wall, away from the enzyme complex (NC).

Nfixing_1The small amount of oxygen is then delivered to the bacteria’s respiratory chain (RC), allowing several ATP molecules to be fed into the enzyme complex, where the reducing agent, NADH, converts the nitrogen into ammonium. The latter is released in aqueous form into the host cell , where it is converted into glutamine, asparagine and urea derivatives of the general form,R-CO-NH-CO NH2, where R can be a different hydrocarbon group.

These products are then transported to the rest of the plant through the xylem (not with sugars, which are distributed by the phloem), and with the abundance of these protein-building blocks, it is not surprising that the seeds of the black, ripe pods of black medic, like those of beans, lentils and other legumes, are rich in proteins.

seed of black medic in my hand

Compared to other plants, legumes seem to be more sensitive to increases in carbon dioxide levels.(Incidentally, we have surpassed the global average concentration of 400 ppm,and you could see how it varies globally here.) Some species produce bigger seeds when the atmosphere is CO2-enriched, and in general, at least in soybeans, extra carbon facilitates the fixation of nitrogen, provided that there are no other stresses such as limited nutrient availability or drought.

I guess that’s another reason why my neighbor was digging up his black medic—better get to it before climate change amplifies his problem.


Will Elevated Carbon Dioxide Concentration Amplify the Benefits of Nitrogen Fixation in Legumes?1
Plant Physiology November 2009 vol. 151 no. 3 1009-1016  (available in its entirety, free of charge)
The Botanical Garden Volume II: Perennials and Annuals. Roger Phillips and Martyn Rix. Firefly. 2002


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