Perfectly Natural: Gardeners’ Love of Chemistry and Chemists’ Love of Plants

When citrus trees are grown from seed, they revert to a wild state and they can take decades to flower. About 15 years after germination I’m still waiting to see grapefruit blossoms in our kitchen, and of course the short days of long winters at high latitudes don’t help the matter. But a few years ago I was lucky enough to visit an organic citrus farm in the Orlando, Florida region, which turned out to be a far more magical treat than any ride at nearby DisneyWorld.

On a single citrus tree we not only see fruits at various stages of ripening but also new flowers. Picture by the author.

Unlike most plants, those of the genus Citrus can simultaneously bloom while fruit is ripening elsewhere on the same tree. And the blossoms include some of the most delightful fragrances one will ever experience. And understanding how some of the compounds are synthesised by tangerines, lemons, grapefruits and plants in general makes one appreciate them even more.

At the level of citrus tissues, we see among different species variations upon a theme, the theme being what all plants of the genus have in common: bee-pollinated, bisexual flowers with usually 5 petals and 5 sepals and superior ovaries which become the fruit’s rind and flesh. Their leaves are evergreen and being part of subtropical trees, even the hardiest among them, the Meyer’s lemon, cannot survive temperatures below -5 °C.  At the biochemical level, in order to produce their special fragrance, there are variations upon themes as well.  Like many other plants they use a common precursor, the  molecule isopentenyl pyrophosphate, and with subtle changes they produce their beautiful characteristic bouquets which diffuse into our nasal receptors.

Using a process relying on thiamine(vitamin B1), among others, plants make isopentenyl pyrophosphate from acetyl coenzyme A, a metabolic byproduct of glucose known as pyruvate.   Isopentenyl pyrophosphate is a useful and ubiquitous molecule containing a 5-carbon atom-building block known as an isoprene unit. Some isopentenyl pyrophosphate molecules isomerize, meaning they rearrange with the same atoms, essentially shifting the double bond from the tail end over to the next pair of carbon atoms. The stable pyrophosphate group then leaves the molecule, leaving behind a reactive positive charge on a carbon atom at the head of the isopentenyl molecule. This is incidentally one of the many reasons plants need to absorb phosphorus from their environment.

Simplified reaction mechanism(enzyme is not shown): electron flow reveals how isopentenyl pyrophosphate bonds to a charged molecule derived from isopentenyl pyrophosphate itself. The product, geranyl pyrophosphate is then used by lemons to make geraniol. Many other fragrant molecules are also derived from geranyl pyrophosphate. See diagram below. Diagram by the author.
The backbone of geranyl pyrophosphate is highlighted in red and is found in three citrus scents.

Notice that I emphasized that only some isopentenyl pyrophosphate isomerize and become ionized. The rest then attack and stick to the positively charged molecules, creating  geranyl pyrophosphate (C10H20O7P2). This molecule can eventually be used to make an important component of cell membranes known as cholesterol, but lemons and some non-citrus plants also use the right enzyme to react it with water to produce geraniol (C10H18O). Although roses produce far more of the scent, it is also a minor component of citrus peels. In addition, lemon plants can oxidize the alcohol group of geraniol to an aldehyde to produce two isomers of citral, A and B. The former has a strong lemon scent and the latter, which has the same formula but with an aldehyde group on the other side of the carbon-double-bond, has a less intense but sweeter odor.

One 2009 study by Citrus Research and Education Center in Florida analyzed the flower scents of 15 species of citrus plants including lemons, limes, sweet oranges and mandarins. Using a relatively new solvent-less technique known as solid phase microextraction (SPME) along with mass spec-gas chromatagrophy, they identified 70 compounds, of which 29 were identified for the first time. The compounds belonged to four different groups of terpenes, compounds that are all derived from previously mentioned isoprene units. One of those oxygenated terpenes, linalool, is an alcohol derivative of geranyl pyrophosphate. Of the two possible isomers of the compound, oranges produce the R-version of linalool, which smells like lavender blended with citrus. It attracts bees and me.

A bee in a lemon flower. Linalool is one of the compounds that attracts the pollinator. Picture by the author.
geranyl pHosp deriv
More variation upon a theme at the molecular level: geranyl pyrophosphate, which is itself built up from two isoprene units, goes on to be the precursor of four other key compounds found in the floral essence of several citrus plants. Structures by the author.

Twenty four and forty five percent of  the blossom-volatiles of sweet oranges and mandarins, respectively, consist of  ß -myrcene. This compound is yet another variation upon the theme of geranyl pyrophosphate. Instead of having an allylic alcoholic head, it has a pair of conjugated double-bonded carbons and a pleasant fragrance. The same fruit blossoms and those of certain limes and lemons also produce of yet another geranyl pyrophosphate-derivative known as E-ocimene. Its aroma has been described as woody, green and tropical, an indication of how difficult it is for humans to describe smells. The difficulty becomes more pronounced when the isolated compounds of the labs force us to perceive “solo performances” while the reality of nature’s citrus blossoms present us with a symphony.


The Botanical Garden. Ryx and Phillips. Firefly.

A comparison of citrus blossom volatiles. Phytochemistry 70 (2009) 1428–1434

Principles of Biochemistry. Lehninger.

The Merck Index. Twelfth Edition

Myrcene as a Natural Base Chemical in Sustainable Chemistry: A Critical Review


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