Benzene: the aromatic circle

My seventh chemical of Christmas is not routinely made in biology, and is actually lethal to most large animals. Crafted by extremely inventive chemists in the 19th Century, benzene is a beautifully symmetric molecule with 6 carbons and 6 hydrogens.

The carbons in benzene are held together by an ‘aromatic’ bond. The word aromatic was coined by those early chemists to describe the smells emitted by these molecules. However, in chemistry the word quickly shifted to define a the chemical properties of this special bond.

Bonds and rings

Bonds are the glue of chemistry, where electrons move amongst atoms. Most bonds are between two atoms. The electron’s favoured path is a loop between two atoms, which binds the two atoms to each other to form a molecule. (This ‘path’ is also called a distribution, as at the quantum scale electrons can coexist between particles and waves. Yup – it doesn’t make a tremendous amount of sense, but that’s the way the world is!)

Occasionally, more than two atoms can be involved in a bond. These multi-atom structures can form rings of atoms. In such cases, some of the electron distribution covers the entire ring. The mathematics of how electron distributions merge favour the symmetry of a ring – making this bond stronger than expected.

These rings are both far more stable than other pairwise structures, and have different properties:

  • The electrons can move their charge easily from one part of the ring to another
  • The ring can participate in charge-related processes as a single entity
  • Aromatic rings can pick up energy from photons and shuffle it off elsewhere in the molecule.

Benzene in nature

The six-carbon benzene ring is the simplest example of an aromatic ring. It is rarely made in nature; rather, it is an everyday product of the petrochemical industry.

That said, rings with one or two decorations or tweaks are commonplace in biology. Three amino acids (phenylalanine, tyrosine and tryptophan) contain six-membered aromatic rings. They get deployed to perform clever bits of chemistry in biology, as the interactions between rings are useful in the mutual recognition of molecules. (Other amino acids contain aromatic five-membered rings, including histidine, an essential amino acid.)

Haem, a monster aromatic

Biology also makes some monster aromatic compounds, notably haems, chlorophyll and other photosynthetic pigments.

Haem (heme in American English) is a large, flat, aromatic compound  containing both carbons and nitrogens. This stable ring of delocalised electrons is big enough to accommodate a metal ion nestled in the middle, making it perfect for reduction / oxidation reactions (wherein an electron is added or subtracted from one molecule to another).

The metal ion – in haem’s case, iron – is the source and sink of the electrons. But the flat ring keeps this ion in a single, defined location, ready to be positioned by a surrounding protein to catalyse a single reaction.

In living systems, haems are mainly used in redox reactions. For humans, its most common deployment is in haemoglobin, the major protein in the blood. It reversibly binds molecular oxygen, transferring oxygen from our lungs to the rest of the body. Here the iron is placed ‘just so’ for the oxygen to be comfortably captured in the lung, but not so comfortable that it diffuses away in our tissues.

The other monster aromatic

The flat planar ring of aromatic compounds is also a key feature of chlorophylls. This broad collection of photosynthesis molecules is critical to the survival of most plants. There are many plantish riffs on chlorophyll: slightly different side chains here, a bit more complexity there… but they all centre on a planar aromatic ring with a magnesium ion in the middle.

For a long time during evolution, these aromatic rings absorbed light energy and used it to boost the redox energy of electrons travelling (through electron transport chains) in the membranes of bacteria.

  • They’d usually start off as a pair of chlorophylls: one an acceptor and one a donor.
  • The high-energy electron would (eventually) be returned in a lower state to the donor via the chain of proteins…
  • but only in exchange for protons either side of the membrane.
  • This set up a proton gradient that could be captured for ATP.

The circle of life

One enterprising cyanobacteria innovated on this scheme in a rather neat way. Rather than perpetuating the cycle of electrons, it split water in order to donate an electron fully to a single chlorophyll. There, the electron performed a similar slalom in the membrane, and was eventually released as captured ‘redox’ energy, in the form of NADPH. The split water ultimately leads to the formation of molecular oxygen, which is a gas and so diffuses easily away.

The runaway success of this process led to the blossoming of life on Earth, with the innovative cyanobacteria captured by enterprising proto-plants to become chloroplasts and the creation of a massive amount of molecular oxygen, reused by life as a source of oxidation power for metabolism.

Aromatic compounds are truly the source of all life.

Benzene in EMBL-EBI data resources

Explore benzene in several of EMBL-EBI’s public data resources