Joining Turtle Shells

When you hear the word organic chemistry, the first thing that comes to your mind might be the turtle shell-shaped molecule of benzene ring (Figure 1). The hexagonal benzene molecules can assemble in many different ways into interesting molecules.

Fig 1 structure of benzene

The Discovery of Benzene Ring
Although the hexagonal structure of benzene is taught in high schools today, it was a big mystery for the chemists in the nineteenth century. It had been expected from the known empirical formula C6H6 that benzene wasn’t made of single bonds alone, but there was the fact that it was much more chemically stable than other compounds containing double and triple bonds. To explain, the chemists came up with various structural formulas. For example, James Dewar proposed the structure shown in Figure 2, and Albert Ladenburg claimed it was a triangular prism (Figure 3).

Fig 2 Dewar benzene Fig 3 Ladenburg benzene

In 1865, the currently used structural formula was proposed by a Czech-native chemist Friedrich August Kekulè (Figure 1.52). The legend is that he thought of the structure after having a dream of six snakes biting the tails of each other in a circle. He reasoned that the single and double bonds of benzene were exchanging so rapidly that they couldn’t be distinguished.
His idea was close but slightly different from the current understanding of benzene, in which the pi electrons are distributed uniformly throughout the six-membered ring and each of the six bonds is considered to have both single and double bond character. Nevertheless, the Kekulè formula (six-membered ring with alternating single and double bonds) is still used today because it is useful for understanding chemical structure and reactivity. The “turtle shell” of benzene is technically called an aromatic ring, and the molecule containing aromatic ring(s) is called an aromatic compound. This is because compounds that contain a benzene ring often have pleasant smell.

Fig 4 equilibrium of benzene

For the six pi electrons to spread out on a benzene ring to stabilize the molecule, the six carbon atoms should ideally be in a single plane as an equilateral hexagon. When this plane is distorted for whatever reason, the interactions among the pi electrons are weakened and the molecule becomes destabilized with lowered aromaticity. The reason that the molecule of fullerene, which essentially consists of twenty benzene rings, shows higher chemical reactivity than other aromatic compounds is because its round shape prevents the rings from staying in one plane.

Joining Turtle Shells
The molecule made by joining two benzene rings is called naphthalene, which is a famous insect repellant (Figure 5). It is a member of aromatic compound family, and you can think of the whole molecule being stabilized by ten pi electrons.

Fig 5 naphthalene

There are longer molecules with more benzene rings added linearly, but they are known to become less and less stable as the length increases (Figure 6, 7). By drawing the structure of these molecules, you can see that only two of the six-membered rings can have three double bonds and it’s not possible to give the rest more than two. Because of this reason the aromaticity decreases gradually and the molecule starts to lose stability.

Fig 6 anthracene Fig 7 tetracene

When benzene rings are connected in zigzag fashion instead, all the rings can accommodate three double bonds. Zigzag aromatic molecules are therefore relatively stable even when they get longer (Fig 8, 9).

Fig 8 phenanthrene Fig 9 chrysene

Isn’t there a triangular molecule made of three benzene rings? The answer is actually no (Figure 10). It becomes clear by drawing that one of the carbon atoms ends up without a double bond, so this triangle doesn’t qualify as an aromatic molecule as a whole. This is, by the way, an example when the aforementioned Kekulè structural formula helps your analysis.

Fig 10 triangular molecule

You can make a larger hexagon by connecting six benzene rings. This molecule is called coronene, after the solar corona (Figure 11). It’s a perfectly flat molecule.

Fig 11 colonene

So far I’ve kept saying that aromatic rings are flat and made of equilateral hexagons. Now, what happens when a large cyclic molecule is formed by joining five hexagons as shown in Figure 1.60? In this case the equilateral hexagons will break if you try to maintain the planarity, and they will be bent out of the plane if their shapes are kept intact. The actual synthesis of this compound corannulene revealed that it has the shape of shallow bowl. This is also a cut-out portion of the soccer ball molecule fullerene and inspired the original idea of fullerene skeleton.

Fig 12 corannulene

Conversely, what if you use seven benzene rings? Joining seven hexagonal papers will show you that the resulting molecule doesn’t fit in a plane, but has a bent shape like a saddle (Figure 12). These cyclic structures consisting of n benzene rings are called [n]circulenes. They are the partial structure of the new popular material carbon nanotubes, and are considered to be a big factor determining their property.

Fig 13 [7]circulene

There is an aromatic molecule that honors Kekulè, who I mentioned earlier as the chemist who elucidated the structure of benzene. It is kekulene, shown in Figure 14.

Fig 14 kekulene

As you can see, kekulene is a large hexagonal molecule composed of twelve benzene rings. The synthesis was completed after the tremendous effort by François Diederich and his coworkers in 1978. The high crystal density due to the molecular symmetry makes the compound high melting (>620°C) and poorly soluble in organic solvents.
Even larger molecule has been synthesized recently. The leading chemist in this field is Professor Klaus Müllen, who has been introducing a number of massive polycyclic hydrocarbon molecules (Figure 15). Extending this sheet of carbon atoms infinitely would make graphite, so it will be interesting to see at which point these molecules begin to show characteristics similar to graphite.

Fig 15 Müllen's giant polyaromatic compound

We have seen a lot of planar molecules, so I think I’m going to introduce a three-dimensional molecule too (Figure 16). By connecting six benzene rings you get a coronene after a full circle, but you should get a helical structure if you twist the molecule in a way that the two ends miss each other. The laboratory of Professor Melvin Newman at Ohio State University synthesized this molecule in 1955 and gave it a perfect name helicene based on its shape. Not surprisingly, the molecule can exist as either right- or left-handed spiral, and it is even possible to separate the two isomers. This was a historical achievement that showed the existence of a chiral molecule having no stereogenic carbon center, but with the crowding within the molecule.

Fig 16 helicene

Benzopyrene: A Carcinogen
I will finish with a little scary story. Some of the aromatic hydrocarbon compounds are potent cancer-inducing agents. Among them, benzopyrene, which is found in things like coal tar and over-scorched fish, is known as the most powerful carcinogen (Figure 17).

Fig 17 benzopyrene

Human body tries to excrete foreign substances with low water solubility by adding oxygen atoms (oxidation) to make them more soluble. Benzopyrene too is oxidized to become the substance shown in Figure 18, but ironically this is a highly reactive chemical species which reacts with nearby DNA molecules to cause damage. Cells with damaged DNA start abnormal growth and eventually develop into cancer cells. Biological defense mechanism is extremely well designed, but this is an unfortunate case when it backfires.

Fig 18 oxidized benzopyrene (potent carcinogen)

The first evidence for the carcinogenicity of these chemical substances was provided in 1915 by Professor Katsusaburo Yamagiwa of Tokyo Imperial University (now Tokyo University). Back then there were many different theories as to what caused cancer. Yamagiwa’s idea that it might be the chemical substance contained in coal tar was based on his observation that chimney cleaning workers had high rate of developing cancer. Despite public criticism, he patiently carried out the experiment in which he smeared coal tar on the ears of rabbit and finally succeeded in artificially inducing tumors after three years.
Around the same time, a Danish scientist Johannes Fibiger reported his research result to claim that cancer was caused by a parasitic organism, and for this he won the Nobel Prize in Physiology or Medicine in 1926. Fibiger’s result, however, was later found to be applicable only to certain types of rat and not to other animals including people. Contemporary oncology is clearly based on the extension of Yamagiwa’s work, but he never received the credit he deserved.
The awardees couldn’t be changed because when it was clear who should have won the prize, both Yamagiwa and Fibiger had already been dead, and the case has remained as the biggest mistake in the history of the Nobel Prize. I have to say Yamagiwa was just so out of luck, missing the opportunity of becoming the first-ever Japanese Nobel laureate. Benzopyrene was isolated as the main carcinogen from coal tar in 1930, and its cancer-triggering mechanism of action was elucidated in 1977. Sometimes it takes a long time for a fact to be recognized.
I’ve gone through the molecules containing the chains of benzene. When Kekulè established the correct structure of benzene, people supposedly said that there was nothing left to solve in organic chemistry, but the history has proved them wrong.
Benzene rings become graphite by flat and endless expansion, and you can turn it into carbon nanotube by rolling or into fullerene by making it a sphere. They are still one of the front runners of science. The chemistry of this organic chemistry icon that began in the nineteenth century will remain as the protagonist in the twenty first century.

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