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The Basis of Biology: Organic Chemistry and the Carbon Factor

11/20/2015

 
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Once upon a time, the though of artificially producing organic materials was though to be impossible. Humans were not supposed to meddle in the matters of life and death. But science marches on. What was once considered taboo became one of the bases of our modern civilisation.

​And it's all thanks to a single, simple, ubiquitous element on the periodic table.
"It may seem odd that a whole discipline is devoted to the study of a single element in the periodic table, when more than 100 elements exist. It turns out, though, that there are far more organic compounds than any other type. Organic chemicals affect virtually every facet of our lives, and for this reason, it is important and useful to know something about them." - Janice G. Smith
In the year 1828, a young German chemist Friedrich Wohler, mad in his laboratory a compound called urea. The news of this accomplishment astounded the scientific world. Urea had been known as a compound made by animal kidneys (including humans of course), and was one of the waste products of a living body. What was so remarkable about Wohler’s making of urea in a laboratory then? Before Wohler’s accomplishment, it had been believed that any of the materials of a living thing – plant or animal – or any of the products of these, contained an ingredient call a “vital spirit”. This vital spirit was believed to be forever beyond human grasp, and belongs exclusively to the realm of the divine, and without it man can never reproduce any of the materials of which living things are made of.

By making urea in a laboratory, Wohler had, at a single stroke, destroyed the vital spirit theory. From then on, the power of life is in human hands. And as soon as the meaning of Wohler’s success was understood, chemists realize that a whole great field of the chemistry of living things had been opened: organic chemistry.

Since this field of chemistry had to do with that of living things – that is, living organisms – it’s not hard to see where the name came from.

As knowledge of the field of organic chemistry grew, it was found that almost all of the tens of thousands of compounds found in living organisms not only contained carbon, but also depended on the properties of carbon, which is why this field was once also known as carbon chemistry.
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Friedrich Wöhler (1800 - 1882)
The Problem With Carbon

Since Wohler’s discovery, organic chemists have studied more than 700,000 carbon compounds. It then became clear that carbon can form more compounds than any other element. Why? We now understand that it’s due to its ability to form into long chains and rings. Most molecules have only a few atoms, but carbon chains may contain hundreds of atoms, such as in organic compounds. Carbon can combine with most other elements, and as a matter of fact, there are more carbon-based compounds than there are of all the other elements put together.

Wood, wool, nylon, rubber, oil, alcohol, fats and plastics are carbon compounds or mixtures of carbon compounds. And then there are hydrocarbons, which are composed only of carbon and hydrogen atoms, which makes up petroleum and coal – itself derived from organic compounds. While others such as carbohydrates gave away their composition from their names alone, in this case carbon, hydrogen and oxygen.

In working with these compounds, the organic chemist takes apart linking carbon chains and puts them together in different combinations. To understand what the organic chemist is doing, you might picture a carbon atom as a tiny ball with four hooks projecting from it at opposing points. These hooks would link up with other hooks on other atoms – hydrogen, oxygen, even another carbon.

All seems to be straightforward enough, until it was discovered that a large number of hydrocarbons are composed of six carbon atoms – benzene. Chemists have been aware of benzene’s empirical formula for quite a while, but the structure itself is a mystery. Organic chemists  soon found that they had a difficult problem when they try to reconcile their notion of chemical bonds with this puzzling compound. Two hooks are used to join a carbon atom with its respective neighbors, one hook to link with hydrogen, but what about the last one?
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This mystery is linked to the tetravalence of carbon – an atom’s valency is the number of its outermost electrons which allows it to bond with other atom, in carbon’s case, four (Greek: tetra). And the same guy who discovered this will again solve the mystery of benzene.

Kekule’s Carbon Hookup

Friedrich August Kekule was born to a humble family on 7 September 1829 (as if preordained, a year after Wohler’s breakthrough) in Darmstadt, of what is now Germany. He had an unremarkable youth, though almost made the mistake of studying architecture at the University of Glessen (apologies to architects, but seriously, we need more chemical engineers) he decided to turn to chemistry after hearing a few lectures on the subject. After brief stints in France, Switzerland and England, he steeled for a teaching position at the University of Ghent where he made his breakthroughs in carbon chemistry.
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With regards to benzene, the solution came in the most unconventional manner there is: a dream. In 1865, as he was asleep (reportedly on a public carriage) he dreamt of carbon atoms dancing and linking arms and legs with each other, though strangely enough some of these links are with both of their arms…Eureka!

Awoke, Kekule immediately sketched his dancing carbons. And as he saw it, the math fits! Thus the discovery of double bonds, where atoms share two valence electrons each. In the case of benzene, a carbon atom links one electron with another carbon, two with the next and one for a single hydrogen atom.
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Kekule’s discovery rationalizes carbon’s prevalence in nature, how it easily forms long chains and rings with other molecules, and therefore forms the basis of organic chemistry, though Wohler is arguably considered as the father of organic chemistry.
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Either way, both Wohler and Kekule had opened up a new field that had stretched beyond their dreams of industrial application (both of them lived during the Industrial Revolution). Organic chemistry is now applicable in medicine, petrochemicals, polymers, and nutrition to name a few. Of course with over 700,000 known possible combinations for a single element, it is indeed a serious business…
  Ponder this

​Wohler's synthetic production of urea was in a way foreshadowed by the discovery of phosphorus (which was first isolated from urea) by Hennig Brand in 1669. Why was there no attempt to reverse the process of turning phosphorus into urea?
​
Silicon have been purported to have a ability to form complex molecules as carbon. Both have four valence electrons, both can be found abundantly in the universe. But how come organic chemistry, at least as it is on Earth, isn't silicon-based?
  Discuss

​Organic chemistry plays a huge part in our civilisation, from the chemical industry to agriculture to construction and engineering and even electronics. Discuss the ubiquity of organic chemicals that play these roles in our daily lives. What are they? Why were they chosen for the specific applications?
  Further readings

Friedrich Wohler, the man who artificially synthesized urea, and the father of organic chemistry.

August Kekule, who solved much of the problems associated with carbon's role in organic chemistry.

The Virtual Textbook of Organic Chemistry, by Professor Emeritus Dr. William Reusch at Michigan State University, a rather comprehensive primer.
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