Topic 6 Organic Chemistry

Organic chemistry is a branch of chemistry that deals with carbon-based compounds.

Figure 6.1: Biomolecules of Life

Carbon is interesting in that it is able to form four covalent bonds with other atoms. Because of this (and its atomic radius), carbon also has the ability to form diverse and complex molecules that are essential to life (i.e., the molecules shown in figure 6.1).

Figure 6.2: History of Organic and Inorganic Chemistry

Up until the 1820s, the terms inorganic and organic chemistry did not appear very often!

6.1 Early Studies on Organic Chemistry

Figure 6.3: Lavoisier’s Experiments on Animal Respiration

While Antoine Lavoisier did conduct experiments on animal respiration, he thought that there was only one kind of chemistry that could explain chemistry in living systems (e.g., a human being) and inanimate systems.

Figure 6.4: Lavoisier’s Account of Fermentation Using Sugar

In Lavoisier’s Traité Élémentaire de Chimie, he even went as far as to describe the makeup of sugar using fermentation.

Figure 6.5: Lavoisier’s Calculations

Lavoisier and other chemists also realized that organic compounds are complex and are made up of oxygen, carbon, and hydrogen. However, the exact makeup of these organic compounds could not be found using the technology that existed during Lavoisier’s days.

6.2 Organic Radicals

Berzelius thought that organic bodies obey the same general laws that regulate the formation of inorganic compounds. He also believed that his electrochemical dualism hypothesis also held true for organic compounds:

Figure 6.6: Berzelius’ Idea

The word radical was coined by Guyton de Morveau in 1787 and refers to a group of atoms that are stable and don’t get changed as it undergoes reactions. Obviously, this idea worked best in inorganic chemistry!

In 1817, Berzelius suggested that organic compounds could take on the following form:

\[\begin{equation} (X_jY_mZ_n)O \end{equation}\]

Where:

1. \(X\), \(Y\), and \(Z\) are carbon, hydrogen, and nitrogen respectively.
2. \(j\), \(m\), and \(n\) are integers greater than or equal to zero.

6.2.1 Organic radicals

In 1832, the scientists Justin Liebig and Fredrich Wöhler published an article on a so-called organic radical: a group that was found to persist through a whole range of reactions:

Figure 6.7: Both Scientists’ Realized Organic Radical

The organic radical both scientists found is known as a benzyl group today.

“…We find that they group themselves about a single compound, which preserves its nature and composition unchanged in nearly all its associations with other bodies. This stability, this sequence in the phenomena, induced us to assume that this group is a compound element and hence to propose for it a special name, that of benzoyl. The composition of this radical we have expressed by the formula 14C + 10H + 2O…”

– Liebig and Wöhler, Annalen der Chemie 3, 249-282 (1832)

Nonetheless, the above blockquote is what both Liebig and Wöhler had to say.

Figure 6.8: Other Scientists’ Organic Radical Discoveries

Other scientists from other nations were also able to discover other such said organic radicals.

6.2.2 Naming organic compounds

Figure 6.9: Naming Conventions in Organic Compounds in the Past

Figure 6.10: More Examples Organic Chemistry Nomenclature

The above two graphics show the history of organic chemistry nomenclature as it relates to today’s IUPAC naming conventions for naming organic compounds.

In 1837, French chemist Jean Baptiste André Duma and Liebig commented the following:

"…It is easy to see that with the 54 elements known today one may, with the aid of a very small number of laws and combinations, and forming all the binary compounds and salts possible, produce not only all the compounds known in the inorganic kingdom but also a great number of analogous compounds. But how apply with some success such ideas to organic chemistry? There, there are encountered no fewer and no less diverse species than in mineral chemistry. There, however, in place of 54 elements, we encounter scarcely more than three or four in the majority of known compounds. In a word, how can we with the aid of the laws of mineral chemistry explain and classify the so varied substances obtained from living matter and which nearly all are formed solely of carbon, hydrogen, and oxygen, elements to which nitrogen is sometimes added?

…actually, to produce with three of four elements combinations as varied as and perhaps more varied than those which form the mineral kingdom, nature has taken a course as simple as it was unexpected; for with the elements she has made compounds which manifest all the properties of elementary substances themselves. And that, we are convinced, is the whole secret of organic chemistry. Thus organic chemistry possesses its own elements which at one time play the role belonging to chlorine or to oxygen in mineral chemistry and at another time, on the contrary, play the role of metals. Cyanogen, amide, benzoyl, the radicals of ammonia, the fatty substances, the alcohols and analogous compounds–these are the true elements on which organic chemistry is founded and not at all the final elements, carbon, hydrogen, oxygen, and nitrogen - elements which appear only when all trace of organic origin has disappeared.

For us, mineral chemistry embraces all substances which result from the direct combination of the elements as such. Organic chemistry, on the contrary, should comprise all substances formed by compound bodies functioning as elements would function. In mineral chemistry the radicals are simple; in organic chemistry the radicals are compound; that is all the difference. The laws of combination and of reaction are otherwise the same in these two branches of chemistry."

– Dumas and Liebig, Comptes Rendus 5, 567-572 (1837)

Long story short, both scientists thought that organic chemistry was similar to inorganic chemistry. One merely needed to identify and isolate the organic radicals involved.

However, observations and experiments that turned up suggested that chemistry doesn’t always adhere to Berzelius’ dualism theory!

6.3 Pioneers of Organic Chemistry: Liebig and Wöhler

Figure 6.11: Artist’s Impression of Liebig

Justos von Liebig (1803 - 1873) was a German organic, food, and an agricultural biological chemist who pioneered teaching in research labs (at the university of Glessen). Many chemists today have roots that trace back to him.

Figure 6.12: A Bottle of Marmite

Liebig was also credited with the discovery that brewer’s yeast could be concentrated, bottled, and eaten - this discovery lead to the invention of marmite.

Figure 6.13: Black and White Photo of Wöhler

Friedrich Wöhler (1800 - 1882) was a German scientist who had a huge influence on chemistry by synthesizing urea.

Figure 6.14: Structural Formula of Urea

He was also a co-discoverer of silicon and beryllium and published papers from 1800 to 1881.

6.3.1 Isomers

In 1824, Liebig published a work on silver fulminate and concluded that it was a salt of AgCNO: fulminic acid.

At the same time, Wöhler was studying silver cyanate and also concluded that it had the same composition of AgCNO.

Figure 6.15: Silver Fulminate and Silver Cyanate

Both silver compounds had very different properties, so it was initially assumed that either Liebig or Wöhler was wrong in their analyses. Liebig (he was more aggressive) accused Wöhler of being a bad experimentalist, only to find that Wöhler was right all along. In 1826, Liebig apologized and the two became best friends.

It was also this predicament that led both scientist to coin the term isomer

6.3.2 Liebig’s Kaliapparat

Figure 6.16: Liebig’s Kaliapparat

The kaliapparat was a trough where substances would be burned.

Figure 6.17: Liebig’s Laboratory

Students from all parts of the world went to his lab to learn and contribute to organic compound anlayses using the kaliapparat.

6.3.3 Wöhler’s synthesis of urea

“Perhaps you still remember the experiment I carried out in that fortunate time when I was working with you, in which I found that whenever one tries to react cyanic acid with ammonia, a crystalline substance appears which is inert, behaving neither like cyanate nor like ammonia.”

– Wöhler to Berzelius in writing

In 1828, Wöhler was studying the reaciton that occured between ammonium chloride and silver cyanate.

Funnily enough, urea was first discovered and isolated from urine by Dutch scientist Herman Boerhaave of Leiden.

Figure 6.18: Structural Formula of Urea

However, instead of getting ammonium cyanate (i.e., Wöhler’s expected products), he found urea instead.

6.3.3.1 Wöhler’s reaction

“I….must tell you that I can make urea without thereby needing to have kidneys, or anyhow, an animal, be it human or dog.”

– Wohler himself

Ammonium cyanate is unstable:

Figure 6.19: Reaction that Wöhler Observed

Upon synthesis, it decomposes to ammonia and cyanic acid: both of which react to give urea.

6.4 Type Theory

Figure 6.20: An Artist’s Rendition of Jean Baptiste André Dumas

Jean Baptiste André Dumas (1800 - 1884) was the most prominent French chemist of his time - he was also Berzelius’ and Liebig’s rivals.

Figure 6.21: Improving on Liebig’s Method of Collecting Nitrogen

6.4.1 Problems with organic radicals dualism theory

Figure 6.22: Chloral Synthesis

In 1834, Dumas reported on experiments involving ethanol and chlorine to yeild chloral (i.e., trichloroacetalhyde).

Thus, chlorine possesses the singular power of removing the hydrogen of certain bodies, replacing it atom for atom. This law of nature, this law or theory of substitutions, has seemed worthy of a particular name, I propose to call it metalepsy…

….Thus chloral is formed by substitution, or by metalepsy; it is one of the metaleptic products of alcohol

– Dumas, 1838

Nonetheless, an electropositive H atom could not be replaced by an electronegativity Cl atom. However, this doesn’t fit well into the idea of electrochemical dualism.

Figure 6.23: Artist’s Rendition of Auguste Laurent

In 1837, Auguste Laurent was ready to take on Berzelius’ dualism theory. Laurent wrote to Berzelius suggesting that electrochemical dualism was far too simplistic for organic chemistry and that perhaps atom arrangements determines the properties more than the identity of the atom.

6.4.2 More problems with radicals

“In a memoir which I had the honor of communicating to the Academy some time ago I showed that chlorine decomposes acetic acid under the influence of solar light and that it gives rise to a new acid which I have named chloroacetic acid.”

– Note on the Constitution of Acetic and Chloroacetic Acids Comptes Rendus 9, 813-815 (1839)

In other words, the above quoteblock referred to the following equation:

\[\begin{equation} \text{Acetic acid } \rightarrow \text{ Chloroacetic acid} \end{equation}\]

And according to Berzelius’ electrochemical dualism theory, both substances should have very different properties.

“This is to say that acetic and chloracetic acids possess the same fundamental chemical properties, as I had established, and belong to the same organic type.”

– Note on the Constitution of Acetic and Chloroacetic Acids Comptes Rendus 9, 813-815 (1839)

Dumas’ solution was to classify organic molecules according to their “organic types” that have similar, fundamental properties and reactions: hence, enter type theory.

6.4.3 “Type” theory

Figure 6.24: Various Types Found by Scientists

Laurent originally developed many ideas, but these ideas were then taken and developed by another scientist called Charles Frédéric Gerhardt:

Figure 6.25: A Photograph of Charles Frédéric Gerhardt

With the help of Gerhardt, type theory was able to reach a logical conclusion.

6.4.3.1 Williamson’s ether synthesis

Figure 6.26: Williamson’s Proposed Type Structure

In 1850, British chemist and student of Liebig Alexander Williamson (1824 - 1904) was attempting to achieve the following reaction:

\[\begin{equation} C_2H_5OK + C_2H_5I \rightarrow C_4H_9OK + HI \end{equation}\]

But Williamson ended up with this reaction instead:

\[\begin{equation} C_2H_5OK + C_2H_5I \rightarrow C_4H_9OC2H5 + KI \end{equation}\]

From this, Williamson made the connection that water, alcohols, and ethers had the structure shown in figure 6.26.

6.5 Structure of Aliphatic and Aromatic Compounds

“We call homologous substances those that have the same chemical properties and whose composition offers certain analogies in the relative proportions of elements”.

– Charles Gerhardt

Homologous series are groups of structures that are similar in property and structure, albeit differing in the amount of carbons they have.

Figure 6.27: Homologous Series for Alkanes

The above table (taken from the lecture slides) show the homologous series for alkanes. As one realizes, all compounds are similar functionally and structurally, albeit each compound is heavier by 14 grams by its predecessor and one carbon longer.

6.5.1 Valence theory

“When the formulae of inorganic chemical compounds are considered, even a superficial observer is impressed with the general symmetry of their construction. The compounds of nitrogen, phosphorus, antimony and arsenic especially exhibit the tendency of these elements to form compounds containing 3 to 5 equivs. of other elements, and it is in these proportions that their affinities are best satisfied; thus in the ternal group we have NO₃, NH₃, NI₃, NS₃, PO₃, PH₃, PCl₃, SbO₃, SbH₃, SbCl₃, AsO₃, AsH₃, AsCl₃, &c.; and in the five-atom group, NO₅, NH₄O, NH₄I, PO₅, PH₄I, &c. Without offering any hypothesis regarding the cause of this symmetrical grouping of atoms, it is sufficiently evident, from the examples just given, that such a tendency or law prevails, and that, no matter what the character of the uniting atoms may be, the combining-power of the attracting element, if I may be allowed the term, is always satisfied by the same number of these atoms.”

– Edward Franklin

The term valence / valency only came into usage after 1865.

6.5.2 From “type” theory to valence

Figure 6.28: Gerhardt’s Four Types Modified

In 1855, scientist William Odling added another type to Gerhardt’s original four types: marsh gas.

"Carbon is, as may easily be shown and I shall explain in detail later, tetrabasic or tetratomic, that is, one atom of carbon = C = 12 is equivalent to 4 atoms of hydrogen…

…it is striking that the amount of carbon which the chemist has known as the least possible, as the atom, always combines with four atoms of a monatomic, or two atoms of a diatomic, element; that generally, the sum of the chemical utilities of the elements which are bound to one atom of carbon is equal to 4. This leads to the view that carbon is tetratomic (or tetrabasic)."

– Kekulé, 1857

From this, the scientist Kekulé noted that carbon is tetravalent in the above blockquote.

"…For substances which contain more atoms of carbon, it must be assumed that at least part of the atoms are held just by the affinity of carbon and that of carbon atoms themselves are joined together, so that naturally a part of the affinity for one for the other will bind an equally great part of the affinity of the other.

The simplest, and therefore the most obvious, case of such linking together of two carbon atoms is this, that one affinity unit of one atom is bound to one of the other. Of the 2×4 affinity units of the two carbon atoms, two are thus used to hold both atoms themselves together…

…the number of hydrogen atoms (chemical units) which is bound with \(n\) atoms of carbon joined together in this way, e.g. will be expressed at n(4 - 2) + 2 = 2n + 2

Hence, the length of the main carbon chain of compounds (i.e., how many carbons and how many hydrogens) in a homologous series can be expressed as \(C_nH_{2n + 2}\), where \(n\) is some integer.

Figure 6.29: The Omnibus Kekulé Saw in His Dreams

Funnily enough, Kekulé claimed that he came up with the above general formula via envisioning the carbon chains on an omnibus ride in London on the way home.

In a daydream, Kekulé saw the carbon atoms joining in some “giddy dance”.

6.5.2.1 Archibald Scott Couper

Figure 6.30: Photograph of Couper

Archibald Scott Couper (1831 - 1892) was the son of a rich man and studied classical physics, metaphysics logic, and moral philosophy.

He first started his studies in Chemistry in Berlin 1855 under Charles Adolphe Wurtz in Paris. In 1858, Couper got into a fight with his superior - he got fired shortly after.

Figure 6.31: Couper’s Molecular Depiction of Glycerine and Glyceric Acid

He then independently came up with the idea of linking carbon atoms with their structure.

Nevertheless, Couper accused Wurtz (i.e., his superior) of delaying the publication of his work. While both Couper’s and Kekulé’s papers were published in 1858, Couper’s paper was published in June and Kekulé’s in May. Kekulé claimed all the credit.

Couper did eventually return to Edinburgh to teach, but he eventually suffered a mental breakdown and stopped doing chemistry for the last three decades of his life.

6.5.3 How do we draw chemical structures?

Figure 6.32: Johann Josef Loschmidt’s Molecular Drawings

Figure 6.33: Alexander Crum Brown’s Molecular Drawings

Figure 6.34: More of Alexander Crum Brown’s Molecular Drawings

The above three figures all show the ways in which chemical structures were determined. This way of representing chemical structures became extensively used by various organic chemists.

In 1866, the circles around the atoms were removed, and this system is still in use today!

6.5.4 Structure of benzene

Figure 6.35: Benzene Structure

In 1825, Faraday (a scientist) isolated what he called the bicarburet of hydrogen, meaning gas oil.

Sometime later in the 1833s, Mitscherlich then renames Faraday’s isolated compound to benzine - a word that came from gum benzoin and luban jawl (meaning frankincense of java from Arabic).

..in all aromatic substances there contained one and the same atom group, or, if you wish, a common nucleus which consists of six carbon atoms….

…a group is obtained which, if it is considered as an open chain, still contains eight nonsaturated affinity units. If another assumption is made, that the two carbon atoms which end the chain are linked together by one affinity unit, then there is obtained a closed chain (a symmetrical ring) which still contains six free affinity units.

From this closed chain now follows all the substances which are usually called aromatic compounds…

– Annalen der Chimie, 137, 129-196 (1865)

Kekulé did mention the above blockquote - presented below is what he thought benzene looked like:

Figure 6.36: Benzene Structure as Proposed by Kekulé

In 1890, Kekulé mentioned the following:

“I turned my chair to the fire and dozed. Again the atoms were gamboling before my eyes. This time the smaller groups kept modestly in the background. My mental eye, rendered more acute by the repeated visions of the kind, could now distinguish larger structures of manifold conformation: long rows, sometimes more closely fitted together; all twining and twisting in snake-like motion. But look! What was that? One of the snakes had seized hold of its own tail, and the form whirled mockingly before my eyes. As if by a flash of lightning I awoke; and this time also I spent the rest of the night in working out the consequences of the hypothesis.”

– Kekulé

The above blockquote referenced something from Egyptian and Greek mythology called the Ouroboros.

6.6 Arrangement of Atoms in a 3D Space

Figure 6.37: A Photograph of Jacobus Henricus van ’t Hoff

Jacobus Henricus van ’t Hoff was a Dutch chemist who worked with Kekulé. He was the first Nobel Laureate in Chemistry in 1901 and had important contributions to physical and organic chemistry.

Figure 6.38: Tetrahedral Carbon Atoms in Space

van Hoff said the following about figure 6.38:

"The theory is brought into accord with the facts if we consider the affinities of the carbon atom directed towards the corners of a tetrahedron of which the carbon atom itself occupies the center.

The number of isomers is then reduced and will be as follows:

One for CH₃R₁, …, CH₂R₁R₂, … Two for CHR₁R₂R₃ or more general, for CR₁R₂R₃R₄…

…When the four affinities of the carbon atom are satisfied by four univalent groups differeing among themselves, two and not more than two different tetrahedrons are obtained, one of which is the reflected image of the other, they cannot be superposed; that is, we have here to deal with two structural formulas isomeric in space

– van Hoff

Nonetheless, van Hoff had a hypothesis: if the bonds of carbon atoms were tetrahedral, then experimental observations can be explained.

6.6.1 Optical chemistry

Figure 6.39: Enantiomers of Lactic Acid

Enantiomers are one of two stereoisomers that are mirror images of one another (i.e., they are non-superimposable).

van Hoff even made a connection between optical activity and chirality:

“All of the compounds of carbon which in solution rotate the plane of polarized light possess an asymmetric carbon atom”.

– van Hoff

A compound’s optical ability is its ability to rotate plane polarized light!

6.6.2 Joseph Archille Le Bei

Figure 6.40: Photograph of Joseph Archille Le Bel

Le Bel was a French chemist who lived from 1847 - 1913.

“Indeed, the group of radicals R, R’, R”, A when considered as material points differing among themselves form a structure which is enantimorphous with its reflected image, and the residue, M, cannot re-establish the symmetry. In general then, it may be stated that if a body is derived from the original type MA4 by the substitution of three different atoms or radicals for A, its molecules will be asymmetric, and it will have rotatory power.”

– Le Bel himself

Le Bel independently came up with the idea of chirality - he published his work two months later after van Hoff. However, his explanations were more theoretical with no figures or diagrams.

Together with van Hoff, Le Bel was awarded the Davy medal in 1893.

6.7 Coordination Chemistry

From the 1850s onwards, most chemists did organic chemistry and inorganic chemistry was neglected.

However, in the late 1800s, chemists start to apply the idea of valency and structural theories to inorganic chemistry - this lead to the development of coordination chemistry.

Figure 6.41: Two Samples of Cobalt Salts

Cobalt salts in particular got a lot of attention because of their color!

6.7.0.1 Alfred Werner

Figure 6.42: Photograph of Alfred Werner

Alfred Werner (1866 - 1919) was a Swiss-German chemist who won the Nobel prize in 1913. Nonetheless, consider the following (transitional) metal ion complex:

Figure 6.43: Metal Ion Complex That Werner Himself Thought Of

Werner thought that if one assumes that in hydrates, metal ammonium salts, and so on, that the radicals are formed by grouping six water molecules, six ammonia molecules, and six monovalent groups around the metal ion, then we may also wonder how we can picture the entire metal ion complex.

Nevertheless, Werner proposed that if one thought about the metal atom as the center of the complex, that we could place the six moleucles bound to it to form the corners of an octahedron.