Organic Chemistry

Some elements will form pairs of atoms of the same element, creating what are known as diatomic (two atoms, same element) molecules. Common examples include O₂, Cl₂, H₂, and N₂. Oxygen will even form rather unstable (very reactive) triplets known as ozone (O₃). A carbon atom, however, is unique in that it can form bonds with as many as four other carbons, even forming double or triple bonds with another carbon, which can link to yet more carbons to create a huge diversity of what can be incredibly complicated carbon compounds. The number and diversity of carbon compounds is so large that the study of compounds in chemistry is divided into two great sub-disciplines: Organic Chemistry (the carbon compounds) and Inorganic Chemistry (everything else).

The ability of carbon to make many diverse compounds is extremely important to life as we know it, so much so that organic chemistry is an integral part of biology which is why carbon compounds are ‘organic.’ There are several very simple carbon compounds that are not considered to be ‘organic’ such as carbon dioxide (CO₂) and carbon monoxide (CO) but the vast majority of carbon compounds are created by and are evidence of some living thing. There is a gray area for the origin of some carbon compounds in the same sense as when does a nonliving coacervate droplet become a living cell? Experiments and observations have now shown that even a simple sugar can be created ‘non-organically’ in space without the involvement of any life, but, at least on Earth, all of those wonderful organic compounds are, today, pretty much the sole province of some life activity.

A hydrocarbon, as the name suggests, is a compound of carbon and hydrogen and nothing else; it is a category of organic compounds. The simplest hydrocarbon is Methane, CH₄, but, since a carbon can link to other carbons, there are a huge quantity of hydrocarbons possible with an almost infinite number of carbons. An organic compound which is a hydrocarbon is shown by its name which ends with the suffix, –ane. The prefix indicates how many carbons are involved in the compound, the first ten being: methane (1 carbon), ethane (2), propane (3), butane (4), pentane (5), hexane (6), heptane (7), octane (8, sound familiar?), nonane (9), and decane (10). Gasoline is usually a mix of octane, nonane, and decane (with some ethyl alcohol and minor additives). As the number of carbons increases, the compounds progress from being gases to liquids, to solids. Some common hydrocarbons which have more than ten carbons include: kerosene, diesel fuel/heating oil, and asphalt.

In order to understand hydrocarbons (and other organic compounds), it is important, not only to know the simple chemical formula, but to know the structural formula of the compound because, even with the exact same number of carbons and hydrogens, how they are arranged can affect their properties. The general simple chemical formula for an alkane is C_nH_2n+2 where n is the number of carbons in the hydrocarbon. The chemical formula for butane, then, is C₄H₁₀ but there is a problem because the carbons could be connected to each other in two different ways, each with the same chemical formula.

There is a sort of hybrid between a chemical formula and a structural formula. In order to give some indication of the configuration of the carbons, the formula, instead of C₄H₁₀, could be written CH₃CH₂CH₂CH₃ which would indicate that the carbons are in a line. The formula might be shortened to CH₃(CH₂)₂CH₃ which still indicates the carbons are arranged in a line which doesn’t seem to save much on writing the formula but which can be much shorter for longer chains like octane which could be written CH₃(CH₂)₆CH₃ instead of CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₃. Note that, although the hydrogens are written between the carbons, they form separate bonds with the carbon to their left; it is not C–H–H–H–C, etc.; the first carbon would be short three bonds and hydrogen does not form two bonds.

It is often useful in organic chemistry to think of more complicated organic compounds as being an assembly of smaller parts, something frequently reflected in the name of the more complicated compounds. These smaller parts (functional groups) are not compounds in themselves because they have a free (unconnected bond) which can be linked to the free bond of another functional group; the combination then becomes a true compound with no hanging (free) bonds. One simple way to make a functional group is take a compound that has a hydrogen in it and pull off the hydrogen. What is left is not a compound, it has a free bond, it is a functional group. One good example is water. Pull one hydrogen off of water and you have –OH which, in inorganic chemistry, would be called a hydroxide anion and be written as OH–. In organic chemistry, it becomes –OH and is called a hydroxyl functional group (note the –yl ending).

You could do the same to methane, CH₄, which would become –CH₃, known as a methyl group. Ethane, C₂H₆, minus one hydrogen, would become an ethyl group and so on. For those hydrocarbons with more than one isomer, assume that the straight (kinked) line (normal) isomer is meant unless an isomer name is used. Remember isobutane? One of its carbons has three other carbons attached to it plus one hydrogen. Pull off that one hydrogen and it becomes a tert-butyl functional group; ‘tert’ is short for ‘tertiary’ (third) which means that this carbon is already attached to three other carbons (this is mentioned because one of the compounds discussed on this website has a tert-butyl functional group).

There are many other functional groups, some of which are parts of organic compounds and some of which are fragments of inorganic compounds (the hydroxyl group is an example of the latter). Some other examples of groups derived from inorganic compounds, groups which do not necessarily end in –yl, include: –NO₂ (nitro), –ClO₂ (chlorite), and –BrO₃ (the latter two of which are parameters in the contaminants section of this website because they can be produced by the disinfection of water).

In addition to the nitro, nitrogen can form amines (amine is the noun, amino is the adjective). Although nitrogen can form as many as five bonds (such as in nitric acid, HNO₃), in organic chemistry it almost always forms three bonds. You could start with ammonia (NH₃), remove one hydrogen, and convert it into a primary amino group, –NH₂. Suppose, however, that, instead of being linked to two hydrogens, one of the bonds of that amino group is linked to another group. A simple example would be –NHCH₃; the amino group is attached to a methyl group which would make the amino a secondary amino group (it has only one hydrogen). Of course, that second group doesn’t have to be a methyl group.

It is the convention in organic chemistry that R is used to indicate another unspecified functional group (usually organic); note that R does not stand for any element which is why it is used. Should that last hydrogen be replaced by yet another group (not hydrogen), that could be indicated with R’ meaning that R and R’ don’t have to be the same. A tertiary amino could generically be indicated as –NRR’. One specific example is –N(CH₃)CH₂CH₃; the tertiary amine is attached to a methyl group and an ethyl group; the parentheses around the methyl group indicate that the methyl group has its own, separate bond with the nitrogen, plus, a methyl group has only one bond which must, then, be attached to the nitrogen, not to the carbon that follows it.

Two very important groups in the water business are the inorganic chloride (–Cl) and bromide (–Br). These two groups (anions in inorganic chemistry) replace hydrogens in many organic compounds to make many of the organic compounds discussed in the contaminants section of this website. The best place to start is with methane itself.

First, a quick review of ‘halogen.’ Halogens are the elements in column 17 of the Periodic Table and include: fluorine, chlorine, bromine, iodine, and beyond. In the water business, chlorine and bromine are normally the important halogens so we will ignore the others. Trihalomethane means that you start with a methane (CH₄) and replace three (tri-) of its hydrogens with a halogen (-halo-; chloride or bromide). Trichloromethane, aka chloroform, is more specific, it is a subset of Trihalomethane in which the three hydrogens are replaced with chlorides (–Cl), producing CHCl₃. If you replace all four hydrogens with chloride, you have Carbon Tetrachloride (tetra = four), CCl₄. If only two hydrogens are replaced with chlorides, you have Dichloromethane (di- means two), CH₂Cl₂, aka methylene chloride. These compounds are a possible consequence of the chlorination of water.

An ether is defined by an oxygen bridge between two functional groups: R–O–R’. An example of a simple ether would be methyl ethyl ether which you should be able to figure out is CH₃–O–CH₂CH₃. A more complicated ether is methyl tert-butyl ether or MTBE (here is that tert-butyl functional group mentioned earlier). Its structural formula is:

Ethylene, C₂H₄, is the simplest alkene (a hydrocarbon with a double bond). If you replace three of the four hydrogens with chlorides, you have Trichloroethylene, C₂HCl₃. If you replace all of the four hydrogens with chlorides, you have Tetrachloroethylene (tetra means four), C₂Cl₄. These compounds are yet another possible consequence of the chlorination of water.

As you might expect, there are quite a few isomers of hexane, C₆H₁₄ but there is another hexane which is not an isomer – it is cyclohexane, C₆H₁₂. Note that cyclohexane has two fewer hydrogens than hexane; this is because the two ends of hexane are joined to form a hexagon. In order to do that, you have to remove a hydrogen from each end of a hexane and then join the ends together. Each carbon now has two hydrogens attached to it. Replace one hydrogen from each carbon with a chloride to produce hexachlorocyclohexane. The very name says it: six (hexa) chlorides on a hexane ring.

As mentioned earlier, organic compounds can be divided into two great divisions, Aliphatic and Aromatic. The latter got its name from the fact that many aromatic compounds do have a distinct odor, although many do not. Loosely put, the aromatics are based on variations and extensions of the six-carbon benzene ring which is hexagonal but should not be confused with cyclohexane; Cyclohexane has only single bonds between the carbons in the ring whereas benzene has alternating double bonds between the carbons. Each carbon in cyclohexane (C₆H₁₂) is bonded with two hydrogens in contrast to benzene (C₆H₆) in which each carbon is linked to only one hydrogen.

One way to make a new compound from benzene is to substitute (replace) one of the hydrogens with a functional group (a generic –R). If the functional group (–R) is a hydroxyl (–OH), you get phenol; a methyl group (–CH₃) makes it Toluene, a nitro group (–NO₂) produces nitrobenzene, and an ethyl group (–CH₂CH₃) changes benzene into Ethylbenzene.

The IUPAC name for Alachlor is 2-Chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide (you can certainly see why everyone but a chemist would prefer to use ‘alachlor’), but the IUPAC name can be used to construct a structural formula for the compound. The CAS number for alachlor is 15972-60-8 (you can find this compound on the net with this CAS number). The simple chemical formula for alachlor is C₁₄H₂₀ClNO₂ which includes five elements (and, yes, there is a rule about in what order the elements should be in the formula). Unfortunately, such a formula includes no information whatsoever about how an alachlor molecule might look; we need the structural formula shown below.

This complicated organic compound illustrates another useful principle in naming the compound. You could think of BEHP as being made of five functional groups: a phthalate group, two ethyl groups, and two hexyl groups. The hexyl group is n-hexane (straight chain, no branches) minus one hydrogen at one end: –CH₂CH₂CH₂CH₂CH₂CH₃. Now number the carbons, starting with the carbon with the free bond. Remove a hydrogen from the second carbon in the hexyl group and attach an ethyl group (–CH₂CH₃) to that carbon. You now have a 2-Ethylhexyl group: –CH₂CH(CH₂CH₃)CH₂CH₂CH₂CH₃. The phthalate group is more complicated but, as seen below, you can see that it is based on a benzene ring. Note too, that the phthalate group has two free bonds.

To make BEHP, attach a 2-Ethylhexyl group to each of the free bonds of the phthalate group. The compound now has two identical 2-Ethylhexyl groups but how do we indicate in the name that there are two of them? We could use another ‘2’ but that could be confusing so we use another way of saying two: Bis, meaning there are two (2-Ethylhexyl) groups attached to the phthalate group. If you really want to get into this, the phthalate group could be thought of as a combination of smaller groups but enough is enough, the point is made.

An acid can be thought of as a proton donor (H⁺).  An acid can ‘donate’ a proton by releasing a hydrogen ion (H⁺); the hydrogen ion is a proton (the rest of the acid is now an anion).  But most compounds are not acids (and there is more than one kind of acid, such as Lewis acids, some of which don’t even have hydrogen).  However, there is a combination that greatly facilitates the release of a hydrogen ion.  Consider the acids shown below, several inorganic acids and one organic acid.  They all have something in common.  

Glyphosate, an aliphatic, has a phosphoric acid group at one end and a carboxylic acid group at the other end (doubly acid). They are linked together with a dimethyl amine group (–CH₂NHCH₂–). The amine is a secondary amine (–NH–) because it is linked to two carbons.

You could replace three of the carbons in a benzene ring with nitrogens to create triazine. Because the nitrogens have only three bonds compared to the four of the carbon, triazine (C₃N₃H₃) has three fewer hydrogens than benzene (C₆H₆). Triazine has three isomers, distinguished by where the nitrogens are in the ring, which can be designated 1,2,3-triazine, 1,2,4-triazine, and 1,3,5-triazine.

Atrazine, or 1-Chloro-3-ethylamino-5-isopropylamino-2,4, 6-triazine, is based on the 1,3,5-triazine isomer. Replace the hydrogen on one of the carbons with a chloride to produce 1-Chloro-2,4,6-triazine. Note that the ring positions have been renumbered; position 1 is now the carbon with the chloride but it is the same triazine isomer.

Now consider ethylamine, CH₃CH₂NH₂. Turn this compound into an ethylamino functional group by removing a hydrogen from the amine to produce CH₃CH₂NH–. Do the same to isopropylamine, CH₃(CH₃)CHNH₂, to convert it into the isopropylamino functional group, CH₃(CH₃)CHNH–. You should be able to see where this is going: attach the ethylamino group to the carbon at position 3 and the isopropyl group to the carbon at position 5 and you have atrazine.

By now you should have an appreciation of functional groups, that they make the visualization and understanding of what could be very complicated organic compounds simpler. You could view them as building blocks but these building blocks also impart certain properties to the fully assembled organic compound. Two examples are the carboxyl group which gives the final compound an acidic property and the hydroxyl group which converts a hydrocarbon into an alcohol. Ethane (CH₃CH₃), with a hydroxyl substitution, becomes ethanol or ethyl alcohol (CH₃CH₂OH). Benzene (C₆H₆), with a hydroxyl substitution, becomes phenol. Note the –ol ending in the name which indicates that the compound is an alcohol.

Phenol is especially interesting because it is both an alcohol and an acid. The resonating benzene ring to which the hydroxyl is attached allows for the separation of a hydrogen ion (proton) from the hydroxyl, making it an acid. Do not, however, make the mistake of thinking that every hydroxyl in a compound is a source of hydrogen ions. Ethanol is not an acid. You need something like an adjacent doubly-bonded oxygen or a benzene ring to ‘loosen’ that potential hydrogen ion.

You may have also noticed that you can work with various sizes and complexity of building blocks, that you can assemble smaller functional groups into larger functional groups. One example is the ethylamino group (CH₃CH₂NH–) mentioned above. You could break it down into two smaller groups, an ethyl group (CH₃CH₂–) and a secondary amino group (–NH–). Or, you could start with a more complicated group like the phthalate group in Bis (2-Ethylhexyl) phthalate.

One caution: thinking of functional groups as building blocks is a useful technique in understanding the structure of an organic compound but it is not necessarily how a particular compound is actually made. Life would be much simpler if we could just pull this off here and add that there but in real life it is often necessary to go through a series of intermediate steps to accomplish what might seem to be a simple joining together of building blocks. It is often the case that conditions have to be just right to cause this to happen rather than that; the synthesis of an organic compound can be a very tedious, and sometimes inefficient, process.

Sometimes the problem is to stop or at least minimize a particular organic compound from forming such as in the unwanted formation of trihalomethanes in the disinfection of water. As is often the case, there are trade-offs. If you didn’t chlorinate the drinking water, trihalomethanes shouldn’t be a problem but chlorination is done for a reason. The consequences of microbial contamination of drinking water are usually greater than the consequences of the formation of unwanted disinfection by-products. If you can remove those unwanted organics at point-of-use, all the better.

There are many, many other organic compounds not mentioned here which could become a recognized concern in the future. One recent example is 6PPD-quinone which is formed when 6PPD (N-(1,3-dimethylbutyl)-N'-phenyl-1,4-benzenediamine) in rubber tires reacts with ozone. 6PPD is one of many chemical additives to tire rubber to improve the quality of the rubber; ozone exposure will cause the rubber to deteriorate. If the rubber has 6PPD, the ozone will be used up oxidizing the 6PPD rather than the rubber. Unfortunately, 6PPD-quinone appears to be very toxic to salmon.

Tires gradually wear from use on roads with the result that tiny particles of rubber are deposited on the roads. A rainstorm will wash those particles into nearby streams and 6PPD-quinone will leach from the particles and enter the stream ecosystem where it has been documented killing coho salmon in the U.S. Pacific Northwest (Why were salmon dying? The answer washed off the road, Erik Stokstad, Science, Vol. 370, Issue 6521, p. 1145, 4 Dec., 2020).

Presumably, 6PPD-quinone is toxic to other fish and it raises the question of what other organisms might find it toxic. Nor would this problem be restricted to the Pacific Northwest especially since cars and highways are everywhere. There is no standard for this compound and, at this time, no health advisories. What other organic compounds are in common products, especially plastics, which will prove to be an ecosystem problem in the future?