The contaminants-in-drinking-water list in this website include some ferocious-looking and possibly confusing organic compounds. What follows is an attempt to give a casual reader a better understanding of the naming and structure of organic compounds that might be found in drinking water. This is not a treatise on organic chemistry, it is not exhaustive, it does not pretend to cover all organic compounds or concepts, nor does it discuss chemical interactions. It is basically descriptive, meant for someone with a general knowledge of science and none of organic chemistry. It does assume that you have read the preceding sections on Physics and Inorganic Chemistry.
The second electron shell of the carbon atom can hold eight electrons but, in carbon, that shell is only half full. In order to reach a shell balance, the carbon atom will make four bonds with other elements but has no strong preference for either accepting or donating electrons, rather, it shares electrons with other atoms to form covalent bonds. If carbon is in a compound, it will always have four bonds. The bonds that it shares are oriented at the corners of a tetrahedron (triangular pyramid). Ideally, the angle between one carbon bond and any other of its bonds is 120°. Sometimes, carbon may share two bonds (double bonds) with another single atom or even three bonds (triple bonds). If it forms a double bond, the two bonds are closer together which makes a double bond less stable and easier to break. A triple bond would be even more unstable and even easier to break. Four bonds with a single other atom do not exist.
Carbon stands at the head of the 14th column of the Periodic Table, a column which also includes silicon, immediately below it, followed by germanium, tin, and lead. Elements in the same column share properties so it should be no surprise that all of those elements form four bonds but only carbon will bond with another carbon because the atoms of those other elements are simply too large, even silicon, to link with another atom of the same element.
Hydrocarbons can be broadly subdivided into two subcategories: Aliphatic (chains of carbons and simple rings) and Aromatic (based on the benzene ring (of which more later). Aliphatic hydrocarbons can be further subdivided into: Alkanes (single bonds only), Alkenes (at least one double bond), Alkynes (at least one triple bond), and Cyclic (usually a simple hexagon ring). The aliphatic hydrocarbon compounds (or organic compounds with other elements based on hydrocarbons) discussed in this website are limited to simple alkanes, two alkenes, and one cyclic (hexagon ring).
Imagine that the four carbons are connected in a line with the two carbons in the middle of the line connected to two other carbons and the two end carbons connected to only one other carbon. Such a configuration would be clearly shown in a structural formula but there are variations of structural formulas. One such would look like this:
All of the carbons and hydrogens are shown in this version of a structural formula, clearly showing how they relate to one another, but the image is misleading in two respects: (1) The carbons are not really linked in a straight line but rather in something that looks like a zig-zag line because of the orientation of the bonds of the carbon. (2) This is a two-dimensional image of something that is really three-dimensional; some of those bonds would rise above the plane of the paper and some would project below it. With those caveats in mind, however, this structural formula does include the information necessary to distinguish between different configurations in a way that a chemical formula cannot.
Before considering the other configuration (isomer), note that there are other variations of a structural formula. One short-hand version looks like a sawtooth blade with, in this case, four zig-zag lines and no Cs or Hs. You have to assume that at the end of each line or where two lines meet, there is a carbon atom. Since a carbon atom shares four bonds with something else, where two lines meet, you assume that there are also two hydrogens attached to the carbon at the juncture of the lines. Where there is a carbon at the end of a line, you assume that, because carbon has four bonds but only one is shown, there are also three hydrogens attached to that carbon; any missing bond is assumed to be a bond to a hydrogen. The zig-zag sawtooth depiction is closer to how the carbons are actually linked and it saves you what could be a very tedious and messy drawing of many, many hydrogens.
The isomer (configuration) discussed above (the ‘straight’ chain) can be indicated in the name thusly: n-butane. The ’n’ stands for ‘normal,’ that the carbons are linked in a (kinked) line. The other isomer? Using yet another variation on a structural formula, the other isomer could be depicted as:
This second, nonlinear isomer, is called isobutane.
Butane is the first in the hydrocarbon sequence that can have more than one configuration (isomer); the carbons in methane, ethane, and propane can only be arranged one way. If you go beyond butane, the number of possible isomers multiplies and naming those isomers can get quite interesting (more later).
Recognize the functional groups?
But there is one more complication. This is one of those instances in which the three-dimensional aspect is important. Those chlorides project either above or below the plane of the hexagon (the hexagon is not really flat either but it doesn’t matter here). There are a number of possible configurations, of combinations in which some chlorides project upward and some project downward (and it matters). Take a hexagon and orient it so that one corner of the hexagon points toward the top of the paper. Starting from that top corner, number each point clockwise from one to six. Gamma-hexachlorocyclohexane (aka Lindane, a brand name) is the configuration in which the chlorides at 1 and 4 project below the plane of the hexagon and the chlorides at 2, 3, 5, and 6 project upward.
In an attempt to convey this 3D aspect of the compound, the bonds that project upward are drawn as very narrow triangles that grow thicker toward the chloride, supposedly to make the chloride look closer to the observer. The bonds that project downward are drawn with a series of short lines that narrow towards the chloride in an attempt to make it look farther away. Other configurations (alpha, beta, etc.) are less stable or have less desirable properties (Lindane is an insecticide).
The alternating double bonds of the carbons in Benzene literally do alternate (resonate), constantly shifting back and forth. In drawing the structural formula of benzene, however, usually only one configuration is shown because it would be a real pain showing the resonance, giving the false impression that the bonds are static; you should simply recognize, whenever you see the alternating bonds, that they do resonate. Sometimes, the structural formula is drawn as a simple hexagon without showing any double bonds, with a large circle inside the hexagon. The circle indicates that there are alternating double bonds that resonate.
You could add a second functional group to the benzene ring but now it can make a difference as to where, in relation to the first substitution, you attach the second group; there are three possible configurations. In drawing the structural formula, as with cyclohexane, arrange the hexagon with one corner pointing toward the top of the paper, label that corner ‘1,’ and, going clockwise, consecutively number the other corners up to six. If you have two methyl groups attached to the benzene ring, you have a Xylene (aka dimethyl benzene). The three xylene variations (isomers) can be distinguished as 1,2 xylene, 1,3 xylene, and 1,4 xylene (note that 1,2 xylene is the same as 1,6 xylene, etc.). Sometimes an alternate naming system is used in that the 1,2 configuration is called ‘ortho,’ the 1,3 is ‘meta,’ and the 1,4 is ‘para.’ Note also that the second group does not have to be the same as the first.
Why stop at two groups? You could put three nitro groups on a benzene ring to produce trinitrotoluene, better known as TNT. The TNT configuration shown below is actually 1,3,5 trinitrotoluene.
As you might imagine, there are a huge number of organic compounds that can be made by modifications of and additions to a benzene ring but we will show only two from the website contaminant list, Alachor and Bis (2-Ethylhexyl) phthalate.
‘Alachlor’ is a trade name (there can be more than one trade name) which illustrates a problem in organic chemistry: name that compound. You have already seen some examples of several different names for the same compound, such as xylene, aka dimethyl benzene. Then there are acronyms: MTBE = methyl tert-butyl ether. And now we have trade names. In an attempt to create some order out of what could be a nomenclature chaos, the International Union of Pure and Applied Chemistry (IUPAC) publishes a recommended list of preferred names for organic compounds (the IUPAC name). Sometimes the IUPAC name is too unwieldy and, therefore, not much used. Nevertheless, you can still expect to find multiple names in use for the same organic compound. Another organization, the Chemical Abstract Service (CAS), produces a unique CAS Registry Number for every organic compound, something quite useful for professional chemists.
What they have in common is an atom of sulfur, nitrogen, phosphorus, or carbon to which is attached a double-bonded oxygen and a hydroxide. That combination allows the hydrogen in the hydroxide to easily separate as a hydrogen ion; the compound is an acid. Note that while the nitric acid has only one hydroxide, the sulfuric and carbonic acids have two and the phosphoric acid has three which means the sulfuric and carbonic acids can release two hydrogen ions and the phosphoric acid three. As an aside, note the high oxidation numbers of the central atom: S (+6), N (+5), P (+5), and C (+4).
What makes the carbon compound acidic is the carbon atom with a doubly-bonded oxygen and a hydroxyl; it is a carboxyl group (which includes a smaller hydroxyl group; groups within groups). The carboxyl group can be written as –COOH with the understanding that both oxygens are linked to the carbon, not to each other. It can link to other groups (R–COOH), forming a diverse collection of carboxylic acids; some are illustrated below. The R for carbonic acid is another hydroxyl (inorganic chemistry says ‘hydroxide’; organic chemistry calls it a ‘hydroxyl’ (group).
The website contaminants list includes a number of organic acids, some not so simple. If one of the hydrogens of the methyl group of an acetic acid (aka vinegar in impure form) is replaced with a halogen (usually sodium or bromine), then the acid becomes a Haloacetic Acid.
2,4-Dichlorophenoxyacetic acid (aka 2,4-D) can be thought of as beginning with phenol (a benzene ring with an attached hydroxyl group; note that phenol, itself, is an organic acid). If the carbon where the hydroxyl group is attached is designated carbon 1 in the benzene ring, then attach two chlorides (dichloro) at carbons 2 and 4 to produce 2,4-Dichlorophenol. Remove the hydrogen of the hydroxyl to create a phenoxy group (actually, in this case, a 2,4-Dichlorophenoxy group). Now remove a hydrogen from the methyl of an acetic acid and join it to the phenoxy group. Note that there is an oxygen bridge in this compound which also makes it an ether.