There are loads of naturally occurring and synthetically created organic molecules (usually compounds composed of carbon and hydrogen but often containing other elements as well). As chemists got busy discovering these substances, they also started coming up with ways to name them in increasingly systematic ways. Very early in an organic chemistry course (or very late in a general chemistry course), students learn that organic chemistry is as much a language course as a science course. Bright students with good language skills figure this out and apply the grammar and syntax accordingly; bright math students sometimes wonder what the heck happened? The way chemical compounds are named is called nomenclature, which means (oddly enough) “name calling” from Latin roots. Before the end of any organic course, some portion of the class usually gets quite busy calling names, although not those of the organic compounds they’ve come to despise (silly students! Succumb! Breathe in that fresh and unusual knowledge!). The professors bear the brunt of the name calling, although teaching assistants and anyone else nearby will do nicely. I probably fell in love with organic chemistry when I realized the nomenclature was systematic and could be applied logically rather than learned by rote memorization. And then there is the rich, rich symbolic language that goes along with the words! So spare and simple! So full of endless possibilities!
Anyway, among the structural idiosyncracies posed by increasingly insightful physical and chemical tests chemists developed was that some organic compounds contained single carbon-to-carbon bonds, some contained shorter double carbon-to-carbon bonds, and some others contained triple bonds between carbons, which were shorter than either of the other two types. Typically, carbon requires four bonds to other elements (carbon, hydrogen, oxygen, nitrogen, sulfur, etc.). When there was a double bond between carbons, the two carbons with the double bond between them only needed another two bonds—a total of three bonds instead of four. When the two carbons had a double bond, the other elements on either side of the double bond were sort of locked in place by the relative rigidity of that double bond (triple bonds are even more rigid). If there were only two carbons in the molecule and each of the carbons were bonded to two hydrogens as well as each other, there was no problem in naming that little nugget. It was called “ethene.” Just to give you something to relate this to, if you take off one of those hydrogen “H” atoms and put on an hydroxyl “OH” bit, this little guy magically becomes ethanol, fuel of dreams, liver-pillager, starter of fights and trips to the ER.
When the chemical moieties are something other than hydrogens, the naming game gets a touch more difficult. For instance, if we are presented with a four-carbon compound that has a double bond between the second and third carbons, it would generally go by the name “but-2-ene” or the arguably simpler 2-butene (there is a global chemistry naming organization called the International Union for Pure and Applied Chemistry (IUPAC) that gets together and sorts this stuff out; but-2-ene is their preference and they have a really colorful website, so let’s go with their approach, which I also adopted with “ethene,” although “ethanol” is the IUPAC name for ethyl alcohol). Here’s but-2-ene:
Oops! But that’s TWO molecules. Yes it is. The thing with that rigid double bond is that once a molecule has one, and there are a sufficient number of carbons or other sufficiently complicated moieties hanging off one end of the double bond or the other, there are two possibilities. The top symbol represents the cis- form, by which it is meant that the two methyl groups (each CH3– group is known as a “methyl” group) are on the same “side” of the double bond as each other (by the way, the double bond makes all of four of the carbons lie in the same plane as each other, so it is essentially a “flat” molecule, although the hydrogens on the methyl groups sort of spoil that by spreading out in their typical tetrahedral patterns). The bottom symbol represents the trans– form, by which it is meant that the two methyl groups are on different “sides” of the double bond. They are two different molecules with different physical properties: cis-but-2-ene boils at 3.7°C, while trans-but-2-ene boils at 1°C (they melt at -138.9°C and -105°C, respectively—a pretty huge difference in melting points for two molecules with exactly the same chemical formula (C4H8)).
For a more three-dimensional look at the difference between cis– and trans-but-2-ene, take a look at the following pages, which allow you to rotate molecular models of these distinct chemicals and shows their “flatness” better than the structures shown above:
(Just click on each with your left mouse button and wiggle them around)
That naming convention worked just fine… until more complicated substituents were inevitably discovered mucking up the nice cis- and trans- simplicity. As an example, let’s look at 1-bromo-2-chloro-2-fluoro-1-iodoethene:
The way this new rule works is that we must take into account the atomic masses of the ethene substituents (ethene (we’ve met before) being that two-carbon-double-bonded bit in the middle of all these halogens (e.g. F, Cl, Br, and I)). Let’s rank these halogens in decreasing atomic mass: iodine (~127 daltons or amu), bromine (~80 amu), chlorine (~35.5 amu), and fluorine (19 amu); (in science, the tilde (~) is used to mean “approximately). The rule is this: if the moieties with the highest atomic masses are on the same side (not the same end, mind you!) of the double bond, then they are “together” or “zusammen,” the German word for “together.” If the highest amu moieties are on different sides of the double bond, they are opposite or “entgegen.” It would be sort of laborious and annoying to spell out “zusammen” and “entgegen” prefixed to every molecule for which this naming convention applies, so instead the letters “Z” and “E” are used. This means compound 9 (above) is named (E)-1-bromo-2-chloro-2-fluoro-1-iodoethene, while compound 10 is named (Z)-1-bromo-2-chloro-2-fluoro-1-iodoethene.
If you’d like to know who to thank for this naming convention, make sure you give credit to R.S. Cahn, C.K. Ingold, and V. Prelog, without whom the Cahn-Ingold-Prelog Rule would not exist. It can be applied in an equivalent manner to any compound in which conformational isomers around a double bond raises some ambiguity about nomenclature. Here is one last picture that shows you how it might apply to other substituents around a double bond:
And, by the way, the Germans (responsible for the words zusammen and entgegen) call the letter “Z” “tzett,” which is close to how those English-speakers on the other side of the pond (i.e. the British, but also Australians, Kiwis, and for that matter, Canadians, who are just across the Great Lake ponds) say it – “Zed.”
If you want to know a bit more, listen to the dulcet tones of Sal Khan as he goes through a few more examples.
Special thanks to my German tutor November Child, who writes excellent poetry and had no idea I was writing about this today.
Featured image: ©2009 Martin Fisch (Some rights reserved).