Chemical nomenclature can be frustrating to learn. It’s a series of conventions which have been patched together over a long period of time, some of which date back to the 19th century. The language contains archaic terms that are past their useful prime, but are lodged deeply in the language of chemistry and almost impossible to excise at this point. The point of this article is to go beyond the common terms cis, trans, (E,Z), (S,R) – which are an absolute must to know – to point out some of the less frequently encountered aspects of nomenclature which might make you furrow your brow and say – “what does that mean?”
1. Bracket notation.
- When it’s used: In condensed formulas.
- What it means: Signifies that a substituent is attached directly to the preceding carbon.
- Example: CH3C(O)CH2CH3 (2-butanone)
- Why it’s useful: Without the bracket, the structure would be written CH3COCH2CH3, which might be confused for an ether. The bracket makes it more clear that it’s a ketone.
- Notes: Although not exactly obscure, it’s an aspect of nomenclature that can lead to confusion.
- When it’s used: for short chain alkanes and alcohols.
- What it means: n- means “normal” – an unbranched chain with the functional group (if present) on the 1-position. s– means “secondary”, t– means “tert“.
- Why it’s useful: Just a shorthand way of describing different structural isomers.
- Notes: n-hexane is another frequently encountered name, which simply represents a linear six-carbon chain. “Hexanes”, which you might see in the lab, refers to a mixture of different (branched) isomers of hexane.(it’s purified by distillation, and the isomers have very similar boiling points, so it’s sold as “hexanes”. Pure n-hexane is more expensive because separating it from its isomers is a royal pain).
3. The N- prefix
- When it’s used: for amines and amides.
- What it means: The N– signifies that the substitutent is connected to the nitrogen.
- Example: N-methyl butylamine, N,N-dimethylformamide.
- Why it’s useful: it removes ambiguity. “Methyl butylamine”, for instance, could refer to an isomer where the methyl group is on the carbon chain.
- Notes; when different substituents are present on the nitrogen, the terminology is N-(substituent),N-(substituent), for instance N-methyl,N-ethylbutylamine.
4. L and D
- When it’s used: for sugars and amino acids.
- What it means: It goes back to Emil Fischer, who designated the two enantiomers of glyceraldehyde (the simplest sugar) L-glyceraldehyde and D-glyceraldehyde. At a time (1890) where techniques for determining absolute structure were not available, he GUESSED(!) that structure of the leveratory (left-rotating) and dextrarotatory (right-rotating) structures of glyceraldehyde was as depicted in the Fischer projection, and gave them the prefixes L and D respectively. Thankfully, when X-ray crystallography was developed, it was found that his guess was correct. In L-sugars, the oxygen on the carbon second from the end is on the left hand side in the Fischer projection. In D-sugars, the oxygen is on the right-hand side.
- Why it’s useful: It was originally used to correlate the absolute structures of sugars to the two glyceraldehydes. It is no longer useful for this purpose, but like the appendix, it hangs around anyway. Like the appendix, it only seems to get noticed when it causes problems.
- Notes: This notation causes a lot of confusion. Just because something is “D” does not mean it rotates polarized light to the right and vice versa [that is the function of (+)- and (–)]. For example D-fructose rotates polarized light to the left (–). Furthermore, any correlation between L/D and S/R is coincidental. The 20 essential amino acids in the body are L-amino acids. They are all (S) except for cysteine, which is (R) (due to the sulfur having higher priority in the Cahn-Ingold-Prelog rules). Racemates are written as DL (for instance, DL-glucose is the racemic mixture).
5. (+) and (–)
- When it’s used: for any optically active compound
- What it means: (+) and (–) refer to the direction in which pure enantiomers of this compound rotate plane-polarized light. (+)-indicates clockwise rotation, while (–)-indicates counterclockwise rotation.
- Example: (+)-glucose, (–)-cysteine
- Why it’s useful: it depicts the direction of optical rotation.
- Notes: Racemic mixtures are referred to as (+/–), e.g. (+/–)-fructose
6. Vicinal and Geminal (vic– and gem-)
- When it’s used: often used in NMR to depict the relationships between hydrogens, also used to describe certain types of products (e.g. bromination produces vic-dibromides).
- What it means: Vicinal refers to two functional groups on adjacent carbons. Geminal refers to two functional groups on the same carbon.
- Why it’s useful: Instead of saying “the protons are on adjacent carbons” or “the protons are on the same carbons”, you can say “the protons are vicinal” or “the protons are geminal”.
- Notes: remember “gem” like “Gemini”, the constellation and astrological sign, meaning “twins”.
7. Methyl, methylene, methine
- When it’s used: most commonly in referring to protons in NMR
- What it means: methyl protons are on a primary carbon (CH3). Methylene protons are on a secondary carbon (CH2). Methine protons are on a tertiary carbon (CH).
- Why it’s useful: In the case of methine, useful shorthand for saying “proton on a tertiary carbon”.
8. Alpha and beta (α/β)
- When it’s used: Predominantly seen in naming sugars. Also used for steroids.
- What it means: When the sugar is drawn in the orientation as shown (carbons 1 through 5 follow a clockwise path), if the anomeric oxygen is UP (equatorial) it is “beta”, and if it is “down” it is alpha. [EDIT: as Bruce notes, this is incomplete and works only for D-sugars. More properly, a sugar is “alpha” if the C-1 OH and the substituent on the penultimate carbon (the CH2OH attached to C5) are on opposite sides of the ring, and “beta” if those two substituents are on the same side. See The Big Damn Post of Sugar Nomenclature for a more thorough description. ]
- Why it’s useful: Useful shorthand for describing the orientation of the anomeric oxygen which can be crucial in biochemistry. Cellulose and starch differ only in how the glucose subunits are linked together. We can digest starch (α-linked) but not cellulose (β-linked)
- Notes: The sugar has to be drawn in this specific orientation in order to apply α,β (it is a convention).
9. Erythro and threo
- When it’s used: Kind of old-fashioned, but indicates a diastereomeric relationship between two compounds with adjacent stereocenters.
- What it means: Erythrose and threose are the 4-carbon aldoses and they are diastereomers. In erythrose, a the oxygens are oriented on the same side in the Fischer projection. In threose, they are oriented trans. The erythro- and threo– prefixes generalize this relationship to other diastereomers.
- Why it’s useful. To be honest, if you’re not going beyond sophomore organic chemistry, it’s probably not all that useful.
Questions, comments, anything missing – as always, I want to hear about it.