Nomenclature roundup

Here are the main types of chemical nomenclature in a nutshell. Well, the post turned out to be a bit longer than I expected. So let’s say “chemical nomenclature in a coconutshell”.

Multiplicative names

Have a look at the structure (a).

(a)

N,N-bis(carboxymethyl)glycine (substitutive) N,N,N-tris(carboxymethyl)amine (substitutive) 2,2′,2″-nitrilotriacetic acid (multiplicative)

Its preferred IUPAC name (PIN) is N,N-bis(carboxymethyl)glycine. This is a classical substitutive name based on functional parent glycine (b). However this name fails to convey the structural feature of (a) that is obvious even to a non-chemist, viz. its threefold symmetry. Alternatively, we can think of (a) as a tertiary amine, that is, ammonia in which each hydrogen atom is substituted by a carboxymethyl group: N,N,N-tris(carboxymethyl)amine. This name clearly tells us that there are three identical groups, but it probably will be frowned upon because carboxy group is senior to amino.

It also can be given a name that reflects both symmetry and the fact that it is a carboxylic acid.

Additive again

As we know, additive nomenclature is widely used in inorganic chemistry. It could be employed for organic structures too, although in a very specific and limited way [1].

I mentioned earlier that the subtractive ‘dehydro’ operation (as in ‘didehydro’, ‘tetradehydro’ etc.) is the opposite of additive ‘hydro’ operation, i.e. hydrogen addition to unsaturated carbon—carbon bond (as in ‘dihydro’, ‘tetrahydro’ etc.).

(a)	(b)	(c)

naphthalene (trivial, parent hydride) 1,2-dihydronaphthalene (trivial + additive) tetralin (trivial) 1,2,3,4-tetrahydronaphthalene (trivial + additive)

For example, adding two hydrogen atoms to carbons 1 and 2 of naphthalene (a) gives us the structure (b) which we call, logically enough, 1,2-dihydronaphthalene; adding two more hydrogens to carbons 3 and 4 we get (c), 1,2,3,4-tetrahydronaphthalene. Easy!

Yet something does not sound quite right here.

Conjunctive names

Here is the eternal problem of organic nomenclature: which part of the molecule is a skeleton and which is a substituent? Let’s have a look at the structure C₆H₅–CH₂–COOH (a).

(a)	(b)	(c)

phenylacetic acid (substitutive) carboxymethylbenzene (substitutive) benzeneacetic acid (conjunctive) benzene (trivial, parent hydride) acetic acid (trivial, functional parent)

Radicofunctional names

I’m sure you came across names such as ‘ethyl alcohol’ or ‘vinyl chloride’. Do they remind you of binary-type names so common in inorganic chemistry? This is because they also consist of two words. There is an important difference though. The inorganic binary-type names always comprise positive/negative pairs, as in ‘sodium chloride’. The names like ‘ethyl alcohol’ consist of “specific” part followed by “generic” part^*. Thus ethyl alcohol is an alcohol. All alcohols have a generic formula R–OH; in our alcohol, R = ethyl group.

These names are easily interpretable in terms of linear formulae. So ethyl alcohol (substitutive name ethanol) has a formula C₂H₅–OH and vinyl chloride (substitutive name chloroethene) is H₂C=CH–Cl.

Cyclo and seco

The prefix ‘cyclo’ is used in chemical names to indicate a ring structure. In additive nomenclature, this prefix is usually italicised and followed by a hyphen, as we have seen for polynuclear entities such as cyclo-tri-μ-oxido-tris(dioxidotungsten). On the other hand, in substitutive nomenclature ‘cyclo’ is not italicised, there is no hyphen, and no other prefixes could be inserted between ‘cyclo’ and the root, as in cyclopropane.

Somewhat confusingly, this prefix is also employed in skeletal modification nomenclature when an additional ring is created [1]. In the names generated thus, ‘cyclo’ has to be preceded by the locants of the skeletal atoms that form a new bond.

(a)	(b)

cycloartane (trivial) 9β,19-cyclolanostane (‘cyclo’) lanostane (trivial, fundamental parent)

Homonames

Both skeletal replacement and ‘nor’-type subtractive naming methods can be considered subtypes of skeletal modification nomenclature. And there are more.

Consider homocysteine (a):

(a)	(b)

homocysteine (trivial + ‘homo’ addition) 2-amino-4-sulfanylbutanoic acid (substitutive) cysteine (trivial) 2-amino-3-sulfanylpropanoic acid (substitutive)

Nornames

A variant of subtractive nomenclature employs the prefix ‘nor’. Probably the most famous example is the neurotransmitter noradrenaline aka norepinephrine (a):

(a)	(b)

noradrenaline (trivial + subtractive) norepinephrine (trivial + subtractive) 4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol adrenaline (trivial) epinephrine (trivial) 4-[(1R)-1-hydroxy-2-(methylamino)ethyl]benzene-1,2-diol

These names are derived from the trivial names of (b), adrenaline or epinephrine. In this particular example, the meaning of ‘nor’ is the same as ‘demethyl’.

Subtractive names

In compositional and additive nomenclatures, we build the names more or less from scratch. The more complex the structure, the longer the name. With substitutive nomenclature, we take the names of parent hydrides or functional parents and modify them adding the names of substituent groups. Once again, the complexity of the name increases with complexity of the structure. In case of both skeletal replacement and functional replacement, a small or no increase in structural complexity still leads to longer names.

Yet there are opposite situations.

(a)	(b)

demethylmirtazapine (trivial + subtractive) 1,2,3,4,10,14b-hexahydropyrazino[2,1-a]pyrido[2,3-c][2]benzazepine mirtazapine (trivial) 2-methyl-1,2,3,4,10,14b-hexahydropyrazino[2,1-a]pyrido[2,3-c][2]benzazepine

You might have noticed that, while the substitutive name of (a) is shorter than that of (b), the reverse is true for their trivial names. This is because the structure of mirtazapine (b) contains a methyl group which is lost in (a), hence ‘demethyl’ bit in demethylmirtazapine.

This method of naming is known as subtractive.

Functional replacement nomenclature

Organic molecules are often thought of as comprising a skeleton, for example a chain or a ring, adorned by functional groups. Having just read about skeletal replacement, you might think that functional replacement has something to do with those functional groups. It’s only logical. But you’d be mistaken.

Let’s name the structure (a):

(a)

[CS(SH)2] trithiocarbonic acid (common + functional replacement) carbonotrithioic acid (functional replacement) sulfidodisulfanidocarbon (additive)

Of course, its formula [CS(SH)₂] gives us a clue: we can call such an entity additively sulfidodisulfanidocarbon. But there is another way to do it.

Skeletal replacement nomenclature

So, in substitutive nomenclature we take a parent hydride or a functional parent, whose name form a root of a term to be created, and replace the hydrogens with substituents, whose names become prefixes or suffixes. Can we do the same with other atoms apart from hydrogens, for the naming purposes?

Yes we can.

(a)	(b)

pentaethylene glycol (trivial) 3,6,9,12-tetraoxatetradecane-1,14-diol (replacement + substitutive) tetradecane

Functional parents

There is a small number of relatively simple organic entities containing at least one characteristic group that also could be treated as parent structures. These entities are known as functional parents.

For example, the preferred IUPAC name of the structure (a) is 2-hydroxybenzoic acid. Why not 2-hydroxybenzenecarboxylic acid? Because (a) is thought of as a derivative of benzoic acid (b). Now (b) contains a characteristic group –COOH and so cannot be called “parent hydride”, while benzene (c), indeed, is a parent hydride of both (a) and (b). However (b) is a functional parent and thus the name “benzoic acid” can be used to construct the substitutive name “2-hydroxybenzoic acid”.

(a)	(b)	(c)

salicylic acid (trivial) 2-hydroxybenzoic acid (substitutive) 2-hydroxybenzenecarboxylic acid (substitutive) benzoic acid (trivial) benzenecarboxylic acid (substitutive) benzene (trivial)

Substitutive names and parent hydrides

Let’s try to name the structure (a).

(a)

CBr4 carbon tetrabromide (compositional) tetrabromidocarbon (additive) tetrabromomethane (substitutive)

We can give it a binary name carbon tetrabromide. We can name it additively tetrabromidocarbon.

Or we can call it in a completely different fashion: tetrabromomethane.

Dealing with dinuclear and polynuclear entities

The additive names are easy to construct for mononuclear entities, that is, when we have to describe an entity with just one central atom. What if we have two?

(a)

[ClO2] OClO• dioxidochlorine(•) μ-chlorido-dioxygen(•)

If we consider the structure (a) a mononuclear entity, [ClO₂], we would call it dioxidochlorine(•). Alternatively, we may think of two oxygen atoms bridged by one chlorine atom, OClO, and call it μ-chlorido-dioxygen(•). Here, a bridging ligand is indicated by the Greek letter μ.

Addi(c)tive names

Let’s have a look at uranium hexafluoride, UF₆. As you remember, in binary-type nomenclature both formulae (e.g. UF₆) and names (e.g. uranium hexafluoride) are divided in two parts, electropositive (or less electronegative) always followed by (more) electronegative. Grammatically, the binary name is a noun phrase consisting of a head noun such as hexafluoride preceded by an attributive noun such as uranium^*.

Neither the compositional name nor formula tell us anything about its structure. For all we know, it could be an ionic compound composed of ions U⁶⁺ and F⁻.

Now let’s say we learn from Wikipedia that this compound consists of discrete molecules which could be represented like this:

(a)

Can we give a name that reflects the structure (a)?

Binary-type, extended

Binary-type nomenclature can be extended beyond simple stoichiometric names. Let’s have a look at the compound with empirical formula HKO. If we were trying to come up with purely stoichiometric name, it would be either potassium hydride oxide or hydrogen potassium oxide, but nobody calls it that. Moreover, it is customary to write its formula not like I did (with element symbols ordered alphabetically), but KOH. Why? Because it is known that KOH is an ionic compound which will dissociate in water into cations K⁺ and anions OH⁻. Attention please: we have just zoomed from (macroscopic) compound to (microscopic) molecular entities.

So we’ve got some extra structural information, viz. that the anion is composed of oxygen and hydrogen. The anion OH⁻ is known as hydroxide and thus our compound is named potassium hydroxide.

Likewise, it is known that NH₄NO₃ dissociates into cations NH₄⁺ and anions NO₃⁻. The NH₄⁺ cation is known as ammonium and the NO₃⁻ anion as nitrate so our compound is is named ammonium nitrate.

Stoichiometric names

The Red Book [1, p. 5] uses the term compositional nomenclature

to denote name constructions which are based solely on the composition of the substances or species being named, as opposed to systems involving structural information.

It is the simplest systematic way of naming chemical substances. Compositional nomenclature can be used for both compounds and elementary substances. In case of compounds, is is also known as binary-type nomenclature [2]. Why “binary”? Because the names of compounds named that way always consist of two parts, positive and negative.

What are compounds anyway?

According to Oxford English Dictionary, “compound” (in chemistry) is

a substance formed from two or more elements chemically united in fixed proportions.

(1)

I quite like this definition. There are four statements in it:

• compound is a substance (therefore, it is macroscopic);
• compound contains at least two (different) elements;
• these elements are “chemically united”, i.e. chemically bound;
• they are bound in fixed proportions.

Elemental haiku

My, the year is almost gone and I, busy with other stuff, didn’t publish a single post. Luckily, I came across Elemental haiku — a periodic table of haikus, one per element, plus one for a hypothetical element 119. Here are my favourites.

2. Helium

Begin universe.
Wait three minutes to enter.
Stay cool. Don’t react.

11. Sodium

Racing to trigger
every kiss, every kind act;
behind every thought.

13. Aluminum/Aluminium

Spent kindergarten
endlessly writing your name.
One i or two i’s?

26. Iron

Anvil, axe, nail, plow,
engine, railway, factory.
Servant, friend, partner.

30. Zinc

Clasp your neighbor tight.
Sound the music while you dance,
trumpet, bugle, horn.

39. Yttrium

That is not a name.
That is a spelling error.
Or a Scrabble bluff.

67. Holmium

The root of the name
elementary, my dear.
Stockholm, not Sherlock.

80. Mercury

Madness the price paid
for your molten alchemy.
Metal. Planet. God.

You can contribute your own on Twitter with hashtag #ChemHaiku.

Cork polycyclic aromatic hydrocarbons

In the spirit of both Christmas and recycling, I decided to build a Christmas tree by gluing together wine corks accumulated during this year. In addition, if you needed one, the intermediates of this process make rather cute models of polycyclic aromatic hydrocarbons.

(a) benzene