Stems, roots, bases

In a number of IUPAC publications, the entities that are referred to as “stems” include

• Latin stems such as ‘argent’, ‘aur’, ‘cupr’, ‘ferr’, etc. used before ‘ide’ or ‘ate’ in anion names [1];
• Stem name ‘carotene’ in nomenclature of carotenoids [2, rule 2];
• Stem ‘calci-’ in nomenclature of vitamin D [3];
• Stem ‘retin-’ in nomenclature of retinoids [4];
• In carbohydrate nomenclature, stem names that designate the chain length of the sugar, e.g. ‘pent-’, ‘hex-’, ‘hept-’ etc. [5];
• Stems such as ‘irene’, ‘irane’, ‘epine’ etc. in Hantzsch-Widman (H-W) nomenclature [6];
• Stem name ‘phosphatidic acid’ [7].

Before we go any further, we have to distinguish between the terms “root”, “stem” and “base”, which are often used interchangeably even in linguistic literature.

Suffixes — or combining forms?

In a number of IUPAC publications, the entities that are referred to as “suffixes” include

• Suffix for the principal characteristic group, such as ‘-amine’, ‘-one’ or ‘-oic acid’ [1];
• Suffixes indicating charge [2, p. 5];
• Suffixes indicating loss or addition of one or more hydrogens from/to parent hydrides, e.g. ‘-ium’, ‘-ylium’, ‘-ide’ or ‘-uide’ [2, p. 105] ;
• Suffixes ‘yl’, ‘ylidene’ or ‘ylidyne’ in the names of radicals and substituent groups [2, p. 108];
• Subtractive suffixes ‘ene’ and ‘yne’ [3];
• Composite suffixes [4, p. 82 ] aka combined suffixes [2, p. 251] that contain multiplicative prefixes, as in ‘diyl’ or ‘triylium’;
• Suffixes ‘quinone’, ‘quinol’, ‘chromenol’ and ‘chromanol’ in names of quinones [5].

Prefixes — or combining forms?

With “endings” out of the way, shall we move on to “prefixes”?

In a number of IUPAC publications, the entities that are referred to as “prefixes” include

• Numerical prefixes [1], aka multiplicative prefixes [2] ‘di’, ‘tri’, ‘tetra’, etc. and ‘bis’, ‘tris’, ‘tetrakis’, etc.;
• Prefixes indicating atoms or groups, either substituents, e.g. ‘hydro’, ‘chloro’, ‘cyano’, or ligands, e.g. ‘hydrido’, ‘chlorido’, ‘cyanido’ [2];
• Prefixes ‘de’ and ‘an’ in subtractive nomenclature as well as their combinations with the names of atoms or groups, e.g. ‘dehydro’, ‘anhydro’, ‘demethyl’, ‘deoxy’, etc.;
• The ‘a’ prefixes for skeletal replacement and Hantzsch-Widman names, e.g. ‘aza’, ‘oxa’, ‘thia’, as well as their combinations with multiplicative prefixes, as in ‘dioxa’ [3];
• Geometrical and structural prefixes such as catena-, arachno-, quadro-, etc. [3];
• Configurational prefixes of inositols such as allo-, chiro-, cis-, epi-, muco-, myo-, neo- and scyllo- [4];
• Prefixes retro- and ‘apo’ in nomenclature of carotenoids [5];
• Configurational prefixes in nomenclature of carbohydrates [6];
• Prefix sn- (for stereospecifically numbered) in nomenclature of glycerol derivatives [7];
• Prefixes ‘abeo’, ‘cyclo’, ‘homo’, ‘nor’ and ‘seco’ in nomenclature of natural products [8];
• Prefix ‘poly’ and qualifiers such as branch-, net-, or star- in polymer names [9].

I like “qualifiers”. I also don’t mind saying “multiplicative prefix” or “configurational prefix” as long as we understand that they actally might be not prefixes, just like vegetarian sausages are not sausages and white chocolate is not chocolate.

Content morphemes

At this point, it might be useful to mention that morphemes could be divided into two classes: content morphemes (i.e. those that have independent meaning) and functional morphemes. All content words contain at least one content morpheme. In English, content words include nouns, adjectives, adverbs and most verbs, while functional morphemes include conjunctions, prepositions, pronouns and articles as well as affixes. These two classes are sometimes referred to as “open class” and “closed class”, respectively. New morphemes are easily added to the former and hardly ever to the latter.

Now to continue with the list that I started earlier.

6. Since chemical names consist of content words (ii), they are open-class.
7. Every content word contains at least one root (iv) which is a content (open-class) morpheme.
8. Affixes are functional (closed-class) morphemes.
9. New chemical names are formed by combining existing content morphemes with functional morphemes or adding new content morphemes.

OK? Still no objections?

Endings

First of all, let’s have a look at endings, also known as inflectional suffixes. In highly inflected languages such as Latin or Russian endings change depending on number, gender and case. In Russian, there are three noun declensions:

Case	feminine (I)		neuter (II)		masculine (II)		feminine (III)
	singular	plural	singular	plural	singular	plural	singular	plural
Nominative	кислота	кислоты	основание	основания	спирт	спирты	соль	соли
Genitive	кислоты	кислот	основания	оснований	спирта	спиртов	соли	солей
Dative	кислоте	кислотам	основанию	основаниям	спирту	спиртам	соли	солям
Accusative	кислоту	кислоты	основание	основания	спирт	спирты	соль	соли
Instrumental	кислотой	кислотами	основанием	основаниями	спиртом	спиртами	солью	солями
Prepositional	кислоте	кислотах	основании	основаниях	спирте	спиртах	соли	солях
	acid	acids	base	bases	alcohol	alcohols	salt	salts

Step back

Those of you who were reading my blog this year might have noticed that words such as “prefix”, “suffix” or “ending” are used extensively in chemical nomenclature. And those of my readers who remember (from their school days perhaps) the basics of morphology also might have been wondering whether these terms have anything to do with their counterparts in linguistics. That’s what happens when you use terms without defining them first.

Before moving any further with nomenclature, it could be helpful to clarify our terminology.

Alas, it looks like the task is more complex than I thought.

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.