Branched hydrocarbons

How can we name the structure (a)?

(a)

[Sn(CH3)3H] hydridotrimethyltin (additive) trimethylstannane (substitutive)

von Hofmann’s footnote

Systematic name formation in chemistry typically happens through compounding, derivation, or mix of both. The semantic modification of a combining form through umlaut-like vowel change as seen in alkanes/alkenes/alkynes appears to be unique. Its origin could be traced to the 1866 publication of August Wilhelm von Hofmann [1]; I probably would never know about it if not for an illuminating blog post by Joe Dixon [2].

In an extended footnote, Hofmann proposed to call the first ten alkanes as follows: methane, ethane, propane, quartane, quintane, sextane, septane, octane, nonane and decane.

Carbon chains

Introduction aside, almost every organic chemistry textbook begins with alkanes, that is, acyclic hydrocarbons with the general formula C_nH_2n+2. Maybe because of that, chemists tend to think of their naming as something too basic and thus boring. I myself thought so until coming across the book by Edward Godly [1] who, in a stroke of genius, put the chapter on silicon chains [1, pp. 19—21] before the chapter on hydrocarbon chains [1, pp. 25—28]. It prompted me to compare the naming of the two classes side-by-side.

Chains and rings

After hours spent looking in my books and searching the internet, I came to the conclusion that chemists talk about chains and rings without explaining what they mean. The only definition I found so far, viz. that of Gold Book, is specific for polymers and seems to be too complex to be used in general chemical nomenclature:

The whole or part of a macromolecule, an oligomer molecule or a block, comprising a linear or branched sequence of constitutional units between two boundary constitutional units, each of which may be either an end-group, a branch point or an otherwise-designated characteristic feature of the macromolecule.

(1)

On the other hand, general dictionary definitions of (chemical) chains are not precise enough. For example, Collins English Dictionary defines chain (chemistry) as

two or more atoms or groups bonded together so that the configuration of the resulting molecule, ion, or radical resembles a chain.

(2)

whereas Merriam-Webster says that it is

a number of atoms or chemical groups united like links in a chain.

(3)

So chain (chemistry) is like a chain. Is it?

Irregularity and suppletion

Now that we’ve established that all chemical names consist of content words and each content word includes at least one base, we can rephrase our original statement ix

9. New chemical names are formed by combining existing content morphemes with functional morphemes or adding new content morphemes

as

9. New chemical names are formed by combining existing bases with functional morphemes or adding new bases.

When we say “combining”, we mean that the parts of our construction set themselves are not changing. Right? In this way, the chemical name-building (out of standardised blocks, like names of atoms, groups, etc.) reflects the actual molecule-building (out of standard blocks, like atoms, groups, etc.).

On the other hand, if we agree that chemical names form part of a natural language, we also have to accept that sometimes they behave in not quite regular fashion. For example, we can figure out that the substituent group called ethenyl is derived from ethene because they share the base ‘ethen’. However, we cannot deduce in the similar fashion that phenyl group is derived from benzene. What’s going on here?

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.