cis and trans

What’s the difference between the structures (a) and (b)?

(a)	(b)

(2Z)-but-2-ene (PIN) cis-but-2-ene (2E)-but-2-ene (PIN) trans-but-2-ene

Enantiomers

Have a look at the structures (a) and (b).

(a)	(b)

(+)-amphetamine (trivial) d-amphetamine (trivial) dextroamphetamine (trivial) dexamfetamine (INN) (2S)-1-phenylpropan-2-amine (substitutive) (−)-amphetamine (trivial) l-amphetamine (trivial) levoamphetamine (trivial) levamfetamine (INN) (2R)-1-phenylpropan-2-amine (substitutive)

Polyhedral symbols and configuration indices

Although structural descriptors such as we’ve seen in the names of boron hydrides, for example catena or closo, provide information on atomic connectivity, they tell us little or nothing about the geometry of the molecule.

Have a look at the structures (a) and (b):

(a)	(b)

(SPY-5)-pentaoxidotungstate(4−) (additive) (TBPY-5)-pentaoxidotungstate(4−) (additive)

Both of them can be named additively pentaoxidotungstate(4−). Yet, as you can see, they have very different shapes.

Boron hydride nomenclature

Can we expand the parent hydride naming philosophy much beyond organic chemistry? Not going too far, let’s have a peek at carbon’s immediate neighbour in the periodic table, boron.

(a)

BH3 borane (preselected name) boron trihydride (binary) trihydridoboron (additive)

The mononuclear hydride (a) is systematically named ‘borane’ while neutral boron hydrides as a class are called boranes.

λ-convention

The whole edifice of substitutive nomenclature is based on concept of parent structures, most importantly parent hydrides. Implicit in parent hydrides are the valencies, or bonding numbers, of non-hydrogen atoms. The standard bonding numbers of neutral atoms in parent hydrides are given thus [1]:

Bonding number n	3*	4	3	2	1
	B	C	N	O	F
	Al	Si	P	S	Cl
	Ga	Ge	As	Se	Br
	In	Sn	Sb	Te	I
	Tl	Pb	Bi	Po	At

These bonding numbers correspond to the number of hydrogen atoms in mononuclear hydrides for elements of Group 13 to Group 17.

Ah, if we only had to name compounds containing just carbon, hydrogen and oxygen. As soon as we move beyond, the trouble starts. Consider phosphorus. We know from school chemistry that this element has valencies of 3 and 5. For trivalent phosphorus compounds we can create substitutive names based on the parent hydride PH₃, phosphane (a). But how to deal with pentavalent phosphorus?

(a)	(b)

Inorganic chains and rings

Let’s name a simple inorganic chain (a):

(a)

1,2-dinitrosodioxidane (substitutive) bis(nitrosyloxygen)(O—O) (additive) 2,5-diazy-1,3,4,6-tetraoxy-[6]catena (ICR)

The shortest systematic name I can think about is 1,2-dinitrosodioxidane, based on the parent hydride dioxidane (aka hydrogen peroxide). Alternatively, we can emphasise the structure’s symmetry by naming it as a dinuclear entity, bis(nitrosyloxygen)(O—O).

Or we can have a go at it employng yet another type of nomenclature developed for inorganic chains and rings (ICR): 2,5-diazy-1,3,4,6-tetraoxy-[6]catena [1, 2 IR-7.4]. What’s going on here?

Phane names

Have a look at the structure (a).

(a)

calix[4]arene (trivial) pentacyclo[19.3.1.13,7.19,13.115,19]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene (von Baeyer) 1,3,5,7(1,3)-tetrabenzenacyclooctaphane (phane)

Applying von Baeyer nomenclature, we get a horrendously long and unwieldy name ‘pentacyclo[19.3.1.1^3,7.1^9,13.1^15,19]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene’. I think it’s a crime to name a beautifully symmetrical structure like (a) in such a fashion. Can’t we create a name that states the obvious: (a) is a big cycle containing four benzene rings?

Ring assemblies

How shall we call the structure (a)?

(a)

biphenyl (trivial) 1,1′-biphenyl (ring assembly, PIN) phenylbenzene (substitutive)

We can name it substitutively, i.e. substituting one hydrogen atom in the parent hydride benzene with phenyl group: phenylbenzene. This name, however, does not reflect the obvious symmetry of the molecule.

Similar story with (b) whose substitutive name, cyclopentylidenecyclopentane, is barely pronounceable.

Spiro names

Observe the structure (a). Doesn’t it look like our old friend housane after a tornado? It kept its roof but only just.

(a)

spiro[2.3]hexane spirohexane

Let us number it in the following fashion:

(a)

The atom 3 is a quaternary carbon while the rest are secondary carbons. Or, using the graph theory language, we can say that in the graph (a) the degree of vertex 3 is 4 and the degrees of the rest of vertices are 2. The atom 3 is also known as a spiro atom [1, SP-0] while the whole structure is an example of spiro union.

Fused ring names

(a)

furan (trivial, retained) oxole (Hantzsch-Widman)

Knowing that the structure (a) is called furan, let’s name the structure (b).

(b)

2-nitrofuran (substitutive)

Easy: 2-nitrofuran.

Keeping that in mind, what kind of structure do you think corresponds to the name ‘2-benzofuran’?

von Baeyer names

Here’s a cute little structure:

(a)

housane (trivial) bicyclo[2.1.0]pentane (von Baeyer)

Drawn like this, (a) looks like a little house and, indeed, is known as a housane. Alexander Senning called this structure “the poor man’s housane” [1, p. 77] while referring to pentaprismane as “the rich man’s housane” [1, p. 78]. Of course, there is a systematic name too.

Bicycles

How many rings has the structure (a)?

(a)

diphenyl ether (functional class) 1,1′-oxydibenzene (multiplicative) phenoxybenzene (substitutive)

Why, there are two, you’ll say. Anybody can see that. And you’ll be right.

What about (b) then?

(b)

norbornane (trivial) bicyclo[2.2.1]heptane (von Baeyer)

The many names of crowns

What is the best way to name the structure (a)?

(a)

1,4,7-trioxonane (Hantzsch-Widman) 1,4,7-trioxacyclononane (replacement) cyclo[tri(oxyethylene)] (organic macrocycle) 9-crown-3 (Pedersen) 9<O3coronand-3> (Vögtle-Weber)

The general naming method is skeletal replacement applied to the corresponding carbocyclic parent hydride, in our case cyclononane, thus 1,4,7-trioxacyclononane. Or we can use extended Hantzsch-Widman (H-W) system and call it 1,4,7-trioxonane. For rings with up to ten members, the H-W names are preferred [1, p. 96].

What about the structures (b)—(d) then? Since all of these rings have more than ten members, we cannot use H-W system, so we have to give them replacement names: 1,4,7,10-tetraoxacyclododecane (b), 1,4,7,10,13-pentaoxacyclopentadecane (c), 1,4,7,10,13,16-hexaoxacyclooctadecane (d). Rather long, completely unambiguous, and very boring.

Hantzsch-Widman names

Are you tired of carbocycles? Let’s have some ring diversity, I say.

Structures that contain two or more different elements in a ring are called heterocyclic. Perhaps because “heteroatom” is really an organic chemistry concept, the word “heterocycle” is commonly (mis)understood as “organic heterocycle”, that is, a carbocycle where at least one carbon atom is replaced by an heteroatom. I blame organic chemists for that.

For a small number of five- and six-membered organic heterocycles the trival names are retained to be used as parent hydride names. Note that, although “trivial” in chemical parlance means “non-systematic”, there is a system to most of those names. For instance, we can see that imidazolidine (a) is a fully saturated version of 1H-imidazole (b):

(a)	(b)

imidazolidine 1H-imidazole

Mancude rings and annulenes

What do the structures (a), (b) and (c) have in common?

(a)	(b)	(c)

[18]annulene cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene (PIN) 1,3,5,2,4,6-triazatriphosphinine thiophene

Well, it is obvious that they all are rings. Also, apart from hydrogens in (a) and (c), they have no side chains. Otherwise, they are quite different. The structure (a) is a hydrocarbon. The ring (b) is purely inorganic while (c) is an organic heterocycle. What else?

You can see that in all these structures single bonds alternate with double bonds. Ring systems like this are referred to as mancude, which is an abbreviation of the “maximum number of non-cumulative double bonds”.

Alicyclic monocycles

Now let us have a look at monocyclic hydrocarbons, starting with cycloalkanes. By the way, I think this term is a bit misleading: cycloalkanes indeed contain cycles but are not alkanes because these latter, by definition, are acyclic. Gold Book defines cycloalkanes as “saturated monocyclic hydrocarbons (with or without side chains)”, where “side chains” are alkyl groups. The general molecular formula of cycloalkanes, with or without side chains, is C_nH_2n. I wish there was an elegant collective term for cycloalkanes-with-no-side-chains, or unsubstituted cycloalkanes, because only this subset of cycloalkanes can be used as parent hydrides in systematic organic nomenclature; I am not aware of any. Here, I will refer to unsubstituted cycloalkanes as ‘cycloalkane parents’^*.

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?