Ants, apples, amber

Let’s turn our attention now to other kind of acids. You know what I’m talking about: carboxylic acids. Here’s the simplest one (a):

(a)

HCOOH formic acid (common, PIN) methanoic acid (substitutive) hydridohydroxidooxidocarbon (additive)

If we compare the structure (a) with that of our old friend, carbonic acid (b), we’ll notice that the only difference between them amounts to one oxygen atom.

Oxoacids and their anions

Many of the chemical names referred today to as “common” or “trivial” — as opposed to “systematic” — at the time were very much systematic. Many of them, in fact, remain systematic because there is a system behind them.

Observe the structure (a):

(a)

H2SO4 [SO2(OH)2] sulfuric acid (common) dihydroxidodioxidosulfur (additive)

Its molecular formula, H₂SO₄, is probably the second most-known formula in the world after H₂O. We can rewrite it as [SO₂(OH)₂]. There’s nothing easier than to create a completely systematic additive name for (a): dihydroxidodioxidosulfur. However, almost nobody uses this name because there is much more famous one: sulfuric acid.

Descriptors, prefixes, combining forms

Systematic chemical names are created, at least in part, on paper, and probably were never meant to be pronounced. It is not only about the length: locants, descriptors, punctuation marks and combinations thereof render many chemical names practically unpronounceable. Yet these names are part of language, and languages tend to change towards pronounceability. Let’s look at a few examples.

There is a class of chemical descriptors known as “geometrical and structural affixes” [1]. You might remember them being used in the names of inorganic polynuclear entities and boron hydrides. It is easy to see that most of them are not affixes but combining forms. Typically, they contain Greek or Latin roots. The descriptor cyclo is identical to ‘cyclo’ in the names of organic alicyclic compounds and cognate to the terminal ‘cycle’ in the inorganic ring nomenclature. Likewise, catena is identical to the terminal ‘catena’ in the inorganic chain names. Moreover, descriptors such as antiprismo, triangulo and hexahedro are “further analysable”, to use Laurie Bauer’s terminology [2]. The same list [1] includes several Greek letters which are pronounceable (as ‘delta’, ‘lambda’, ‘kappa’, etc.) but do not have any intrinsic semantics related to chemical structures.

The descriptors ‘cis’ and ‘trans’, however, are true prefixes. They are easily recognisable by non-chemists because they are identical to the corresponding Latin prefixes. Historically, they have been employed in geographical names, e.g. Cisjordan “on this side of the River Jordan”, Transjordan “on the other side of the River Jordan”, Transylvania “beyond the woods”, Cisplatina “on this side of the Río de la Plata”^*, etc. More recently, the use of ‘cis’ and ‘trans’ in the context of gender became widespread (and widely criticised). In systematic and semi-systematic chemical names, cis and trans are italicised and followed by dashes. In trivial names, which are much more likely to be spoken, there is no need for these decorations. Remember cisplatin (a) and transplatin (b)?

(a)	(b)

cisplatin (INN, English) cisplatina (INN, Spanish) cisplatine (INN, French) cisplatinum (INN, Latin) cis-diamminedichloridoplatinum(II) (additive) (SP-4-2)-diamminedichloridoplatinum (additive) transplatin (trivial) trans-diamminedichloridoplatinum(II) (additive) (SP-4-1)-diamminedichloridoplatinum (additive)

In the nomenclature of natural products like carotenoids and retinoids, the descriptor ‘all’ in conjunction with ‘cis’ and ‘trans’ indicates that all double bond configurations are identical [3]. For instance, the structure (c) can be named all-trans-retinol, which is way shorter than (2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol.

(c)

(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol (substitutive) all-trans-retinol (natural product) retinol (INN) vitamin A1 (trivial)

The descriptors ‘(+)’, ‘(−)’, ‘d’, ‘l’ indicate that the compound in question as a whole has optical activity. Easy to write, awkward to say aloud. Luckily, there are alternatives ‘dextro’, ‘dex’ (from the Latin dexter, “right”) and ‘laevo’, ‘levo’, ‘lev’ (from the Latin laevus, “left”) that can be used to create rather euphonious names. They are not prefixes but content morphemes^†.

As we’ve seen on the example of amphetamine, the “right” and “left” of optical rotation descriptors do not correspond to the “right” and “left” of the absolute configuration descriptors: dextroamphetamine (d) is the S-isomer and levoamphetamine (e) is the R-isomer.

(d)	(e)

(+)-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)

What about stereodescriptors ‘R’ and ‘S’? Curiously enough, they too found their way to trivial names of arketamine (f) and esketamine (g).

(f)	(g)

(2R)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone (substitutive) (R)-ketamine (trivial) (R)-(+)-ketamine (trivial) arketamine (trivial) (2S)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone (substitutive) (S)-ketamine (trivial) (S)-(−)-ketamine (trivial) esketamine (INN)

Of course, ‘ar’ and ‘es’ are nothing else than ‘R’ and ‘S’, once again stripped of their (unpronounceable) decorations. I don’t know whether we can or should consider them prefixes. Nor whether they always sound good. Try saying, for example, ‘arnorreticuline’ for (R)-norreticuline (I am making this up) or ‘eszopiclone’ for R-isomer of zopiclone (true story).

To sum up: pronounceable chemical descriptors can form parts of trivial names. Some of them end up as prefixes, some as combining forms and yet others as something else.

*	The name of historical Cisplatina province (now Uruguay) is cognate to cisplatina, the Spanish international nonproprietary name (INN) of cisplatin. This is because the Spanish word platina “platinum” is a diminutive of plata “silver”. Cisplatina was a Brazilian province and “on the same side of <the Río de la> Plata” really means “on the same side of the Río de la Plata as Brazil”.
†	In English, the cognates of dexter include standalone words dexterity and dextrous. Apart from chemistry, the root laevo/levo can be found in medical terms, laevocardia, levoscoliosis and so on.

References

1. Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005. Royal Society of Chemistry, Cambridge, 2005, p. 259, Table V.
2. Bauer, L. (1983) English Word-Formation. Cambridge University Press, 1983, pp. 20—22.
3. Favre, H.A. and Powell, W.H. Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names. Royal Society of Chemistry, Cambridge, 2014, P-101.6.3.

α and β again

The descriptors ‘α’ and ‘β’ are also used in carbohydrate nomenclature to specify configuration of cyclic monosaccharides [1, P-102.3.4.2.1]. You may remember that aldehydo-glucose, the open-chain form of glucose, has four chiral centres. Consider the structures (a) and (b):

(a)	(b)

aldehydo-D-gluco-hexose (carbohydrate) aldehydo-D-glucose (carbohydrate) (2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanal (substitutive) aldehydo-L-gluco-hexose (carbohydrate) aldehydo-L-glucose (carbohydrate) (2S,3R,4S,5S)-2,3,4,5,6-pentahydroxyhexanal (substitutive)

Upon cyclisation of either enantiomer, an extra chiral centre is created at the position 1. This centre is referred to as anomeric centre [2, 2-Carb-6.1] and two resulting stereoisomers are anomers. For example, cyclisation of aldehydo-D-glucose (a) brings about two major forms of D-glucose, (c) and (d):

(c)	(d)

α, β, ξ

Here’s a molecule everybody must have heard about: testosterone (a).

(a)

testosterone (INN) 17β-hydroxyandrost-4-en-3-one (fundamental parent + substitutive) (1S,3aS,3bR,9aR,9bS,11aS)-1-hydroxy-9a,11a-dimethyl-1,2,3,3a,3b,4,5,8,9,9a,9b,10,11,11a-tetradecahydro-7H-cyclopenta[a]phenanthren-7-one (fused ring + additive + substitutive)

Planar chirality

In most organic chemistry textbooks, double bond cis/trans isomerism is exemplified by alkenes. It is also observed in cycloalkenes such as cyclooctene that can exist as either cis (a) or trans (b) isomer:

(a)	(b)

(Z)-cyclooctene (PIN) cis-cyclooctene (E)-cyclooctene (PIN) trans-cyclooctene

To the trans isomer, there is a twist — and the pun is fully intended. Have a look at the structures (c) and (d) (or at their 3-D models here, Fig. 2 and Fig. 3, respectively).

(c)	(d)

(1E,1P)-cyclooct-1-ene (PIN) (E,P)-cyclooctene (E,Rp)-cyclooctene (1E,1M)-cyclooct-1-ene (PIN) (E,M)-cyclooctene (E,Sp)-cyclooctene

Axial chirality

Have a look at the structures (a) and (b). They are the stereoisomers of laballenic acid, with (a) is naturally occurring in plants of the Lamiaceae family. What kind of stereoisomers are they?

(a)	(b)

(−)-laballenic acid (trivial) (5M)-octadeca-5,6-dienoic acid (substitutive, PIN) (5Ra)-octadeca-5,6-dienoic acid (substitutive) (+)-laballenic acid (trivial) (5P)-octadeca-5,6-dienoic acid (substitutive, PIN) (5Sa)-octadeca-5,6-dienoic acid (substitutive)

If there was just one double bond in the middle of the molecule, we’ll be dealing with cis/trans isomerism. But we have two cumulative double bonds, which makes our molecules chiral, even though there are no chiral atoms. Why?

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.