InChI metal-reconnected layer

While I wasn’t looking, the InChI folks implemented the metal-reconnected layer. Isn’t it nice? I discovered it quite by chance thanks to the Beilstein-Institut ChemInfo Labs page. You can see how it works on InChI Web Demo.

Consider ferrocyanide (a):

(a)

[Fe(CN)6]4− hexacyanidoferrate(4−) (additive) ferrocyanide (trivial)

Its standard InChI is:

InChI=1S/6CN.Fe/c6*1-2;/q;;;;;;-4

(1)

The main layer contains two types of entities: 6CN (i.e. six CN molecules) and Fe (one iron atom). If we try to convert (1) back to structure, using the same Web Demo tool, we get six free-floating CN^• radicals and a separate Fe⁴⁻ anion. Ew. But if we tick the “Include Bonds to Metal” box in the Web Demo tool, we have

InChI=1/6CN.Fe/c6*1-2;/q;;;;;;-4/rC6FeN6/c8-1-7(2-9,3-10,4-11,5-12)6-13/q-4

(2)

where the metal-reconnected layer (/r) appears. It looks like an alternative InChI added directly after the standard one, with its own connectivity (/c) and charge (/q) sublayers. In this layer, there is only one entity: C6FeN6, i.e. [Fe(CN)₆]. The string (2) is correctly converted back to the structure (a).

Now let’s look at the structure of a salt known as Prussian Blue (b):

(b)

Fe4[Fe(CN)6]4− iron(3+) hexacyanidoferrate(4−) (additive) ferric ferrocyanide (trivial) Prussian Blue (trivial)

Its standard InChI is:

InChI=1S/18CN.7Fe/c18*1-2;;;;;;;/q;;;;;;;;;;;;;;;;;;3*-4;4*+3

(3)

The main layer contains two types of entities: 18CN (i.e. 18 CN molecules) and 7Fe (seven iron atoms). Converting (3) to structure brings about a horrible mess. With “bonds to metal”, however, we get

InChI=1/18CN.7Fe/c18*1-2;;;;;;;/q;;;;;;;;;;;;;;;;;;3*-4;4*+3/r3C6FeN6.4Fe/c3*8-1-7(2-9,3-10,4-11,5-12)6-13;;;;/q3*-4;4*+3

(4)

In the metal-reconnected layer (/r) we see two different types of entities: 3C6FeN6 (i.e. three [Fe(CN)₆]) and 4Fe. The string (4) is correctly converted back to the structure (b).

Years ago, I was complaining (to the universe) about different InChIs for the same molecular entity, viz. chromate (c—e). I’ve revisited it with the new version of InChI.

(c)	(d)	(e)

[CrO4]2− chromate (trivial) tetraoxidochromate(2−) (additive) tetraoxidochromate(VI) (additive)

Alas, the standard InChIs for the representations (c), (d) and (e) remain different. Try to convert them back to structures: they also are all different and all wrong (all have extra hydrons). Nevertheless, I see a sign of progress: the metal-reconnected layers for the corresponding strings (5), (6) and (7) are identical!

(c)	InChI=1/Cr.4O/q;;;2*-1/rCrO4/c2-1(3,4)5/q-2	(5)
(d)	InChI=1/Cr.4O/q-2;;;;/rCrO4/c2-1(3,4)5/q-2	(6)
(e)	InChI=1/Cr.4O/q+2;4*-1/rCrO4/c2-1(3,4)5/q-2	(7)

Moreover, all three strings, (5), (6) and (7), are converted back to the structure (c).

What about our old friend ferrocene? Depends how you draw it. I’ll stick to the ChEBI’s decacoordinate-iron representation (f):

(f)

bis(η5-cyclopentadienyl)iron (additive) ferrocene (trivial)

The standard InChI for ferrocene is:

InChI=1S/2C5H5.Fe/c2*1-2-4-5-3-1;/h2*1-5H;

(8)

Converting (8) to structure results in two standalone cyclopentadienyl radicals and a neutral iron atom. With “bonds to metal”:

InChI=1/2C5H5.Fe/c2*1-2-4-5-3-1;/h2*1-5H;/rC10H10Fe/c1-2-4-5-3(1)11(1,2,4,5)6-7(11)9(11)10(11)8(6)11/h1-10H

(9)

In the /r layer we see a single entity, C10H10Fe, i.e. [Fe(C₅H₅)₂]. The string (9) is correctly converted back to the structure (f).

Seniority criteria

Last time I took part in the Intra-Universal Panel of Astronomical Chemistry, I had a most edifying and enjoyable discussion with an alien (to me) colleague who, for reasons unknown, showed an interest in terrestrial chemical nomenclature. I can’t tell you her name, and not due to confidentiality considerations: I am simply unable either pronounce or write it^*.

We got along very well. Even though she spoke with a thick Arcturian accent, I understood most of her English. What she made of my English, I know not, but she assured me that the latest Google Translate app was doing a decent job despite ignoring important words like “not”.

I told her that chemical nomenclature, with all its shortcomings, is the best scientific nomenclature developed on Earth because, knowing the rules, one can reconstruct the structure from the name. Looking back, I wish I hadn’t said that. I guess now she doesn’t think much of our science as a whole.

Her interest in nomenclature was intriguing given that she regarded it, along with other prescriptive systems, a form of authoritarianism. Among Arcturians, she explained, it’s considered to be poor taste to talk about that, but she’s always had a rebellious streak.

One thing we agreed on was that any nomenclature system requires some seniority criteria. These criteria better be both objective and consistent, and the fewer of them the better.

Atomic number

And if there is one truly universal criterion of seniority for elements — universal in the sense that it will be accepted anywhere in our Universe — it must be atomic number. Consider the atoms i and j with corresponding atomic numbers Z_i and Z_j. Saying that if Z_i > Z_j then atom i is senior to atom j should stir no controversy whatsoever. So you would expect the atomic number criterion to be the main ordering principle in chemical nomenclature, or at least to be used a lot. You’d be wrong.

Nevertheless, atomic number is used consistently in the Cahn–Ingold–Prelog (CIP) sequence rules. Now there are many rules, but the first among them is this one [1, P-92.1.3.1a]:

higher atomic number precedes lower.

How curious, says the Arcturian. She has nothing against atomic numbers, it is just that in her view “senior” means what it means: elder. Hydrogen, helium, lithium and beryllium have been around the longest, practically since the Big Bang, so they must be senior to the rest. And the superheavies are the newest, the youngest. In other words, junior. Also, they die young, so they’ll never grow to be seniors. For me, she says, if Z_j > Z_i then atom i is senior to atom j. But please, go on.

Let’s see how it works, I continue. If all atoms directly attached to the chiral centre are different, applying the CIP rules is straightforward. This is the case of the enantiomers of halothane, (a) and (b).

(a)	(b)

(S)-halothane (trivial) (2S)-2-bromo-2-chloro-1,1,1-trifluoroethane (substitutive) (R)-halothane (trivial) (2R)-2-bromo-2-chloro-1,1,1-trifluoroethane (substitutive)

The chiral centre (C-2) is linked to four different atoms: Br, C, Cl and H. On the diagram (a), the chiral centre is positioned in such a way that the least-preferred ligand — in this case, hydrogen — points away from the viewer. The rest of the ligand sequence, Br > Cl > C, go anticlockwise, therefore, the configuration of the chiral carbon is ‘S’. The complete name of (a) is (2S)-2-bromo-2-chloro-1,1,1-trifluoroethane and of its mirror image (b) is (2R)-2-bromo-2-chloro-1,1,1-trifluoroethane.

If at the chiral centre there are two or more atoms of the same element, we can assign priorities according to the atoms directly attached to them [1, P-92.2.1.1.2]. Consider two common amino acids, L-serine (c) and L-cysteine (d) [1, P-103.1.1.1]:

(c)	(d)

L-serine (retained) (2S)-2-amino-3-hydroxypropanoic acid (substitutive) L-cysteine (retained) (2R)-2-amino-3-sulfanylpropanoic acid (substitutive)

In both amino acids, the order of preference at the chiral centre (C-2) is N > C = C > H. But no, not all carbons are equal. In L-serine (c), the carbon (C-1) of the carboxy group, –COOH, is linked to two oxygen atoms, and therefore is senior to the other carbon (C-3) that is linked to only one oxygen, that of a hydroxy group, –OH. The hydrogen at C-2 points away from the viewer and the rest of the ligand sequence, N > C-1 > C-3, go anticlockwise, so the configuration of the chiral carbon is ‘S’. On the other hand, in L-cysteine (d), the carbon (C-3) bears a sulfanyl group, –SH. Since sulfur is senior to oxygen, the ligand sequence N > C-3 > C-1 go clockwise and the configuration of C-2 is ‘R’.

Element sequence

Could it be that the atomic number criterion is so obvious that Earth chemists felt embarrassed to use it for nomenclature? Anyhow, they came up with a different seniority sequence for elements, the one based on electronegativity [2, IR-2.15.3.1, IR-4.4.2.1]. The element sequence is the reason why we (are supposed to) say hydrogen chloride and write HCl (rather than chlorine hydride and ClH). The main purpose of the element sequence is to order the atoms in binary compounds, but it is “also adhered to when ordering central atoms in polynuclear compounds for the purpose of constructing additive names” [2, IR-1.6.3].

Here is an updated version of the element sequence [3]:

	(1)

In general, electronegativity decreases when we go from top to bottom in a group and from right to left in a period. This is how the element sequence (1) is organised: zigzagging, starting from the group 17 (F > Cl > Br, etc.), then groups 16, 15 and so on until the group 1 (Li > Na > K etc.) and then to the group 18 (He > Ne > Ar, etc.). Interestingly, hydrogen is placed not in the group 1 but on a “hedge” between groups 16 (chalcogens) and 15 (pnictogens)^†.

Wait, my Arcturian colleague interrupts. This couldn’t be right. No matter whether you choose Pauling or Allen scale, caesium is not more electronegative than krypton, and hydrogen is not more electronegative than nitrogen, or even carbon. So you should write H₃N instead of NH₃. On the other hand, tellurium is less electronegative than hydrogen. So you should say tellurium dihydride, not dihydrogen telluride.

I don’t really know how to counter it. Perhaps, I wager, this is not true electronegativity for each element but average electronegativity in a group?

The Arcturian smiles, a bit condescendingly. How can you deal with the fact that electronegativity of Group 11 (individual or average) is higher than that of Group 12? And you still didn’t explain what the noble gases are doing in the very end of the element sequence. Why on Earth you use a criterion that does not even have an accepted definition?

Indeed. To make matters worse, chemists came up with a number of other element sequences. The Red Book gives the following sequence for ordering mononuclear parent hydrides [2, IR-2.15.3.2]:

N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Al > Ga > In > Tl > O > S > Se > Te > C > F > Cl > Br > I	(2)

Here, it goes from the group 15, then group 14 starting from silicon, then group 13, then group 16, then carbon, then group 17. Confusing? You bet. To select senior atoms in parent structures and to choose between rings and chains, the Blue Book recommends the variant of (2) without halogens [1, P-44.1.2, P-68.1.5]:

N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Al > Ga > In > Tl > O > S > Se > Te > C	(3)

While for skeletal replacement (‘a’) and in Hantzsch-Widman (H-W) names, the seniority order of heteroatoms is as follows [1, P-22.2.3.1]:

F > Cl > Br > I > O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Al > Ga > In > Tl	(4)

Naturally, not being a heteroatom, carbon is not even here. And sometimes, a shorter (halogen-less) variant of sequence (4) is used [1, P-23.3.2.2, P-25.4.2.3.1, P-26.5.4.2, P-28.4.2]:

O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Al > Ga > In > Tl	(5)

It’s a mess, the Arcturian shrugs. I concur.

Chains and rings: size matters

You may recall that the names of branched hydrocarbons are constructed using the longest-chain method. For example, (e) is named 3-methylpentane and not 2-ethylbutane because its principal chain is the one that contains the greater number of skeletal atoms, viz. pentane.

(e)

CH3–CH2–CH(CH3)–CH2–CH3 3-methylpentane (substitutive, PIN)

Likewise, in cyclic hydrocarbons larger rings (rings with the greater number of skeletal atoms) are senior to smaller ones [1, P-61.2.2]. Thus, (f) is named cyclopropylcyclohexane and not cyclohexylcyclopropane. Two rings are senior to one ring, so (g) is named 1-phenylnaphthalene, not (naphthalen-1-yl)benzene (or 1-naphthylbenzene). It’s only logical. My alien friend nods in agreement.

(f)	(g)

cyclopropylcyclohexane (substitutive, PIN) 1-phenylnaphthalene (substitutive, PIN)

Other seniority criteria applied are rather arbitrary, I admit. For instance, the structure (h) is called cyclohexylbenzene because “benzene has more multiple bonds than cyclohexane” [1, P-61.2.2]. This is because, caeteris paribus, priority is given to the system with greater number of multiple bonds [1, P-44.4.1]. The Arcturian counters saying that the number of atoms in saturated rings or chains is always higher than in the corresponding unsaturated ones and, therefore, the “size” criterion can be applied more consistently if we give seniority to saturated structures.

(h)

cyclohexylbenzene (substitutive, PIN)

What if we have a system consisting of rings and chains? We can call the structure (i) hexylcyclopentane (ring is senior to chain) or 1-cyclopentylhexane (chain has greater number of skeletal atoms) but the preferred IUPAC name will be the former one [1, P-44.1.2.2]. Again, my colleague is not convinced: rings-senior-to-chains sounds like a matter of taste, she says.

(i)

hexylcyclopentane (substitutive, PIN) 1-cyclopentylhexane (substitutive)

Organic classes

Substitutive nomenclature employs an order of seniority for classes of organic compounds [1, P-4, Table 4.1]. As discussed earlier [4], it is the most senior characteristic group that gives a name to a class — and corresponding “suffix” to a systematic name. Thus, L-serine (c) is named substitutively (2S)-2-amino-3-hydroxypropanoic acid and not (1S)-1-carboxy-2-hydroxyethanamine because acids are senior to amines. If we take away a hydron from (c), we’ll get L-serinate (j), or (2S)-2-amino-3-hydroxypropanoate (anions > amines).

(j)	(k)	(l)

L-serinate (retained) (2S)-2-amino-3-hydroxypropanoate (substitutive) L-serinium (retained) (1S)-1-carboxy-2-hydroxyethanaminium (substitutive) L-serine zwitterion (retained) (2S)-2-ammonio-3-hydroxypropanoate (substitutive)

On the other hand, if we add a hydron to (c), we’ll get L-serinium (k). Its substitutive name is (1S)-1-carboxy-2-hydroxyethanaminium because cations are senior to acids. Finally, L-serine zwitterion (l) is sytematically named as (2S)-2-ammonio-3-hydroxypropanoate (anions > cations).

As you can see, there is no great structure change here, just moving a hydron around. There’s no intrinsic reason why the carboxy group –COOH should be senior to amino group –NH₂ but “junior” to the aminium group –NH₃⁺.

Compounds such as halothane (a) and (b) are at the bottom of the seniority order [1, P-41, Table 4.1]:

λ¹ Halogen compounds in the order F > Cl > Br > I

In substitutive nomenclature they don’t qualify to be expressed by “suffixes” even if there are no other characteristic groups. (I find it discriminatory, says my alien colleague.) The quoted element sequence explains why halothane is named 2-bromo-2-chloro-1,1,1-trifluoroethane and not 1-bromo-1-chloro-2,2,2-trifluoroethane (fluorine is senior to the rest of halogens and thus gets the lower locant). The substituents ‘bromo’, ‘chloro’ and ‘fluoro’ are ordered alphabetically.

Alphanumerical order

Which brings us to the last ordering criterion for today. The substituents that appear as “prefixes” are cited in alphabetical order. The Blue Book prefers the term alphanumerical order, “to convey the message that both letters and numbers are involved” (in ordering principles) [1, P-14.5].

In some cases, locants are assigned according to alphanumerical order [1, P-14.4 (g)]. E.g., preferred name for (m) is 1-chloro-2-nitrobenzene, not 1-nitro-2-chlorobenzene:

(m)

1-chloro-2-nitrobenzene (substitutive, PIN)

Herold [5] notes that we have to be careful when translating English systematic names because alphabetical order in other languages is often not the same. He exemplifies his point with 3-methyl-5-phenylpyridine: its correct translation to Spanish, Italian and Portuguese will be 3-fenil-5-metilpiridina. In both names the substituent cited first get lower locants. In case of 1-chloro-2-nitrobenzene (m), its Russian systematic name will be 1-нитро-2-хлорбензол because the alphabetical order of substituents is opposite to that of the English name.

You should have seen my colleague’s face when I came to this bit. And how does that work in Chinese, she inquired. Somewhat naïvely, she thought I speak every Earth language. We decided to stop right there because it was almost dinner time.

We never came back to discuss chemical nomenclature: she flew back to Arcturus stream early the following morning. I sent her an email, of the it-was-nice-to-meet-you persuasion, but I fear I won’t receive an answer in my lifetime.

*	I assumed that my colleague was a “she”, although I can’t be completely sure. She never introduced herself stating her gender; come to think about it, neither did I. I addressed her as “you” and she did likewise. It didn’t cause any problem because nobody else in the room spoke Modern English.
†	More specifically, between livermorium and nitrogen (Lv > H > N); in earlier recommendations, between polonium and nitrogen [2, p. 260, Table VI].

References

1. Favre, H.A. and Powell, W.H. Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names. Royal Society of Chemistry, Cambridge, 2014.
2. 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.
3. Hartshorn, R.M., Hellwich, K.-H., Yerin, A., Damhus, T. and Hutton, A.T. (2015) Brief guide to the nomenclature of inorganic chemistry (IUPAC technical report). Pure and Applied Chemistry 87, 1039—1049.
4. Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020) Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). Pure and Applied Chemistry 92, 527—539.
5. Herold, B. (2013) Lost in nomenclature translation. Chemistry International 35, no. 3, 12—15.

Hydrogen names

Let us come back to inorganic oxoacids and their anions. Observe the structures (a) through (c):

(a)	(b)	(c)

[CO(OH)2] carbonic acid (common, PIN) dihydrogencarbonate (simplified hydrogen) dihydrogen(trioxidocarbonate) (hydrogen) dihydroxidooxidocarbon (additive) [CO2(OH)]− bicarbonate (common, not recommended) hydrogencarbonate (simplified hydrogen) hydrogen(trioxidocarbonate)(1−) (hydrogen) hydroxidodioxidocarbonate(1−) (additive) [CO3]2− carbonate (common, PIN) trioxidocarbonate(2−) (additive)

You may remeber that (a) is carbonic acid and (c) is its fully deprotonated anion, carbonate. What about (b)? Well, it’s called ‘hydrogencarbonate’ in the Red Book [1, IR-8.4] and ‘hydrogen carbonate’ in the Blue Book [2, P-65.6.2.3.2]. What’s the difference?

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.

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.

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?

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.

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.

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

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?

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].

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”.

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

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.