One-electron carbon—carbon bond

What is a covalent bond? We learn in school that it is a chemical bond formed by shared pairs of electrons between atoms. The Gold Book provides a bit more careful definition:

A region of relatively high electron density between nuclei which arises at least partly from sharing of electrons and gives rise to an attractive force and characteristic internuclear distance.

Well, now the textbook definition will have to be changed [1]. In the study published this week in Nature [2], Shimajiri and co-authors

report the isolation of a compound with a one-electron σ-bond between carbon atoms by means of the one-electron oxidation of a hydrocarbon with an elongated C—C single bond. The presence of the C•C one-electron σ-bond (2.921(3) Å at 100 K) was confirmed experimentally by single-crystal X-ray diffraction analysis and Raman spectroscopy, and theoretically by density functional theory calculations.

Cf. the length of single C—C bond in diamond: 1.54 Å. In 2018, Ishigaki et al. [3] reported much longer two-electron C—C bond of 1.806(2) Å in a polycyclic hydrocarbon, dispiro[(dibenzo[a,d]cycloheptatriene)-5,1′-(1′,2′-dihydropyracylene)-2′,5″-(dibenzo[a,d]cycloheptatriene)]^* (10c):

Now the same team took the compound 10c of [3] and crystallised it with iodine. In the resulting stable salt (10c^•+)(I₃⁻), the C1—C2 bond lost one electron to I₃.

This is not the first one-electron bond observed (see [2] and references 1—4 therein) but the first involving carbon atoms.

The crystal structures of (10c^•+)(I₃⁻) are deposited with CCDC, entries 2301032 through 2301039.

*

This is the name given to the compound by Shimajiri [4]. ‘Pyracylene’ is a trivial name of cyclopent[fg]acenaphthylene. Saturating the bond of the cyclopentane ring, we get 1,2-dihydrocyclopent[fg]acenaphthylene. In spiro nomenclature, the locants of the second component are primed (and of the third component doubly primed, etc.), thus 1′,2′-dihydrocyclopent[fg]acenaphthylene. Therefore, the fully systematic name should be dispiro[(dibenzo[a,d]cycloheptatriene)-5,1′-(1′,2′-dihydrocyclopent[fg]acenaphthylene)-2′,5″-(dibenzo[a,d]cycloheptatriene)].

References

1. Bourzac, K. (2024) Carbon bond that uses only one electron seen for first time: ‘It will be in the textbooks’. Nature, online ahead of print.
2. Shimajiri, T., Kawaguchi, S., Suzuki, T. and Ishigaki, Y. (2024) Direct evidence for a carbon—carbon one-electron σ-bond. Nature, online ahead of print.
3. Ishigaki, Y., Shimajiri, T., Takeda, T., Katoono, R. and Suzuki, T. (2018) Longest C—C single bond among neutral hydrocarbons with a bond length beyond 1.8 Å. Chem 4, 795—806.
4. Shimajiri, T. (2022) The nature of ultralong C—C bonds: Demonstration of the longest Csp³—Csp³ single bond beyond 1.8 Å and discovery of flexible covalent bonds. Doctoral dissertation, Hokkaido University.

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?

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