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.

Colourful Compound Interest

I discovered Andy Brunning’s Compound Interest last year and got absolutely hooked on it – and I don’t even teach chemistry! If, perchance, you do teach chemistry and don’t yet know what CI is all about, then you probably should check it out. (And if you want to use the material in the classroom, you can download the high-resolution PDF files.) The topics range from general chemistry to material science, chemical warfare and everyday compounds. You’ve got answers to many questions you always wanted to ask but never had time to find out for yourself, like, “is it worth (not) to refrigerate tomatoes?”. The Undeserved Reputations section is a perfect antidote to the “oh my God, our food is still full of chemicals” stream of rubbish published by your Facebook friends.

Here are ten the top ten some of my CI favourites.

Metal Ion Flame Test Colours Chart

1. This is how (I’d like to think) I’ve got interested in chemistry. We used to have a gas hob in our kitchen. I loved the fact that the flame was blue. One day, my brother told me that you can make the flame bright orangey-yellow if you sprinkle it with table salt or bicarbonate of soda. “Why?”, I asked. “Sodium”, was the answer. Unsatisfactory as it was, it stayed in my memory. Yes, chemistry won’t be of any interest to me if not for flame and colours.



Colours of Transition Metal Ions in Aqueous Solution

2. When they are not busy burning or, better still, exploding stuff, your archetypal chemists are often imagined (and therefore portrayed; or is it the other way round?) as hiding behind the test tubes filled with colourful solutions. Which is just as well. The test tubes filled with colourless solutions would be really boring.



What Causes the Colour of Gemstones?

3. Who didn’t dream of finding a treasure, that is, a pirate’s chest filled with gold and jewels? Wait. I still dream of that. I remember how surprised I was when, back in elementary school, I read in some book that ruby and sapphire are basically the same mineral corundum, the only difference is in a type of impurity. Well it’s quite an important difference then. Without impurities, most gemstones would be colourless.



The Chemistry of The Colours of Blood

4. My interest in bioinorganic chemistry (even though at the time I didn’t know at it was called that) was also awakened in school, when I learned that some animals have blue blood. I also discovered that, contrary to what anatomy textbooks show, veins do not carry blue blood in humans. I am not sure if I was relieved or disappointed. Later, already in the university, I read about a Soviet-developed fluorocarbon-based blood substitute nicknamed “Blue Blood”. Fascinating stuff.



The Chemicals Behind the Colours of Autumn Leaves

5. I remember, as a child, reading, or rather browsing, an illustrated book about plants (translated from English), with many beautiful colour photographs. “This apple is yellow because of anthocyanin”. Next page: “This apple is yellow because of carotene”. Next page: “This apple is green because of chlorophyll”. The realisation dawned that, apple-wise, being green is not only necessary but sometimes sufficient.

   But what about leaves? When autumn comes, chlorophyll starts to break down and we get to see other pigments in them. Apart from caroteinoids and flavonoids, there are also coloured chlorophyll degradation products, termed “rusty pigments”.



The Chemistry of Stain Removal

6. Sometimes, however, we want to get rid of all these beautiful colours. The infographic shows the chemical methods of achieving that, although I am not sure that “enzymatic stains” is a correct name for stains caused by blood or grass (yes, haem and chlorophyll again!).



The Atmospheres of the Solar System

7. Alchemists associated seven metals with seven planets (which included the sun and the moon). At the time, it seemed to be quite reasonable. Now that nobody expects Mercury to be made of mercury (and, for that matter, Pluto to be made of plutonium), precious little is known about composition of these planets. About their atmospheres, we’ve learned a bit more. Hey, isn’t it amazing that Mercury’s atmosphere has by far highest percentage of molecular oxygen (42%) compared to any other atmosphere in Solar system? We still won’t be able to breathe there though, because its atmosphere is way too thin (its surface pressure is less than 10⁻¹⁴ bar).



The Metals in UK Coins

8. Compared to gemstones, coins are so much duller, especially now that we don’t come across either gold or silver coins any longer. Continuing the alchemical tradition, we can say that modern British coins of 20 pence and higher are mostly from Venus (that is, copper), while 1 p, 2 p, 5 p and 10 p coins are mostly from Mars (i.e. iron). Of course, you can find much more metal variety in commemorative coins.



The Metal Reactivity Series

9. In contrast to their salts, aqueous complexes and gemstones, pure metals do not offer a great variety of colours. Copper is red, gold is yellow and caesium is yellowish; the rest are coming in many shades of grey. But their chemical behaviour is wildly different, as this infographics shows. You don’t need a sophisticated lab equipment or fancy reagents, just water and some (diluted) acids. If there’s no reaction whatsoever, you’ve got a precious metal. Easy!



Analytical Chemistry – Infrared (IR) Spectroscopy

10. Did I tell you that my first love, as far as the world of analytical chemistry is concerned, was vibrational spectroscopy? If not, I’m telling you now. I’ve never got to do any experiment worthy of a publication, because if I did, believe me, it would have been awesome. This infographics reminded me of happy days of my studenthood when I knew and cared more about amide bands (bless them) than about money or my future career.

Iron stars

According to Freeman Dyson, in rather unimaginable 10¹⁵⁰⁰ years from now, and in case proton decay does not happen, most of nuclei will either fuse or decay into iron. This will leave the universe inhabited by “cold spheres of pure iron”. I think it is cool, even if I won’t live that long to see it. However, I came across a report of recent (2006) observation of ‘iron star’ with NASA’s Spitzer Space Telescope. I don’t think these objects are the same as Dyson’s iron stars though, just the next best thing.

Metal snow, anyone?

It was snowing heavily yesterday, at least by English standards. Can I find something related to both snow and metal on the web? The googling for “metal snow” does not bring that many interesting results, mostly it’s all about metal tools related to snowy weather. All moderately interesting finds are rather old news. There are couple of papers from 1978 entitled “Plasma cooling by metal snow” (this and this). There, “metal snow” refers to the metal dust “liberated” from the walls of Tokamaks as a result of surface cracking. Another old news item concerns the heavy metal snow discovered on Venusian mountain tops back in 1995. According to Laura Schaefer and Bruce Fegley from Washington University in St. Louis (2004), this “snow” consists of compounds such as galena (lead sulfide), bismuthite (bismuth sulfide), and/or lead-bismuth sulfosalts. The most recent find (2008) is a photo promisingly titled Metal Snow Girl which does not show any snow either, but a snowman-like figure made of metal balls.

Circumnames

I came across these “circumnames” quite by chance: several compounds were mentioned in this paper and some other can be found in this astrochemistry database. Is there any elegant way to name them systematically?

(a) circumpyrene

(b) ovalene

(c) pyrene

For instance, ACD/Name gives the molecule (a) a systematic name dinaphtho[2,1,8,7-hijk:2',1',8',7'-stuv]ovalene, i.e. two naphtho groups are fused to the top and bottom of the ovalene (b) molecule, while the non-systematic name “circumpyrene” means that pyrene (c) core is completely encircled by fused benzene rings. Unfortunately, I was unable to generate ACD/Names for bigger molecules, such as circumcoronene (d) [i.e. coronene (e) encircled by fused benzene rings] and circumovalene (f). Apparently, ACD/Name cannot name compounds with more than 15 fused rings.

(d) circumcoronene

(e) coronene

(f) circumovalene

If the “core” structure is surrounded by two rows of fused benzene rings, the doubly “circum” names like circumcircumpyrene (g) and circumcircumcoronene (h) appear.

(g) circumcircumpyrene

(h) circumcircumcoronene