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.

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?

Content morphemes

At this point, it might be useful to mention that morphemes could be divided into two classes: content morphemes (i.e. those that have independent meaning) and functional morphemes. All content words contain at least one content morpheme. In English, content words include nouns, adjectives, adverbs and most verbs, while functional morphemes include conjunctions, prepositions, pronouns and articles as well as affixes. These two classes are sometimes referred to as “open class” and “closed class”, respectively. New morphemes are easily added to the former and hardly ever to the latter.

Now to continue with the list that I started earlier.

6. Since chemical names consist of content words (ii), they are open-class.
7. Every content word contains at least one root (iv) which is a content (open-class) morpheme.
8. Affixes are functional (closed-class) morphemes.
9. New chemical names are formed by combining existing content morphemes with functional morphemes or adding new content morphemes.

OK? Still no objections?

Stoichiometric names

The Red Book [1, p. 5] uses the term compositional nomenclature

to denote name constructions which are based solely on the composition of the substances or species being named, as opposed to systems involving structural information.

It is the simplest systematic way of naming chemical substances. Compositional nomenclature can be used for both compounds and elementary substances. In case of compounds, is is also known as binary-type nomenclature [2]. Why “binary”? Because the names of compounds named that way always consist of two parts, positive and negative.

What are compounds anyway?

According to Oxford English Dictionary, “compound” (in chemistry) is

a substance formed from two or more elements chemically united in fixed proportions.

(1)

I quite like this definition. There are four statements in it:

• compound is a substance (therefore, it is macroscopic);
• compound contains at least two (different) elements;
• these elements are “chemically united”, i.e. chemically bound;
• they are bound in fixed proportions.

Elemental haiku

My, the year is almost gone and I, busy with other stuff, didn’t publish a single post. Luckily, I came across Elemental haiku — a periodic table of haikus, one per element, plus one for a hypothetical element 119. Here are my favourites.

2. Helium

Begin universe.
Wait three minutes to enter.
Stay cool. Don’t react.

11. Sodium

Racing to trigger
every kiss, every kind act;
behind every thought.

13. Aluminum/Aluminium

Spent kindergarten
endlessly writing your name.
One i or two i’s?

26. Iron

Anvil, axe, nail, plow,
engine, railway, factory.
Servant, friend, partner.

30. Zinc

Clasp your neighbor tight.
Sound the music while you dance,
trumpet, bugle, horn.

39. Yttrium

That is not a name.
That is a spelling error.
Or a Scrabble bluff.

67. Holmium

The root of the name
elementary, my dear.
Stockholm, not Sherlock.

80. Mercury

Madness the price paid
for your molten alchemy.
Metal. Planet. God.

You can contribute your own on Twitter with hashtag #ChemHaiku.

The end of unun*iums is announced

So that’s it, then. Four new elements, ununtrium, ununpentium, ununseptium and ununoctium [1] are to be officially named nihonium (symbol Nh), moscovium (Mc), tennessine (Ts), and oganesson (Og), respectively [2]. So that for a while the periodic table will be free of ungainly “unun” names. The provisional recommendation is out [3], comments by 8 November 2016. I am going to send mine to IUPAC, but I’d like to share them with my readers first.

Let’s start with naming conventions [4]:

In keeping with tradition, elements are named after:

1. a mythological concept or character (including an astronomical object),
2. a mineral, or similar substance,
3. a place, or geographical region,
4. a property of the element, or
5. a scientist.

Unfortunately, it is not required for the names to be aesthetically pleasing.

In absence of minerals (all four elements are artificial) and properties (apart from half-lives, which aren’t that long) to speak about, we are left with three options. Don’t you agree that the option (a) is the most interesting one? However, the discoverers have chosen easy and boring options (c) and (e). Well, I like nihonium, named after Nihon (ニホン), one of the Japanese names for Japan (literally, “the sun’s origin”). I can’t say the same about the rest.

Take moscovium:

It is proposed that the name moscovium and symbol Mc are given to element 115. Moscovium is recommended in recognition of the Moscow region and honoring the ancient Russian land that is home to the Joint Institute for Nuclear Research, where the discovery experiments were conducted using the Dubna Gas-Filled Recoil Separator in combination with the heavy-ion accelerator capabilities of the Flerov Laboratory of Nuclear Reactions, JINR.

I see. Not content with dubnium (element 105), Russian scientists™ insist on honouring Dubna one more time. But Dubna is not Moscow. The town is at least as old as the Russian capital and is situated on the very edge of Moscow Oblast, or Podmoskovye (Подмосковье). Shouldn’t dubnium 2.0 be called podmoskovium then? And why mention Moscow at all? After all, there are four elements named after Ytterby. The variations like dubinium, dubonium, or poddubnium spring to mind. Needless to say, “Mc” will have to go.

Personally, I would prefer the element 115 to be named lemmium in honour of the late Motörhead frontman Lemmy Kilmister. Alas, IUPAC’s set of absurd rules (see above) restricts people after whom the new elements could be named to “scientists”. I’ll come to that in a minute.

Now let’s look at tennessine. The ending -ine, by analogy with English names of other halogens, appears to be natural. However it simply shows that the authors of this proposal (from Tennessee region, I guess) did not think about languages other than English, although they should have, for “the names for new chemical elements in English should allow proper translation into other major languages” [3]. For instance, in Latin the halogen names are fluorum, clorum, bromum, iodum and astatum, in Spanish they are flúor, cloro, bromo, yodo and astato, while in German they are simply Fluor, Chlor, Brom, Iod und Astat. So in these languages the element 117 must be named tennessum, teneso and Tenness, respectively.

As for the symbol, I was about to complain that Ts is is a bad choice for an element symbol as Ts is widely used for tosyl group, and why not to use Tn given that TN is also an abbreviation for Tennessee. There was a similar story with copernicium a few years ago (originally proposed symbol Cp was later changed to Cn). It’s not that the authors of the recommendation aren’t aware of potential confusion:

NB: We are aware of the fact that Ts is often used as abbreviation for the tosyl chemical group. However, this was not considered to be a valid objection, given the fact that we also use the symbols Ac and Pr for chemical elements, while chemists also use these as abbreviations for the acyl and the propyl groups. Very common items like AcOH and PrOH are usually not taken for the hydroxides of actinium and praseodymium and a possible confusion with the tosyl group seem extremely low. On the other hand, the abbreviation Tn, that might have been a natural suggestion, is impossible given the earlier (1923) CIAAW-IUPAC acceptance of that symbol for thoron (²²⁰Rn), and its regular usage since then, see e.g. Journal of Environmental Radioactivity.

Still, I don’t find this convincing. If we ever get enough of ununseptium, we’ll find that its chemistry is nothing like that of actinium or praseodymium. Think of tosyl chloride, abbreviated TsCl. Now think of its tennessine analogue, abbreviated TsTs. That’s just silly. It’s a shame we can’t use “Tn” as TN is an abbreviation for the state of Tennessee. What about Tq then, after Tanasqui, the first recorded version of this toponym?

Finally, oganesson. Does it have to end with -on? Yes, most noble gases do (and, in contrast to meaningless -ine, the ending -on is present in other languages). Except helium, that is. Helium was named after Helios, the Greek god of the Sun, and is the only noble gas following the naming principle (a). Several “on” names are of Greek origin, namely νέον “new”, ἀργόν “inactive”, κρυπτόν “hidden” and ξένον “foreign”, whereas radon is a contraction of “radium emanation”. But oganesson... Please! It’s two syllables too many and feels out of place.

And another thing. I don’t know about you, but naming anything after a living person makes me uneasy. Seeing his surname mutilated this way should make Yuri Oganessian uneasy too. Come on, did we ran out of deserving dead scientists whose names, incidentally, can be used for the heaviest known element? For example, we can honour John Dalton, an English polymath best known for development of atomic theory; among other things, he invented his own symbols for chemical elements [5]. Or J. J. Thomson, discoverer of the electron. Or Francis W. Aston, discoverer of many naturally occurring isotopes. Or Arthur Compton, known for Compton scattering. Or C. T. R. Wilson, inventor of the cloud chamber. Or Fritz London, after whom the London dispersion forces are named. Or Ernest Walton, the first person to artificially split the atom.

To summarise: political considerations, inflated egos, and lack of imagination all may be responsible for some of the dismal proposals above. It does not mean we have to swallow them without fight. If you have better suggestions — and I’m sure you do — I urge you to write to IUPAC before 8 November.

1. IUPAC announces the verification of the discoveries of four new chemical elements: The 7th period of the periodic table of elements is complete. IUPAC Press Release, 30 December 2015.
2. IUPAC is naming the four new elements nihonium, moscovium, tennessine, and oganesson. IUPAC Press Release, 8 June 2016.
3. Öhrström, L. and Reedijk, J. (2016) Names and symbols of the elements with atomic numbers 113, 115, 117 and 118. IUPAC Provisional Recommendation.
4. Koppenol, W.H., Corish, J., García-Martínez, J., Meija, J. and Reedijk, J. (2016) How to name new chemical elements (IUPAC Recommendations 2016). Pure and Applied Chemistry 88, 401—405.
5. Dalton, J. (1808) A New System of Chemical Philosophy, vol. I.

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.

Periodic Videos

It’s been a while since I posted anything on this blog, but now I’m back.

This is a very cool collection of videos, “a lesson about every single element on the periodic table”. Featuring Professor and a really awesome reaction, here’s one about one of my favourite elements. Yes, iron is in my blood! (In yours too.)

Metals

From A Dictionary of Symbols by Juan Eduardo Cirlot (translated by Jack Sage):

In astrology they are called ‘terrestrial’ or ‘subterranean planets’, because of the analogous correspondences between the planets and the metals. For this reason astrologers consider that there are only seven metals (influenced by the same number of spheres), which does not mean that mankind during the astrobiological period did not recognize more. As Piobb has pointed out, some engineers have noted that the seven planetary metals make up a series which is applicable to the system of the twelve polygons. But, apart from the theory of correspondences, the metals symbolize cosmic energy in solidified form and, in consequence, the libido. On this basis, Jung has asserted that the base metals are the desires and the lusts of the flesh. Extracting the quintessence from these metals, or transmuting them into higher metals, is equivalent to setting creative energy free from the fetters of the sense world, a process identical with what esoteric tradition and astrology regard as liberation from the ‘planetary influences’. The metals can be grouped within a progressive ‘series’ in which each metal displays its hierarchical superiority over the one preceding it, with gold as the culminating point of the progression. This is why, in certain rites, the neophyte is required to divest himself of his ‘metals’ — coins, keys, trinkets — because they are symbolic of his habits, prejudices and characteristics, etc. We, for our part, however, are inclined to believe that in each particular pairing of planet with metal (as Mars with iron) there is an essential element of the ambitendent, in that its positive quality tends one way and its negative defect tends the other. Molten metal is an alchemic symbol expressing the coniunctio oppositorum (the conjunction of fire and water), related to mercury, Mercury and Plato’s primordial, androgynous being. And at the same time, the solid or ‘closed’ properties of matter emphasize its symbolism as a liberator — hence the connexion with Hermes the psychopomp <...> . The correspondences between the planets and the metals, from inferior to superior, are: Saturn — lead, Jupiter — tin, Mars — iron, Venus — copper, Mercury — mercury, Moon — silver, Sun — gold.

Binary pnictogen halides

Here’s a tricky (trick?) question from the final exam of MITx course Introduction to Solid State Chemistry:

Which compound has the higher boiling point, phosphorus trifluoride (PF₃) or phosphorus pentafluoride (PF₅)?

Naturally, you are supposed to figure this out from the first principles, or rather, from some principles taught in this course, not from Wikipedia (or “by googling”, as some put it).

(a)	(b)

The problem is, the “right” answer, PF₃, is actually, factually wrong. Even though this question cost only two points (of 150), a rather animated debate followed the exam.

Those who defended the “right” but factually wrong answer (a) were proposing that what the problem was testing our thinking rather than actual knowledge, and our thinking should have been along the lines of VSEPR model. VSEPR rules correctly predict PF₃ to be trigonal pyramidal and PF₅ to be trigonal bipyramidal. The dipole moment of a polar molecule PF₃ should make it less volatile than apolar PF₅. Those who chose the “wrong” but factually correct answer (b) were arguing that polarisability of larger PF₅ is higher than that of PF₃ and therefore the London dispersion forces in PF₅ would beat dipole-dipole interactions in PF₃. The (a) party were saying that making the answer you’d get by applying principles different to the one you’d get by “googling” is a good protection against cheating. The (b) party were retorting that this is a silly way of protection, that the question asked was what has the higher boiling point, not what could be expected to have the higher boiling point, and that expecting students to come up with the factually wrong answer is not exactly pedagogical.

Truth to be told, the methods of estimating boiling or melting points of materials were simply not a part of this course. The only thing one could do was to determine whether the molecule has a non-zero dipole moment. But there is no way to figure out which effect will be stronger, the increase in dispersion forces or dipole-dipole interactions.

One would think that the physical properties of such simple compounds as binary halides of Group 15 elements (pnictogens) are studied well and long ago. Not really. I tried to compile a table of dipole moments and melting/boiling points for pnictogen tri- and pentahalides, MX₃ and MX₅, using various resources [1—5]. As you can see, there are still many gaps.

Trihalide	μ (D)	mp (°C)	bp (°C)	Pentahalide	mp (°C)	bp (°C)
NF3	0.234	–207	–129	—
PF3	1.03	–151.5	–101.8	PF5	–93.7	–84.5
AsF3	2.59	–6.0	62.8	AsF5	–79.8	–52.8
SbF3	?	290	345	SbF5	8.3	141
BiF3	?	649	900	BiF5	154.4	230
NCl3	0.6	–40	71	—
PCl3	0.97	–93.6	76.1	PCl5	167	160s
AsCl3	2.15	–16.0	130.8	AsCl5	–50	?
SbCl3	2.75	73.4	223	SbCl5	4	140
BiCl3	4.6	233.5	441	BiCl5	?	?
NBr3	?	?	?	—
PBr3	?	–41.5	173.2	PBr5	<100d	106d
AsBr3	1.66	31	221	AsBr5	?	?
SbBr3	2.47	96	288	SbBr5	?	?
BiBr3	3.6	219	462	BiBr5	?	?
NI3	?	–20s	?	—
PI3	~0	61.1	227	PI5	41	?
AsI3	?	141	400	AsI5	?	?
SbI3	1.58	170.5	401	SbI5	79	401
BiI3	?	408.6	~542	BiI5	?	?

d, decomposition
s, sublimation

What, if any, trends can we see?

• The dipole moment of MX₃ grows larger down the group of the central atom M, e.g. μ(NF₃) < μ(PF₃) < μ(AsF₃), and grows smaller down the group of ligand atom X, e.g. μ(SbCl₃) > μ(SbBr₃) > μ(SbI₃).
• As the sizes of both central atom and ligands go up, so do the melting and boiling points.
• As dipole moments go up, so do the melting and boiling points.

Something curious happens, though, when one crosses the phosphorus—arsenic borderline. AsF₃ has a dipole moment of 2.59 debye. As expected, both mp and bp of AsF₃ are, respectively, higher than those of AsF₅. PF₃, however, has much lower moment of 1.03 D. Both mp and bp of PF₃ are, respectively, lower than those of PF₅. Similarly, mp of AsCl₃ is higher than mp of AsCl₅, whereas mp of PCl₃ is lower than mp of PCl₅. Similarly... but no, there are too many gaps in the table “down there”.

Which shows, by the way, that “googling” does not help if the data is not available. For the future, the course authors may consider asking a very similar question about a pair of compounds from “down there”. Thus the whole conflict between the (as yet unknown) “truth” and “expected answer” could be easily avoided.

Since the electronegativities decrease down the group for both M and L, the most polar M—L bond must be Bi—F bond and BiF₃ should have the largest dipole moment. Well I couldn’t find its value. But it is known that bismuth trifluoride has ionic structure, and has the highest melting (649 °C) and boiling (900 °C) points of all binary pnictogen halides. On the other side of the spectrum, we have extremely sensitive nitrogen triiodide. A feather tickle, a loud noise and, I suppose, any attempt to measure its dipole moment will set off an explosive decomposition (see the video below):

2 NI₃ → N₂ + 3 I₂

References

1. Earnshaw, A. and Greenwood, N. (1997) Chemistry of the Elements, 2^nd Edition. Butterworth-Heinemann, Oxford.
2. Nelson, R.D., Jr., Lide, D.R., Jr. and Maryott, A.A. (1967) Selected values of electric dipole moments for molecules in the gas phase. National Standard Reference Data Series — National Bureau of Standards 10, Washington, DC.
3. Cotton, S. (2001) Nitrogen triiodide. Molecule of the Month collection, University of Bristol.
4. WebElements
5. atomistry.com

IUPAC periodic table?

The cover of the latest issue of Chemistry International features a fragment of Homenatge als elements (Hommage to the Elements) by the Catalan artist Eugènia Balcells. The display in the atrium of the Physics and Chemistry Library at the University of Barcelona takes the shape of the periodic table where each chemical element is represented by its emission spectrum [1]. According to the artist’s website, it “was born as a counterpoint” to the video installation Freqüències (Frequencies).

The Periodic Table Project at the University of Waterloo, Canada is another work of art,

designed by chemistry students from all Canadian provinces and territories, 20 U.S. states, and 14 countries. It can be viewed online and is available as a printed poster.

Also, as a free app for Apple or Android.

Both the Periodic Table Project and Hommage to the Elements use the medium-long form periodic table. The “IUPAC Periodic Table of the Elements” as published at the back of Chemistry International (in this issue, for the first time it includes flerovium and livermorium) has the same shape. Why the quotes? Because, as a matter of fact, there is no such thing as IUPAC-approved periodic table. Jeffery Leigh wrote three years ago that “there is unlikely to be a definitive IUPAC-recommended form of the periodic table” [2]. In my humble opinion, this is unfortunate that IUPAC refuses to take a position on this matter. Eric Scerri takes a view that “IUPAC should in fact take a stance on the membership of particular groups even if this has not been the practice up to this point” [3]. To illustrate this point, he goes to address the Group 3 question. He argues that the most logical composition of this group is Sc, Y, Lu and Lr (rather than Sc, Y, La and Ac), as shown below.

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

H

He

Li

Be

B

C

N

O

F

Ne

Na

Mg

Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe

Cs

Ba

La

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

Hf

Ta

W

Re

Os

Ir

Pt

Au

Hg

Tl

Pb

Bi

Po

At

Rn

Fr

Ra

Ac

Th

Pa

U

Np

Pu

Am

Cm

Bk

Cf

Es

Fm

Md

No

Lr

Rf

Db

Sg

Bh

Hs

Mt

Ds

Rg

Cn

Nh

Fl

Mc

Lv

Ts

Og

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

In addition to arranging all the elements in a more correct sequence of increasing atomic numbers, the decision to move to a long-form or 32-column table forces the periodic table designer towards just one possible option regarding the question of which elements to place in group 3.

I entirely agree with that. And yet Scerri stops short of proposing that IUPAC should support the 32-column (or “long, long form”, as Leigh put it) periodic table; in fact he explicitly states that he is not suggesting a change of IUPAC policy, viz. that of doing nothing about it. Why? That would be one of the most important and immediately noticeable changes sponsored by IUPAC in decades.

The problem is, sorting out the Group 3 does not resolve the problem how to number the f-block columns. If we stick with 18 groups (blue numbering on the top of the table), that would be really unfair towards the lanthanoids and actinoids. Why don’t we simply number groups from 1 to 32 (red numbers on the bottom of the table)? Sc, Y, Lu and Lr will find themselves in Group 17. So what? It’s not that many people will miss the current Group 17 — nobody really calls these elements anything but “halogens”. And 32 is even more convenient number than 18. I think it’s about time IUPAC took the lead and said how exactly the periodic table should look like.

1. Alvarez, S. (2012) An artist’s hommage to the elements. Chemistry International 34, 5.
2. Leigh, J. (2009) Periodic tables and IUPAC. Chemistry International 31, 4—6.
3. Scerri, E. (2012) Mendeleev’s periodic table is finally completed and what to do about group 3? Chemistry International 34, 28—31.