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?

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.

Visualising hexabenzocoronene

A few years ago, I wrote that we do not know how to draw ferrocene or a nitro group. (Still true.) Is the situation with polycyclic aromatic hydrocarbons any better?

Take hexabenzo[bc,ef,hi,kl,no,qr]coronene, one of the subjects of the single-molecule visualisation study published last week in Science [1]. One way to draw it shown in diagram (a):

(a)

I chose this one (out of many other possible Kekulé representations) because I can reproduce it on a paper napkin (beermat, Post-it note, you name it). If you look carefully, you will notice that the central ring and the six outermost rings are connected with single bonds.

(b)

Continuing the paper-napkin-doodle argument, it is even easier to draw a circle inside of each ring as in all-delocalised representation (b). However, that would not be a preferred diagram from IUPAC point of view [2, GR-6.5]: for example, benzene ⏣ is acceptable but ⌬ is preferred. Moreover, “it is generally not acceptable to use curves in two adjacent fused rings”. Still, I’d stick with circles.

The question is, do I have to draw a circle within each ring? Of course not. If I draw seven aromatic rings and connect the with single bonds as shown in (c), the resulting structure will be the same. In this way, I can even save some ink (graphite, chalk, etc.)

(c)

Without the circles, the six rings that surround the central ring in (c) start to look, well, more empty. Using the noncontact atomic force microscopy (NC-AFM), the team behind the study [1] were able to show (and in this case “to show” really means “to show”), that those rings are indeed slightly larger. The C—C bonds in the central ring (i-bonds, 1.417 Å) are 0.03 Å shorter than the bonds connecting that ring with the six outermost rings (j-bonds, 1.447 Å).

1. Gross, L., Mohn, F., Moll, N., Schuler, B., Criado, A., Guitián, E., Peña, D., Gourdon, A. and Meyer, G. (2012) Bond-order discrimination by atomic force microscopy. Science 337, 1326—1329.
2. Brecher, J. (2008) Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008). Pure Appl. Chem. 80, 277—410.

What is a correct InChI for chromate?

During the IUPAC International Chemical Identifier (InChI) Subcommittee meeting in Glasgow last month, we touched upon the issue of normalisation of metal complexes. I did not realise before that even simple entity such as chromate(2−), drawn in different ways (a)—(c), will give different InChIs. (And different standard InChIs as well; and InChIKeys too.) This is, I am told, because the current InChI algorithm involves “disconnection” of metals before “normalisation”, while it really should do normalisation first. Bother.

InChI=1/Cr.4O/q;;;2*-1	InChI=1/Cr.4O/q-2;;;;	InChI=1/Cr.4O/q+2;4*-1
(a)	(b)	(c)

Metal carbonyls

Remember the nitro group? Let us consider even ‘simpler’ case of carbon monoxide. Almost invariably, the chemical databases represent CO as a charge-separated molecule (a) even though it would be as correct to draw it with triple bond and two lone pairs (b). I guess the reason to chose the representation (a) is that the software used for drawing/validating concerns itself with electron accountancy of separate atoms rather than whole molecule.

(a)	(b)

What about metal carbonyls? For instance, hexacarbonylvanadium, drawn with charge separation (c), looks really ugly. On the other hand, the software (e.g. ChemSketch) objects to the representation (d) (which, apparently, is preferred; cf. tetracarbonylnickel on p. 408 of IUPAC Recommendations) because it ‘wants’ the positive charge on triple-bonded oxygen.

(c)	(d)

How to draw a nitro group

In our IUPAC Recommendations, section GR-8, “the nitro problem” is discussed in detail. To quote:

“The nitro problem” is one of the most familiar issues in chemical informatics: How should a nitro group be best represented? Experimentally, the two oxygen atoms are equivalent, so it would make sense to depict them symmetrically. However, any way to depict them symmetrically will either violate the popular “octet rule” or force a double positive charge on the nitrogen atom. Conversely, any attempt to honor the octet rule results in oxygen atoms that appear to be non-equivalent. Similar problems arise for molecules based on sulfur, phosphorus, and related elements. Furthermore, all of these are fairly common functional groups, and cannot readily be pushed aside as “unusual” cases.

The recommended representation of nitrobenzene is either (a) or (c) while (b) is not acceptable. Needless to say, (b) is exactly the way this compound is drawn in Beilstein database, while the search with charge-separated nitro query will not work.

(a)	(b)	(c)

But what is wrong with representation using “pentavalent” nitrogen? In my view, nothing. How else one should draw nitrogen dioxide (d)? One can think of nitro group as of nitrogen dioxide with a single bond instead of the unpaired electron.

(d)

For purely aesthetic reasons, the multiple charge-separated nitro groups are not good: too many charges without good reason. For example, hexanitroplatinate(2–) looks much nicer when the sketch shows only one charge, 2– (e), rather than 13 assorted charges as in (f).

(e)	(f)

Drawing ferrocene

Ferrocene was discovered in 1951 and we still do not know the proper way to draw it. CrossFire example recommends to connect every carbon atom of the ring to the central metal atom. Which is fair enough and will be a valid query for CrossFire Gmelin database. Similarly, both ChEBI and NIST Webbook use decacoordinate iron in ferrocene structure (a). In this representation, all carbon—carbon bonds are single. But, according to IUPAC Recommendations, section GR-1.7.2,

coordination bonds to contiguous atoms (most commonly representing a form of π-bonding) should be drawn to indicate most clearly that special bonding pattern. Depictions that imply a regular covalent bond — and especially, depictions that show a regular covalent bond to each member of a delocalized system — are not acceptable.

In other words, the preferred representation is the one with bicoordinate iron and delocalised bond system (b). The problem with that is there is no agreed (as far as chemoinformaticans are concerned) way to do that, even though solutions for different applications (e.g. for Marvin Sketch) do exist. In MolBase, the coordination number of iron in ferrocene is 6 (and I do remember Mark Winter confirming that this is true). On yet another hand, Beilstein and ChemIDplus databases represent ferrocene as a standalone Fe²⁺ and two standalone cyclopenta-2,4-dienide anions (c), thus avoiding the question of coordination number altogether. Naturally, the decacoordinate-iron query will not work in Beilstein. (For InChI implications, see this discussion.)

(a)	(b)	(c)

PubChem takes liberties with hydrogens

The submitted structure (a) is C₃H₅O₅P, the PubChem shows C₃H₄O₅P⁺ (b). How did that happen? Why the deposited molecule lost hydride (H^–)?

(a)	(b)

In the case of structure C₁₆H₃₆MoN₆O₄P₂ (c), presumably submitted by NIST, it has acquired two hydrons in PubChem to become [C₁₆H₃₈MoN₆O₄P₂]²⁺ (d).

(c)	(d)

Impossible figures

I am sure everybody can see that the drawing (a) is an impossible figure. So I expect nobody will draw cubane like this; the correct drawing is (b).

(a)

(b)

In fact, if you pay attention, you will notice that the chemical databases are full of impossible figures. I just have corrected the drawing in ChEBI entry for codeinone (c). Next release, it will look like (d).

(c)

(d)