The Game is Afoot

November 9, 2006

I’m whiling away a few minutes trying to work out Peter’s mystery molecule. IANAChemist, and although I’ve been working with them for 10 months now, I fear that very little has rubbed off. However, Peter reckons that you can’t work it out chemically, so I figure that not being a chemist shouldn’t be too much of a handicap. Like betting on the novices at Newmarket.

I leapt off to Pubchem, and used the molecular weight limits. Restricted to 240-260 (the syntax is 240:260[mw]). Nearly 14,000 compounds. Hmmm. Narrowing it down, 245-255 gives under 7000. Still needle in a haystack.

Need to assess what we know, and make some inferences. Hopefully the lazy web will mean some kindly chemist can fix my broken logic.

OK, so what do we know? It seems to be fairly commonly observed, so I’m guessing its structure was discovered a while ago. Well, you can’t limit in PubChem on a range of CIDs, but you can limit to NCI as the source of the data. This didn’t reduce the hit count.

We also know that Peter was trying to do co-ordination chemistry at the time. I didn’t know what that co-ordination chemistry is (I told you, I’m really not a chemist), but wikipedia soon sorted me out. So there are probably either metal ions or organic ligands. My A level chemistry and the variety of colours of the crystals suggest that the metal ions are in the molecule. So I added a limit requiring a heavy atom into pubchem (I know this doesn’t necessarily mean metal ions). Only 14 Hits, whoppee! Probably the wrong 14, but hey.

So my best guess is molecular iodine, which Peter assures me is wrong.

Where is my logic broken? Is it possible to find this molecule by search?

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2 Responses to “The Game is Afoot”


  1. […] Jim Downing is stuck on a mystery molecule, and wonders whether the answer can be found via search. Well, I doubt that conventional chemical informatics search will do him. Google Suggest, on the other hand, may be his friend. It seems that Peter Murray-Rust is being coy about a certain critical piece of information, something that’s normally unimportant that may be considered to be a dead giveaway. Well, it’s a giveaway because of linguistics. You see, there’s a couple of collocations that describe the molecule in question, and if you can guess one half of the collocation – or systematically search through the available values (there’s a finite set, and not too large) using publicly available tools trained on the entire web as a corpus – then the other half will leap right out at you. […]


  2. […]  Jim Downing blogs: I’m whiling away a few minutes trying to work out Peter’s mystery molecule. IANAChemist, and although I’ve been working with them for 10 months now, I fear that very little has rubbed off. However, Peter reckons that you can’t work it out chemically, so I figure that not being a chemist shouldn’t be too much of a handicap. Like betting on the novices at Newmarket. […]


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