As my chemist's eyes flitted across the page, I smiled at some familiar friends on p. 51 - line structures of nucleotide base cytosine. Just
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| Source: Discover 5.2013 |
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See that nitrogen at the bottom? In the language of my sophomore organic professor, it's "very unhappy" that way. Nitrogen usually gets three bonds and a lone pair of electrons; I won't over-critique the missing dots, but there needs to be one of three things on that structure:
1. A generic R-group (meaning a new carbon chain)
2. A proton (indicating the free cytosine base)
3. A "minus" sign (indicating an anion)
Kudos to the graphic artist, though, who actually used standard chemical notation here. Many general science mags would have just used a colored-in hexagon.
*Update, 6/17/13 - As commenters have piled on, we note the empty valences on the two aromatic carbons (carbanions?), as well as questions over whether a methyl group counts as a "compound."
*Update, 6/17/13 - As commenters have piled on, we note the empty valences on the two aromatic carbons (carbanions?), as well as questions over whether a methyl group counts as a "compound."
But you have no qualms with the two carbanions?
ReplyDeleteWell, see, in an aromatic system, I'm OK with implied H's at carbon vertices. That N, though, sticks out to me like a sore appendix.
DeleteGenerally the H/Cless notation doesn't show either C or H explicitly, but abbreviates C with a junction of lines, and assumes the Hs. If you're going to make the Cs explicit, then it's not reasonable to assume implicit Hs.
DeleteSince the drawing isn't for chemists, having everything explicit makes lots of sense, but then, everything (including the Hs) should be explicit.
The figure also stated that "methyl group is an organic compound". Really?
ReplyDeleteGood catch!
DeleteDepends on how you define 'compound'. I'd refer to it as a moiety or radical, personally. But I don't think it's necessarily silly to refer to it as a compound as the distinctions between these things aren't necessarily that clear-cut.
DeleteI can't find a definition of 'compound' on the IUPAC Gold Book (http://goldbook.iupac.org/C.html). If I had to define it, I would define it (roughly) as an isolable substance (as opposed to a molecule) composed of multiple elements that cannot be separated through physical means. This allows contrast with atoms, elements, molecules, and mixtures. By this definition, the methyl group is a (not particularly stable) molecule rather than a compound, as it is not really isolable. Feel free to criticise this definition.
That N is attached to a ribose molecule: http://schools-wikipedia.org/wp/d/DNA.htm
ReplyDeleteOh, certainly in cytiDINE, it is. In cytOSINE, it just needs a proton. Either way, it's certainly not OK as-is!
DeleteA compound is a molecule made up of more than one element. It HAS to be a compound whether it (or any of its vagaries) are isolable here on earth or not. But the term compound is not the correct jargon-y descriptor in this case. Same as with no H's on the N. It's easily confusing to chemists (but perfectly logical to chemists) why we need to write H's on N, O, et al and NOT C. Its an easy mistake to make.
ReplyDeleteFair comment. I'm actually inclined to agree, I was probably too hasty earlier and would agree that CH3 is a compound (otherwise it's what - an element or a mixture. Not sure what else there is.) But to distract you from my retraction I'm going to muddy the waters a bit. :D
DeleteThis is part of a broader problem we have of actually being a bit wooly with our terms. For example: define "element". I'd say something like: an element is the set of all atoms having the same number of protons. But it also refers to molecules composed of that element: both H and H2 fall into this definition. That's not a problem, but it is a little vague, as H (the ideal, isolated, individual atom) and H the substance are different, but both elemental, but... it's a bit wooly what I'm referring to when I say "an element". And what about H-D? Is that still an element? Or is it a compound?
It gets worse. What's H2O? Is it the liquid, or is it the molecule? After all: even ultra-pure water contains molecular species that are not strictly H-O-H. Or is that behaviour implicit in the definition?
I don't think any of these problems are actually that important or difficult to resolve - they simply provide work for philosophers and pedants - but they point to a degree of ambiguity in our language, and a healthy practicality in our approach to our science. This, in turn, tells me that we probably ought not to worry too much about whether CH3 is a compound or not; a little vagueness around the edges of our definitions isn't going to adversely affect science.
(unless you count funding lost due to Twitter debates... :D )