Ten days ago I asked my readers if two molecules were the same or not. I guessed\nthey were not, when I was asked Are these organic molecules the same?\nThe people who replied to my post were quite convinced they were, and Peter\ngave the context of the pub quiz: assumptions may not be correct.
\n\nIndeed, I assumed there were hydrogens missing (implicit), and that line corners\nindicate places where carbons are. But the key to this problem was that I also\nassumed that the E/Z stereochemistry for the two double bonds were properly\ndefined. Or, more accurately, I assumed that because I was comparing the two\nmolecules, the E/Z stereochemistry for the double bond between the rings was\nidentical in both drawings. We all did.
\n\nUnder that assumption, these two molecules are indeed not the same. However,\nif the E/Z stereochemistry is actually not the same for that double bond, …\nwell, you get the point. Perhaps this was not the best of examples, as it is\nquite conventional to use 2D coordinates to determine E/Z stereochemistry…\nwe even have a special drawing style to indicate the E/Z stereochemistry is unknown.\nThen again, how often does the organic chemist really use that.
\n\nA more convincing example was also drawn in the pub, and I should have given\nthat one. Peter posted those later.\nThese involve a spiro compounds.\nHere too, I assumed that the stereochemistry around the spiro carbon was identical.\nMy bad. There was one person in the pub who spotted the problem: David Jessop.
\n\nUnderlying issue, of course, is those stupid 2D drawings. Jmol has been around\nfor more than 10 years now (and non-free tools too), and we still use 2D drawings…\nwhy, oh why? 3D coordinates and explicit hydrogens, that is what our molecular\ndata should be represented with. Henry does this right, over and over again,\nin his brilliant blog. Well, most of the\ntime anyway. Look for the ‘Click for 3D’ statements behind the figures, and\njust give it a try, e.g. in this post on I(CN)7.
\n\nBTW, a clear example of McPrinciple #2 .
", "summary": "Ten days ago I asked my readers if two molecules were the same or not. I guessed they were not, when I was asked Are these organic molecules the same? The people who replied to my post were quite convinced they were, and Peter gave the context of the pub quiz: assumptions may not be correct.", "date_published": "2010-10-23T00:00:00+00:00", "date_modified": "2026-10-05T00:00:00+00:00", "tags": ["mcprinciples"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }