B.R.S.M. Help! I'm trapped in a molecule factory!

16Oct/1110

Black dot… I mean Linstead notation.

Anyone who's read some of the older chemical literature (or even recent papers by old school chemists) has probably noticed the 'black dot' notation used to depict stereochemistry at ring junctions, particularly by chemists in the US and Canada. Here's a recent example, so you'll know what I'm on about if you don't already.

thud1

From Angew. Chem. Int. Ed., 2010, 49, 4864 – 487.[1]

I don't know how things are in the US, but at no point during my chemical education do I ever remember having this notation explained to me. I recall encountering it for the first time at the start of my PhD, asking around a bit, and then just working it out for myself. Turns out it's actually really simple - a black dot at a ring junction just means that the hydrogen there is on the β-face, i.e. above the plane of the paper. To this day I've never seen this explained in a textbook, and have wondered from time to time where the heck it came from. As named reactions become canonised, the references the seminal papers slowly disappear, and clearly the same thing has happened here, as with many other conventions and nomenclatures. However, not having a name for this notation I'd never been able to trace where it started. Until now.

I recently saw that R. B. Woodward, in his full paper on the synthesis of quinine, gave Harvard colleague R. P. Linstead credit as the creator of this convention, but as our library didn't have the 1937 Chemistry and Industry paper referenced I gave up.[2] However, I saw today another Linstead paper published two years later on the stereochemistry of the hydrogenation of phenanthrene which explains all:

linstead 1

From J. Chem. Soc., 1939, 842.

Strangely, googling 'Linstead notation' and variants thereof doesn't seem to turn up many chemical hits - unfortunately it seems that Linstead didn't get the recognition he deserved. Is anyone aware of this being taught to undergrads or postgrads, or is it something we just have to work out?

Etc

1. This essay on the vinylcyclopropane - cyclopentene rearrangement by Tomas Hudlicky is actually quite interesting. You can read it for free here (kindly hosted on the group website).

2. Sir Reginald Patrick Linstead CBE, DSc, HonDSc, DIC, HonFCGI, HonMIMM, FRS (!), was a British chemist and a professor at Harvard with Woodward from 1939.

Comments (10) Trackbacks (0)
  1. I was never taught of this notation. Fascinating post, good to learn something new from you again!

  2. Thanks for sorting this out. I had no idea that the dots implied stereochemisty even. The only stereochemical oddity I remember being taught is that the dashed “into the paper” bond has its thick end attached to stereogenic atom in Europe, while Americans draw it the other way around. When naming complex structures using common software, one must use the American style, or names might come out wrong; something I have learned the hard way. I wonder if ACD Name or ChemDraw’s “structure to name” understand dots!

  3. I had never been taught this in undergrad and in fact the first time I saw it was about a month ago (I am in my first semester of my PhD so similar situation to when you first saw it). I saw it being used by a fellow first year so apparently this is being taught at her undergrad- Trinity University in San Antonio.

  4. At the risk of revealing my age I was disappointed that the reference to Linstead omitted to mention his most visible discovery, phthalocyanine pigments. Until that time the manufacture of blue inks and coatings was a route to disappointment. Nowadays anything pigmented blue is likely to be an acknowledgement of his greatness in this area.

  5. This notation is actually used a lot in physics for vectors in R^3 (the space). If one imagines the vector as an arrow, which is perpendicular to the plane of the screen, it can have to directions: pointing into the screen or outside the screen.

    If one further imagines the arrow as a real one, having a round tip and a tail with 4 little wings to stabilize it, you will either see a dot or a cross, depending if it’s pointing outside the screen or into, respectively.

    This smells a lot like that.

  6. I too never encountered this during my undergrad and it wasn’t until my first semester of my PhD that I encountered it and was taught what it meant.

  7. I actually was taught this nomenclature, in a 4th year undergrad class. No explanation was given as to the origin, we were simply told that the dot represented the hydrogen atom above the plane of the molecule, and that was the end of it. I am from a Canadian university, however, so perhaps you may be on to something in claiming it to be more of a North American convention.

  8. Also, if I’m not mistaken, white circles simetimes mean “hydrogen down”.

    • I’ve only seen that once or twice – wasn’t really sure what it meant. It certainly seems to be much rarer. I think there’s some kind of radical notation that also involves hollow circles, but I can’t think where I saw it.

  9. It was exhaustively used in steroid chemistry where it indicated ring junction.


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