This reaction emerged a few years ago (thanks Alan!) as a tutorial problem in organic chemistry, in which students had to devise a mechanism for the reaction and use this to predict the stereochemical outcome at the two chiral centres indicated with *. It originates in a brief report from R. B. Woodward’s group in 1973 describing a prostaglandin synthesis,[cite]10.1021/ja00801a066[/cite] the stereochemical outcome being crucial. Here I take a look at this mechanism using computation.
Archive for the ‘Interesting chemistry’ Category
A tutorial problem in stereoelectronic control. The Tiffeneau-Demjanov rearrangement as part of a prostaglandin synthesis.
Monday, November 23rd, 2015Interactions responsible for the lowest energy structure of the trimer of fluoroethanol.
Friday, October 23rd, 2015Steve Bachrach on his own blog has commented on a recent article[cite]10.1002/anie.201505934[/cite] discussing the structure of the trimer of fluoroethanol. Rather than the expected triangular form with three OH—O hydrogen bonds, the lowest energy form only had two such bonds, but it matched the microwave data much better. Here I explore this a bit more.
Impressions of China 2: The colour of porcelain.
Wednesday, October 14th, 2015In Jingdezhen an Imperial Kiln was built in 1369 to produce porcelain that was “white as jade, thin as paper, bright as a mirror and tuneful as a bell”. It’s the colours of the glazes that caught my eye, achieved by a combination of oxidative and reductive firing in the kiln, coupled with exquisite control of the temperature.
Impressions of China. New units of speed and old ways of counting.
Friday, October 9th, 2015This comes to you from China, and the city of Suzhou. To set the scene, cities in China have a lot of motorbikes. Electric ones. With their own speed units, a % of Panda speed. 
Isoelectronic games: the CO analogue of diazirines as an intriguing species?
Thursday, September 24th, 2015How does an anaesthetic work? Surprisingly, it is only recently[cite]10.1038/nchembio.1340[/cite] that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling.[cite]10.1016/j.bmc.2011.06.066[/cite] A propofol analogue was constructed[cite]10.1038/nchembio.1340[/cite] by replacing one of the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen and forms a carbene as a reactive species, which with further chemistry binds covalently[cite]10.1016/j.bmc.2011.06.066[/cite] to adjacent amino acids in the binding pocket.These modified segments could then be analysed by mass spectrometry.[cite]10.1038/nchembio.1340[/cite] An isomer of diazirine is diazomethane, which is some 11 kcal/mol lower in free energy, but fortunately the diazirene is preventing from thermally isomerising to this species by a large kinetic barrier. That was the intro; now for a connection.‡ I recently attended a presentation on another medical topic, the therapeutic uses of carbon monoxide.[cite]10.1038/nrd3228[/cite] In higher concentrations it is notoriously lethal, but with appropriate delivery it can be therapeutic. So, intertwingling, I asked myself what the properties of the carbon monoxide isoelectronic analogue of a diazirine might be (X=C, Y=O below).
Intermolecular atom-atom bonds in crystals? The O…O case.
Saturday, July 25th, 2015I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[cite]10.1107/S2052252515002006[/cite] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[cite]10.1021/ja02261a002[/cite] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack's article: "The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions" I thought I might explore this point a bit further in this post.
Electrides (aka solvated electrons).
Wednesday, July 8th, 2015Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of solvated electrons. An organic chemist knows this species as “e–” and it occurs in ionic compounds known as electrides; chloride = the negative anion of a chlorine atom, hence electride = the negative anion of an electron. It struck me how very odd these molecules are and so I thought I might share here some properties I computed after the lecture for a specific electride known as GAVKIS.[cite]10.1107/S0108270188002847[/cite] If you really want to learn (almost) everything about these strange species, go read the wonderful review by Zurek, Edwards and Hoffmann,[cite]10.1002/anie.200900373[/cite] including a lesson in the history of chemistry stretching back almost 200 years.
R-X≡X-R: G. N. Lewis’ 100 year old idea.
Friday, May 22nd, 2015As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[cite]10.1021/ja02261a002[/cite] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene, R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.
Ionizing yet more ultra-strong acids with water molecules.
Friday, March 20th, 2015This might be seen as cranking a handle by producing yet more examples of acids ionised by a small number of water molecules. I justify it (probably only to myself) as an exercise in how a scientist might approach a problem, and how it linearly develops with time, not necessarily in the directions first envisaged. A conventional scientific narrative published in a conventional journal tells the story often with the benefit of hindsight, but rarely how the project actually unfolded chronologically.‡ So by devoting 7 posts to this, you can judge for yourself how my thoughts might have developed (and I am prepared to acknowledge this may only serve to show my ignorance).