Archive for the ‘Interesting chemistry’ Category

Quintuple bonds: resurfaced.

Sunday, January 31st, 2016
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Six years ago, I posted on the nature of a then recently reported[1] Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a sub-topic on the nature of the higher order bonding in C2. The comment made a connection between that discussion and the Cr-Cr bond alluded to above. I responded briefly to that comment, but because I want to include 3D rotatable surfaces, I expand the discussion here and not in the comment.

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References

  1. C. Hsu, J.K. Yu, C. Yen, G. Lee, Y. Wang, and Y. Tsai, "Quintuply-Bonded Dichromium(I) Complexes Featuring Metal-Metal Bond Lengths of 1.74 Å", Angewandte Chemie International Edition, vol. 47, pp. 9933-9936, 2008. http://dx.doi.org/10.1002/anie.200803859

I’ve started so I’ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles.

Sunday, January 10th, 2016
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Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came models for both water and the general base catalysed ionization of indolinones. Here I explore general acid catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid, one involving proton transfer (PT) from neutral water in the presence of covalent un-ionized HCl (1) and one with PT from a protonated water resulting from ionised HCl (2).

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I’ve started so I’ll finish. The mechanism of diazo coupling to indoles – forty (three) years on!

Thursday, December 24th, 2015
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The BBC TV quiz series Mastermind was first broadcast in the UK in 1972, the same time I was starting to investigate the mechanism of diazocoupling to substituted indoles as part of my Ph.D. researches. The BBC program became known for the catch phrase I've started so I'll finish; here I will try to follow this precept with the project I started then. Indole diazocoupling In 1972, one measured the rates of chemical reactions to gain insights into the transition state kinetic model. To obtain more data, we used isotopes such as 2H or 3H, together with substituents such as R-t-butyl to modify the potential energy surfaces of the reactions by inducing steric effects.[1],[2] We found that the kinetics for this reaction were actually complex (in part because of pH dependence) involving a Wheland intermediate (the formation of which is shown with red curly arrows above) followed by the collapse of this intermediate to the diazo-coupled product (blue arrows). Coupling to 2-methyl indole (R=X=H, R'=Me), 2-t-butyl indole (R=H, R'=t-butyl) and 4-methyl-2-t-butyl indole (R=Me, R'=t-butyl) revealed that the kinetic isotope effects induced by replacing H by D or T were "not apparent" (i.e. close to 1), the inference being that the rate constant k1 for those systems was slower than k2; the formation of the Wheland intermediate was rate determining (the rds) for the reaction. But with 2-methyl-4,6-di-t-butyl indole (R=t-butyl, R'=Me) this changed and a deuterium isotope effect of ~7 was observed. The rate determining proton removal from the Wheland intermediate k2 was now slower than k1. With 2,4,6-tri-t-butyl indole, we ended by noting that the reaction become almost too slow to observe and furthermore was accompanied by loss of a t-butyl cation as well as a proton. At this point we attempted to infer some transition state models consistent with these observations. Note that we had relatively little data with which to derive our 3D models (one needs to define a geometry using 3N-6 variables, along with its relative energy and force constants). The text and diagram of our attempt is shown below. TS1 The main points of this argument were;

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References

  1. B.C. Challis, and H.S. Rzepa, "The mechanism of diazo-coupling to indoles and the effect of steric hindrance on the rate-limiting step", J. Chem. Soc., Perkin Trans. 2, pp. 1209, 1975. http://dx.doi.org/10.1039/P29750001209
  2. Rzepa, Henry S.., "Hydrogen transfer reactions of Indoles", 1974. http://dx.doi.org/10.5281/zenodo.18777

The atom and the molecule: A one-day symposium on 23 March, 2016 celebrating Gilbert N. Lewis.

Friday, December 11th, 2015
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You might have noticed the occasional reference here to the upcoming centenary of the publication of Gilbert N. Lewis’ famous article entitled “The atom and the molecule“.[1] A symposium exploring his scientific impact and legacy will be held in London on March 23, 2016, exactly 70 years to the day since his death. A list of the speakers and their titles is shown below; there is no attendance fee, but you must register as per the instructions below.

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References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", J. Am. Chem. Soc., vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002

More stereo electronics: the Eschenmoser double fragmentation and guerrilla tutorials.

Thursday, December 10th, 2015
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The layout of floor 2 of the chemistry department here contains a number of small rooms which function as tutorial areas. Each has a (non-interactive) whiteboard used by students and tutors for, inter-aliathought-showering. It was in one such room that I found myself with three colleagues this monday afternoon. We soon all sensed something not quite right about the room; it slowly dawned that the whiteboard was entirely devoid of thoughts (it is normally left adorned with chemical hieroglyphics). Before we departed, one of our number crept up to the board and showered the following (the red bit only followed by a ?; thanks Willie!). The chemistry equivalent you might say of Guerrilla gardening. The product shown in blue below is for your benefit here. It is an example of a double fragmentation reaction; by an odd coincidence following on nicely from the previous post.

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A tutorial problem in stereoelectronic control. A Grob alternative to the Tiffeneau-Demjanov rearrangement?

Saturday, November 28th, 2015
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In answering tutorial problems, students often need skills in deciding how much time to spend on explaining what does not happen, as well as what does. Here I explore alternatives to the mechanism outlined in the previous post to see what computation has to say about what does (or might) not happen.

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A tutorial problem in stereoelectronic control. The Tiffeneau-Demjanov rearrangement as part of a prostaglandin synthesis.

Monday, November 23rd, 2015
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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,[1] the stereochemical outcome being crucial. Here I take a look at this mechanism using computation.

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References

  1. R.B. Woodward, J. Gosteli, I. Ernest, R.J. Friary, G. Nestler, H. Raman, R. Sitrin, C. Suter, and J.K. Whitesell, "Novel synthesis of prostaglandin F2.alpha.", J. Am. Chem. Soc., vol. 95, pp. 6853-6855, 1973. http://dx.doi.org/10.1021/ja00801a066

Interactions responsible for the lowest energy structure of the trimer of fluoroethanol.

Friday, October 23rd, 2015
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Steve Bachrach on his own blog has commented on a recent article[1] 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.

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References

  1. J. Thomas, X. Liu, W. Jäger, and Y. Xu, "Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer", Angewandte Chemie International Edition, vol. 54, pp. 11711-11715, 2015. http://dx.doi.org/10.1002/anie.201505934

Impressions of China 2: The colour of porcelain.

Wednesday, October 14th, 2015
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In 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.

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Impressions of China. New units of speed and old ways of counting.

Friday, October 9th, 2015
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This 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. image

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