January 6th, 2013
The benzidine rearrangement is claimed to be an example of the quite rare [5,5] sigmatropic migration[1], which is a ten-electron homologation of the very common [3,3] sigmatropic reaction (e.g. the Cope or Claisen). Some benzidine rearrangements are indeed thought to go through the [3,3] route[2]. The topic has been reviewed here[3].
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References
- H.J. Shine, K.H. Park, M.L. Brownawell, and J. San Filippo, "Benzidine rearrangements. 19. The concerted nature of the one-proton rearrangement of 2,2'-dimethoxyhydrazobenzene", Journal of the American Chemical Society, vol. 106, pp. 7077-7082, 1984. https://doi.org/10.1021/ja00335a035
- H.J. Shine, L. Kupczyk-Subotkowska, and W. Subotkowski, "Heavy-atom kinetic isotope effects in the acid-catalyzed rearrangement of N-2-naphthyl-N'-phenylhydrazine. Rearrangement is shown to be a concerted process", Journal of the American Chemical Society, vol. 107, pp. 6674-6678, 1985. https://doi.org/10.1021/ja00309a041
- H.J. Shine, "Reflections on the π‐complex theory of benzidine rearrangements", Journal of Physical Organic Chemistry, vol. 2, pp. 491-506, 1989. https://doi.org/10.1002/poc.610020702
Tags: higher energy, Historical, π-complex, pericyclic, Reaction Mechanism
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January 5th, 2013
A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)/H-O σ* NBO interaction in that ring, indicated a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the π-electrons of an alkene as the electron donor.
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Tags: energy gap
Posted in Interesting chemistry | 4 Comments »
January 4th, 2013
Tags: basic search, Cambridge, CF 3, conformational analysis, gauche, metal, search takes, similar, Tutorial material
Posted in crystal_structure_mining, Interesting chemistry | 8 Comments »
January 3rd, 2013
One frequently has to confront the question: will a hydrogen bond form between a suitable donor (lone pair or π) and an acceptor? One of the factors to be taken into consideration for hydrogen bonds which are part of a cycle is the ring size. Here I explore one way of quantifying the effect for the series below, n=1-5 (4-8 membered rings).
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Tags: Cambridge, energy, energy gap, interaction energy, Tutorial material
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January 3rd, 2013
I return to this reaction one more time. Trying to explain why it is enantioselective for the epoxide product poses peculiar difficulties. Most of the substituents can adopt one of several conformations, and some exploration of this conformational space is needed.
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Tags: catalysis, conformational analysis, energy, epoxide product, free energy, Reaction Mechanism, similar systems, Tutorial material
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December 24th, 2012
tpap[1], as it is affectionately known, is a ruthenium-based oxidant of primary alcohols to aldehydes discovered by Griffith and Ley. Whereas ruthenium tetroxide (RuO4) is a voracious oxidant[2], its radical anion countered by a tetra-propylammonium cation is considered a more moderate animal[3]. In this post, I want to try to use quantum mechanically derived energies as a pathfinder for exploring what might be going on (or a reality-check if you like).
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References
- S.V. Ley, J. Norman, W.P. Griffith, and S.P. Marsden, "Tetrapropylammonium Perruthenate, Pr<sub>4</sub>N<sup>+</sup>RuO<sub>4</sub>
<sup>-</sup>, TPAP: A Catalytic Oxidant for Organic Synthesis", Synthesis, vol. 1994, pp. 639-666, 1994. https://doi.org/10.1055/s-1994-25538
- D.G. Lee, U.A. Spitzer, J. Cleland, and M.E. Olson, "The oxidation of cyclobutanol by ruthenium tetroxide and sodium ruthenate", Canadian Journal of Chemistry, vol. 54, pp. 2124-2126, 1976. https://doi.org/10.1139/v76-304
- D.G. Lee, Z. Wang, and W.D. Chandler, "Autocatalysis during the reduction of tetra-n-propylammonium perruthenate by 2-propanol", The Journal of Organic Chemistry, vol. 57, pp. 3276-3277, 1992. https://doi.org/10.1021/jo00038a009
Tags: catalysis, energy, free energy, low energy elimination, metal, react freq, Reaction Mechanism, RuO4+ ethanol, triplet state energy, Tutorial material
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December 20th, 2012
I have written earlier about dihydrocostunolide, and how in 1963 Corey missed spotting the electronic origins of a key step in its synthesis.[1]. A nice juxtaposition to this failed opportunity relates to Woodward’s project at around the same time to synthesize vitamin B12. The step in the synthesis that caused him to ponder is shown below.
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References
- E.J. Corey, and A.G. Hortmann, "The Total Synthesis of Dihydrocostunolide", Journal of the American Chemical Society, vol. 87, pp. 5736-5742, 1965. https://doi.org/10.1021/ja00952a037
Tags: dispersion energy, free energy, Historical, pericyclic
Posted in Interesting chemistry, pericyclic, reaction mechanism | No Comments »
December 19th, 2012
The Sharpless epoxidation of an allylic alcohol had a big impact on synthetic chemistry when it was introduced in the 1980s, and led the way for the discovery (design?) of many new asymmetric catalytic systems. Each achieves its chiral magic by control of the geometry at the transition state for the reaction, and the stabilizations (or destabilizations) that occur at that geometry. These in turn can originate from factors such as stereoelectronic control or simply by the overall sum of many small attractions and repulsions we call dispersion interactions. Here I take an initial look at these for the binuclear transition state shown schematically below.
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Tags: asymmetric catalytic systems, Bob Hanson, catalysis, Julia Contreras-Garcia, little web site, NCI, non-covalent-analysis, Reaction Mechanism, terminal =CH
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December 17th, 2012
Part one on this topic showed how a quantum mechanical model employing just one titanium centre was not successful in predicting the stereochemical outcome of the Sharpless asymmetric epoxidation. Here in part 2, I investigate whether a binuclear model might have more success. The new model is constructed using two units of Ti(OiPr)4, which are likely to assemble into a dimer such as that shown below (in this crystal structure, some of the iPr groups are perfluorinated).
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Tags: catalysis, catalytic metal centre, Enantioselective, free energy difference, Reaction Mechanism, Sharpless epoxidation, t-butyl, This free energy difference, Tutorial material
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December 9th, 2012
Sharpless epoxidation converts a prochiral allylic alcohol into the corresponding chiral epoxide with > 90% enantiomeric excess[1],[2]. Here is the first step in trying to explain how this magic is achieved.
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References
- J.M. Klunder, S.Y. Ko, and K.B. Sharpless, "Asymmetric epoxidation of allyl alcohol: efficient routes to homochiral .beta.-adrenergic blocking agents", The Journal of Organic Chemistry, vol. 51, pp. 3710-3712, 1986. https://doi.org/10.1021/jo00369a032
- R.M. Hanson, and K.B. Sharpless, "Procedure for the catalytic asymmetric epoxidation of allylic alcohols in the presence of molecular sieves", The Journal of Organic Chemistry, vol. 51, pp. 1922-1925, 1986. https://doi.org/10.1021/jo00360a058
Tags: animation, asymmetric epoxidation, catalysis, Enantioselective, free energy, lower energy conformations, Reaction Mechanism, Tutorial material
Posted in Interesting chemistry | 1 Comment »
