January 11th, 2013
Kinetic isotope effects have become something of a lost art when it comes to exploring reaction mechanisms. But in their heyday they were absolutely critical for establishing the mechanism of the benzidine rearrangement[1]. This classic mechanism proceeds via bisprotonation of diphenyl hydrazine, but what happens next was the crux. Does this species rearrange directly to the C-C coupled intermediate (a concerted [5,5] sigmatropic reaction) or does it instead form a π-complex, as famously first suggested by Michael Dewar[2] [via TS(NN] and only then in a second step [via TS(CC)] form the C-C bond? Here I explore the isotope effects measured and calculated for this exact system.
Read the rest of this entry »
References
- H.J. Shine, H. Zmuda, K.H. Park, H. Kwart, A.G. Horgan, and M. Brechbiel, "Benzidine rearrangements. 16. The use of heavy-atom kinetic isotope effects in solving the mechanism of the acid-catalyzed rearrangement of hydrazobenzene. The concerted pathway to benzidine and the nonconcerted pathway to diphenyline", Journal of the American Chemical Society, vol. 104, pp. 2501-2509, 1982. https://doi.org/10.1021/ja00373a028
- M. Dewar, and H. McNicoll, "Mechanism of the benzidine rearrangement", Tetrahedron Letters, vol. 1, pp. 22-23, 1959. https://doi.org/10.1016/s0040-4039(01)82765-9
Tags: Henry Shine, Michael Dewar, Reaction Mechanism, TS(CC), Yamabe and co
Posted in Interesting chemistry | 1 Comment »
January 10th, 2013
This is an interesting result I got when studying the [1,4] sigmatropic rearrangement of heptamethylbicyclo-[3.1.0]hexenyl cations. It fits into the last lecture of a series on pericyclic mechanisms, and just before the first lecture on conformational analysis. This is how they join.
Read the rest of this entry »
Tags: conformational analysis, energy profile, pericyclic, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 2 Comments »
January 8th, 2013
In this post, I looked at some hydrogen bonds formed by interaction of a π-system with an acidic hydrogen. Unlike normal lone pair donors, π-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors.
Read the rest of this entry »
Tags: π-hydrogen bonded systems, π-systems
Posted in Interesting chemistry | No Comments »
January 8th, 2013
Eagle-eyed footnote readers might have spotted one at the bottom of the post on the benzidine rearrangement. I was comparing the N-N bond lengths in crystal structures of known diprotonated hydrazines (~1.45Å) with the computed N-N bond length at the start point of the intrinsic reaction coordinate for the [5,5] sigmatropic rearrangement of di-N-protonated diphenylhydrazine (the active species in the benzidine rearrangement itself), which was some 1Å longer. This post explores the implications of this oddity.
Read the rest of this entry »
Tags: free energy barrier, Reaction Mechanism
Posted in Uncategorised | 3 Comments »
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].
Read the rest of this entry »
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
Posted in Interesting chemistry | 4 Comments »
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.
Read the rest of this entry »
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).
Read the rest of this entry »
Tags: Cambridge, energy, energy gap, interaction energy, Tutorial material
Posted in Interesting chemistry | 2 Comments »
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.
Read the rest of this entry »
Tags: catalysis, conformational analysis, energy, epoxide product, free energy, Reaction Mechanism, similar systems, Tutorial material
Posted in Interesting chemistry | No Comments »
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).
Read the rest of this entry »
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
Posted in Interesting chemistry | 2 Comments »
