Ribulose-1,5-bisphosphate reacts with carbon dioxide to produce 3-keto-2-carboxyarabinitol 1,5-bisphosphate as the first step in the biochemical process of carbon fixation. It needs an enzyme to do this (Ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCO) and lots of ATP (adenosine triphosphate, produced by photosynthesis). Here I ask what the nature of the uncatalysed transition state is, and hence the task that might be facing the catalyst in reducing the activation barrier to that of a facile thermal reaction. I present my process in the order it was done‡.
Posts Tagged ‘free energy’
Enantioselective epoxidation of alkenes using the Shi Fructose-based catalyst. An undergraduate experiment.Tuesday, April 15th, 2014
The journal of chemical education can be a fertile source of ideas for undergraduate student experiments. Take this procedure for asymmetric epoxidation of an alkene. When I first spotted it, I thought not only would it be interesting to do in the lab, but could be extended by incorporating some modern computational aspects as well.
- A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", J. Chem. Educ., vol. 77, pp. 271, 2000. http://dx.doi.org/10.1021/ed077p271
In the previous post, I showed how modelling of unbranched alkenes depended on dispersion forces. When these are included, a bent (single-hairpin) form of C58H118 becomes lower in free energy than the fully extended linear form. Here I try to optimise these dispersion forces by adding further folds to see what happens.
The diazo-coupling reaction dates back to the 1850s (and a close association with Imperial College via the first professor of chemistry there, August von Hofmann) and its mechanism was much studied in the heyday of physical organic chemistry. Nick Greeves, purveyor of the excellent ChemTube3D site, contacted me about the transition state (I have commented previously on this aspect of aromatic electrophilic substitution). ChemTube3D recruits undergraduates to add new entries; Blue Jenkins is one such adding a section on dyes.
- S.B. Hanna, C. Jermini, H. Loewenschuss, and H. Zollinger, "Indices of transition state symmetry in proton-transfer reactions. Kinetic isotope effects and Bronested's .beta. in base-catalyzed diazo-coupling reactions", J. Am. Chem. Soc., vol. 96, pp. 7222-7228, 1974. http://dx.doi.org/10.1021/ja00830a009
- J.E. Kwon, S. Park, and S.Y. Park, "Realizing Molecular Pixel System for Full-Color Fluorescence Reproduction: RGB-Emitting Molecular Mixture Free from Energy Transfer Crosstalk", J. Am. Chem. Soc., vol. 135, pp. 11239-11246, 2013. http://dx.doi.org/10.1021/ja404256s
A reader asked me about the mechanism of the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the Boekelheide Rearrangement). He wrote ” I don’t understand why the system should prefer to go via fragmentation-recombination (… the evidence being that oxygen labelling shows scrambling) when there is an easy concerted pathway available (… a [3,3]sigmatropic shift). Furthermore, is it possible for two pathways to co-exist?” Here is how computation might enlighten us.
- A. Massaro, A. Mordini, A. Mingardi, J. Klein, and D. Andreotti, "A New Sequential Intramolecular Cyclization Based on the Boekelheide Rearrangement", European Journal of Organic Chemistry, vol. 2011, pp. 271-279, 2010. http://dx.doi.org/10.1002/ejoc.201000936
Sometimes the originators of seminal theories in chemistry write a personal and anecdotal account of their work. Niels Bohr was one such and four decades later Robert Woodward wrote “The conservation of orbital symmetry” (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249; it is not online and so no doi can be given). Much interesting chemistry is described there, but (like Bohr in his article), Woodward lists no citations at the end, merely giving attributions by name. Thus the following chemistry (p 236 of this article) is attributed to a Professor Fonken, and goes as follows (excluding the structure in red):
- N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Z. Physik, vol. 9, pp. 1-67, 1922. http://dx.doi.org/10.1007/BF01326955
In a previous post on the topic, I remarked how the regiospecific ethanolysis of propene epoxide could be quickly and simply rationalised by inspecting the localized NBO orbital calculated for either the neutral or the protonated epoxide. This is an application of Hammond’s postulate[ in extrapolating the properties of a reactant to its reaction transition state. This approach implies that for acid-catalysed hydrolysis, the fully protonated epoxide is a good model for the subsequent transition state. But is this true? Can this postulate be tested? Here goes.
The mechanism of ester hydrolysis is a staple of examination questions in organic chemistry. To get a good grade, one might have to reproduce something like the below. Here, I subject that answer to a reality check.