We are approaching 1 million recorded crystal structures (actually, around 716,000 in the CCDC and just over 300,00 in COD). One delight with having this wealth of information is the simple little explorations that can take just a minute or so to do. This one was sparked by my helping a colleague update a set of interactive lecture demos dealing with stereochemistry. Three of the examples included molecules where chirality originates in stereogenic centres with just three attached groups. An example might be a sulfoxide, for which the priority rule is to assign the lone pair present with atomic number zero. The issue then arises as to whether this centre is configurationally stable, i.e. does it invert in an umbrella motion slowly or quickly. My initial intention was to see if crystal structures could cast any light at all on this aspect.
Posts Tagged ‘energy’
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‡.
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.
By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations.  Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends.. Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58 appears to be fully extended, (an early report of a low quality structure for C36H74 also appears to show it as linear).‡ Here I explore how standard DFT theories cope with these structures.
- N.O.B. Lüttschwager, T.N. Wassermann, R.A. Mata, and M.A. Suhm, "The Last Globally Stable Extended Alkane", Angew. Chem. Int. Ed., vol. 52, pp. 463-466, 2012. http://dx.doi.org/10.1002/anie.201202894
- N. Cocherel, C. Poriel, J. Rault-Berthelot, F. Barrière, N. Audebrand, A.M.Z. Slawin, and L. Vignau, "New 3π-2Spiro Ladder-Type Phenylene Materials: Synthesis, Physicochemical Properties and Applications in OLEDs", Chemistry - A European Journal, vol. 14, pp. 11328-11342, 2008. http://dx.doi.org/10.1002/chem.200801428
- S.C. Nyburg, and A.R. Gerson, "Crystallography of the even n-alkanes: structure of C20H42", Acta Cryst Sect B, vol. 48, pp. 103-106, 1992. http://dx.doi.org/10.1107/S0108768191011059
- R. Boistelle, B. Simon, and G. Pèpe, "Polytypic structures of n-C28H58 (octacosane) and n-C36H74 (hexatriacontane)", Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, vol. 32, pp. 1240-1243, 1976. http://dx.doi.org/10.1107/S0567740876005025
- H.M.M. Shearer, and V. Vand, "The crystal structure of the monoclinic form of n-hexatriacontant", Acta Crystallographica, vol. 9, pp. 379-384, 1956. http://dx.doi.org/10.1107/S0365110X5600111X
Paul Schleyer sent me an email about a pattern he had spotted, between my post on F3SSF and some work he and Michael Mauksch had done 13 years ago with the intriguing title “Demonstration of Chiral Enantiomerization in a Four-Atom Molecule“. Let me explain the connection, but also to follow-up further on what I discovered in that post and how a new connection evolved.
- P.V.R. Schleyer, and M. Mauksch, "Demonstration of Chiral Enantiomerization in a Four‐Atom Molecule ", Angewandte Chemie International Edition, 2000. http://doi.org/d8g2nw
- 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