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.
Archive for March, 2013
A sideways look at the mechanism of ester hydrolysis.
Friday, March 29th, 2013A (very) short history of shared-electron bonds.
Tuesday, March 26th, 2013The concept of a shared electron bond and its property of an order is almost 100 years old in modern form, when G. N. Lewis suggested a model for single and double bonds that involved sharing either 2 or 4 electrons between a pair of atoms[1]. We tend to think of such (even electron) bonds in terms of their formal bond order (an integer), recognising that the actual bond order (however defined) may not fulfil this value. I thought I would very (very) briefly review the history of such bonds.
References
- G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
Concerted vs stepwise (Meisenheimer) mechanisms for aromatic nucleophilic substitution.
Monday, March 25th, 2013My two previous explorations of aromatic substitutions have involved an electrophile (NO+ or Li+). Time now to look at a nucleophile, representing nucleophilic aromatic substitution. The mechanism of this is thought to pass through an intermediate analogous to the Wheland for an electrophile, this time known as the Meisenheimer complex[1]. I ask the same question as before; are there any circumstances under which the mechanism could instead be concerted, by-passing this intermediate?
References
- J. Meisenheimer, "Ueber Reactionen aromatischer Nitrokörper", Justus Liebigs Annalen der Chemie, vol. 323, pp. 205-246, 1902. https://doi.org/10.1002/jlac.19023230205
To be cyclobutadiene, or not to be, that is the question? You decide.
Thursday, March 21st, 2013A quartet of articles has recently appeared on the topic of cyclobutadiene.[1],[2],[3],[4]. You will find a great deal discussed there, but I can boil it down to this essence. Do the following coordinates (obtained from a (disordered) previously published[5] x-ray refinement) correspond to a van der Waals complex of 1,3-dimethyl cyclobutadiene and carbon dioxide, or do they instead represent a covalent interaction between these two components resulting in a compound with the chemical name 2-oxabicyclo[2.2.0]hex-5-en-3-one (i.e. not a cyclobutadiene)?
References
- H.S. Rzepa, "A Computational Evaluation of the Evidence for the Synthesis of 1,3‐Dimethylcyclobutadiene in the Solid State and Aqueous Solution", Chemistry – A European Journal, vol. 19, pp. 4932-4937, 2013. https://doi.org/10.1002/chem.201102942
- M. Shatruk, and I.V. Alabugin, "Reinvestigation of “Single‐Crystal X‐ray Structure of 1,3‐dimethylcyclobutadiene”", Chemistry – A European Journal, vol. 19, pp. 4942-4945, 2013. https://doi.org/10.1002/chem.201103017
- Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van der Lee, and M. Barboiu, "A Constrained Disorder Refinement: “Reinvestigation of “Single‐Crystal X‐ray Structure of 1,3‐Dimethylcyclobutadiene” by M. Shatruk and I. V. Alabugin”", Chemistry – A European Journal, vol. 19, pp. 4946-4950, 2013. https://doi.org/10.1002/chem.201203234
- Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van der Lee, and M. Barboiu, "Reply to A Computational Evaluation of the Evidence for the Synthesis of 1,3‐Dimethylcyclobutadiene in Solid State and Aqueous Solution—Beyond the Experimental Reality", Chemistry – A European Journal, vol. 19, pp. 4938-4941, 2013. https://doi.org/10.1002/chem.201203235
- Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010. https://doi.org/10.1126/science.1188002
The mysterious (aromatic) structure of n-Butyl lithium.
Sunday, March 17th, 2013n-Butyl lithium is hexameric in the solid state[1] and in cyclohexane solutions. Why? Here I try to find out some of its secrets.
References
- T. Kottke, and D. Stalke, "Structures of Classical Reagents in Chemical Synthesis: (<i>n</i>BuLi)<sub>6</sub>, (<i>t</i>BuLi)<sub>4</sub>, and the Metastable (<i>t</i>BuLi · Et<sub>2</sub>O)<sub>2</sub>", Angewandte Chemie International Edition in English, vol. 32, pp. 580-582, 1993. https://doi.org/10.1002/anie.199305801
William Henry Perkin: The site of the factory and the grave.
Monday, March 11th, 2013William Henry Perkin is a local chemical hero of mine. The factory where he founded the British (nay, the World) fine organic chemicals industry is in Greenford, just up the road from where we live. The factory used to be close to the Black Horse pub (see below) on the banks of the grand union canal. It is now commemorated merely by a blue plaque placed on the wall of the modern joinery building occupying the location (circled in red on the photo).
Kinetic vs Thermodynamic control. Subversive thoughts for electrophilic substitution of Indole.
Sunday, March 10th, 2013I mentioned in the last post that one can try to predict the outcome of electrophilic aromatic substitution by approximating the properties of the transition state from those of either the reactant or the (presumed Wheland) intermediate by invoking Hammond’s postulate[1]. A third option is readily available nowadays; calculate the transition state directly. Here are the results of exploring this third variation.
References
- G.S. Hammond, "A Correlation of Reaction Rates", Journal of the American Chemical Society, vol. 77, pp. 334-338, 1955. https://doi.org/10.1021/ja01607a027
Understanding the electrophilic aromatic substitution of indole.
Sunday, March 3rd, 2013The electrophilic substitution of indoles is a staple of any course on organic chemistry. Indoles also hold a soft-spot for me, since I synthesized not a few as part of my Ph.D. studies.[1],[2] The preference for substitution in the 3-position is normally explained using the arrows shown below (position 3=green,2=blue,1=red). Here I explore how these arrows might be interpreted in terms of various quantum mechanical properties.
References
- 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", Journal of the Chemical Society, Perkin Transactions 2, pp. 1209, 1975. https://doi.org/10.1039/p29750001209
- B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids", Journal of the Chemical Society, Perkin Transactions 2, pp. 281, 1977. https://doi.org/10.1039/p29770000281