April 17th, 2013
This is another in the occasional series of “what a neat molecule”. In this case, more of a “what a neat idea”. The s-triazine below, when coordinated to eg ZnI2, forms what is called a metal-organic-framework, or MOF. A recent article[1] shows how such frameworks can be used to help solve a long-standing problem in structure determination, how to get a crystal structure on a compound that does not crystallise on its own.
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References
- Y. Inokuma, S. Yoshioka, J. Ariyoshi, T. Arai, Y. Hitora, K. Takada, S. Matsunaga, K. Rissanen, and M. Fujita, "X-ray analysis on the nanogram to microgram scale using porous complexes", Nature, vol. 495, pp. 461-466, 2013. https://doi.org/10.1038/nature11990
Tags: chair, marine natural product, metal, radiation, X-ray
Posted in Interesting chemistry | 2 Comments »
April 14th, 2013
A recent theme here has been to subject to scrutiny well-known mechanisms supposedly involving intermediates. These transients can often involve the creation/annihilation of charge separation resulting from proton transfers, something that a cyclic mechanism can avoid. Here I revisit the formation of an oxime from hydroxylamine and propanone, but with one change. In the earlier post, I used two molecules of water to achieve the desired proton transfer. Now I look to see what effect replacing those two water molecules by a guanidine has.
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Tags: Reaction Mechanism
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April 4th, 2013
Back in the days (1893) when few compounds were known, new ones could end up being named after the discoverer. Thus Feist is known for the compound bearing his name; the 2,3 carboxylic acid of methylenecyclopropane (1, with Me replaced by CO2H). Compound 1 itself nowadays is used to calibrate chiroptical calculations[1], which is what brought it to my attention. But about four decades ago, and now largely forgotten, both 1 and the dicarboxylic acid were famous for the following rearrangement that gives a mixture of 2 and 3[2]. I thought I might here unpick some of the wonderfully subtle stereochemical analysis that this little molecule became subjected to.
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References
- E.D. Hedegård, F. Jensen, and J. Kongsted, "Basis Set Recommendations for DFT Calculations of Gas-Phase Optical Rotation at Different Wavelengths", Journal of Chemical Theory and Computation, vol. 8, pp. 4425-4433, 2012. https://doi.org/10.1021/ct300359s
- J.J. Gajewski, "Hydrocarbon thermal degenerate rearrangements. IV. Stereochemistry of the methylenecyclopropane self-interconversion. Chiral and achiral intermediates", Journal of the American Chemical Society, vol. 93, pp. 4450-4458, 1971. https://doi.org/10.1021/ja00747a019
Tags: chemical synthesis, chemical transformations, lower energy triplet state, Reaction Mechanism, rearrangement products, Tutorial material
Posted in Interesting chemistry | 2 Comments »
April 2nd, 2013
My previous dissection of the mechanism for ester hydrolysis dealt with the acyl-oxygen cleavage route (red bond). There is a much rarer[1] alternative: alkyl-oxygen cleavage (green bond) which I now place under the microscope.
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References
- C.A. Bunton, and J.L. Wood, "Tracer studies on ester hydrolysis. Part II. The acid hydrolysis of tert.-butyl acetate", Journal of the Chemical Society (Resumed), pp. 1522, 1955. https://doi.org/10.1039/jr9550001522
Tags: acetic acid, analogous energy, energy, lower energy route, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 3 Comments »
March 29th, 2013
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.
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Tags: ALSO, co-operative, energy, energy well, ester hydrolysis, free energy, Reaction Mechanism, shallow energy, solvation energy, Tutorial material
Posted in Uncategorised | 16 Comments »
March 26th, 2013
The 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.
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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
Tags: double bond, high energy, Historical, quadruple bond, quintuple bond, single bond, triple bond
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March 25th, 2013
My 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?
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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
Tags: Meisenheimer, Reaction Mechanism
Posted in Interesting chemistry | 3 Comments »
March 21st, 2013
A 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)?
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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
Tags: crystallography, cyclobutadiene, Waals complex, X-ray
Posted in Interesting chemistry | 4 Comments »
March 17th, 2013
n-Butyl lithium is hexameric in the solid state[1] and in cyclohexane solutions. Why? Here I try to find out some of its secrets.
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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
Tags: Cambridge, chemical shifts, conformational analysis, cyclohexane solutions, hexameric, spherical aromaticity, Tutorial material
Posted in Interesting chemistry | 16 Comments »
March 16th, 2013
Functionalisation of a (hetero)aromatic ring by selectively (directedly) removing protons using the metal lithium is a relative mechanistic newcomer, compared to the pantheon of knowledge on aromatic electrophilic substitution. Investigating the mechanism using quantum calculations poses some interesting challenges, ones I have not previously discussed on this blog.
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Tags: carbon-metal bond, lithiation, metal, metal alkyls, metal lithium, pericyclic, Reaction Mechanism, Tutorial material
Posted in Hypervalency, Interesting chemistry | 2 Comments »