Archive for the ‘Interesting chemistry’ Category
Monday, May 6th, 2013
In a previous post on the topic, I remarked how the regiospecific ethanolysis of propene epoxide[1] 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[[2] 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.
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References
- H.C. Chitwood, and B.T. Freure, "The Reaction of Propylene Oxide with Alcohols", Journal of the American Chemical Society, vol. 68, pp. 680-683, 1946. https://doi.org/10.1021/ja01208a047
- 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
Tags:CF 3 CO, free energy, good model for the subsequent transition state, lower free energy barrier, Reaction Mechanism
Posted in Interesting chemistry | 1 Comment »
Monday, April 29th, 2013
A few posts back, I explored the “benzidine rearrangement” of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement. So replacing both NHs by O to form diphenyl peroxide (Ph-O-O-Ph) completes this homologous series. I had speculated that PhNHOPh might exist if all traces of catalytic acid were removed, but could the same be done to PhOOPh? Not if it continues the trend and requires no prior protonation at all!
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Tags:actual initial product, energy, energy transition state, Michael Dewar, New Hampshire, Reaction Mechanism
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Sunday, April 28th, 2013
I recently got an email from a student asking about the best way of rationalising epoxide ring opening using some form of molecule orbitals. This reminded me of the famous experiment involving propene epoxide.[1]
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References
- H.C. Chitwood, and B.T. Freure, "The Reaction of Propylene Oxide with Alcohols", Journal of the American Chemical Society, vol. 68, pp. 680-683, 1946. https://doi.org/10.1021/ja01208a047
Tags:10.1021, energy, lowest energy, predominant product, Reaction Mechanism, Tutorial material
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Wednesday, 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 »
Sunday, 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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Thursday, 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 »
Tuesday, 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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Monday, 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 »
Thursday, 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 »
Sunday, 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 »