Archive for September, 2016
Wednesday, September 28th, 2016
The story so far. Imines react with a peracid to form either a nitrone (σ-nucleophile) or an oxaziridine (π-nucleophile).[1] The balance between the two is on an experimental knife-edge, being strongly influenced by substituents on the imine. Modelling these reactions using the “normal” mechanism for peracid oxidation did not reproduce this knife-edge, with ΔΔG (π-σ) 16.2 kcal/mol being rather too far from a fine balance.
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References
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D.R. Boyd, P.B. Coulter, N.D. Sharma, W. Jennings, and V.E. Wilson, "Normal, abnormal and pseudo-abnormal reaction pathways for the imine-peroxyacid reaction", Tetrahedron Letters, vol. 26, pp. 1673-1676, 1985. http://dx.doi.org/10.1016/S0040-4039(00)98582-4
Tags:addition product, free-energy pathway, Functional groups, Imine, Nitrone, Nucleophile, Organic chemistry, Oxaziridine
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Thursday, September 22nd, 2016
Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago[1] and the article included an inspection of the computed wavefunction. However this did not look at the potential stereoelectronics in this species, which I now address here.
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References
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A. Wierzbicki, E.A. Salter, E.A. Cioffi, and E.D. Stevens, "Density Functional Theory and X-ray Investigations of P- and M-Hexamethylene Triperoxide Diamine and Its Dialdehyde Derivative", The Journal of Physical Chemistry A, vol. 105, pp. 8763-8768, 2001. http://dx.doi.org/10.1021/jp0123841
Tags:Amines, Artemisinin, Chemistry, Functional groups, Hexamethylene triperoxide diamine, Interesting chemistry, Organic chemistry, Organic peroxides, Peroxide, perturbation energy interaction, Stereoelectronics
Posted in Uncategorised | 1 Comment »
Wednesday, September 21st, 2016
Nucleophiles are species that seek to react with an electron deficient centre by donating a lone or a π-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine or H2NOH. I previously discussed how for this example, the energetics allow the nitrogen lone pair (Lp) to win out over the O Lp. Here, I play a similar game, but this time setting an NLp up against a π-pair.
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Posted in crystal_structure_mining, reaction mechanism | No Comments »
Monday, September 19th, 2016
I previously explored stabilized “carbenes” with the formal structures (R2N)2C:, concluding that perhaps the alternative ionic representation R2N+=C–NR2 might reflect their structures better. Here I take a broader look at the “carbene” landscape before asking the question “what about nitrenes?”
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Posted in crystal_structure_mining | 1 Comment »
Sunday, September 11th, 2016
To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or persistent carbene. This type is of interest because of its ability to act as a ligand to an astonishingly wide variety of metals, with many of the resulting complexes being important catalysts. The Wiki page on persistent carbenes shows them throughout in form 1 below, thus reinforcing the belief that they have a valence of two and by implication six (2×2 shared + 2 unshared) electrons in the valence shell of carbon. Here I consider whether this name is really appropriate.
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Tags:Carbenes, chemical bonding, energy barrier, free energy, Functional groups, General, Ligand, Mesoionic carbene, Organometallic chemistry, Persistent carbene, quantum mechanical solution, Reactive intermediates, Transition metal carbene complex, Valence, Valence electron
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Thursday, September 1st, 2016
Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity. 
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References
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D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chemical Communications, vol. 52, pp. 11219-11222, 2016. http://dx.doi.org/10.1039/C6CC06395K
Tags:chemical bonding, chemical reaction, Chemistry, Delocalized electron, double bond, energy, energy difference, HOMO/LUMO, lowest energy, Molecular orbital, Natural bond orbital, Nature, Physics, Quantum chemistry, stable HOMO-1
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