The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).
Archive for the ‘reaction mechanism’ Category
This is a spin-off from the table I constructed here for further chemical examples of the classical/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its minimum. So is square planar methane a true transition state for inversion (of configuration) of carbon?
The story so far. Inspired by the report of the most polar neutral compound yet made, I suggested some candidates based on the azulene ring system that if made might be even more polar. This then led to considering a smaller π-analogue of azulene, m-benzyne. Here I ponder how a derivative of this molecule might be made, using computational profiling as one reality check.
The story so far. Imines react with a peracid to form either a nitrone (σ-nucleophile) or an oxaziridine (π-nucleophile). 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.
- 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
σ or π? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks.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.
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? Here I explore the difference between two different and very simple approaches to predicting its reactivity.
- D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chem. Commun., vol. 52, pp. 11219-11222, 2016. http://dx.doi.org/10.1039/C6CC06395K