Archive for the ‘reaction mechanism’ Category

The conformation of enols: revealed and explained.

Thursday, April 6th, 2017
No Gravatar

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.

(more…)

What is the (calculated) structure of a norbornyl cation anion-pair in water?

Saturday, April 1st, 2017
No Gravatar

In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation. Most calculations indicate the force constant for an “isolated” symmetrical cation is +ve, which means it is a true minimum and not a transition state for a [1,2] shift. The latter would have been required if the species equilibrated between two classical carbocations. I then pondered what might happen to both the magnitude and the sign of this force constant if various layers of solvation and eventually a counter-ion were to be applied to the molecule, so that a bridge of sorts between the different states of solid crystals, superacid and aqueous solutions might be built.

(more…)

Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.

Monday, March 20th, 2017
No Gravatar

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).

(more…)

Pyrophoric metals + the mechanism of thermal decomposition of magnesium oxalate.

Sunday, March 19th, 2017
No Gravatar

A pyrophoric metal is one that burns spontaneously in oxygen; I came across this phenomenon as a teenager doing experiments at home. Pyrophoric iron for example is prepared by heating anhydrous iron (II) oxalate in a sealed test tube (i.e. to 600° or higher). When the tube is broken open and the contents released, a shower of sparks forms. Not all metals do this; early group metals such as calcium undergo a different reaction releasing carbon monoxide and forming calcium carbonate and not the metal itself. Here as a prelude to the pyrophoric reaction proper, I take a look at this alternative mechanism using calculations.

(more…)

How does silane invert (its configuration)?

Thursday, March 16th, 2017
No Gravatar

In the previous post, I found intriguing the mechanism by which methane (CH4) inverts by transposing two of its hydrogens. Here I take a look at silane, SiH4.

(more…)

How does methane invert (its configuration)?

Thursday, March 16th, 2017
No Gravatar

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?

(more…)

Forming a stabilized m-benzyne.

Friday, January 20th, 2017
No Gravatar

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.

(more…)

The smallest C-C-C angle?

Monday, October 31st, 2016
No Gravatar

Is asking a question such as “what is the smallest angle subtended at a chain of three connected 4-coordinate carbon atoms” just seeking another chemical record, or could it unearth interesting chemistry?

(more…)

σ or π nucleophilic reactivity of imines? A mechanistic reality check using substituents.

Sunday, October 9th, 2016
No Gravatar

Previously, a mechanistic twist to the oxidation of imines using peracid had emerged. Time to see how substituents respond to this mechanism.

(more…)

σ or π nucleophilic reactivity of imines? A mechanistic twist emerges.

Wednesday, September 28th, 2016
No Gravatar

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.

(more…)

References

  1. 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