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).
Posts Tagged ‘energy’
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
An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride.Friday, May 27th, 2016
In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation. Here I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.,,
- L. Wozniak, M. Cypryk, J. Chojnowski, and G. Lanneau, "Optically active silyl esters of phosphorus. II. Stereochemistry of reactions with nucleophiles", Tetrahedron, vol. 45, pp. 4403-4414, 1989. http://dx.doi.org/10.1016/S0040-4020(01)89077-3
- L.H. Sommer, and H. Fujimoto, "Stereochemistry of asymmetric silicon. X. Solvent and reagent effects on stereochemistry crossover in alkoxy-alkoxy exchange reactions at silicon centers", Journal of the American Chemical Society, vol. 90, pp. 982-987, 1968. http://dx.doi.org/10.1021/ja01006a024
- D.N. Roark, and L.H. Sommer, "Dramatic stereochemistry crossover to retention of configuration with angle-strained asymmetric silicon", Journal of the American Chemical Society, vol. 95, pp. 969-971, 1973. http://dx.doi.org/10.1021/ja00784a081
The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre occurs with inversion of configuration at the carbon, the mechanism being known by the term SN2 (a story I have also told in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which I here quantify with some calculations.
Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.
Ammonium hydroxide (NH4+…OH–) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+…OH–. The measured concentrations [H3O+] ≡ [OH–] give rise of course to the well-known pH 7 of pure water, and converting this ionization constant to a free energy indicates that the solvated ion-pair must be some ~19.1 kcal/mol higher in free energy than water itself.♣ So can a quantum calculation reproduce pH7 for water?
Hypervalency is defined as a molecule that contains one or more main group elements formally bearing more than eight electrons in their valence shell. One example of a molecule so characterised was CLi6 where the description "“carbon can expand its octet of electrons to form this relatively stable molecule“ was used. Yet, in this latter case, the octet expansion is in fact an illusion, as indeed are many examples that are cited. The octet shell remains resolutely un-expanded. Here I will explore the tiny molecule CH3F2- where two extra electrons have been added to fluoromethane.
- H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. http://dx.doi.org/10.1038/355432a0