Henry Rzepa's Blog Chemistry with a twist

March 20, 2017

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

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).


March 2, 2017

More tetrahedral fun. Spherical aromaticity (and other oddities) in N4 and C4 systems?

The thread thus far. The post about Na2He introduced the electride anionic counter-ion to Na+ as corresponding topologically to a rare feature known as a non-nuclear attractor. This prompted speculation about other systems with such a feature, and the focus shifted to a tetrahedral arrangement of four hydrogen atoms as a dication, sharing a total of two valence electrons. The story now continues here.


April 14, 2016

Hydronium hydroxide: the why of pH 7.

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?


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