Organic chemistry (III)

The mechanism of the H5C5x (free radical intramolecular hydrogen abstraction followed by intramolecular addition to an alkene) reaction represented as an animation of the energy profile as well as the SOMO (singly occupied molecular orbital) wave functions.

We provide the animation in three formats in case that the two first are not compatible with all browsers. If any given image is not animated, please, move down to the next format (they should work in recent versions of Firefox and Chrome). The animated images are too heavy to be embedded here, they can be downloaded from the following links:

APNG version.

WEBP version.



The QM calculations were carried out with ORCA at the UHF/RI-MP2/ma-def2-TZVP level of theory, whereas the orca_plot program was used to generate the Cube files that were subsequently rendered with VMD with the help of a customised vmd_cube script (Python 2).

Other tools employed include Gabedit, ImageMagick, Inkscape, img2webp, ffmpeg and Matplotlib, powered by Manjaro Linux.

This work is inspired by the second part of my PhD thesis.

Even though they are not intended for distribution, I can make available the Python 3 and Bash scripts I wrote in order to automatise the tasks.