Friday 21 December 2018

Benzene excimer

I created this picture to illustrate excimer formation in the benzene dimer after light irradiation. We start with a slip-stacked geometry shown on the upper left and irradiate this with light. Then, as the molecules align during the first few hundred femtoseconds, the coupling increases and we get an energy transfer from the lower to the upper benzene. As the coupling increases, an excimer is formed. In our dynamics, this excimer decays later on as there is no way to dissipate the excess energy.

The corresponding paper just appeared in PCCP (DOI: 10.1039/c8cp06354k) and we are trying to send a slightly adapted version of the above picture as a front cover to PCCP.

The pictures shown were created with PyMOL after creating cube files with Q-Chem. As a memo to myself and anyone who might want to try this out, these are the main commands for PyMOL:

1. Load all the coordinate and cube files. If you set it up in a way that all the coordinate and cube files have the same names, then everything is loaded into different frames of the same object in pymol, which is needed for step 4.
pymol S_*/plots/coord.mol S_*/plots/singlet_A_1_elec.cube
2. Create an isosurface for the density
isosurface elec, singlet_A_1_elec, 0.0015
3. Change the color of the isosurface, and for some reason it seems you have to write the command from 2. again afterwards.

4. To create the pictures of the different frames, you can use the integrated movie functionality of PyMOL
set ray_trace_frames=1
set cache_frames=0
mpng fig
That's it!

I was previously talking about how to create surfaces automatically in VMD and even created a script for that. But actually, I am quite impressed by how well this works in the current PyMOL version. And the nice thing about PyMOL is that you can have a transparent background for the structures, which adds flexibility for creating the final image.

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