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
mclear
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.

Monday, 17 December 2018

PhD studentship at Loughborough University

A fully funded PhD studentship starting in October 2019 will be opening in my group at Loughborough University. If you are just finishing your Master's in chemistry, are interested in quantum chemistry and ambitious about learning new things, then go for it and apply!

The official announcement is shown here:

Unravelling the electronic structure properties of functional molecular materials

Functional molecular materials play an important role in modern science with applications in solar energy conversion, lighting, and data processing. Nowadays, computer simulations are an indispensable component in the study of these systems due to constant improvements in computer power. However, these computations have become so complicated that it is often a major challenge to make full sense of the results. To overcome this problem, a versatile computational analysis toolkit has been developed by Dr Plasser and co-workers, and it is the goal of this project to apply and further develop these tools. The student working on this project will develop skills in terms of applying modern quantum chemistry methods to various molecules of current scientific interest and will be given the opportunity to turn recently developed methods into high-impact scientific publications. In addition, programming skills will be developed, and the student will have the chance to work in an interdisciplinary setting with inputs from chemistry, physics and computer science.

The pictures shown pertain to a new method for visualising electron correlation in the excited state. Here, the excitation hole (red) is moved through the system and one observes how the excited electron (blue) adjusts to the position of the hole for the different excited states. I will talk about this idea some more once the underlying paper is published.

The tasks to be carried out during the project revolve around the topic of excited-state wavefunction analysis. First, we would be applying some of the recently developed tools, available within TheoDORE, Q-Chem, and Molcas. This work would be similar to this post or this post. Subsequent work will be a combination of programming and/or scripting tasks together with applications.

You can find the official announcement and guidelines here. I guess the main point to realise is that we can only pay a stipend to UK/EU graduates. Others would just get their non-UK/EU tuition fee covered and not obtain a stipend on top of that.

If you are interested, go ahead and check out my new group's homepage. Feel free to contact me if you have any specific questions about the work to be done.

Monday, 12 November 2018

Electron donating and withdrawing groups

Aside from the fact that I do not believe in the existence of HOMOs and LUMOs, it is sometimes good to know how they work. In particular, I can never remember how electron-donating and withdrawing groups work. Here is how I understand it:

  • An electron-donating group adds more electrons to the system and thus increases electron-electron repulsion (or decreases the effective nuclear charge). As a consequence the HOMO and LUMO energies increase.
  • An electron-withdrawing group removes electrons and, thus decreases the HOMO and LUMO energies.
  • An electron-donating group usually acts through an occupied non-bonding orbital. This is energetically close to the HOMO. Therefore, it has a stronger effect on the HOMO than on the LUMO (at least in organic molecules).
  • An electron-withdrawing group acts through a virtual orbital, which interacts more strongly with the LUMO.
  • As a consequence, electron-donating and withdrawing groups are both expected to lower the HOMO-LUMO gap in organic molecules.
  • Things are different for transition metal complexes. For example an electron-withdrawing fluorine group still lowers orbital energies. But it can affect the HOMO more strongly and increase the overall gap in fluorinated iridium complexes, see this Ref.

Wednesday, 10 October 2018

Cheap nonadiabatic dynamics simulations II

Staying true to the topic of cheap nonadiabatic dynamics simulations, here is another paper by us: Surface hopping within an exciton picture - An electrostatic embedding scheme that just appeared in JCTC. The idea in this case was to speed up the efficiency of photodynamics simulations by doing computations on individual chromophores and combining the results through a Frenkel exciton model.



Friday, 5 October 2018

Cheap nonadiabatic dynamics simulations

What is the cheapest way to run nonadiabatic dynamics simulations and get results that are at least better than a random number generator? How about parameterising a linear vibronic coupling Hamiltonian using only a single excited-state computation and running surface hopping dynamics with it. This is what we tried in our new paper "Highly efficient surface hopping dynamics using a linear vibronic coupling model" that just appeared in PCCP. And to our surprise, the results were actually a lot better than a random number generator. We could reproduce the main physics of the dynamics of intersystem crossing in SO2, the presence/absence of ultrafast internal conversion in adenine/2-aminopurine, as well as ultrafast intersystem crossing in 2-thiocytosine. Only for 5-azacytosine we were somewhat off the mark.


Some of the referees were a little bit "not amused" because it almost seems like kind of an unfair trick to run dynamics using such a simple setup. But if it works and if it gives you relevant information about the real world, why should you not do it?