Monday, 25 January 2021

Chemical shielding tensors

How do you visualise a tensor field? A 3x3 tensor as a function of the 3 spatial coordinates makes a 12-dimensonal object. How do we visualise a 12-dimensional object using a 2-dimensional screen? This is the problem we encountered trying to visualise the chemical shielding tensor, which is a common aromaticity criterion. The solution: we compute the principal axes of the tensor and represent those using little dumb-bells at different points in space providing us at least a coarse-grained description.

 To get the full story, check out our preprint “3D Visualisation of chemical shielding tensors to elucidate aromaticity and antiaromaticity” available on ChemRxiv or this blog post.

Here, I just wanted to show a few more computer graphics. This, for example, are the in-plane shielding tensors shown with our new VIST method in connection with the ACID isosurface as computed via GIMIC.

For comparison, the NICS(1) tensors along with the magnetically induced current densities also computed using GIMIC. Diatropic currents, giving rise to positive shielding are shown in blue; paratropic currents in red. Diatropic currents dominate, hence we see positive (blue) shielding.

The code will be released through TheoDORE once I have the time to make it reasonbly well documented and user friendly.

Friday, 26 June 2020

Virtual Open Day with Jmol

I prepared some interactive Jmol molecular models for our Department's Virtual Open Day research showcase. There are some bits with molecular orbitals and molecular vibrations, which look quite nice I think. I am not quite sure if any of our prospective undergrads went there or if they liked it. Anyway, my 5-year old son likes it - but he already had a pre-existing appreciation of molecules ;)

Sunday, 7 June 2020

Full economic cost

According to the official numbers from our Research Office the full economic cost of one hour of my time comes out at about 75 pounds. 75 pounds for every hour of research, 75 pounds for every hour of teaching, 75 pounds for every hour of debugging code, 75 pounds for every seminar visit, 75 pounds for every hour of target tracking, 75 pounds for every hour of shuffling around Excel sheets, and 75 pounds for every hour of filling out forms to claim back 75 pounds. I am not saying that this is what I am paid but it is the full cost of having me sit in my office including the heating, cleaning the halls, mowing the lawn outside, and keeping up the flower bed at the main entrance.

Obviously, this averaged and linear view does not tell the whole story, neither of the costs nor of productivity, but it is still a bit disturbing to think about all this cost involved. I am not quite sure what the moral of the story is but I guess it is that we should be a bit more careful regarding our colleagues' time and that institutions might be a bit more generous in terms of allocating funds.

I am in charge of organising the seminars here. Would all 26 full-time equivalents of academics show up to our seminar, this would be a bill of 2k pounds. Adding in all the PhD students and postdocs would move us well above 5k, almost three times the yearly seminar budget! As much as I believe in the importance of seminars, this is why I am not too pushy in making people come.

Another interesting factoid: If I had to pay myself with my own startup budget, then I could finance about 26 hours of my work time. I would be out of money on Thursday at 11am of the first week of the financial year!

Saturday, 2 May 2020


If the electronic ground state of a molecule has double-excitation character and the excited state only single-excitation character, then you can view the molecule as being "de-excited." Electrons are taken from a higher lying orbital and moved into a lower lying orbital. A recent paper tries to formalise this idea by computing an expectation value of the particle-hole permutation operator. We take the two-body exciton wavefunction, switch the electron and hole and see how much it resembles the original wavefunction. If the hole resides purely in the occupied orbitals and the electron purely in the virtual orbitals, this has to yield zero. But with a correlated ground state it does not vanish.

The striking thing is that this expectation value of the particle-hole permutation operator seems to agree between TDDFT and wavefunction based methods in, both, magnitude and sign. This means that de-excitations are a "real thing" rather than just an artifact of TDDFT - not physically observable but a well-defined property of the wavefunction. For more on this, see PCCP 2020, 22, 6058.

Thursday, 5 March 2020

From eV to kJ/mol

What is the conversion factor from eV to kJ/mol? To go from eV to J, you have to multiply with the unit charge (formally speaking you insert the e into eV). To go to J/mol you multiply with Avogadro's number. What is the product of the unit charge and Avogadro's number - the Faraday constant. And if you were treated to Chemistry Olympiad at school then, hopefully, you are still able to blurt out its value even when woken up in the middle of the night: 96 485 C/mol. If we divide this by 1000, we get the desired result 1 eV is 96.485 kJ/mol. Or more broadly speaking, you just have to multiply with a factor of 100 if you want to go from eV to kJ/mol. I have never realised that connection before.