Thursday, 5 January 2017

Simulating Light-Induced Processes in DNA

We planned to write a short perspective of our experience of simulating UV excitations in DNA but ended up with a quite comprehensive article: "Challenges in Simulating Light-Induced Processes in DNA", which just appeared in the journal Molecules. The aim of this work was to illustrate the different tasks that are involved in the simulation of DNA and its components: (i) quantum chemistry, (ii) description of the excitation processes, (iii) nonadiabatic dynamics, (iv) comparison to experiment, and (v) analysis of the results. In all these cases significant challenges can occur, and a wide range of methods to tackle these have been developed by numerous researchers. For someone entering the field or even for active researchers, it is sometimes difficult to keep all this in mind. We hope that this new article will be provide a useful summary of the work that has been done.

Friday, 23 December 2016

Rational Design

One of the amazing things in chemistry is that people can actually predict the properties of molecules just by pushing around electron pairs on paper. In our newest article "Color Fine Tuning of Optical Materials Through Rational Design" that appeared in ChemPhysChem, we put this idea to the test. A set of oligothiophene derivatives are created by connecting different cap and linker groups, which are chosen according to chemical reasoning. These molecules are subsequently synthesized and characterized spectroscopically. And to check, we also perform TDDFT/M06-2X computations. The outcome: It all fits together. Chemical reasoning provides the correct qualitative trends. Computation predicts the outcome quantitatively.


Monday, 18 July 2016

Research proposals vs. research excellence

There is generally no reason to assume that the research you are funded to do should exactly coincide with the best possible research that you are capable of doing. Research is unpredictable by its very definition and new ideas, insights, results, etc., that change your optimal course of action, pop up all the time. This makes me wonder what is the higher imperative: Doing what you are funded to do, or doing the most excellent research you are capable of? Let's examine some reasons in favor of the former:
  1. You should do what you are funded for simply because you signed a contract to so. End of discussion. But the point is: It is actually not in the best interest of the funding agency to hold you back in case you found a more exciting topic along the way. Are you obliged to comply with the funding agency against its own interest?
  2. Your funding agency may not be interested in general research excellence but may have more narrow interests. But even in this case there could be ways to satisfy those more narrow interests outside of your original proposal. Should you grab that opportunity?
  3. Your original proposal was certified by peer-review to be productive and worthwhile, switching to a different topic is too risky. But I don't think this makes sense either: It puts the opinion of your "peers" above yours about your own very special research topic.
If I look at my two most cited papers, then I find out that both were not part of a research proposal. The first one, concerned with polyradical character in graphene nanoribbons, was not in a proposal, since we did not expect that graphene nanoribbons would show polyradical character. The second one, about a wavefunction analysis strategy for excitons, was not in the proposal for my scholarship, since I had no idea at the start of my PhD that I would actually be doing that. Do I have to somehow feel bad for writing these papers and working on the related computer codes?

Is a research proposal a "lower bound" to your research and should you modify parts of it as you go along? Or is it cast in stone? Any opinions, experience?

Wednesday, 13 July 2016

Comparing Wavefunctions by their Overlap

Ever since starting in quantum chemistry I have been trying to avoid looking at orbitals. One reason is laziness. I just do not like sitting there clicking and waiting for all the orbitals to be rendered (even though this can be improved by using the proper scripts and programs). The other reason is a formal one: Orbitals, being one-body functions, can never tell us the whole truth about the many-body wavefunctions. Even worse, the same wavefunction may appear differently depending on the orbital set used to describe it (canonical orbitals, natural orbitals, natural transition orbitals, ...)

Assume that we performed two computations with different computational methods. When we look at the results we find out that, both, the molecular orbitals and wavefunction listings changed between the calculations. Does this mean that the two computations produced different wavefunctions? Not necessarily! The changes in the orbitals might be compensated by changes in the wavefunction expansion, at least in part. If we want to compare such wavefunctions we have to take into account the changes in the MOs and wavefunctions in a consistent fashion. In our newest Communication in J. Chem. Phys. "Unambiguous comparison of many-electron wavefunctions through their overlaps" we suggest to use the many-body wavefunction overlap for this task, i.e. the scalar product in the full many-body Hilbert space.

The outcome looks like this:

What we are doing is computing the 4 lowest excited states with CASSCF(12,9) and with MR-CIS(12,12). And then we compute the overlaps for all pairs of states and summarize them in pie charts. Every chart corresponds to one CASSCF wavefunction and the colors correspond to the MR-CIS wavefunctions. For example the second chart tells us that the Ψ1' wavefunction at CASSCF has a 67% overlap with the Ψ1 wavefunction at MR-CIS. But there are also smaller contributions of the Ψ2 and Ψ3 wavefunctions (as seen by the green and yellow bits).

The analysis gives us a quick overview of the relations between the wavefunctions computed at the different levels. There are two immediate conclusions: First, the overall state ordering is the same for both methods. Second, the wavefunctions are generally quite different, as seen by the large chunks of the pies missing.

The overlap code described here is actually a side product of a development we did for the nonadiabatic dynamics program SHARC (see this post). It will be released from the SHARC homepage as a standalone module, I hope soon ...

Thursday, 19 May 2016

Entanglement Entropy of Electronic Excitations

There is more to excited states than meets the eye. Just looking at the orbitals will not tell you everything there is to know about the many-body wavefunctions. The purpose of my newest paper "Entanglement Entropy of Electronic Excitations," that just appeared in J. Chem. Phys., was to quantify the amount of information that is hidden from view. For this purpse, I used the idea of mutual information from quantum information theory.

The focus of this paper is the eigenvalue spectrum of the natural transition orbital (NTO) decomposition. There is information in the eigenvalue spectrum independent of the orbitals themselves. To illustrate the point, we can look at the first excited singlet state of two interacting ethylene molecules at 6.0 Å
and at 3.5 Å
The orbitals in both cases look similar but the eigenvalues λ1 and λ2 are different. For the larger separation both are equal at about 0.45. For the smaller separation, there is one dominant one at 0.86. Clearly, these are different wavefunctions, but what is the significance?

In the paper I am arguing that only the first case is consistent with the idea of a Frenkel exciton, i.e. two coupled local excitations. The second case can be seen as one homogeneous transition. This automatically means that there is admixture of charge transfer, since the orbitals are distributed evenly. And indeed when we apply our charge transfer measures, we find charge resonance character in the second case.

The whole formalism employed is somewhat abstract, unfortunately, and too much for one single blogpost. But the take home message is the following: Quantum and correlation effects appear even for rather simple excited state calculations. In critical cases these may mislead us when interpreting the calculations. Luckily, there is a solution to this conundrum - our wavefunction analysis tools TheoDORE and libwfa :)