Samstag, 17. Mai 2014

looking at molecules 1

this is the first part of an upcoming multi-post guide, in which I want to describe how to address photochemical questions about a certain molecule or class of molecules. Therefore, I think it is a good approach to first line out the process of the quantum chemical investigation in a step-like structure and then go into details of each step in future posts. So lets start from the beginning:

For starters, I want to get an overview about the molecules inner (electronic) structure and reactivity. But before I turn on the electric heating of the server room I thoroughly consult existing literature and any available scientists about reactivity and photochemical behaviour of the molecule(s). This helps to avoid getting lost in the vast amount of information that the quantum-chemical machinery can provide you with.

Secondly, on the basis of the literature and my experience I hypothesize about the electronic structure of the molecule and only afterwards start my calculations. At this point, you inevitably face the choice of the methodology. Depending on the size of the system, I usually start off with some solid double-zeta (SVP) ab-initio treatment (if doable CCSD, otherwise SCS/MOS-MP2) and double-hybrid functional (B2-PLYP). At this point, the calculations are limited to ground state geometry of the molecule and I try to get familiar with the MOs. To assure reliability, it is always a good idea to compare the outcome various methods and learn from the differences in the predictions. This way you can  e.g. identify highly correlated states whose energy changes a lot when going from second- to third-order methods or charge-transfer states when using TDDFT.

The third part of my guide will be concerned with the identification of the relevant coordinates of the system under investigation. Since most photochemical processes involve multi-state degeneracies (e.g. conical intersections and/or intersystem crossing), a key step in any quantum-chemical investigations is to learn along which geometrical parameters the involves states exhibit a different run and intersect. This can be intra-molecular coordinates such as bond length and angles or an inter-molecular distance coordinate along which a charge-transfer state of a molecular complex intersects with locally excited state.

The fourth and last section is about getting the numbers right. While in the first three parts we were satisfied with an approximate treatment of our system, we now want to get as quantitative as possible. Therefore, you should have some experimental numbers at hand to compare-to and a thorough insight into the electronic structure in the system as well as the experiments.

Now that I laid out the tasks, the next posts will be dealing with the first of those steps.


On the molecular mechanism of non-radiative decay in nitrobenzene and the unforseen molecular challenges this small molecule holds for electronic structure theory

This lengthy title is from our recently published paper that had been mentioned earlier in this blog. Amongst with some other things, this paper or rather the work that went into it also was the reason for the long pause since the last post. Now that it finally completed the process of publication, I will continue with a tutorial on how I look at molecules with the tools of a theoretical chemist.
There will be multiple posts on this topic in the upcoming weeks, but first, here is the link:

So long!