Sunday 12 July 2009


Nice, I just noticed that my Master's thesis article is already available online [1]. Well, you can take a look at it if you are interested in excited state proton transfer or if you want to know what I did for my Master's thesis. I'll put some additional things here that did not make it there. This is basically what happens:

Bipyridyl-diol has two intramolecular hydrogen bonds. You excite it with UV light wait a few femtoseconds and the protons get transferred. It was understood that the double-transfer product DK is finally formed. The main question was wether there were sequential and/or concerted transfers. The general idea was that there would be a branched reaction path: An ultrafast (100 fs) first step that was either a single or double proton transfer and a "very fast" (10 ps) step from MK to DK. According to us it looks more like there is no branched reaction but rather a dynamical equilibrium between MK and DK that cools toward DK. Well I hope some experimental groups are still interested enough in this system to test for this hypothesis.

This is one trajectory, a simulation of the molecule for 300 fs after UV excitation.[2] You can see a very quick initial transfer and then some more transfers.

Actually I wanted also to show the development of the normal modes in the video. To compare them with the results of Stock et al.'s experiment. But this does not seem to work out here because the videos need to have a fixed 4:3 format. So I'll just show a figure. The important thing is that there is strong participation of the totally symmetric modes (blue, red) even if the process does not conserve the symmetry. Another very interesting thing is that activation of the non-totally symmetric (black) mode is a violation of the Franck-Condon rules. A way to explain this is that the Franck-Condon rules work only under ideal assumptions and not with a strongly anharmonic reactive potential.

Here is another trajectory for comparison. In this case the second proton transfer occured only a little bit later.

Actually another nice figure would be this one. What I am doing is projecting the trajectories onto a normal mode. And then I can average for every time step over the 36 trajectories that we ran. This time-dependent average should represent the coherent motions. Here I am showing 17ag, an aromatic breathing vibration, which is the classical case for a coherent Franck-Condon excitation (in the context of proton transfer the lower frequency skeletal modes were of more interest). In the harmonic vibrational analysis that we did at the DK equilibrium geometry, the mode has a wavenumber of 682/cm. This corresponds to a period of about 49 fs. Well and there really is a coherent oscillation with just that frequency. So we see that the harmonic vibrational analysis at the minimum and the dynamics nicely work together. If I compute the standard deviation over time of this time-dependent average then I get only one number per normal mode. These numbers are what we are showing in Fig. 10. And by the way: The tools to do this are in the new Newton-X version (aside from many other nice things ...).

[1] And interestingly there is a direct link to facebook which of course I had to click.

[2] One of these 300 fs RI-CC2/SVP-SV trajectories takes about a month on one processor.

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