It's about time for me to put up another post here. What I chose as a topic is to present little bit of the work that I have been doing over the last year. Of course it went a lot slower than we thought it would but at least we already understand what the problems are...
And I can already make movies that I think are pretty cool. What I am showing here is the charge transfer dynamics of the ethylene-formaldehyde-ethylene complex radical cation. This is of course a somewhat artificial system. But it is good for understanding the physics and the computational problems related to such processes.
The main point of interest is the non-adiabatic coupling between electronic and nuclear degrees of freedom. The Born-Oppenheimer approximation breaks down because electron tunneling between the ethylene molecules happens on the same time scale as the nuclear dynamics. This phenomenon is traditionally described by Marcus theory. Here we are applying semi-classical surface hopping dynamics, as provided by the Newton-X program package.
In the movie the charge is shown in red. It can be seen how it hops between the ethylene molecules. But not every passage of the transition region leads to a charge transfer. It may be inhibited by non-adiabatic coupling. In these simulations this is represented through a "surface hoppping" to the excited state. In the video it is shown as a yellow background.
For comparison I am also showing the static picture here. Plot (b) shows the location of the charge and can be compared with the red color in the above movie. (a) is the energy gap and it is marked if the trajectory is in the excited state. (c) shows the CC distances of the ethylene molecules.
Macrocycles, flexibility and biological activity: A tortuous pairing - Here's an interesting paper from the Jacobson, Wells and Walsh labs at UCSF and Stanford that seeks to demonstrate how restricting the flexibility of macr...
3 days ago