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Home > Seminars > 2009

Shedding light on photochemical reactions : Computer simulation as an aid for time-resolved spectroscopy

Gerrit Groenhof, Max-Planck-Institut (Göttingen, Allemagne)

Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption. These reactions typically occur at femto- to picosecond timescales. As the relevant time and spatial resolutions are notoriously hard to access experimentally, Molecular Dynamics (MD) simulations are the method of choice to study such ultra-fast processes.

In our simulations, we use a multi-configurational quantum mechanical (QM) description (CASSCF, CASPT2) to model the electronic rearrangement for those parts of the system that are involved in the absorption. For the remainder, typically consisting of the apoprotein and the solvent, a simple forcefield model (MM) suffices. QM/MM gradients are computed on-the-fly, and a diabatic surface hopping procedure is used to model the excited state decay. We have demonstrated the validity of this hybrid QM/MM approach for photobiological reactions in recent applications on photoactivation of photoreceptor proteins, on photo-switching of fluorescent proteins and on benign and malign photochemical reactions in DNA. In addition to providing quantities that are experimentally accessible, such as structural intermediates, fluorescence lifetimes, quantum yields and spectra, the simulations provide also information that is much more difficult to measure experimentally, such as reaction mechanisms and the influence of individual amino acid residues.