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ResearchZernike (ZIAM)Theoretical ChemistryFaraji Group


Currently we are pursuing the following research projects in our group:

I. Dynamics and Mechanism of DNA Repair by Photolyases

Dynamics and mechanism of DNA repair by photolyases
Dynamics and mechanism of DNA repair by photolyases

Using hybrid quantum mechanical/molecular mechanical (QM/MM) dynamics, we have carried out series of simulations to completely map out the entire evolution of functional processes involved in the molecular mechanism of DNA photolyases. We have demonstrated that the electron catalyzing the repair is generated via an intermolecular Coulombic decay (ICD) process. We have presented the most energetically feasible electron-induced splitting mechanism in which the initial step is electron-coupled proton transfer from the protonated Histidine to the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state. The experimental spectroscopic signature of the detected 6-4PP intermediate is assigned theoretically to a specific molecular structure determining the operating molecular mechanism of the electron-induced restoration of (6-4) photolesions. Thereby, all pieces of the (6-4) photolesion repair puzzle are finally put together.

II. Excited-state Dynamics of Photoactive Proteins

In this project we are studying excited-state processes of far-red fluorescent proteins (FPs), which are relevant to deep-tissue in vivo imaging. Recently, we found that the Stokes shift in mPlum originates from the hydrogen-bond rearrangement around the chromophore in the excited states. Our theoretical findings provide support to a recent experimental study of the Stokes shifts in mPlum and its mutants.

III. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM

IV. Non-adiabatic effects and Vibronic Coupling Model

V. Multidimensioanl Quantum Dynamics: Wave-packet Propagation

Last modified:06 July 2017 10.30 p.m.