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Mondal_2018.pdf (2.86 MB)
Azobenzene as a Photoregulator Covalently Attached to RNA: A Quantum Mechanics/Molecular Mechanics-Surface Hopping Dynamics Study
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submitted on 05.01.2018 and posted on 05.01.2018by Padmabati Mondal, Giovanni Granucci, Dominique Rastädter, Maurizio Persico, Irene Burghardt
The photoregulation of nucleic acids by azobenzene photoswitches has
recently attracted considerable interest in the context of emerging
biotechnological applications. To understand the mechanism of
photoinduced isomerisation and conformational control in these complex
biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface
Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are
investigated, both of which contain the azobenzene chromophore
covalently attached to an RNA double strand via a beta-deoxyribose
linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.