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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

preprint
submitted on 05.01.2018, 00:14 and posted on 05.01.2018, 15:30 by 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.

Funding

Deutsche Forschungsgemeinschaft

History

Topic

  • Computational chemistry and modeling

Email Address of Submitting Author

burghardt@chemie.uni-frankfurt.de

Email Address(es) for Other Author(s)

padmabati.mondal@gmail.com, maurizio.persico@unipi.it

Institution

Goethe University Frankfurt

Country

Germany

ORCID For Submitting Author

0000-0002-9727-9049

Declaration of Conflict of Interest

There are no conflicts to declare.

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