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Int. J. Mol. Sci. 2004, 5(3), 75-83; doi:10.3390/i5030075

Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics

1,* , 2 and 3
1 Department of Biophysics, Molecular Biology & Genetics, University of Calcutta, 92 APC Road, Kolkata 700009, India 2 Department of Biophysics, University of P. J. Safarik, Jesenna 5, 04S 54 Koˇsice, Slovak Republic 3 Physical Chemistry Division, Arrhenius Laboratory, Stockholm University, S 106 91, Stockholm, Sweden
* Author to whom correspondence should be addressed.
Received: 30 April 2003 / Accepted: 10 October 2003 / Published: 20 February 2004
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We have theoretically characterized the ground state and the excited state properties of wybutine, a naturally fluorescent modified base occuring in tRNAs, using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods. Both gas phase excited state properties and solvent effects, modelled through Onsager reaction field method, were considered. In addition to vertical excitation energies, the fluorescence transitions were calculated, based on S1 equilibrium geometry optimized at CIS level. Our computations show encouraging agreement with known experimental data either directly (TDDFT) or after applying empirical scaling (CIS). The fluorescence Stokes’ shift for the S0 Ã S1 transition is computed taking into account the contributions from both intramolecular and solvent reorganization processes. The results suggest that intramolecular relaxation of the S1 state accounts for the major part of the magnitude of the Stokes’ shift, while the role of solvent reorganization seems to be of less importance.
Keywords: CIS; TDDFT; modified base; reaction field; fluorescence lifetime CIS; TDDFT; modified base; reaction field; fluorescence lifetime
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Lahiri, A.; Ulicny, J.; Laaksonen, A. Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics. Int. J. Mol. Sci. 2004, 5, 75-83.

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