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

Abstract

Abstract: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 S 1 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 S 0 ← S 1 transition is computed taking into account the contributions from both intramolecular and solvent reorganization processes. The results suggest that intramolecular relaxation of the S 1 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.

The 2.1Å Crystal Structure of the Far-red Fluorescent Protein HcRed: Inherent Conformational Flexibility of the Chromophore

“…22,23 Our results for the cis coplanar model agree closely with previous published calculations done at an identical theoretical level with a slightly less truncated chromophore model, 17 differing only by 0.03 eV in the absorption energy. The assignment of the absorption and excitation maxima to trans non-coplanar and cis coplanar forms implies that the fluorescence quantum yield of the cis coplanar conformation is substantially higher than for the trans non-coplanar form.…”

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

“…low, intermediate and high rotational mobilities of Y37 base have also been investigated in another fluorescence study [29]. Ground state and excited state properties of wybutine were studied by using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods [30]. It has been demonstrated by using semi-empirical quantum chemical AM1 calculations that some noticeable conformational change occurs in the wybutine side chain at 37th position when first uracil of codon UUC binds to the A36 of anticodon GAA of tRNA Phe [31].…”

Synthesis, characterization, and DFT calculation of a Pd(II) Schiff base complex

“…Two scale factors, 0.9648 and 0.72, were used for correction of the calculated harmonic vibrational frequencies and singlet-singlet calculated excitations, respectively. 32,33…”