Uracil conical intersections

Figure 11-5. Energy level diagram of minima and conical intersections involved in the radiationless decay in uracil. Energies and structures taken from Ref. [147, 224]...

Figure 11-6. Structures of representative conical intersections Sj/Sq in the pyrimidine bases, uracil, thymine, and cytosine. Uracil structures (a,d) are taken from Ref. [147, 210]. Thymine structures (b,e) are taken from Ref. [152], Cytosine structures (c,f) are taken from Ref. [157]...

The ab initio molecular dynamics study by Hudock et al. discussed above for uracil included thymine as well [126], Similarly to uracil, it was found that the first ultrafast component of the photoelectron spectra corresponds to relaxation on the S2 minimum. Subsequently a barrier exists on the S2 surface leading to the conical intersection between S2 and Si. The barrier involves out-of-plane motion of the methyl group attached to C5 in thymine or out-of-plane motion of H5 in uracil. Because of the difference of masses between these two molecules, kinematic factors will lead to a slower rate (longer lifetime) in thymine compared to uracil. Experimentally there are three components for the lifetimes of these systems, a subpicosecond, a picosecond and a nanosecond component. The picosecond component, which is suggested to correspond to the nonadiabatic S2/S1 transition, is 2.4 ps in uracil and 6.4 ps in thymine. This difference in the lifetimes could be explained by the barrier described above. 

Figure 11-16. Diagram of the energy levels at the two- and three-state conical intersections in uracil and adenine calculated at the MRCI level, ciIJK represents conical intersection between states Sj, S j, S -. (From Ref. [210])...

The effect of solvation on uracil and thymine photophysics has been studied by Gustavvson and coworkers, who have studied uracil with four explicit water molecules and PCM to study distorted geometries [92,93,149], The conical intersection connecting Si to the ground state that was found in the gas phase is also present in solution. The barrier connecting the Si minimum to the conical intersection is lower in solution, however, causing much shorter lifetimes. So the nanosecond lifetime which is observed in the gas phase is not observed in solution but a picosecond lifetime is observed. 

Matsika S (2004) Radiationless decay of excited states of uracil through conical intersections. J Phys Chem A 108 7584... 

Figure 5 (a) Pathway from a displacement along the g direction of the conical intersection Si -Sq. Following the gradient of the So surface leads to the So minimum. The energies of the So, Si, and S2 states relative to the minimum of So are plotted as a function of a dihedral angle. Reproduced with permission from Refs. 56. (b) Geometries of uracil at the minima of So, Si and at the conical intersections S2-S1 and Si-So. 

Figure 6 Energy levels at the two- and three-state conical intersection points using MRCI, (a) the So, Si, Si states of uracil and (b) the So, Si, Si, S3, S4 states of adenine. Rx(ciIJ) and Rx(ciIJK) denote conical intetsection between states /,/ ot I,J,K, tespectively. Reproduced with petmission from Ref. 94.

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