Three-State Conical Intersections in Nucleic Acid Bases

Abstract

The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S 0 , S 1 , and S 2 states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S 2 and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S 1 , S 2 , and S 3 states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.

Singlet excited state dynamics of uracil and thymine derivatives: A femtosecond fluorescence upconversion study in acetonitrile

“…This picture is very similar to that obtained in water [17], suggesting that the intramolecular mechanism of the ground state recovery (v. infra) is the same in these two On the balance the results obtained in acetonitrile can be usefully interpreted within the same mechanistic framework we have developed in our previous studies in aqueous solution [17,32]. Confirming the results obtained by Matsika in the gas phase [18,19], the key step leading to the conical intersection between the ground (S 0 ) and the /* excited state (S  ) consists of the pyramidalization of the C5 carbon atom and in the out of the plane motion of the C5 substituent. Our calculations in aqueous solution indicates that this geometry rearrangement for thymine and, especially, for 5-fluorouracil should be more difficult than for uracil, giving account of the ordering of the excited-state lifetime [17].…”

“…In general, the mechanism responsible for the ultrafast non-radiative deactivation (internal conversion) has not yet been completely assessed, even if several theoretical studies point towards the existence of near barrier-less paths, implying important ring deformation, leading from the excited state through a conical intersection to the ground state both in uracil [17][18][19][20][21], cytosine [8,[22][23][24] and adenine [19,[25][26][27][28][29]. Even if the proposed deactivation mechanism is not identical for the three bases (therefore one should not think of it in terms of a general mechanism, common for all DNA bases), the present picture is thus that the ultrafast decays observed for the various bases are due to purely intramolecular mechanisms, little or not affected by the solvent.…”

Solvent Effect on the Singlet Excited-state Dynamics of 5-Fluorouracil in Acetonitrile as Compared with Water

“…As a matter of fact, CASSCF calculations predicts that a Conical Intersection between S n and S π states (hereafter CI n/π ) does exist in vacuo for a geometry close to planarity. The structure of CI n/π is very similar to that found for uracil in the gas phase by Matsika at the CASSCF level, 5,29 and PCM/TDPBE0 calculations confirm that this CI is present also in CH 3 Even if the present computational analysis does not allow excluding the possibility that the solvent can modulate also the barrier heights on the path towards the CI S1/S0 conical intersection, the comparison of the computational results obtained for 5FU in acetonitrile with those obtained for water solution 10 strongly suggests that it affects the S π lifetime mainly by tuning the relative energy of the S π state and the close lying S n dark state. The stability of π/π* states increases both with the polarity and, especially, the hydrogen bonding ability of the solvent, implying that in water the dynamics on S π is not influenced by S n .…”

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy

“…64 Our calculations are in favor of ∼0.2 eV gap between L b and L a , placing the L a state higher in energy in agreement with results from previous studies using wave function-based methods. 52,[64][65][66][67][68] Experiments in aqueous solution assign a weak band at 4.6 eV to the L b transition (denoted as band I in Table I), while a more intense peak around 4.8 eV is believed to arise from a transition to the L a state (band II in Table I). Vapor experiments report only a peak at 4.9 eV, which we tentatively assign to the more intense L a transition.…”