A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

Abstract

It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.

Chart 1. Uracil (1), Its Photohydrate (2), and Photohydration Mechanism Hypothesized in ref (5)a

Chart 2. A Reactive Intermediate Proposed in This Worka

Figure 1

(a) Evolution of the population of the adiabatic S₀–S₃ states during the NAMD simulations. The time constants of the monoexponential fit of the S₂ population and the biexponential fit of S₀ are also shown. The margins of error were determined by bootstrapping. (b) Evolution of the HC₅C₆H dihedral angle (φ) during the NAMD simulations. The red circles show the S₂ → S₁ nonadiabatic transitions (surface hops), and the blue circles the S₁ → S₀ nonadiabatic transitions. The dashed horizontal lines show the dihedral angle values in the structures given to the right of the plot (see the text for more details). (c) MEPs on the S₂ (blue), S₁ (red), and S₀ (black) PESs of uracil obtained using the nudged elastic band (NEB) optimization^, in connection with the MRSF-TDDFT/BH&HLYP/6-31G* method. The MEPs are described in terms of the HC₅C₆H dihedral angle (denoted as φ) and the BLA distortion. The relative energies (in electronvolts) are given with respect to the S₀ equilibrium geometry of uracil. The (BLA (Å), φ (deg), ΔE (eV)) values of the critical structures are (0, 0, 6.09) for FC, (0.13, 0.36, 5.58) for CI_21,BLA, (0.19, 48.0, 5.27) for CI_21,+ , (0.21, 2.00, 4.23) for S_1,min, (0.02, 118.21, 4.35) for CI_10,+, and (−0.04, 176.33, 3.54) for S_0,min+. The green arrows show the relaxation paths characterized by distinct decay constants, τ₁–τ₃. The S_1,min → CI_10,+ path merges with the CI_21,+ → CI_10,+ MEP (at BLA = 0.013 Å, φ = 152.4°, and ΔE = 4.32 eV). (d) Structure and frontier orbitals of intermediate 4.

Chart 3. (a) Conformations of Hydroxo-uracila and (b) Relative Energies (kilocalories per mole) of the Intermediate Species in the Mechanism of Uracil 1 Hydration Obtained Using the BH&HLYP/cc-pVTZ Method on the PES of the Electronic Ground Stateb

Chart 4. Mechanism of Uracil Photohydration Suggested in This Worka