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.

Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy

“…A similar lifetime has also been obtained using MRSF-TDDFT. 48 Although it is not readily discernible in Figure 7b, the 1 ππ* lifetime for Ura is even shorter than that for Thy. The signal intensity integrated over 4−5.4 eV decays in 15 ± 1 fs (Figure 7d), and the global fitting analysis provides time constants of 17 ± 1 fs, 0.44 ± 0.01 ps, 3.48 ± 0.03 ps, and >30 ps (Figure S19).…”

Ultrafast Excited State Aromatization in Dihydroazulene

“…In particular, because the photon absorption results in a π → π* transition in the S 1 state, this leads to recoupling of the single and double bonds in the molecule, − which manifests itself in the bond length alternation (BLA) displacement. − This is because the bright ππ * transition is mainly composed of a HOMO (π) to LUMO (π*) single electron excitation yielding a π 1 π 1 * configuration, which effectively eliminates a single π bonding from its π-conjugation network. Therefore, in the vicinity of the Franck–Condon (FC) geometry on the excited state potential energy surface (PES) there exists a substantial slope in the BLA direction, which results in a rapid motion along this mode. − However, the period of oscillatory BLA motion is rather short (∼20 fs) − and the experimental observation of coherent BLA motion should require pump pulses of extremely short duration, i.e., a very broad bandwidth, a condition that is not usually fulfilled in the experiments.…”

Accurate Spin-Orbit Coupling and Intersystem Crossing by Relativistic Mixed-Reference Spin-Flip (MRSF)-TDDFT

“…These advantages allow the MRSF to overcome the major limitations of the conventional TDDFT variants, while reliably reproducing the results of the more expensive multi-reference ab initio wave function theories. 9 In a series of studies, 8,12,[14][15][16][17][18][19][20][21][22] it has been demonstrated that the MRSF approach can also yield accurate nonadiabatic coupling matrix elements (NACMEs), 15,17 enabling reliable non-adiabatic molecular dynamics (NAMD) simulations, [22][23][24] a topologically correct description of conical intersections, 8,18,21 and accurate values of singlet-triplet gaps. 14,16 This method has also been successfully used in designing high-performance optoelectronic materials.…”