A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

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.

Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State

Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S₁(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.

Mechanism of photocatalytic water splitting with triazine-based carbon nitrides: insights from ab initio calculations for the triazine–water complex

Valuable theoretical insights into the mechanism of photocatalytic water-splitting using triazine as a model system for carbon-nitride materials.

Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution

The mechanistic details of well-known photohydrate lesions are explored using state-of-the-art computational methods.

Reversible Photohydration of Trenbolone Acetate Metabolites: Mechanistic Understanding of Product-to-Parent Reversion through Complementary Experimental and Theoretical Approaches

Photolysis experiments (in H2O and D2O) and quantum chemical calculations were performed to explore the pH-dependent, reversible photohydration of trenbolone acetate (TBA) metabolites. Photohydration of 17α-trenbolone (17α-TBOH) and 17β-trenbolone (17β-TBOH) occurred readily in simulated sunlight to yield hydrated products with incorporated H(+) at C4 and OH(-) at either C5 (5-OH-TBOH) or C12 (12-OH-TBOH) in the tetracyclic steroid backbone. Although unable to be elucidated analytically, theory suggests preferred orientations of cis-12-OH-TBOH (relative to C13 methyl) and trans-5-OH-TBOH, with the former most thermodynamically stable overall. Both experiment and theory indicate limited stability of trans-5-OH-TBOH at acidic pH where it undergoes concurrent, carbocation-mediated thermal rearrangement to cis-12-OH-TBOH and dehydration to regenerate its parent structure. Experiments revealed cis-12-OH-TBOH to be more stable at acidic pH, which is the only condition where its reversion to parent TBA metabolite occurred. At basic pH cis-12-OH-TBOH decayed quickly via hydroxide/water addition, behavior that theory attributes to the formation of a stable enolate resistant to dehydration but prone to thermal hydration. In a noteworthy deviation from predicted theoretical stability, 17α-TBOH photohydration yields major trans-5-OH-TBOH and minor cis-12-OH-TBOH, a distribution also opposite that observed for 17β-TBOH. Because H(+) and OH(-) loss from adjacent carbon centers allows trans-5-OH-TBOH to dehydrate at all pH values, the presumed kinetically controlled yield of 17α-TBOH photohydrates results in a greater propensity for 17α-TBOH reversion than 17β-TBOH. Additional calculations explored minor, but potentially bioactive, trenbolone analogs that could be generated via alternative rearrangement of the acidic carbocation intermediate.

Lithium intercalation and diffusion in TiO2 nanotubes: a first-principles investigation

The effective diffusion barriers between the outer and inner surfaces of the O_2c–TiO₂ NT can be as low as 0.53 eV.

Theoretical investigations on stability of pyridylpentazoles, pyridazylpentazoles, triazinylpentazoles, tetrazinylpentazoles, and pentazinylpentazole searching for a replacement of phenylpentazole as N5 (-) source

Stabilities of pyridylpentazoles, pyridazylpentazoles, triazinylpentazoles, tetrazinylpentazoles, and pentazinylpentazole were studied using density functional theory to assess their potentials as the source of pentazole anion (N5 (-)) for replacement of phenylpentazole (PhN 5 ). Replacing the aryl group of PhN 5 by six-member heterocycle weakens pentazole ring. Compared to PhN 5 , title molecules have longer N-N bonds and lower activation energy (E a,1) needed for the N5 ring breaking. E a,1 decreases with the increasing number of nitrogen atoms of heterocycle. The ortho nitrogen of heterocycle most obviously lowers the stability of pentazole. The central C-N bond dissociation energies (BDEs) of title molecules are lower than that of PhN 5 . For the molecule with 0~1 ortho-nitrogen, H rearrangement happens during the central C-N bond breaking. The energy (E a,2) required for H rearrangement is considerably smaller than the corresponding BDE. ΔE a,2 (E a,2(PhN5) - E a,2 = 7.5~35.7 kJ mol(-1)) is larger than ΔE a,1 (E a,2(PhN5) - E a,2 = 4.6~15.5 kJ mol(-1)), while ΔE a,2/E a,2(PhN5) (2~9.5 %) is smaller than ΔE a,1/E a,1(PhN5) ( 4.4~15.0 %). The larger ΔE a,1/E a,1(PhN5) suggests that title molecules can not be the better N5 (-) than PhN 5 .

Pyridylpentazole and its derivatives: a new source of N5−?

Pyridylpentazole (PyN₅) and its derivatives with 1–2 electron withdrawing groups were studied using the density functional theory to assess their potentials as the source of pentazole anion N₅⁻ for replacement of phenylpentazole (PhN₅).