A Combined Experimental and Theoretical Approach to the Photogeneration of 5,6-Dihydropyrimidin-5-yl Radicals in Nonaqueous Media

Abstract

The chemical fate of radical intermediates is relevant to understand the biological effects of radiation and to explain formation of DNA lesions. A direct approach to selectively generate the putative reactive intermediates is based on the irradiation of photolabile precursors. But, to date, radical formation and reactivity have only been studied in aqueous media, which do not completely mimic the microenvironment provided by the DNA structure and its complexes with proteins. Thus, it is also important to evaluate the photogeneration of nucleoside-based radicals in nonaqueous media. The attention here is focused on the independent generation of 5,6-dihydropyrimidin-5-yl radicals in organic solvent through the synthesis of new lipophilic tert-butyl ketone precursors. Formation of 5,6-dihydro-2'-deoxyuridin-5-yl and 5,6-dihydrothymidin-5-yl radicals has first been confirmed by using a new nitroxide-derived profluorescent radical trap. Further evidence has been obtained by nanosecond laser flash photolysis through detection of long-lived transients. Finally, the experimental data are corroborated by multiconfigurational ab initio CASPT2//CASSCF methodology.

Mechanism of the OH Radical Addition to Adenine from Quantum-Chemistry Determinations of Reaction Paths and Spectroscopic Tracking of the Intermediates

“…The current research sheds light on the latter issue and the solvent effects. It has been proposed that solvent accessibility in the microenvironment of nucleic acids is somewhat restricted due to the hydrophobic character of the double strand and, among other factors, the presence of DNA–protein complexes, suggesting that DNA/RNA macromolecules should not be considered completely solvated. Actually, a recent measurement of the dielectric constant of DNA yielded a value of ∼8, which is ca .…”

“…The present CASPT2//CASSCF computational approach has been demonstrated to provide accurate results compared to experimental recordings, 26 and has been previously used by the authors of the present work to correctly assign experimental transient absorption spectroscopy signals of uracil, thymine, and cytosine radicals. 26,66 All of the multiconfigurational calculations have been performed with the MOLCAS 8 software package. 67…”

“…Oscillator strengths ( f ) have been computed according to the formula where the TDM stands for the CASSCF transition dipole moment between the initial φ 1 and final φ 2 electronic states, and TDM = ⟨φ 1 |d⃗|φ 2 ⟩, where d⃗ is the dipole moment operator. The present CASPT2//CASSCF computational approach has been demonstrated to provide accurate results compared to experimental recordings, and has been previously used by the authors of the present work to correctly assign experimental transient absorption spectroscopy signals of uracil, thymine, and cytosine radicals. , …”

“…Difficulties in the determination of the C4/C5 regioselectivity arise not only from the fast decomposition of the A4OH/A5OH species, which undergoes − OH loss on the microsecond scale, hampering its experimental detection. The chemical structure of A also complicates the resolution, since the C4 and C5 positions do not allow substitutions, making the synthesis of photolabile precursors of C4-or C5-centered radicals impossible, a strategy recently used in pyrimidine NBs (see ref 26 and references cited therein). Both A4OH and A5OH are transformed to the oxidant (A− H) • species, identified as the radical dehydrogenated from the −NH 2 group (ANH).…”

Hydroxyl Radical Addition to Thymine and Cytosine and Photochemistry of the Adducts at the C6 Position

“…Finally, the water radiolysis exerted by ionizing radiation, relevant in more specific situations such as space travel, nuclear plants’ environments or cancer treatment, among many others, yields . OH and other types of reactive species like hydrated electrons and hydrogen atoms …”