How Does Thymine DNA Survive Ultrafast Dimerization Damage?

Synergetic argentophilic and through space electronic interactions in a single-crystal-to-single-crystal photocycloaddition reaction: a mechanistic study

Ag(I) is able to mediate single-crystal-to-single-crystal transformation through [2+2] photocycloaddition to prepare high-conductivity materials. However, the intrinsic mechanism of Ag(I) mediation, the detailed photophysical and photochemical processes as well as the origin of the enhanced conductivity of nanocrystals are still unclear. In this work, the comprehensive kinetic scheme and regulation mechanism are established by the accurate QM/MM calculations at the CASPT2//CASSCF/AMBER level of theory with consideration of the crystal environment. We find that the argentophilic interaction and through space electronic interaction are the key factors that promote Ag(I)-mediated [2+2] PCA reactions and may account for the enhancement of conductivity. These mechanistic insights into the Ag(I)-regulated photo-dimerization in the crystal surrounding are beneficial for the design of the structurally and electrically favorable skeletons of a metal-organic coordination polymer.

Intermolecular-Type Conical Intersections in Benzene Dimer

The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT) as well as using the multiconfigurational complete active space self-consistent field (CASSCF) method considering the minimally augmented def2-TZVPP and the 6-31G(d,p) basis sets. It was found that the stacking distance between the benzene monomers decreases by about 0.5 Å in the first electronic excited state, due to the stronger intermolecular interaction energy, bringing the two monomers closer together. Intermolecular-type conical intersection (CI) geometries can be formed between the two benzene molecules, when (i) both monomer rings show planar deformation and (ii) weaker (approximately 1.6-1.8 Å long) C-C bonds are formed between the two monomers, with parallel and antiparallel orientation with respect to the monomer. These intermolecular-type CIs look energetically more favorable than dimeric CIs containing only one deformed monomer. The validity of the dimer-type CI geometries obtained by SF-TDDFT was confirmed by the CASSCF method. The nudged elastic band method used for finding the optimal relaxation path has confirmed both the accessibility of these intermolecular-type CIs and the possibility of the radiationless deactivation of the electronic excited states through these CI geometries. Although not as energetically favorable as the previous two CI geometries, there are other CI geometries characterized by the relative rotation of monomers at different angles around a vertical C-C axis.

On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution

UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.

The Behavior of Triplet Thymine in a Model B-DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations†

Among the naturally occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B-DNA environment. The energy gap varies between 305 and 329 kJ mol^-1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double-stranded 16-bp oligonucleotide. The energy of triplet state decreases up to 300 kJ mol^-1 , due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ mol^-1 ), and our theoretical exploration opens the door to investigations toward other more complex and biologically relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semi-empirical approaches such as density functional-based tight-binding, allowing to further rationalize sequence effects.

Mechanistic insight into photocrosslinking reaction between triplet state 4-thiopyrimidine and thymine

Multiple nonadiabatic pathways greatly facilitate the proceeding of photocrosslinking reactions between 4-thiopyrimidine and thymine.

Photorelaxation and Photorepair Processes in Nucleic and Amino Acid Derivatives

Understanding the fundamental interaction between electromagnetic radiation and matter is essential for a large number of phenomena, with significance to civilization.[...].

Stepwise photosensitized thymine dimerization mediated by an exciton intermediate

ABSTRACT

Cyclobutane thymine dimerization is the most prominent DNA photoinduced damage. While the ultrafast mechanism that proceeds in the singlet manifold is nowadays well established, the triplet-state pathway is not completely understood. Here we report the underlying mechanism of the photosensitized dimerization process in the triplet state. Quantum chemical calculations, combined with wavefunction analysis, and nonadiabatic molecular dynamics simulations demonstrate that this is a stepwise reaction, traversing a long-lived triplet biradical intermediate, which is characterized as a Frenkel exciton with very small charge-transfer character. The low yield of the reaction is regulated by two factors: (i) a relatively large energy barrier that needs to be overcome to form the exciton intermediate, and (ii) a bifurcation of the ground-state potential-energy surface that mostly leads back to the Franck-Condon region because dimerization requires a very restricted combination of coordinates and velocities at the event of non-radiative decay to the ground state.

GRAPHICAL ABSTRACT