On the Intrinsically Low Quantum Yields of Pyrimidine DNA Photodamages: Evaluating the Reactivity of the Corresponding Minimum Energy Crossing Points

Nonadiabatic molecular dynamics with subsystem density functional theory: application to crystalline pentacene

In this work, we report the development and assessment of the nonadiabatic molecular dynamics approach with the electronic structure calculations based on the linearly scaling subsystem density functional method. The approach is implemented in an open-source embedded Quantum Espresso/Libra software specially designed for nonadiabatic dynamics simulations in extended systems. As proof of the applicability of this method to large condensed-matter systems, we examine the dynamics of nonradiative relaxation of excess excitation energy in pentacene crystals with the simulation supercells containing more than 600 atoms. We find that increased structural disorder observed in larger supercell models induces larger nonadiabatic couplings of electronic states and accelerates the relaxation dynamics of excited states. We conduct a comparative analysis of several quantum-classical trajectory surface hopping schemes, including two new methods proposed in this work (revised decoherence-induced surface hopping and instantaneous decoherence at frustrated hops). Most of the tested schemes suggest fast energy relaxation occurring with the timescales in the 0.7-2.0 ps range, but they significantly overestimate the ground state recovery rates. Only the modified simplified decay of mixing approach yields a notably slower relaxation timescales of 8-14 ps, with a significantly inhibited ground state recovery.

Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering

Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.

Sequence dependent UV damage of complete pools of oligonucleotides

Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.

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.

SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide

Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.

On the Importance of Ligand-Centered Excited States in the Emission of Cyclometalated Ir(III) Complexes

The photophysical behavior of the cyclometalating Ir(III) complexes [Ir(ppy)₂(bpy)]⁺, where Hppy is 2-phenylpyridine and bpy is 2,2′-bipyridine (complex 1), and [Ir(diFppy)₂(dtb-bpy)]⁺, where diFppy is 2-(2,4-difluorophenyl)pyridine and dtb-bpy is 4,4′-di-tert-butyl-2,2′-bipyridine (complex 2), has been theoretically investigated by performing density functional theory calculations. The two complexes share the same molecular skeleton, complex 2 being derived from complex 1 through the addition of fluoro and tert-butyl substituents, but present notable differences in their photophysical properties. The remarkable difference in their emission quantum yields (0.196 for complex 1 in dichloromethane and 0.71 for complex 2 in acetonitrile) has been evaluated by characterizing both radiative and nonradiative decay paths. It has emerged that the probability of decaying through the nonradiative triplet metal-centered state, normally associated with the loss of the emission quantum yield, does not appear to be the reason behind the reported substantially different emission efficiency. A more critical factor appears to be the ability of complex 2 to emit from both the usual metal-to-ligand charge-transfer state and from two additional ligand-centered states, as supported by the fact that the respective minima belong to the potential energy surface of the lowest triplet T₁ state and that their phosphorescence lifetimes are in the same order of magnitude. In contrast, the emission of complex 1 can be originated only from the metal-to-ligand charge-transfer state, being the only emissive T₁ minimum. The results constitute a significant case in which the emission from ligand-centered states is the key for determining the high emission quantum yield of a complex.

The reasons behind the significant increase in the emission quantum yield of the [Ir(diFppy)₂(dtb-bpy)]⁺ complex with respect to [Ir(ppy)₂(bpy)]⁺ are rationalized on the basis of DFT, TDDFT, and TDDFT-SOC calculations, revealing the key role that low-lying LC states can play in the emission properties of the complex.