Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil.

DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.

The copious photochemistry of 2,6-diaminopurine: Luminescence, triplet population, and ground state recovery.

9H- and 7H-2,6-Diaminopurine (26DAP) photoinduced events in vacuum were studied at the MS-CASPT2/cc-pVDZ level of theory. The S1 1 (ππ* La ) state is initially populated evolving barrierless towards its minimum energy structure, from where two photochemical events can take place in both tautomers. The first is the return of the electronic population to the ground state via the C6 conical intersection (CI-C6). The second involves an internal conversion to the ground through the C2 conical intersection (CI-C2). According to our geodesic interpolated paths connecting the critical structures, the second route is less favorable in both tautomers, due to the presence of high energy barriers. Our calculations suggest a competition between fluorescence and ultrafast relaxation to the electronic ground state via internal conversion process. Based on our calculated potential energy surfaces and experimental excited state lifetimes from the literature, we can infer that the 7H- must have a greater fluorescence yield than the 9H-tautomer. We also explored the triplet state population mechanisms on the 7H-26DAP to understand their long-lived components observed experimentally.

Water Solvated Zn(II)-Guanine Complex: Structural Aspects and Luminescence Properties.

Understanding the role of metal ions in living organisms and their interactions with biological compounds is fundamental for our health and for developing technological devices for bioinorganic applications. In this work, structural aspects and photophysical mechanisms involved in the luminescence of the Zn(II)-guanine complex in water were studied by using computational quantum chemical methods, providing molecular-level explanations for reported experimental findings. Structural aspects were investigated with def2-SVP basis sets, Density Functional Theory, Resolution of Identity Algebraic Diagrammatic Construction in Second-Order (RI-ADC(2)), Polarizable Continuum Model (PCM), and Conductor-like Screening Model (COSMO) methods. Spectroscopic properties and photophysical deactivation mechanisms were explored with the atomic natural orbital basis sets including relativistic and semicore correlation (ANO-RCC-VDZP) basis sets, Multistate Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2), and Polarizable Continuum Model (PCM) methods. Our results indicate that Zn(II) ions bind preferentially to the N7 position, and three water molecules in its coordination sphere are sufficient for describing the photophysical properties. The complexation with Zn(II) ions and solvation effects favor fluorescence because the minimum energy region of the S1 (La) (1ππ*) ((La)min) potential energy hypersurface is stabilized, the (La/GS) crossing region is destabilized, and a high energetic barrier along the pathway from the (La)min and (La/GS) regions hampers fast nonradiative return of the electronic population to the ground state, as observed for isolated 9H-guanine.

Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA.

UV-VIS photoinduced events of tz A and tz G embedded into DNA and RNA are described by combining the Extended Multi-State Second-Order Perturbation Theory (XMS-CASPT2) and electrostatic embedding molecular mechanics methods (QM/MM). Our results point out that the S1 1 (ππ* La ) state is the bright state in both environments. After the photoexcitation to the S1 1 (ππ* La ) state, the electronic population evolves barrierless towards its minimum, from where the excess of energy can be dissipated by fluorescence. As the minimum energy crossing point structure between the ground and first bright states lies in a high-energy region, the direct internal conversion to the ground state is an unviable mechanism. Other spectroscopic properties (for instance, absorption and Stokes shifts) and comparisons with photochemical properties of canonical nucleobases are also provided.

Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-aza-7-deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet†.

The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art extended multi-state complete active space second-order perturbation theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10- to 30-fold slower relaxation (depending on solvent) compared with guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared with guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemically active to adjacent nucleobases than guanine or other nucleobases within DNA.

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water.

Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S2 state that converts internally to the dark S1 state, from which the population is transferred to the triplet T2 state via intersystem crossing and finally to the lowest T1 state. This S2 → S1 → T2 → T1 deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T1 lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T1/S0 crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ1 = 131 fs and τ2 = 191 fs) that are in excellent agreement with the experimentally reported value (τexp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.

Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil.

The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.

On the population of triplet states of 2-seleno-thymine.

The population and depopulation mechanisms leading to the lowest-lying triplet states of 2-Se-Thymine were studied at the MS-CASPT2/cc-pVDZ level of theory. Several critical points on different potential energy hypersurfaces were optimized, including minima, conical intersections, and singlet-triplet crossings. The accessibility of all relevant regions on the potential energy hypersurfaces was investigated by means of minimum energy paths and linear interpolation in internal coordinates techniques. Our analysis indicates that, after the population of the bright S2 state in the Franck-Condon region, the first photochemical event is a barrierless evolution towards one of its two minima. After that, three viable photophysical deactivation paths can take place. In one of them, the population in the S2 state is transferred to the T2 state via intersystem crossing and subsequently to the T1 state by internal conversion. Alternatively, the S1 state could be accessed by internal conversion through two distinct conical intersections with S2 state followed by singlet-triplet crossing with the T2 state. The absence of a second minimum on the T1 state and a small energy barrier on pathway along the potential energy surface towards the ground state from the lowest triplet state are attributed as potential reasons to explain why the lifetime of the triplet state of 2-Se-Thymine might be reduced in comparison with its thio-analogue.

Excited-State Properties and Relaxation Pathways of Selenium-Substituted Guanine Nucleobase in Aqueous Solution and DNA Duplex.

The excited-state properties and relaxation mechanisms after light irradiation of 6-selenoguanine (6SeG) in water and in DNA have been investigated using a quantum mechanics/molecular mechanics (QM/MM) approach with the multistate complete active space second-order perturbation theory (MS-CASPT2) method. In both environments, the S1 1(nSeπ5*) and S2 1(πSeπ5*) states are predicted to be the spectroscopically dark and bright states, respectively. Two triplet states, T1 3(πSeπ5*) and T2 3(nSeπ5*), are found energetically below the S2 state. Extending the QM region to include the 6SeG-Cyt base pair slightly stabilizes the S2 state and destabilizes the S1, due to hydrogen-bonding interactions, but it does not affect the order of the states. The optimized minima, conical intersections, and singlet-triplet crossings are very similar in water and in DNA, so that the same general mechanism is found. Additionally, for each excited state geometry optimization in DNA, three kind of structures ("up", "down", and "central") are optimized which differ from each other by the orientation of the C═Se group with respect to the surrounding guanine and thymine nucleobases. After irradiation to the S2 state, 6SeG evolves to the S2 minimum, near to a S2/S1 conical intersection that allows for internal conversion to the S1 state. Linear interpolation in internal coordinates indicate that the "central" orientation is less favorable since extra energy is needed to surmount the high barrier in order to reach the S2/S1 conical intersection. From the S1 state, 6SeG can further decay to the T1 3(πSeπ5*) state via intersystem crossing, where it will be trapped due to the existence of a sizable energy barrier between the T1 minimum and the T1/S0 crossing point. Although this general S2 → T1 mechanism takes place in both media, the presence of DNA induces a steeper S2 potential energy surface, that it is expected to accelerate the S2 → S1 internal conversion.

Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI.

The photophysical relaxation pathways of tzA, tzG, and tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying 1(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the 1(ππ*)min region, the conical intersection with the ground state ((ππ*/GS)CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.

Photochemical Relaxation Pathways of 9 H-8-Azaguanine and 8 H-8-Azaguanine.

The photochemical reaction path approach, the MS-CASPT2 quantum-chemical method, and double-ζ basis sets (cc-pVDZ) were used to study 9 H-8-azaguanine and 8 H-8-azaguanine relaxation pathways. Several potential energy hypersurfaces were characterized by means of equilibrium geometries, surface crossings (conical intersections and singlet-triplet intersystem crossings), minimum energy paths, and linear interpolation in internal coordinates. The 9 H-8-azaguanine main photochemical event begins with the direct population of the 1(ππ* La) state, which evolves toward a conical intersection with the ground state after surmounting a small energy barrier, explaining why it is nonfluorescent. For 8 H-8-azaguanine, two relaxation mechanisms are possible, depending on the excitation energy. If the S1 1(ππ*) state is initially populated (lower-energy region), the system evolves barrierless to the S1 1(ππ*)min region, from where the excess energy is released. If the 1(ππ* La) state is populated (higher-energy radiation), the system will encounter conical intersections with the S2 1(nOπ*) and S1 1(ππ*) states before evolving to the 1(ππ* La)min region, from where a conical intersection with the ground state is accessible, favoring radiationless deactivation to the ground state. However, because a fraction of the population can be transferred from 1(ππ* La) to the S1 1(ππ*) state, emission from the S1 1(ππ*)min region is also expected, although weaker than it would be if the S1 1(ππ*) state were populated directly. Irrespective of the excitation energy, the emissive state is the same and a single fluorescence band is observed, with the strongest emission occurring upon excitation in the lower-energy region, as observed experimentally. Therefore, our computational study corroborates experimental results, attributing the emission of the neutral form of 8-azaguanine in solution to the presence of the minor 8 H-8-azaguanine tautomer, while the 9 H-8-azaguanine major tautomer is nonfluorescent.

Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories.

In this computational work, we assessed the performance of ab initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single-state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI-CC2, RI-ADC2 and EOM-CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2-IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.

Photoinduced processes in nucleic acids.

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.

The low-lying electronic states of ReB.

The ground and low-lying electronic states of ReB were studied at the CASPT2//CASSCF level (multiconfigurational second-order perturbation theory) and quadruple-ζ ANO-RCC basis sets. Spectroscopic constants, potential energy curves, wavefunctions, and Mulliken population analysis are given. The ground state of ReB is of X(5)Σ(+) symmetry (R e = 1.817 Å, ω e = .909 cm(-1), and µ = 2.87 D), giving rise to a Ω = 0(+) ground state after including spin-orbit coupling.

Relaxation Mechanisms of 5-Azacytosine.

The photophysics and deactivation pathways of the noncanonical 5-azacytosine nucleobase were studied using the CASPT2//CASSCF protocol. One of the most significant differences with respect to the parent molecule cytosine is the presence of a dark (1)(nNπ*) excited state placed energetically below the bright excited state (1)(ππ*) at the Franck-Condon region. The main photoresponse of the system is a presumably efficient radiationless decay back to the original ground state, mediated by two accessible conical intersections involving a population transfer from the (1)(ππ*) and the (1)(nNπ*) states to the ground state. Therefore, a minor contribution of the triplet states in the photophysics of the system is expected, despite the presence of a deactivation path leading to the lowest (3)(ππ*) triplet state. The global scenario on the photophysics and photochemistry of the 5-azacytosine system gathered on theoretical grounds is consistent with the available experimental data, taking especially into account the low values of the singlet-triplet intersystem crossing and fluorescence quantum yields observed.

On the population of triplet excited states of 6-aza-2-thiothymine.

The mechanisms of population of the lowest excited triplet states of 6-aza-2-thiothymine were investigated by means of CASPT2//CASSCF quantum-chemical calculations, with extensive atomic natural orbital basis sets of double-ζ quality (ANO-L-VDZP). Several key structures corresponding to equilibrium geometries, surface crossings, minimum energy paths, and linear interpolation in internal coordinates were used to explain the ability to sensitize molecular oxygen. After population of the S2(1)(ππ*) state, the system evolves to the state minimum. At this point, and along the minimum energy path of the (1)(ππ*) state, two main mechanisms related to the triplet and singlet manifolds can be visualized, leading the system to the lowest triplet state, T1(3)(ππ*).

On the mechanisms of triplet excited state population in 8-azaadenine.

The photophysics of 8-azaadenine (8-AA) has been studied with the CASPT2//CASSCF protocol and ANO-L double-ζ basis sets. Stationary equilibrium structures, surface crossings, minimum energy paths, and linear interpolations have been used to study possible mechanisms to populate the lowest triplet state, T(1)(3)(ππ*), capable of sensitizing molecular oxygen. Our results show that two main mechanisms can occur after photoexcitation to the S(2)(1)(ππ*) state. The first one is through the S(2)/S(1) conical intersection (((1)ππ*/(1)nπ*)(CI)), leading to the S(1) ((1)nπ*) state minimum, (S(1) ((1)nπ*))(min), where a singlet-triplet crossing, ((1)nπ*/(3)ππ*)(STC), is accessible. The second one starts with the ((1)ππ*/(3)nπ*)(STC) at the (S(2)((1)ππ*))(min), from which the system can evolve to the (T(2) ((3)nπ*))(min), with subsequent population of the T(1) excited electronic state, due to the ((3)nπ*/(3)ππ*)(CI) conical intersection.

On the deactivation mechanisms of adenine-thymine base pair.

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)], and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

On the relaxation mechanisms of 6-azauracil.

The nonadiabatic photochemistry of 6-azauracil has been studied by means of the CASPT2//CASSCF protocol and double-ζ plus polarization ANO basis sets. Minimum energy states, transition states, minimum energy paths, and surface intersections have been computed in order to obtain an accurate description of several potential energy hypersurfaces. It is concluded that, after absorption of ultraviolet radiation (248 nm), two main relaxation mechanisms may occur, via which the lowest (3)(ππ*) state can be populated. The first one takes place via a conical intersection involving the bright (1)(ππ*) and the lowest (1)(nπ*) states, ((1)ππ*/(1)nπ*)(CI), from which a low-energy singlet-triplet crossing, ((1)nπ*/(3)ππ*)(STC), connecting the (1)(nπ*) state to the lowest (3)(ππ*) triplet state is accessible. The second mechanism arises via a singlet-triplet crossing, ((1)ππ*/(3)nπ*)(STC), leading to a conical intersection in the triplet manifold, ((3)nπ*/(3)ππ*)(CI), evolving to the lowest (3)(ππ*) state. Further radiationless decay to the ground state is possible through a (gs/(3)ππ*)(STC).

Electronic structure and chemical bonding in the lowest electronic states of TcN.

Multiconfiguration second-order perturbation theory, with the inclusion of relativistic effects and spin-orbit coupling, was employed to investigate the nature of the ground and low-lying Lambda-S and Omega states of the TcN molecule. Spectroscopic constants, effective bond order, and potential energy curves for 13 low-lying Lambda-S states and 5 Omega states are given. The computed ground state of TcN is of Omega = 3 symmetry (R(e) = 1.605 A and omega(e) = 1085 cm(-1)), originating mainly from the (3)Delta Lambda-S ground state. This result is contrasted with the nature of the ground state for other VIIB transtion-metal mononitrides, including X(3)Sigma(-) symmetry for MnN and Omega = 0(+) symmetry for ReN, derived also from a X(3)Sigma(-) state.