Photoinduced processes in nucleic acids

The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study

Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.

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.

Temperature effects on the internal conversion of excited adenine and adenosine

This work aims to elucidate the dependence of the excited-state lifetime of adenine and adenosine on temperature. So far, it has been experimentally shown that while adenine's lifetime is unaffected by temperature, adenosine's lifetime strongly depends on it. However, the non-Arrhenius temperature dependence has posed a challenge in explaining this phenomenon. We used surface hopping to simulate the dynamics of adenine and adenosine in the gas phase at 0 and 400 K. The temperature effects were observed under the initial conditions via Wigner sampling with thermal corrections. Our results confirm that adenine's excited-state lifetime does not depend on temperature, while adenosine's lifetime does. Adenosine's dependency is due to intramolecular vibrational energy transfer from adenine to the ribose group. At 0 K, this transfer reduced the mean kinetic energy of adenine's moiety so much that internal conversion is inhibited, and the lifetime elongated by a factor of 2.3 compared to that at 400 K. The modeling also definitively ruled out the influence of viscosity, which was proposed as an alternative explanation previously.

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.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution

The excited-state properties and photophysics of cytosine aza-analogues, i.e., 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S₁(ππ*) state decay back to the S₀ state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S₁, S₂, T₁, T₂, and S₀ states. Upon photoexcitation to the bright S₁(ππ*) state, 2,4-DT quickly relaxes to its S₁ minimum and then overcomes a small energy barrier of 5.1 kcal mol^-1 to approach a S₁/S₀ conical intersection, where the S₁ system hops to the S₀ state through S₁ → S₀ internal conversion (IC). In addition, at the S₁ minimum, the system could partially undergo intersystem crossing (ISC) to the T₁ state, followed by further ISC to the S₀ state via the T₁/S₀ crossing point. In the T₁ state, an energy barrier of 7.9 kcal mol^-1 will trap 2,4-DT for a while. In parallel, for 2-AT, the system first relaxes to the S₁ minimum and then S₁ → S₀ IC or S₁ → T₁ → S₀ ISCs take place to the S₀ state by surmounting a large barrier of 15.3 kcal mol^-1 or 11.9 kcal mol^-1, respectively, which heavily suppress electronic transition to the S₀ state. Different from 2,4-DT, upon photoexcitation in the Franck-Condon region, 2-AT can quickly evolve in an essentially barrierless manner to nearby S₂/S₁ conical intersection, where the S₂ and T₁ states can be populated. Once it hops to the S₂ state, the system will overcome a relatively small barrier (6.6 kcal mol^-1vs. 15.3 kcal mol^-1) through IC to the S₀ state. Similarly, an energy barrier of 11.9 kcal mol^-1 heavily suppresses the T₁ state transformation to the S₀ state. The present work manifests that the amination/deamination of the triazine rings can affect some degree of different vertical and adiabatic excitation energies and nonradiative decay pathways in solution. It not only rationalizes excited-state decay dynamics of 2,4-DT and 2-AT in aqueous solution but could also provide insights into the understanding of the photophysics of aza-nucleobases.

Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies

ConspectusThe interaction between light and multichromophoric assemblies (MCAs) is the primary event of many fundamental processes, from photosynthesis to organic photovoltaics, and it triggers dynamical processes that share remarkable similarities at the molecular scale: light absorption, energy and charge transfer, internal conversions, emission, and so on. Those events often involve many chromophores and different excited electronic states that are coupled on an ultrafast time scale. This Account aims to discuss some of the chemical physical effects ruling these processes, a fundamental step toward their control, based on our experience on nucleic acids.In the last 15 years, we have, indeed, studied the photophysics and photochemistry of DNA and its components. By combining different quantum mechanical methods, we investigated the molecular processes responsible for the damage of the genetic code or, on the contrary, those preventing it by dissipating the excess energy deposited in the system by UV absorption. Independently of its fundamental biological role, DNA, with its fluctuating closely stacked bases stabilized by weak nonbonding interactions, can be considered a prototypical MCA. Therefore, it allows one to tackle within a single system many of the conceptual and methodological challenges involved in the study of photoinduced processes in MCA.In this Account, by using the outcome of our studies on oligonucleotides as a guideline, we thus highlight the most critical modellistic issues to be faced when studying, either experimentally or computationally, the interaction between UV light and DNA and, at the same time, bring out their general relevance for the study of MCAs.We first discuss the rich photoactivated dynamics of nucleobases (the chromophores), highlighting the main effects modulating the interplay between their excited states and how the latter can affect the photoactivated dynamics of the polynucleotides, either providing effective monomer-like nonradiative decay routes or triggering reactive processes (e.g., triplet generation).We then tackle the reaction paths involving multiple bases, showing that in the DNA duplex the most important ones involve two stacked bases, forming a neutral excimer or a charge transfer (CT) state, which exhibit different spectral signatures and photochemical reactivity. In particular, we analyze the factors affecting the dynamic equilibrium between the excimer and CT, such as the fluctuations of the backbone or the rearrangement of the solvent.Next, we highlight the importance of the effects not directly connected to the chromophores, such as the flexibility of the backbone or the solvent effect. The former, affecting the stacking geometry of the bases, can determine the preference between different deactivation paths. The latter is particularly influential for CT states, making very important an accurate treatment of dynamical solvation effects, involving both the solvent bulk and specific solute-solvent interactions.In the last section, we describe the main methodological challenges related to the study of polynucleotide excited states and stress the benefits derived by the integration of complementary approaches, both computational and experimental. Only exploiting different point of views, in our opinion, it is possible to shed light on the complex phenomena triggered by light absorption in DNA, as in every MCA.

Role of the Hydrogen Bond on the Internal Conversion of Photoexcited Adenosine

Experiments and theory have revealed that hydrogen bonds modify the excited-state lifetimes of nucleosides compared to nucleobases. Nevertheless, how these bonds impact the internal conversion is still unsettled. This work simulates the non-adiabatic dynamics of adenosine conformers in the gas phase with and without hydrogen bonds between the sugar and adenine moieties. The isomer containing the hydrogen bond (syn) exhibits a significantly shorter excited-state lifetime than the isomer without it (anti). However, internal conversion through electron-driven proton transfer between sugar and adenine plays only a minor (although non-negligible) role in the photophysics of adenosine. Either with or without hydrogen bonds, photodeactivation preferentially occurs following the ring-puckering pathways. The role of the hydrogen bond is to avoid the sugar rotation relative to adenine, shortening the distance to the ring-puckering internal conversion.

Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside

2'-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark ¹ nπ* state with a lifetime of ∼3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.

Integrated Renewable Production of Sorbitol and Xylitol from Switchgrass

This work deals with the design of integrated facilities for the production of xylitol and sorbitol from lignocellulosic biomass. Xylitol can be obtained from xylose via fermentation or catalytic hydrogenation. Sorbitol is obtained from glucose, but preferably from fructose, and also via fermentation or catalytic hydrogenation. Fructose can be obtained from glucose via isomerization. Thus, a superstructure of alternatives is formulated to process switchgrass, corn stover, miscanthus, and other agricultural and forestry residues. Different pretreatments, such as dilute acid or ammonia fiber explosion (AFEX), for the fractionation of the biomass are evaluated. Next, after hydrolysis, the C5 and C6 sugars are processed separately for which a catalytic or a fermentation stage are considered. Glucose has to be isomerized before it can be processed. Finally, crystallization in a multistage evaporator system is used for purification. The optimization of the system is done by the use of dilute acid and the catalytic system. A system of 3 crystallizers is selected. For a facility that produces 145 kt/yr of xylitol and 157.6 kt/yr of sorbitol, the investment adds up to 120.74 M€ for a production cost of 0.28 €/kg products. The inverse engineering of biomass was also performed resulting in a composition of 15% water, 20% cellulose, 40% hemicellulose, 15% lignin, and 5% ash. The closest biomass corresponds to Sargassum (brown algae), which is capable of producing 230.5 kt/yr of xylitol and 116 kt/yr of sorbitol with investment and production costs of 120.5 M€ and 0.25 €/kg products, respectively.

Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tz, tz, and tz

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.

Simulation of Excitation by Sunlight in Mixed Quantum-Classical Dynamics

This paper proposes a method to simulate nonadiabatic dynamics initiated by thermal light, including solar radiation, in the frame of mixed quantum-classical (MQC) methods, like surface hopping. The method is based on the Chenu-Brumer approach, which treats the thermal radiation as an ensemble of coherent pulses. It is composed of three steps: (1) sampling initial conditions from a broad blackbody spectrum, (2) dynamics propagation using conventional methods, and (3) ensemble averaging considering the field and realization time of the pulses. The application of MQC dynamics with pulse ensembles (MQC-PE) to a model system of nucleic acid photophysics showed the emergence of a steady excited-state population. In another test case, modeling retinal photophysics, MQC-PE predicted that although the photoisomerization occurs within 200 fs, it may take tens of microseconds of continuous solar irradiation to photoactivate a single retinal. Such emergent long timescales may impact our understanding of biological and technological phenomena occurring under solar radiation.

Simulation of Excitation by Sunlight in Mixed Quantum-Classical Dynamics

This paper proposes a method to simulate nonadiabatic dynamics initiated by thermal light, including solar radiation, in the frame of mixed quantum-classical (MQC) methods, like surface hopping. The method is based on the Chenu–Brumer approach, which treats the thermal radiation as an ensemble of coherent pulses. It is composed of three steps: (1) sampling initial conditions from a broad blackbody spectrum, (2) dynamics propagation using conventional methods, and (3) ensemble averaging considering the field and realization time of the pulses. The application of MQC dynamics with pulse ensembles (MQC-PE) to a model system of nucleic acid photophysics showed the emergence of a steady excited-state population. In another test case, modeling retinal photophysics, MQC-PE predicted that although the photoisomerization occurs within 200 fs, it may take tens of microseconds of continuous solar irradiation to photoactivate a single retinal. Such emergent long timescales may impact our understanding of biological and technological phenomena occurring under solar radiation.

Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study

The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (π_Hπ_L^*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (n_Oπ_L^*). The population of the second ππ* state decays almost completely, in <100 fs, not only to π_Hπ_L^* and to n_Oπ_L^* states but also to another nπ_L^* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.

Initial excited-state structural dynamics of 2′-deoxyadenosine

Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.

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* L_a) 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* L_a) state is populated (higher-energy radiation), the system will encounter conical intersections with the S₂ ¹(n_Oπ*) and S₁ ¹(ππ*) states before evolving to the ¹(ππ* L_a)_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* L_a) 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.

Nonadiabatic dynamics: The SHARC approach

We review the Surface Hopping including ARbitrary Couplings (SHARC) approach for excited-state nonadiabatic dynamics simulations. As a generalization of the popular surface hopping method, SHARC allows simulating the full-dimensional dynamics of molecules including any type of coupling terms beyond nonadiabatic couplings. Examples of these arbitrary couplings include spin-orbit couplings or dipole moment-laser field couplings, such that SHARC can describe ultrafast internal conversion, intersystem crossing, and radiative processes. The key step of the SHARC approach consists of a diagonalization of the Hamiltonian including these couplings, such that the nuclear dynamics is carried out on potential energy surfaces including the effects of the couplings-this is critical in any applications considering, for example, transition metal complexes or strong laser fields. We also give an overview over the new SHARC2.0 dynamics software package, released under the GNU General Public License, which implements the SHARC approach and several analysis tools. The review closes with a brief survey of applications where SHARC was employed to study the nonadiabatic dynamics of a wide range of molecular systems. This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and KineticsSoftware > Simulation MethodsSoftware > Quantum Chemistry.

Surface hopping dynamics including intersystem crossing using the algebraic diagrammatic construction method

We report an implementation for employing the algebraic diagrammatic construction to second order [ADC(2)] ab initio electronic structure level of theory in nonadiabatic dynamics simulations in the framework of the SHARC (surface hopping including arbitrary couplings) dynamics method. The implementation is intended to enable computationally efficient, reliable, and easy-to-use nonadiabatic dynamics simulations of intersystem crossing in organic molecules. The methodology is evaluated for the 2-thiouracil molecule. It is shown that ADC(2) yields reliable excited-state energies, wave functions, and spin-orbit coupling terms for this molecule. Dynamics simulations are compared to previously reported results using high-level multi-state complete active space perturbation theory, showing favorable agreement.

Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations

The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.

Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments

Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential energy surfaces, requires the powerful interplay between experimental measurements and state of the art molecular simulations. In this review, we provide an overview on the photophysics of natural nucleobases’ thioanalogs, which covers the last 30 years and both experimental and computational contributions. For all the canonical nucleobase’s thioanalogs, we have compiled the main steady state absorption and emission features and their interpretation in terms of theoretical calculations. Then, we revise the main topographical features, including stationary points and interstate crossings, of their potential energy surfaces based on quantum mechanical calculations and we conclude, by combining the outcome of different spectroscopic techniques and molecular dynamics simulations, with the mechanism by which these nucleobase analogs populate their triplet excited states, which are at the origin of their photosensitizing properties.

Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides

For the first time, ultrafast deactivations of photoexcited water-solvated pyrimidine nucleosides are mapped employing hybrid QM(CASPT2)/MM(AMBER) optimizations that account for explicit solvation, sugar effects, and dynamically correlated potential energy surfaces. Low-energy S₁/S₀ ring-puckering and ring-opening conical intersections (CIs) are suggested to drive the ballistic coherent subpicosecond (<200 fs) decays observed in each pyrimidine, the energetics controlling this processes correlating with the lifetimes observed. A second bright ¹π₂π* state, promoting excited-state population branching and leading toward a third CI with the ground state, is proposed to be involved in the slower ultrafast decay component observed in Thd/Cyd. The transient spectroscopic signals of the competitive deactivation channels are computed for the first time. A general unified scheme for ultrafast deactivations, spanning the sub- to few-picosecond time domain, is eventually delivered, with computed data that matches the experiments and elucidates the intrinsic photoprotection mechanism in solvated pyrimidine nucleosides.

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted ¹(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents

We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.

Multiconfigurational Second-Order Perturbation Theory with Frozen Natural Orbitals Extended to the Treatment of Photochemical Problems

A new flavor of the frozen natural orbital complete active space second-order perturbation theory method (FNO-CASPT2, Aquilante et al., J. Chem. Phys. 131, 034113) is proposed herein. In this new implementation, the virtual space in Cholesky decomposition-based CASPT2 computations (CD-CASPT2) is truncated by excluding those orbitals that contribute the least toward preserving a predefined value of the trace of an approximate density matrix, as that represents a measure of the amount of dynamic correlation retained in the model. In this way, the amount of correlation included is practically constant at all nuclear arrangements, thus allowing for the computation of smooth electronic states surfaces and energy gradients-essential requirements for theoretical studies in photochemistry. The method has been benchmarked for a series of relevant biochromophores for which large speed-ups have been recorded while retaining the accuracy achieved in the corresponding CD-CASPT2 calculations. Both vertical excitation energies and gradient calculations have been carried out to establish general guidelines as to how much correlation needs to be retained in the calculation for the results to be consistent with the CD-CASPT2 findings. Our results feature errors within a tenth of an eV for the most difficult cases and have been validated to be used for gradient computations where an up to 3-fold speed-up is observed depending on the size of the system and the basis set employed.

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate

The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.