Mechanisms of Ultrafast Excited-State Deactivation in Adenosine

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54±11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

Ribose and Deoxyribose Group Alter Excited-State Dynamics of 5-Azacytosine in Solution

5-Azacytosine (5-AC) is one of the best interesting noncanonical nucleobases due to its functionalization and structural imitation of natural bases. 5-AC can be used as the scaffold of two important chemotherapeutic medicines, 5-azacytidine and 2'-deoxy-5-azacytidine. Furthermore, increased sensitivity to UV leads to the photochemical effects of 5-AC also attracted attention. Yet, no study has been reported to explore the effect of glycosyl groups on the photophysical and photochemical properties of 5-AC, which can help to reveal the photostability of related actual clinic drugs. In this study, the excited-state dynamics of 5-azacytidine and 2'-deoxy-5-azacytidine are studied by femtosecond transient absorption and quantum-chemical calculations while revisiting that of 5-AC with a wider probe spectral range. It is shown that glycosyl substitution on the N1 position leads to ultrafast excited-state relaxation within several picoseconds in both nucleosides, which is distinct compared with the 17 ps lifetime seen in 5-AC. It is proposed that these changes are due to altering the energy level of the dark nπ* state. Moreover, our results suggest that it should be cautioned to simply replace sugar groups with methyl groups when doing a theoretical calculation study on nucleobases and their derivatives.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Revealing the excited-state dynamics of cytidine and the role of excited-state proton transfer process

The high photostability of DNAs and RNAs is inextricably related to the photochemical and photophysical properties of their building blocks, nucleobases and nucleosides, which can dissipate the absorbed UV light energy in a harmless manner. The deactivation mechanism of the nucleosides, especially the decay pathways of cytidine (Cyd), has been a matter of intense debate. In the current study, we employ high-level electronic structure calculations combined with excited state non-adiabatic dynamic simulations to provide a clear picture of the excited state deactivation of Cyd in both gas phase and aqueous solution. In both environments, a barrierless decay path driven by the ring-puckering motion and a relaxation channel with a small energy barrier driven by the elongation motion of CO bond are assigned to <200 fs and sub-picosecond decay time component, respectively. The presence of ribose group has a subtle effect on the dynamic behavior of Cyd in gas phase as the ribose-to-base hydrogen/proton transfer process is energetically inaccessible with a sizable energy barrier of about 1.4 eV. However, this energy barrier is significantly reduced in water, especially when an explicit water molecule is present. Therefore, we argue that the long-lived decay channel found in aqueous solution could be assigned to the Cyd-water intermolecular hydrogen/proton transfer process. The present study postulates a novel scenario toward deep understanding the intrinsic photostability of DNAs and RNAs and provides solid evidence to disclose the long history debate of cytidine excited-state decay mechanism, especially for the assignment of experimentally observed time components.

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.

Dynamic Role of the Intramolecular Hydrogen Bonding in the S1 State Relaxation Dynamics Revealed by the Direct Measurement of the Mode-Dependent Internal Conversion Rate of 2-Chlorophenol and 2-Chlorothiophenol

The dynamic role of the intramolecular hydrogen bond in the S1 relaxation of cis-2-chlorophenol (2-CP) or cis-2-chlorothiophenol (2-CTP) has been investigated in a state-specific manner. Whereas ultrafast internal conversion is dominant for 2-CP, the H-tunneling competes with internal conversion for 2-CTP even at the S1 origin. The S0-S1 internal conversion rate of 2-CTP could be directly measured from the S1 lifetimes of 2-CTP-d1 (Cl-C6H4-SD) as the D-tunneling is kinetically blocked, allowing distinct estimations of tunneling and internal conversion rates with increasing the energy. The internal conversion rate of 2-CTP increases by two times at the out-of-plane torsional mode excitation, suggesting that the internal conversion is facilitated at the nonplanar geometry. It then sharply increases at ∼600 cm-1, indicating that the S1/S0 conical intersection is readily accessible at the extended C-Cl bond length. The strength of the intramolecular hydrogen bond should be responsible for the distinct dynamic behaviors of 2-CP and 2-CTP.

The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects

Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.

Surface hopping modeling of charge and energy transfer in active environments

An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.

The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics

The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping simulation provides the essential information to understand the geometric evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A "hierarchical" protocol based on the dimensionality reduction and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.

Understanding How a New Hachimoji Nucleobase Alters Photodynamics of Genetic Building Blocks

This article is a highlight of the paper by Krul et al. in this issue of Photochemistry and Photobiology. It describes the excited state dynamics of 5-aza-7-deazaguanine (^5N7C G), which has recently been proposed as an alternative nucleobase. Upon UV absorption to the lowest energy ¹ ππ* state, ^5N7C G returns to the electronic ground state an order of magnitude more slowly than guanine with a corresponding greater fluorescence quantum yield. These findings are significant because they suggest that ^5N7C G is less UV photostable that its canonical nucleobase equivalent, which would have been a selective disadvantage in prebiotic conditions.

Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides

Potentially prebiotic chemical reactions leading to RNA nucleotides involve periods of UV irradiation, which are necessary to promote selectivity and destroy biologially irrelevant side products. Nevertheless, UV light has only been applied to promote specific stages of prebiotic reactions and its effect on complete prebiotic reaction sequences has not been extensively studied. Here, we report on an experimental and computational investigation of the photostability of 2-thiooxazole (2-TO), a potential precursor of pyrimidine and 8-oxopurine nucleotides on early Earth. Our UV-irradiation experiments resulted in rapid decomposition of 2-TO into unidentified small molecule photoproducts. We further clarify the underlying photochemistry by means of accurate ab initio calculations and surface hopping molecular dynamics simulations. Overall, the computational results show efficient rupture of the aromatic ring upon the photoexcitation of 2-TO via breaking of the C-O bond. Consequently, the initial stage of the divergent prebiotic synthesis of pyrimidine and 8-oxopurine nucleotides would require periodic shielding from UV light either with sun screening chromophores or through a planetary scenario that would protect 2-TO until it is transformed into a more stable intermediate compound, e.g. oxazolidinone thione.

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.

A combined experimental and computational study on the deactivation of a photo-excited 2,2'-pyridylbenzimidazole-water complex via excited-state proton transfer

In this report, we present solvent assisted excited-state proton transfer coupled to the deactivation of a photo-excited 2,2'-pyridylbenzimidazole bound to a single water molecule. Experimentally, the mass-selected 1 : 1 complex was probed using two-colour resonant two-photon ionization (2C-R2PI) and UV-UV hole-burning (HB) spectroscopy in a supersonically jet-cooled molecular beam. Computationally, three structural isomers were identified as the normal, the tautomer and the proton transfer product of the PBI-H₂O complex in the excited S₁ state using B3LYP-D4/def2-TZVPP and ADC(2) (MP2)/cc-pVDZ levels of theory. The most stable form in the ground state, i.e., the normal form, was identified using the excitation spectrum in the 30 544 to 30 936 cm^-1 region. The 2C-R2PI spectrum showed a sudden break-off above the 000 + 392 cm^-1 region, even though the Frack-Condon activity of the S₁ ← S₀ transition was measured beyond 000 + 1000 cm^-1 in the HB spectrum. The intensity of the bands associated with the excited state intermolecular vibrational modes near the break-off region was found to be drastically decreased, which indicates efficient quantum mechanical tunnelling along the hydrogen transfer coordinate. The sudden disappearance of the intermolecular vibrational modes in the spectrum revealed the existence of a deactivation channel in the PBI-H₂O complex near 392-450 cm^-1 above the 000 transition. The computational investigation predicted that the deactivation of the excited-state occurred via the intersection between the S₁ and S₀ states, which was associated with the proton transfer from the H₂O to the PBI molecule along the O(3)-H(4)→N(5) coordinate. The highest energy structure was identified as the point of intersection between the nπ* (S₂) and ππ* (S₁) states. The associated barrier height was experimentally determined to be 392-450 cm^-1, which showed a reasonable agreement with the calculated excited-state proton transfer barrier. Competing reaction channels such as dissociation and tautomerization were found to be highly energetically inaccessible.

Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage

UV-induced photolysis of aqueous guanine nucleosides produces 8-oxo-guanine and Fapy-guanine, which can induce various types of cellular malfunction. The mechanistic rationale underlying photodestructive processes of guanine nucleosides is still largely obscure. Here, we employ accurate quantum chemical calculations and demonstrate that an excited-state non-bonding interaction of guanosine and a water molecule facilitates the electron-driven proton transfer process from water to the chromophore fragment. This subsequently allows for the formation of a crucial intermediate, namely guanosine photohydrate. Further (photo)chemical reactions of this intermediate lead to the known products of guanine photodamage.

Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems

The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

We present experimental evidence for soft X-ray induced intramolecular hydrogen transfer in the protonated synthetic tri-oligonucleotide d($^{\mbox{\footnotesize{F}}}$UAG) in the gas-phase. The trinucleotide cations were stored in a cryogenic ion trap...

Excited State Deactivation Mechanisms of Protonated Adenine: a Theoretical study

Quantum chemical computational method as well as the adiabatic dynamics simulation have been employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We have located three...

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.

Excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate

Minor structural modifications to the DNA and RNA nucleobases have a significant effect on their excited state dynamics and electronic relaxation pathways. In this study, the excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate are investigated in aqueous solution and in a mixture of methanol and water using femtosecond broadband transient absorption spectroscopy following excitation at 267 nm. The transient spectra are collected using photon densities that ensure no parasitic multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily using a two- or three-component kinetic model. By analyzing the results from steady-state, time-resolved, computational calculations, and the methanol-water mixture, the following general relaxation mechanism is proposed for both molecules, L_b → L_a → ¹πσ^*(ICT) → S₀, where the ¹πσ^*(ICT) stands for an intramolecular charge transfer excited singlet state with significant πσ^* character. In general, longer lifetimes for internal conversion are obtained for 7-deazaguanosine compared to guanosine 5'-monophosphate. Internal conversion of the ¹πσ^*(ICT) state to the ground state occurs on a similar time scale of a few picoseconds in both molecules. Collectively, the results demonstrate that substitution of a single nitrogen atom for a methine (C-H) group at position seven of the guanine moiety stabilizes the ¹ππ^* L_b and L_a states and alters the topology of their potential energy surfaces in such a way that the relaxation dynamics in 7-deazaguanosine are slowed down compared to those in guanosine 5'-monophosphate but not for the internal conversion of ¹πσ^*(ICT) state to the ground state.

Caveat when using ADC(2) for studying the photochemistry of carbonyl-containing molecules

Several electronic-structure methods are available to study the photochemistry and photophysics of organic molecules. Among them, ADC(2) stands as a sweet spot between computational efficiency and accuracy. As a result, ADC(2) has recently seen its number of applications booming, in particular to unravel the deactivation pathways and photodynamics of organic molecules. Despite this growing success, we demonstrate here that care has to be taken when studying the nonradiative pathways of carbonyl-containing molecules, as ADC(2) appears to suffer from a systematic flaw.

Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues

Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil⁺ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C₅H₉O₄⁺ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition.

This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.

Theoretical insights on the excited-state-deactivation mechanisms of protonated thymine and cytosine

Ab initio and surface-hopping nonadiabatic dynamics simulation methods were employed to investigate relaxation mechanisms in protonated thymine (TH⁺) and cytosine (CH⁺). A few conical intersections were located between ¹ππ* and S₀ states for each system with the CASSCF (8,8) theoretical model and relevant contributions to the deactivation mechanism of titled systems were addressed by the determination of potential energy profiles at the CASPT2 (12,10) theoretical level. It was revealed that the relaxation of the ¹ππ* state of the most stable conformer of both systems to the ground state is mostly governed by the accessible S₁/S₀ conical intersection resulting from the barrier-free out-of-plane deformation. Interestingly, it was exhibited that the ring puckering coordinate driven from the C₆ position of the heterocycle ring in TH⁺ and CH⁺ plays the most prominent role in the deactivation mechanism of considered systems. Our ab initio results are also supported by excited-state nonadiabatic dynamics simulations based on ADC(2), describing the ultrashort S₁ lifetime of TH⁺/CH⁺ by analyzing trajectories leading excited systems to the ground. It was confirmed that the excited-state population mostly relaxes to the ground via the ring puckering coordinate from the C₆ moiety. Overall, the theoretical results of this study shed light on the deactivation mechanism of protonated DNA bases.

Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study

Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH⁺) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH⁺ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH⁺ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH⁺ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.

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.

The effect of hydrogen bonds on the ultrafast relaxation dynamics of a BODIPY dimer

The influence of hydrogen bonds (H-bonds) in the structure, dynamics, and functionality of biological and artificial complex systems is the subject of intense investigation. In this broad context, particular attention has recently been focused on the ultrafast H-bond dependent dynamical properties in the electronic excited state because of their potentially dramatic consequences on the mechanism, dynamics, and efficiency of photochemical reactions and photophysical processes of crucial importance for life and technology. Excited-state H-bond dynamics generally occur on ultrafast time scales of hundreds of femtoseconds or less, making the characterization of associated mechanisms particularly challenging with conventional time-resolved techniques. Here, 2D electronic spectroscopy is exploited to shed light on this still largely unexplored dynamic mechanism. An H-bonded molecular dimer prepared by self-assembly of two boron-dipyrromethene dyes has been specifically designed and synthesized for this aim. The obtained results confirm that upon formation of H-bonds and the dimer, a new ultrafast relaxation channel is activated in the ultrafast dynamics, mediated by the vibrational motions of the hydrogen donor and acceptor groups. This relaxation channel also involves, beyond intra-molecular relaxations, an inter-molecular transfer process. This is particularly significant considering the long distance between the centers of mass of the two molecules. These findings suggest that the design of H-bonded structures is a particularly powerful tool to drive the ultrafast dynamics in complex materials.

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(n_Seπ₅^*) and S₂ ¹(π_Seπ₅^*) states are predicted to be the spectroscopically dark and bright states, respectively. Two triplet states, T₁ ³(π_Seπ₅^*) and T₂ ³(n_Seπ₅^*), 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(π_Seπ₅^*) 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.

Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies

We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the ¹ππ* state of enol-enol form (EE⁺) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S₁ lifetime of this species. For the second most stable isomer (EK⁺), however, a significant barrier predicted in the CASPT2 S₁ potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.

Oxidative Addition of Singlet Oxygen to Model Building Blocks of the Aerucyclamide A Peptide: A First-Principles Approach

Singlet oxygen (¹O₂) is a significant source of biodamage in living organisms. ¹O₂ is a highly reactive excited electronic-state spin-configuration of molecular oxygen and is usually prepared via organic molecule sensitization. Despite the wealth of experimental studies on the ¹O₂-induced oxidation of several bio-organic molecules, the detailed mechanism of the oxidation process is largely unknown. Using high-level quantum chemical methods, we compute the potential energy profiles of the various electronic states associated with the [4 + 2]-cycloaddition reaction of O₂ with a class of model peptide precursors that are based on derivatives of oxazole and thiazole. Experiments have shown that such oxazole/thiazole-based model peptides show a favorable reaction with ¹O₂. Upon increasing the molecular complexity, the bimolecular rate constant decreases and is attributed to the π-perturbing effects of the substituent of the oxazole/thiazole moiety. Our theoretical predictions are in excellent agreement with the experimental measurements and reveal a deep insight into the myriad electronic states that may hinder/promote the reaction of a given bio-organic molecule with ¹O₂.

UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ* states

Formation of an excited-state complex enables ultrafast photorelaxation of dark nπ* states in GC and HC base pairs.

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.

Photodynamics of alternative DNA base isoguanine

Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.

UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level

The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright ¹ππ* and the lowest energy dark ¹nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the ¹n_Oπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional ¹n_Nπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the ¹n_Oπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.

Photostability of oxazoline RNA-precursors in UV-rich prebiotic environments

Pentose aminooxazolines and oxazolidinone thiones are considered as the key precursors which could have enabled the formation of RNA nucleotides under the conditions of early Earth. UV-irradiation experiments and quantum-chemical calculations demonstrate that these compounds are remarkably photostable and could accumulate over long periods of time in UV-rich prebiotic environments to undergo stereoisomeric purification.

Photochemical relaxation pathways of S6-methylthioinosine and O6-methylguanosine in solution

S6-Methylthioinosine and O6-methylguanosine are byproducts resulting from the enzymatic reactions of sulfur-substituted prodrugs in cells and from the interaction of alkylating agents with cellular DNA, respectively. Their photochemistry has not been investigated, and it is currently unknown whether light absorption by these byproducts may pose any threat to the cell. In this contribution, their photoinduced processes upon absorption of UVB radiation are reported using broadband transient absorption spectroscopy. Plausible electronic relaxation mechanisms are proposed for both biological molecules, which are supported by steady-state absorption and emission measurements, and by singlet and triplet vertical excitation energies performed on a large subset of ground-state optimized conformational isomers in solution. The results are compared to the body of knowledge gathered in the scientific literature about the light-induced processes in the sulfur-substituted and canonical purine monomers. In particular, it is shown that S6-methylation decreases the rate to populate the lowest-energy triplet state and blueshifts the ground-state absorption spectrum compared to those for the sulfur-substituted prodrugs and for the 6-thioguanosine metabolite. Similarly, O6-methylation decreases the rate of internal conversion to the ground state observed in the guanine monomers by more than 10-fold in acetonitrile and 40-fold in aqueous solution, while it redshifts the ground-state absorption spectrum. Collectively, this investigation provides relevant new insights about the relationship between structural modifications of the purine chromophore and the electronic relaxation mechanisms in this important group of biological molecules.

Photoprotection: extending lessons learned from studying natural sunscreens to the design of artificial sunscreen constituents

Evolution has ensured that plants and animals have developed effective protection mechanisms against the potentially harmful effects of incident ultraviolet radiation (UVR). Tanning is one such mechanism in humans, but tanning only occurs post-exposure to UVR. Hence, there is ever growing use of commercial sunscreens to pre-empt overexposure to UVR. Key requirements for any chemical filter molecule used in such a photoprotective capacity include a large absorption cross-section in the UV-A and UV-B spectral regions and the availability of one or more mechanisms whereby the absorbed photon energy can be dissipated without loss of the molecular integrity of the chemical filter. Here we summarise recent experimental (mostly ultrafast pump-probe spectroscopy studies) and computational progress towards unravelling various excited state decay mechanisms that afford the necessary photostability in chemical filters found in nature and those used in commercial sunscreens. We also outline ways in which a better understanding of the photophysics and photochemistry of sunscreen molecules selected by nature could aid the design of new and improved commercial sunscreen formulations.

Ultrafast excited-state dynamics of isocytosine

The alternative nucleobase isocytosine has long been considered as a plausible component of hypothetical primordial informational polymers. To examine this hypothesis we investigated the excited-state dynamics of the two most abundant forms of isocytosine in the gas phase (keto and enol). Our surface-hopping nonadiabatic molecular dynamics simulations employing the algebraic diagrammatic construction to the second order [ADC(2)] method for the electronic structure calculations suggest that both tautomers undergo efficient radiationless deactivation to the electronic ground state with time constants which amount to τketo = 182 fs and τenol = 533 fs. The dominant photorelaxation pathways correspond to ring-puckering (ππ* surface) and C[double bond, length as m-dash]O stretching/N-H tilting (nπ* surface) for the enol and keto forms respectively. Based on these findings, we infer that isocytosine is a relatively photostable compound in the gas phase and in these terms resembles biologically relevant nucleobases. The estimated S1 [radiolysis arrow - arrow with voltage kink] T1 intersystem crossing rate constant of 8.02 × 10(10) s(-1) suggests that triplet states might also play an important role in the overall excited-state dynamics of the keto tautomer. The reliability of ADC(2)-based surface-hopping molecular dynamics simulations was tested against multireference quantum-chemical calculations and the potential limitations of the employed ADC(2) approach are briefly discussed.

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments

The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.

A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs

The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Hydrogen detachment driven by a repulsive 1πσ* state – an electron localization function study of 3-amino-1,2,4-triazole

Electron localization function analysis reveals the details of a charge induced hydrogen detachment mechanism of 3-amino-1,2,4-triazole, identified recently as responsible for phototautomerization of the molecule.

Electronic structure and absorption spectra of fluorescent nucleoside analogues

This work presents a systematic investigation of the electronic and conformational properties of five new fluorescent nucleobases belonging to the alphabet based on the isothiazole[4,3-d]pyrimidine molecule, very recently synthesized. This is of particular importance in the characterization of the main electronic aspects of these fluorescent nucleosides. The solvent effects of 1,4-dioxane and water were included combining the Sequential Monte Carlo/CASPT2 and the Free Energy Gradient (FEG) methods. For comparison, the Polarizable Continuum method was also used. The geometries of all compounds were optimized in solvent with the largest effects observed in water using the average solvent electrostatic configuration (ASEC) and the FEG approaches. Statistical analysis of the solute-solvent hydrogen bonds is performed and their effect on the absorption spectra analyzed. The dipole moments were calculated and the value obtained from the ASEC-FEG method in water follows the same trend as the natural canonical bases (adenine → uracil → guanine → cytosine). The theoretical results for the absorption spectra obtained from CASPT2(18,13) calculations using the geometries obtained with the ASEC-FEG procedure are in very good agreement with the experimental data. A detailed elucidation of the main aspects of the absorption spectra of the five new fluorescent nucleoside analogues is successfully attempted.