A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils

Structure-Photophysical Property Relationships in Noncanonical and Synthetic Nucleobases

This review provides focused coverage of the photophysical properties of noncanonical and synthetic nucleobases reported over the past decade. It emphasizes key research findings and physical insights gathered for prebiotic and fluorescent nucleobase analogs, sulfur- and selenium-substituted nucleobases, aza-substituted nucleobases, epigenetic nucleobases and their oxidation products, and nucleobases utilized for expanding DNA/RNA to reveal central structure-photophysical property relationships. Further research and development in this emerging field, coupled with machine learning methods, will enable the effective harnessing of nucleobases' modifications for applications in biotechnology, biomedicine, therapeutics, and even the creation of live semisynthetic organisms.

Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs

The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.

The impact of the chalcogen-substitution element and initial spectroscopic state on excited-state relaxation pathways in nucleobase photosensitizers: a combination of static and dynamic studies

The substitution of oxygen with chalcogen in carbonyl group(s) of canonical nucleobases gives an impressive triplet generation, enabling their promising applications in medicine and other emerging techniques. The excited-state relaxation S2(ππ*) → S1(nπ*) → T1(ππ*) has been considered the preferred path for triplet generation in these nucleobase derivatives. Here, we demonstrate enhanced quantum efficiency of direct intersystem crossing from S2 to triplet manifold upon substitution with heavier chalcogen elements. The excited-state relaxation dynamics of sulfur/selenium substituted guanines in a vacuum is investigated using a combination of static quantum chemical calculations and on-the-fly excited-state molecular dynamics simulations. We find that in sulfur-substitution the S2 state predominantly decays to the S1 state, while upon selenium-substitution the S2 state deactivation leads to simultaneous population of the S1 and T2,3 states in the same time scale and multi-state quasi-degeneracy region S2/S1/T2,3. Interestingly, the ultrafast deactivation of the spectroscopic S3 state of both studied molecules to the S1 state occurs through a successive S3 → S2 → S1 path involving a multi-state quasi-degeneracy S3/S2/S1. The populated S1 and T2 states will cross the lowest triplet state, and the S1 → T intersystem crossing happens in a multi-state quasi-degeneracy region S1/T2,3/T1 and is accelerated by selenium-substitution. The present study reveals the influence of both the chalcogen substitution element and initial spectroscopic state on the excited-state relaxation mechanism of nucleobase photosensitizers and also highlights the important role of multi-state quasi-degeneracy in mediating the complex relaxation process. These theoretical results provide additional insights into the intrinsic photophysics of nucleobase-based photosensitizers and are helpful for designing novel photo-sensitizers for real applications.

Thieno[3,4-d]pyrimidin-4(3H)-thione: an effective, oxygenation independent, heavy-atom-free photosensitizer for cancer cells

All-organic, heavy-atom-free photosensitizers based on thionation of nucleobases are receiving increased attention because they are easy to make, noncytotoxic, work both in the presence and absence of molecular oxygen, and can be readily incorporated into DNA and RNA. In this contribution, the DNA and RNA fluorescent probe, thieno[3,4-d]pyrimidin-4(1H)-one, has been thionated to develop thieno[3,4-d]pyrimidin-4(3H)-thione, which is nonfluorescent and absorbs near-visible radiation with about 60% higher efficiency. Steady-state absorption and emission spectra are combined with transient absorption spectroscopy and CASPT2 calculations to delineate the electronic relaxation mechanisms of both pyrimidine derivatives in aqueous and acetonitrile solutions. It is demonstrated that thieno[3,4-d]pyrimidin-4(3H)-thione efficiently populates the long-lived and reactive triplet state generating singlet oxygen with a quantum yield of about 80% independent of solvent. It is further shown that thieno[3,4-d]pyrimidin-4(3H)-thione exhibits high photodynamic efficacy against monolayer melanoma cells and cervical cancer cells both under normoxic and hypoxic conditions. Our combined spectroscopic, computational, and in vitro data demonstrate the excellent potential of thieno[3,4-d]pyrimidin-4(1H)-thione as a heavy-atom-free PDT agent and paves the way for further development of photosensitizers based on the thionation of thieno[3,4-d]pyrimidine derivatives. Collectively, the experimental and computational results demonstrate that thieno[3,4-d]pyrimidine-4(3H)-thione stands out as the most promising thiobase photosensitizer developed to this date.

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 (τ_exp = 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.

Attosecond spectroscopy for the investigation of ultrafast dynamics in atomic, molecular and solid-state physics

Since the first demonstration of the generation of attosecond pulses (1 as = 10^-18s) in the extreme-ultraviolet spectral region, several measurement techniques have been introduced, at the beginning for the temporal characterization of the pulses, and immediately after for the investigation of electronic and nuclear ultrafast dynamics in atoms, molecules and solids with unprecedented temporal resolution. The attosecond spectroscopic tools established in the last two decades, together with the development of sophisticated theoretical methods for the interpretation of the experimental outcomes, allowed to unravel and investigate physical processes never observed before, such as the delay in photoemission from atoms and solids, the motion of electrons in molecules after prompt ionization which precede any notable nuclear motion, the temporal evolution of the tunneling process in dielectrics, and many others. This review focused on applications of attosecond techniques to the investigation of ultrafast processes in atoms, molecules and solids. Thanks to the introduction and ongoing developments of new spectroscopic techniques, the attosecond science is rapidly moving towards the investigation, understanding and control of coupled electron-nuclear dynamics in increasingly complex systems, with ever more accurate and complete investigation techniques. Here we will review the most common techniques presenting the latest results in atoms, molecules and solids.

Time-Resolved Optical Pump-Resonant X-ray Probe Spectroscopy of 4-Thiouracil: A Simulation Study

We theoretically monitor the photoinduced ππ* → nπ* internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ππ* and nπ* absorption features. The lowest sulfur K-edge shows strong absorption for both ππ* and nπ*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ππ* and an approximate timing of the conical intersection via its depletion. A spectral signature of the nπ* transition, not accessible by UV-vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. The ππ*/nπ* coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.

Ultrafast Excited-State Decay Mechanisms of 6-Thioguanine Followed by Sub-20 fs UV Transient Absorption Spectroscopy

Understanding the primary steps following UV photoexcitation in sulphur-substituted DNA bases (thiobases) is fundamental for developing new phototherapeutic drugs. However, the investigation of the excited-state dynamics in sub-100 fs time scales has been elusive until now due to technical challenges. Here, we track the ultrafast decay mechanisms that lead to the electron trapping in the triplet manifold for 6-thioguanine in an aqueous solution, using broadband transient absorption spectroscopy with a sub-20 fs temporal resolution. We obtain experimental evidence of the fast internal conversion from the S₂(ππ*) to the S₁(nπ*) states, which takes place in about 80 fs and demonstrates that the S₁(nπ*) state acts as a doorway to the triplet population in 522 fs. Our results are supported by MS-CASPT2 calculations, predicting a planar S₂(ππ*) pseudo-minimum in agreement with the stimulated emission signal observed in the experiment.

Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy

The conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states.

Imaging the charge flow in photoexcited molecules would provide key information on photophysical and photochemical processes. Here the authors demonstrate tracking in real time after photoexcitation the change in charge density at a specific site of 2-thiouracil using time-resolved X-ray photoelectron spectroscopy.

Coherent vibrational modes promote the ultrafast internal conversion and intersystem crossing in thiobases

Thionated nucleobases are obtained by replacing oxygen with sulphur atoms in the canonical nucleobases. They absorb light efficiently in the near-ultraviolet, populating singlet states which undergo intersystem crossing to the...

Mechanistic photophysics and photochemistry of unnatural bases and sunscreen molecules: insights from electronic structure calculations

Photophysics and photochemistry are basic subjects in the study of light-matter interactions and are ubiquitous in diverse fields such as biology, energy, materials, and environment. A full understanding of mechanistic photophysics and photochemistry underpins many recent advances and applications. This contribution first provides a short discussion on the theoretical calculation methods we have used in relevant studies, then we introduce our latest progress on the mechanistic photophysics and photochemistry of two classes of molecular systems, namely unnatural bases and sunscreens. For unnatural bases, we disclose the intrinsic driving forces for the ultrafast population to reactive triplet states, impacts of the position and degree of chalcogen substitutions, and the effects of complex environments. For sunscreen molecules, we reveal the photoprotection mechanisms that dissipate excess photon energy to the surroundings by ultrafast internal conversion to the ground state. Finally, relevant theoretical challenges and outlooks are discussed.

Femtosecond intersystem crossing to the reactive triplet state of the 2,6-dithiopurine skin cancer photosensitizer

Site-selected sulfur-substituted nucleobases are a class of all organic, heavy-atom-free photosensitizers for photodynamic therapy applications that exhibit excellent photophysical properties such as strong absorption in the ultraviolet-A region of the electromagnetic spectrum, near-unity triplet yields, and a high yield of singlet oxygen generation. Recent investigations on doubly thionated nucleobases, 2,4-dithiothymine, 2,4-dithiouracil, and 2,6-dithiopurine, demonstrated that these set of dithionated nucleobases outperform the photodynamic efficacy exhibit by 4-thiothymidine-the most widely studied singly substituted thiobase to date. Out of the three dithionated nucleobases, 2,6-dithiopurine was shown to be the most effective, exhibiting inhibition of cell proliferation of up to 63% when combined with a low UVA dose of 5 J cm^-2. In this study, we elucidated the electronic relaxation pathways leading to the population of the reactive triplet state of 2,6-dithiopurine. 2,6-Dithiopurine populates the triplet manifold in less than 150 fs, reaching the nπ* triplet state minimum within a lifetime of 280 ± 50 fs. Subsequently, the population in the nπ* triplet state minimum internally converts to the long-lived ππ* triplet state within a lifetime of 3 ± 1 ps. The relatively slow internal conversion lifetime is associated with major conformational relaxation in going from the nπ* to ππ* triplet state minimum. A unity triplet yield of 1.0 ± 0.1 is measured.

In Silico Ultrafast Nonlinear Spectroscopy Meets Experiments: The Case of Perylene Bisimide Dye

Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.

Mechanistic Photophysics of Tellurium-Substituted Uracils: Insights from Multistate Complete-Active-Space Second-Order Perturbation Calculations

The photophysical mechanisms of tellurium-substituted uracils were studied at the multistate complete-active-space second-order perturbation level with a particular focus on how the position and number of tellurium substitutions affect their nonadiabatic relaxation processes. Electronic structure analysis reveals that the lowest several excited states are closely concerned with the n and π orbitals at the Te₇-C₂ [Te₈-C₄] moiety of 2-tellurouracil (2TeU) [4TeU and 24TeU]. Both planar and twisted minima were optimized for 2TeU, whereas only planar ones were obtained for 4TeU and 24TeU, except for a twisted T₁ minimum of 4TeU. Based on intersection structures and linearly interpolated internal coordinate paths, we proposed several feasible excited-state deactivation paths. It is found that the relaxation channels for 2TeU are more complicated than those of 4TeU and 24TeU. The electronic population transfer to the T₁ state for 2TeU is easier than that for 4TeU and 24TeU in consideration of the barrier heights from the S₂ Franck-Condon point to the S₂/S₁ or S₂/T₂ intersections. In addition, the recovery of the ground state from the T₁ state for 2TeU will be more efficient than that for the other two systems as well.

Electronic Relaxation Pathways in Heavy-Atom-Free Photosensitizers Absorbing Near-Infrared Radiation and Exhibiting High Yields of Singlet Oxygen Generation

Heavy-atom-free photosensitizers (HAF-PSs) based on thionation of carbonyl groups of readily accessible organic compounds are rapidly emerging as a versatile class of molecules. However, their photochemical properties and electronic relaxation mechanisms are currently unknown. Investigating the excited-state dynamics is essential to understand their benefits and limitations and to develop photosensitizers with improved photochemical properties. Herein, the photochemical and electronic-structure properties of two of the most promising HAF-PSs developed to date are revealed. It is shown that excitation of thio-4-(dimethylamino)naphthalamide and thionated Nile Red with near-infrared radiation leads to the efficient population of the triplet manifold through multiple relaxation pathways in hundreds of femtoseconds. The strong singlet-triplet couplings in this family of photosensitizers should enable a broad range of applications, including in photodynamic therapy, photocatalysis, photovoltaics, organic LEDs, and photon up-conversion.

Investigating the mapping of chromophore excitations onto the electron detachment spectrum: photodissociation spectroscopy of iodide ion-thiouracil clusters

Laser photodissociation spectroscopy (3.1-5.7 eV) has been applied to iodide complexes of the non-native nucleobases, 2-thiouracil (2-TU), 4-thiouracil (4-TU) and 2,4-thiouracil (2,4-TU), to probe the excited states and intracluster electron transfer as a function of sulphur atom substitution. Photodepletion is strong for all clusters (I-·2-TU, I-·4-TU and I-·2,4-TU) and is dominated by electron detachment processes. For I-·4-TU and I-·2,4-TU, photodecay is accompanied by formation of the respective molecular anions, 4-TU- and 2,4-TU-, behaviour that is not found for other nucleobases. Notably, the I-·2TU complex does not fragment with formation of its molecular anion. We attribute the novel formation of 4-TU- and 2,4-TU- to the fact that these valence anions are significantly more stable than 2-TU-. We observe further similar behaviour for I-·4-TU and I-·2,4-TU relating to the general profile of their photodepletion spectra, since both strongly resemble the intrinsic absorption spectra of the respective uncomplexed thiouracil molecule. This indicates that the nucleobase chromophore excitations are determining the clusters' spectral profile. In contrast, the I-·2-TU photodepletion spectrum is dominated by the electron detachment profile, with the near-threshold dipole-bound excited state being the only distinct spectral feature. We discuss these observations in the context of differences in the dipole moments of the thionucleobases, and their impact on the coupling of nucleobase-centred transitions onto the electron detachment spectrum.

Excited States of Thio-2'-deoxyuridine Bearing an Extended π-Conjugated System: 3',5'-Di-O-acetyl-5-phenylethynyl-4-thio-2'-deoxyuridine

A new thio-2'-deoxyuridine with an extended π-conjugated group was successfully synthesized: 3',5'-di-O-acetyl-5-phenylethynyl-4-thio-2'-deoxyuridine. The thio-2'-deoxyuridine derivative has a large red-shifted absorption band in the UVA region and also shows fluorescence, a rare photo-property among thionucleobases/thionucleosides. The triplet-triplet absorption spectrum and the rate constants (the intrinsic decay rate constant of the triplet state, the self-quenching rate constant, and the quenching rate constant of the triplet state by an oxygen molecule) of the thio-2'-deoxyuridine were obtained by transient absorption spectroscopy. The quantum yield of intersystem crossing and the quantum yield of singlet molecular oxygen formation (ϕ_Δ) under an oxygen atmosphere were also determined. The ϕ_Δ value of the new thio-2'-deoxyuridine was found to be substantially higher than all reported values of other thio-2'-deoxyribonucleosides in low oxygen concentrations similar to cancer cell environments. The fluorescence quantum yield depended on the excitation wavelength, revealing certain photochemical reactions in the higher excited singlet states. However, when excited into the higher excited state with non-resonant two-photon absorption, the ϕ_Δ of the thio-2'-deoxyuridine derivative was found to remain sufficiently large. These findings should be very useful for the development of thio-2'-deoxyribonucleoside-based pharmaceuticals as DNA-specific photosensitizers for photochemotherapy.

Spectral Tuning and Photoisomerization Efficiency in Push-Pull Azobenzenes: Designing Principles

This work demonstrates how push–pull substitution can induce spectral tuning toward the visible range and improve the photoisomerization efficiency of azobenzene-based photoswitches, making them good candidates for technological and biological applications. The red-shifted bright ππ* state (S₂) behaves like the lower and more productive dark nπ* (S₁) state because less potential energy along the planar bending mode is available to reach higher energy unproductive nπ*/S₀ crossing regions, which are responsible for the lower quantum yield of the parent compound. The stabilization of the bright ππ* state and the consequent increase in isomerization efficiency may be regulated via the strength of push–pull substituents. Finally, the torsional mechanism is recognized here as the unique productive route because structures with bending values attributable to the inversion mechanism were never detected, out of the 280 ππ* time-dependent density functional theory (RASPT2-validated) dynamics simulations.

Role of Multistate Intersections in Photochemistry

It has been generally accepted that the intersection of potential energy surfaces can facilitate nonadiabatic transitions and plays a crucial role in photochemistry. Although most previous studies have focused on the conical intersection of two electronic states, multistate intersections are common in polyatomic molecules, and their key roles in photochemistry have been uncovered by electronic structure calculations and nonadiabatic dynamics simulations. In this Perspective, the algorithms for searching two- or three-state intersections are first examined with an emphasis on the latest development in a general algorithm for location of multistate intersections. Then, we focus on intersystem crossing (ISC) that occurs in the region of multistate intersection, paying more attention to how the state-specific spin-orbit coupling interaction influences nonadiabatic ISC processes. Finally, the interweaving of nonadiabatic dynamics simulation and electronic structure calculation has been recognized as a correct way to ascertain the vital roles of multistate intersections in photochemical reactions.

Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going

Computational spectroscopy is becoming a mandatory tool for the interpretation of the complex, and often congested, spectral maps delivered by modern non-linear multi-pulse techniques. The fields of Electronic Structure Methods, Non-Adiabatic Molecular Dynamics, and Theoretical Spectroscopy represent the three pillars of the virtual ultrafast optical spectrometer, able to deliver transient spectra in silico from first principles. A successful simulation strategy requires a synergistic approach that balances between the three fields, each one having its very own challenges and bottlenecks. The aim of this Perspective is to demonstrate that, despite these challenges, an impressive agreement between theory and experiment is achievable now regarding the modeling of ultrafast photoinduced processes in complex molecular architectures. Beyond that, some key recent developments in the three fields are presented that we believe will have major impacts on spectroscopic simulations in the very near future. Potential directions of development, pending challenges, and rising opportunities are illustrated.

Internal conversion and intersystem crossing dynamics of uracil upon double thionation: a time-resolved photoelectron spectroscopy study in the gas phase

The photophysical properties of 2,4-dithiouracil (2,4-DTU) in the gas phase are studied by time-resolved photoelectron spectroscopy (TRPES) with three different excitation wavelengths in direct extension of previous work on uracil (U), 2-thiouracil (2-TU) and 4-thiouracil (4-TU). Non-radiative deactivation in the canonical nucleobases like uracil mainly occurs via internal conversion (IC) along singlet excited states, although intersystem crossing (ISC) to a long-lived triplet state was confirmed to play a minor role. In thionated uracils, ISC to the triplet state becomes ultrafast and highly efficient with a quantum yield near unity; however, the lifetime of the triplet state is strongly dependent on the position of the sulfur atom. In 2-TU, ISC back to the ground state occurs within a few hundred picoseconds, whereas the population remains trapped in the lowest triplet state in the case of 4-TU. Upon doubling the degree of thionation, ISC remains highly efficient and dominates the photophysics of 2,4-DTU. However, several low-lying excited states contribute to competing IC and ISC pathways and a complex deactivation mechanism, which is evaluated here based on TRPES measurements and discussed in the context of the singly thionated uracils.

Observation of Enhanced Dissociative Photochemistry in the Non-Native Nucleobase 2-Thiouracil

We present the first study to measure the dissociative photochemistry of 2-thiouracil (2-TU), an important nucleobase analogue with applications in molecular biology and pharmacology. Laser photodissociation spectroscopy is applied to the deprotonated and protonated forms of 2-TU, which are produced in the gas-phase using electrospray ionization mass spectrometry. Our results show that the deprotonated form of 2-thiouracil ([2-TU-H]⁻) decays predominantly by electron ejection and hence concomitant production of the [2-TU-H]· free-radical species, following photoexcitation across the UVA-UVC region. Thiocyanate (SCN⁻) and a m/z 93 fragment ion are also observed as photodecay products of [2-TU-H]⁻ but at very low intensities. Photoexcitation of protonated 2-thiouracil ([2-TU·H]⁺) across the same UVA-UVC spectral region produces the m/z 96 cationic fragment as the major photofragment. This ion corresponds to ejection of an HS· radical from the precursor ion and is determined to be a product of direct excited state decay. Fragment ions associated with decay of the hot ground state (i.e., the ions we would expect to observe if 2-thiouracil was behaving like UV-dissipating uracil) are observed as much more minor products. This behaviour is consistent with enhanced intersystem crossing to triplet excited states compared to internal conversion back to the ground state. These are the first experiments to probe the effect of protonation/deprotonation on thionucleobase photochemistry, and hence explore the effect of pH at a molecular level on their photophysical properties.

Photoinduced Forward and Backward Pedalo-Type Motion of a Molecular Switch

Photoresponsive molecular switches enable spatial and temporal control of molecular processes and are therefore crucial for the development of smart functional materials. Because the light-induced dynamics of these switching units are at the core of the resulting functionality, a detailed insight into their structural time evolution is fundamental for molecular embedding. Here, we performed a hybrid quantum mechanics (CASPT2 and TDDFT)/molecular mechanics (QM/MM) study to elucidate the photodynamics of an azodicarboxamide-based molecular switch, which is a promising candidate for implementation in highly dense environments such as polymers. In particular, we report a detailed picture of the molecular motion at the atomic level based on a relevant number of excited-state trajectories. We show that the azodicarboxamide-based molecular switch undergoes both a forward and backward pedalo-type motion upon excitation. Trans-cis photoisomerization on the other hand, which is well-known to occur for other azo-based chromophores, is shown to be a negligible pathway. By validating the volume-conserving pedalo-type motion, we provide a rational basis for the design of novel types of photoresponsive functional materials in which the active component must operate in a confined space.

Modern quantum chemistry with [Open]Molcas

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

The excited-state relaxation mechanism of potential UVA-activated phototherapeutic molecules: trajectory surface hopping simulations of both 4-thiothymine and 2,4-dithiothymine

Recent experimental investigations of the photochemical properties of a series of sulfur-substituted pyrimidine derivatives provide insights into the phototherapeutic potential of these nucleobase variants. Herein we elucidate the triplet formation mechanism of two prospective UVA-activated phototherapeutic molecules, 4-thiothymine and 2,4-dithiothymine, upon photo-excitation by applying the trajectory surface hopping dynamics at the LR-TDDFT level. Our simulations reasonably reproduce the experimental time constants and demonstrate the preferred triplet formation pathway which starts from the S₁(n_Sπ*) state for both molecules. It is found that deactivation of the first bright state to the S₁(n_Sπ*) state proceeds through a mechanism involving elongation of the C5-C6 and C4-S8 bond-lengths and C2-pyramidalization in 4-thiothymine and involving elongation of the C5-C6 and C2-S7 bond-lengths in 2,4-dithiothymine. The intersystem crossing of 2,4-dithiothymine occurs either at geometries characterized by elongated C5-C6 and C2-S7 bond-lengths or at geometries showing elongated C5-C6 and C4-S8 bond-lengths as seen in 4-thiothymine. The solvents are found to affect the S₂ state decay of 4-thiothymine, leading to a competing pathway between S₂→ S₁ and S₂→ T₃. This study provides a molecular-level understanding of the underlying excited-state relaxation of the two UVA-activated thiopyrimidines, which may be linked to their potential applications in pharmacological science and also prove helpful for designing more effective phototherapeutic agents.

Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique

Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers.