Excited state dynamics of DNA bases

Electronic spectroscopy of isolated DNA polyanions

We address whether action spectroscopy could be used to investigate structural changes in gas-phase biomolecule (e.g. nucleic acid) ions, owing to changes in the environments of their chromophores, while taking advantage of the additional spectrometric separation of complex mixtures.

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.

Simulated and Experimental Time-Resolved Photoelectron Spectra of the Intersystem Crossing Dynamics in 2-Thiouracil

We report time-dependent photoelectron spectra recorded with a single-photon ionization setup and extensive simulations of the same spectra for the excited-state dynamics of 2-thiouracil (2TU) in the gas phase. We find that single-photon ionization produces very similar results as two-photon ionization, showing that the probe process does not have a strong influence on the measured dynamics. The good agreement between the single-photon ionization experiments and the simulations shows that the norms of Dyson orbitals allow for qualitatively describing the ionization probabilities of 2TU. This reasonable performance of Dyson norms is attributed to the particular electronic structure of 2TU, where all important neutral and ionic states involve similar orbital transitions and thus the shape of the Dyson orbitals do not strongly depend on the initial neutral and final ionic state. We argue that similar situations should also occur in other biologically relevant thio-nucleobases, and that the time-resolved photoelectron spectra of these bases could therefore be adequately modeled with the techniques employed here.

Photoprotection or photodamage: a direct observation of nonradiative dynamics from 2-ethylhexyl 4-dimethylaminobenzoate sunscreen agent

Apart from being an analogue of the prototype for photoinduced intramolecular charge transfer (ICT), 2-ethylhexyl 4-dimethylaminobenzoate (EHDMABA) is also one of the earliest patented and most commonly used sunscreen components. There is, however, little documented information about the photophysics and factors affecting the photophysics of this molecule. Such information is of importance for both the understanding of the ICT reaction and assessing the underlying process of photoprotection, especially in view of the "sunscreen controversy" that has arisen from the contrasting in vivo vs. in vitro photobiological results on this and related UV filters. We report herein a femtosecond broadband time-resolved fluorescence (fs-TRF), complemented by transient absorption (fs-TA) to allow a full probe of the excited state cascades for EHDMABA and two of its derivatives in solvents of varied properties. The results provide direct evidence for a nearly solvent independent inner sphere ICT reaction occurring on the sub-picosecond time scale, and an ensuing solvent dictated deactivation of the ICT state. The ICT state in the aprotic solvent acetonitrile decayed solely through the intrinsic intersystem crossing (ISC) to produce a potentially harmful triplet excited state. In the protic solvent, the solvation and formation of ICT-induced solute-solvent hydrogen (H)-bonding opened the originally inaccessible internal conversion (IC) channel of the ICT state, leading to the rapid reformation of the ground state molecule with a unitary efficiency in the aqueous solution. This H-bonding-mediated IC restrained or eliminated the intrinsic ISC, providing a mechanism at the molecular level for the benign dissipation of the electronic excitation. The precise rate of IC was observed to vary with the alkoxy substituent and its efficiency was affected by the H-bonding capacity of the solvent. The findings of this work demonstrate the pivotal role of the microenvironment and the direct participation of solvent molecules through H-bonding in drastically altering the nonradiative dynamics and promoting or inhibiting photostability and photoprotection. This may assist in developing next-generation UV filters and help in improving formulation design for the optimal efficacy of sunscreen products. The pronounced H-bonding-induced fluorescence quenching and variation in the fluorescence wavelength imply that these molecules may also serve as a sensitive fluorescence probe for the H-bonding properties of the microenvironment.

Wet Sunscreens in the Gas Phase: Structures of Isolated and Microsolvated Oxybenzone

New insights into the structural intricacies of solvated sunscreen compounds are presented. Using high-resolution rotational spectroscopy with supersonic jets and quantum-chemistry calculations, we navigate the conformational space of oxybenzone and oxybenzone-water clusters. We unambiguously assign the global minimum structure, resolving any prevailing ambiguities, and locate the primary hydration sites of the ground-state enol conformer. Two microsolvated molecular models of oxybenzone are validated by rotational spectroscopy of isotopically enriched species. Theoretical predictions based on these models suggest that water influences the ground-state enol-keto energetic constraints and that its effect is biased depending on which water docking-site is at play.

Unveiling the complex vibronic structure of the canonical adenine cation

Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.

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.

Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry

The photodynamic properties of molecules determine their ability to survive in harsh radiation environments. As such, the photostability of heterocyclic aromatic compounds to electromagnetic radiation is expected to have been one of the selection pressures influencing the prebiotic chemistry on early Earth. In the present study, the gas-phase photodynamics of uracil, 5-methyluracil (thymine) and 2-thiouracil-three heterocyclic compounds thought to be present during this era-are assessed in the context of their recently proposed intersystem crossing pathways that compete with internal conversion to the ground state. Specifically, time-resolved photoelectron spectroscopy measurements evidence femtosecond to picosecond timescales for relaxation of the singlet (1)ππ* and (1)nπ* states as well as for intersystem crossing to the triplet manifold. Trapping in the excited triplet state and intersystem crossing back to the ground state are investigated as potential factors contributing to the susceptibility of these molecules to ultraviolet photodamage.

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.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3)

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA⁺, N-phenylacetamide), AA⁺-(H₂O)_n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν_OH, ν_NH, ν_CH, amide A, 2800-3800 cm^-1) and fingerprint (amide I-II, 1000-1900 cm^-1) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA⁺-(H₂O)_n structures, the H₂O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H₂O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH₃) on the shape of the intermolecular potential and the structure of the hydration shell.

Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole

Prebiotically credible activator of non-enzymatic RNA template-copying, 2-aminoimidazole, is protected from destructive photochemistry by photoacidity.

How nature covers its bases

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

Sequential microhydration of cationic 5-hydroxyindole (5HI+): infrared photodissociation spectra of 5HI+–Wn clusters (W = H2O, n ≤ 4)

The hydrogen-bonding properties of the acidic OH and NH groups of the 5-hydroxyindole cation are probed by infrared spectroscopy and DFT calculations of its microhydrated clusters.

Photorelaxation and Photorepair Processes in Nucleic and Amino Acid Derivatives

Understanding the fundamental interaction between electromagnetic radiation and matter is essential for a large number of phenomena, with significance to civilization.[...].

Excited-State Dynamics of Isocytosine: A Hybrid Case of Canonical Nucleobase Photodynamics

We present resonant two-photon ionization (R2PI) spectra of isocytosine (isoC) and pump-probe results on two of its tautomers. IsoC is one of a handful of alternative bases that have been proposed in scenarios of prebiotic chemistry. It is structurally similar to both cytosine (C) and guanine (G). We compare the excited-state dynamics with the Watson-Crick (WC) C and G tautomeric forms. These results suggest that the excited-state dynamics of WC form of G may primarily depend on the heterocyclic substructure of the pyrimidine moiety, which is chemically identical to isoC. For WC isoC we find a single excited-state decay with a rate of ∼10¹⁰ s^-1, while the enol form has multiple decay rates, the fastest of which is 7 times slower than for WC isoC. The excited-state dynamics of isoC exhibits striking similarities with that of G, more so than with the photodynamics of C.

Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation

The photophysical properties of natural nucleobases and their respective nucleotides are ascribed to the sub-picosecond lifetime of their first singlet states in the UV-B region (260-350 nm). Electronic transitions of the ππ* type, which are stronger than those in the UV-B region, lie at the red edge of the UV-C range (100-260 nm) in all isolated nucleobases. The lowest energetic excited states in the UV-B region of nucleobases have been investigated using a plethora of experimental and theoretical methods in gas and solution phases. The sub-picosecond lifetime of these molecules is not a general attribute of all nucleobases but specific to the five primary nucleobases and a few xanthine and methylated derivatives. To determine the overall UV photostability, we aim to understand the effect of more energetic photons lying in the UV-C region on nucleobases. To determine the UV-C initiated photophysics of a nucleobase system, we chose a halogen substituted purine, 6-chloroguanine (6-ClG), that we had investigated previously using resonance Raman spectroscopy. We have performed quantitative measurements of the resonance Raman cross-section across the Bb absorption band (210-230 nm) and constructed the Raman excitation profiles. We modeled the excitation profiles using Lee and Heller's time-dependent theory of resonance Raman intensities to extract the initial excited state dynamics of 6-ClG within 30-50 fs after photoexcitation. We found that imidazole and pyrimidine rings of 6-ClG undergo expansion and contraction, respectively, following photoexcitation to the Bb state. The amount of distortions of the excited state structure from that of the ground state structure is reflected by the total internal reorganization energy that is determined at 112 cm(-1). The contribution of the inertial component of the solvent response towards the total reorganization energy was obtained at 1220 cm(-1). In addition, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale of less than 30 fs following photoexcitation.

Probing ultrafast ππ*/nπ* internal conversion in organic chromophores via K-edge resonant absorption

Many photoinduced processes including photosynthesis and human vision happen in organic molecules and involve coupled femtosecond dynamics of nuclei and electrons. Organic molecules with heteroatoms often possess an important excited-state relaxation channel from an optically allowed ππ* to a dark nπ* state. The ππ*/nπ* internal conversion is difficult to investigate, as most spectroscopic methods are not exclusively sensitive to changes in the excited-state electronic structure. Here, we report achieving the required sensitivity by exploiting the element and site specificity of near-edge soft X-ray absorption spectroscopy. As a hole forms in the n orbital during ππ*/nπ* internal conversion, the absorption spectrum at the heteroatom K-edge exhibits an additional resonance. We demonstrate the concept using the nucleobase thymine at the oxygen K-edge, and unambiguously show that ππ*/nπ* internal conversion takes place within (60 ± 30) fs. High-level-coupled cluster calculations confirm the method's impressive electronic structure sensitivity for excited-state investigations.Many photo-induced processes such as photosynthesis occur in organic molecules, but their femtosecond excited-state dynamics are difficult to track. Here, the authors exploit the element and site selectivity of soft X-ray absorption to sensitively follow the ultrafast ππ*/nπ* electronic relaxation of hetero-organic molecules.

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.

Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study

Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H₂O)₁, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H₂O)₁ conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H₂O)₁ and AAP(CO)-(H₂O)₁ conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H₂O)₁, [syn- and anti-AAP(OH)-(H₂O)₁ and syn- and anti-AAP(CO)-(H₂O)₁], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H₂O)₁ conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H₂O)₁ conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H₂O)₁ conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H₂O)₁ have been found in this study.

Competition between stacked and hydrogen bonded structures of cytosine aggregates

The four bases of DNA constitute what is known as the “alphabet of life”.

Microsolvation of the pyrrole cation (Py+) with nonpolar and polar ligands: infrared spectra of Py+–Ln with L = Ar, N2, and H2O (n ≤ 3)

IR spectra and dispersion-corrected density functional calculations of pyrrole cluster ions with Ar, N₂, and H₂O reveal the competition between H-bonding and π-stacking motifs of this prototypical heterocyclic aromatic cation in a hydrophobic and hydrophilic solvent.

Nonadiabatic dynamics simulation of keto isocytosine: a comparison of dynamical performance of different electronic-structure methods

Different reaction channels are obtained in the nonadiabatic dynamics simulations of isocytosine at CASSCF and ADC(2) levels.

2-Thiouracil intersystem crossing photodynamics studied by wavelength-dependent photoelectron and transient absorption spectroscopies

The excitation-wavelength dependence of the intersystem crossing (ISC) dynamics of 2-thiouracil was studied in gas-phase and solution.

Water–chromophore electron transfer determines the photochemistry of cytosine and cytidine

Irradiation of aqueous cytidine may result in a water–chromophore electron transfer process which explains numerous experimental observations, including photodamage.

Ultrafast dynamics in the DNA building blocks thymidine and thymine initiated by ionizing radiation

Ultrafast dynamics and fragmentation of thymidine and thymine after ionization by attosecond extreme ultraviolet radiation studied in the time-domain.

Ultrafast structural dynamics of photoexcited adenine

Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the L_a (260 nm) and B_b (210 nm) excited states.

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.

Non-radiative processes in protonated diazines, pyrimidine bases and an aromatic azine

The excited state lifetimes of DNA bases are often very short due to very efficient non-radiative processes assigned to the ππ*-nπ* coupling. A set of protonated aromatic diazine molecules (pyridazine, pyrimidine and pyrazine C4H5N2(+)) and protonated pyrimidine DNA bases (cytosine, uracil and thymine), as well as the protonated pyridine (C5H6N(+)), have been investigated. For all these molecules except one tautomer of protonated uracil (enol-keto), electronic spectroscopy exhibits vibrational line broadening. Excited state geometry optimization at the CC2 level has been conducted to find out whether the excited state lifetimes measured from line broadening can be correlated to the calculated ordering of the ππ* and nπ* states and the ππ*-nπ* energy gap. The short lifetimes, observed when one nitrogen atom of the ring is not protonated, can be rationalized by relaxation of the ππ* state to the nπ* state or directly to the electronic ground state through ring puckering.

Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture

The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

Monitoring Ultrafast Chemical Dynamics by Time-Domain X-ray Photo- and Auger-Electron Spectroscopy

The directed flow of charge and energy is at the heart of all chemical processes. Extraordinary efforts are underway to monitor and understand the concerted motion of electrons and nuclei with ever increasing spatial and temporal sensitivity. The element specificity, chemical sensitivity, and temporal resolution of ultrafast X-ray spectroscopy techniques hold great promise to provide new insight into the fundamental interactions underlying chemical dynamics in systems ranging from isolated molecules to application-like devices. Here, we focus on the potential of ultrafast X-ray spectroscopy techniques based on the detection of photo- and Auger electrons to provide new fundamental insight into photochemical processes of systems with various degrees of complexity. Isolated nucleobases provide an excellent testing ground for our most fundamental understanding of intramolecular coupling between electrons and nuclei beyond the traditionally applied Born-Oppenheimer approximation. Ultrafast electronic relaxation dynamics enabled by the breakdown of this approximation is the major component of the nucleobase photoprotection mechanisms. Transient X-ray induced Auger electron spectroscopy on photoexcited thymine molecules provides atomic-site specific details of the extremely efficient coupling that converts potentially bond changing ultraviolet photon energy into benign heat. In particular, the time-dependent spectral shift of a specific Auger band is sensitive to the length of a single bond within the molecule. The X-ray induced Auger transients show evidence for an electronic transition out of the initially excited state within only ∼200 fs in contrast to theoretically predicted picosecond population trapping behind a reaction barrier. Photoinduced charge transfer dynamics between transition metal complexes and semiconductor nanostructures are of central importance for many emerging energy and climate relevant technologies. Numerous demonstrations of photovoltaic and photocatalytic activity have been performed based on the combination of strong light absorption in dye molecules with charge separation and transport in adjacent semiconductor nanostructures. However, a fundamental understanding of the enabling and limiting dynamics on critical atomic length- and time scales is often still lacking. Femtosecond time-resolved X-ray photoelectron spectroscopy is employed to gain a better understanding of a short-lived intermediate that may be linked to the unexpectedly limited performance of ZnO based dye-sensitized solar cells by delaying the generation of free charge carriers. The transient spectra strongly suggest that photoexcited dye molecules attached to ZnO nanocrystals inject their charges into the substrate within less than 1 ps but the electrons are then temporarily trapped at the surface of the semiconductor in direct vicinity of the injecting molecules. The experiments are extended to monitor the electronic response of the semiconductor substrate to the collective injection from a monolayer of dye molecules and the subsequent electron-ion recombination dynamics. The results indicate some qualitative similarities but quantitative differences between the recombination dynamics at molecule-semiconductor interfaces and previously studied bulk-surface electron-hole recombination dynamics in photoexcited semiconductors.

UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical

UV excitation of mass-selected hexachloroplatinate–nucleobase clusters provides detailed insight into the photophysics and photochemistry of a model DNA photopharmaceutical.

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H₂O)₅ cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S₀ state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H₂O)₅ cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.