The origin of efficient triplet state population in sulfur-substituted nucleobases

Nonadiabatic dynamics: The SHARC approach

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

Selective prebiotic conversion of pyrimidine and purine anhydronucleosides into Watson-Crick base-pairing arabino-furanosyl nucleosides in water

Prebiotic nucleotide synthesis is crucial to understanding the origins of life on Earth. There are numerous candidates for life's first nucleic acid, however, currently no prebiotic method to selectively and concurrently synthesise the canonical Watson-Crick base-pairing pyrimidine (C, U) and purine (A, G) nucleosides exists for any genetic polymer. Here, we demonstrate the divergent prebiotic synthesis of arabinonucleic acid (ANA) nucleosides. The complete set of canonical nucleosides is delivered from one reaction sequence, with regiospecific glycosidation and complete furanosyl selectivity. We observe photochemical 8-mercaptopurine reduction is efficient for the canonical purines (A, G), but not the non-canonical purine inosine (I). Our results demonstrate that synthesis of ANA may have been facile under conditions that comply with plausible geochemical environments on early Earth and, given that ANA is capable of encoding RNA/DNA compatible information and evolving to yield catalytic ANA-zymes, ANA may have played a critical role during the origins of life.

Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases

Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.

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

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

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.

Mechanism of enhanced triplet decay of thionucleobase by glycosylation and rate-modulating strategies

Functionalization of the sugar group can be used to control the triplet decay rate of thionucleosides.

Incorporating spin–orbit effects into surface hopping dynamics using the diagonal representation: a linear-response time-dependent density functional theory implementation with applications to 2-thiouracil

Evaluation of SOC values employs Casida's wave functions and the Breit–Pauli spin–orbit Hamiltonian with effective charge approximation.

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.[...].

Spatial Factors for Triplet Fusion Reaction of Singlet Oxygen Photosensitization

First-principles quantum-chemical description of photosensitized singlet oxygen generation kinetics is challenging because of the intrinsic complexity of the underlying triplet fusion process in a floppy molecular complex with open-shell character. With a quantum-chemical kinetic model specifically tailored to deal with this problem, the reaction rates are investigated as a function of intermolecular incidence direction, orientation, and distance between O₂ and the photosensitizer. The adopted photosensitizer, 6-azo-2-thiothymine, combines practical interest and prototypical variability. The study quantitatively determined maximum singlet oxygen generation rates for 15 incidence/orientation directions, showing that they span 5 orders of magnitude between the largest and the smallest rate. Such information may provide a hands-on guideline for the experimental molecular design of new photosensitizers as well as further higher-level theoretical research.

Evidence for a Double Well in the First Triplet Excited State of 2-Thiouracil

The computationally predicted presence of two structurally distinct minima in the first triplet excited (T₁) state of 2-thiouracil (2TU) is substantiated by sub-picosecond transient vibrational absorption spectroscopy (TVAS) in deuterated acetonitrile solution. Following 300 nm ultraviolet excitation to the second singlet excited state of 2TU, a transient infrared absorption band centered at 1643 cm^-1 is observed within our minimum time resolution of 0.3 ps. It is assigned either to 2TU molecules in the S₁ state or to vibrationally hot T₁-state molecules, with the latter assignment more consistent with recent computational and experimental studies. The 1643 cm^-1 band decays with a time constant of 7.2 ± 0.8 ps, and there is corresponding growth of several further bands centered at 1234, 1410, 1424, 1443, 1511, 1626, and 1660 cm^-1 which show no decline in intensity over the 1 ns time limit of our measurements. These spectral features are assigned to two different conformations of 2TU, corresponding to separate energy minima on the T₁-state potential energy surface, on the basis of their extended lifetimes, computed infrared frequencies, and the observed quenching of the bands by addition of styrene. Corresponding measurements for the 4-thiouracil (4TU) isomer show sub-picosecond population of the T₁ state, which vibrationally cools with a time constant of 5.2 ± 0.6 ps. However, TVAS measurements in the carbonyl stretching region do not distinguish the two computed T₁-state conformers of 4TU because of the similarity of their vibrational frequencies.

The Synthesis and Photophysical Analysis of a Series of 4-Nitrobenzochalcogenadiazoles for Super-Resolution Microscopy

A series of 4-nitrobenzodiazoles with atomic substitution through the chalcogen group were synthesised and their photophysical properties analysed with a view for use in single-molecule localisation microscopy. Sub-diffraction resolution imaging was achieved for silica nanoparticles coated with each dye. Those containing larger atoms were favoured for super-resolution microscopy due to a reduced blink rate (required for stochastic events to be localised). The sulfur-containing molecule was deemed most amenable for widespread use due to the ease of synthetic manipulation compared to the selenium-containing derivative.

Excited State Dynamics of 6-Thioguanine

Here we present the excited state dynamics of jet-cooled 6-thioguanine (6-TG), using resonance-enhanced multiphoton ionization (REMPI), IR-UV double resonance spectroscopy, and pump-probe spectroscopy in the nanosecond and picosecond time domains. We report data on two thiol tautomers, which appear to have different excited state dynamics. These decay to a dark state, possibly a triplet state, with rates depending on tautomer form and on excitation wavelength, with the fastest rate on the order of 10¹⁰ s^-1. We also compare 6-TG with 9-enolguanine, for which we observed decay to a dark state with a 2 orders of magnitude smaller rate. At increased excitation energy (∼+500 cm^-1) an additional pathway appears for the predominant thiol tautomer. Moreover, the excited state dynamics for 6-TG thiols is different from that recently predicted for thiones.

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

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

Photochemical Reactivity of dTPT3: A Crucial Nucleobase Derivative in the Development of Semisynthetic Organisms

In 2017, the Romesberg group successfully developed the dTPT3·dNaM unnatural base pair to create a semisynthetic organism with enhanced genetic fidelity and the ability to store additional genetic information indefinitely. It is also desirable that the newly developed genetic material remains stable upon exposure to radiation. However, the photochemical properties of dTPT3 are presently unknown. In this contribution, excitation of dTPT3 with near-visible radiation is shown to efficiently populate a reactive triplet state in high yield and on a sub-1 ps time scale; a state that is able to survive for up to a few microseconds in aqueous solution. The triplet state can also generate singlet oxygen in ca. 30% yield, suggesting that dTPT3 can act as a pervasive photosensitizer to accelerate oxidatively generated damage within DNA and to other biological molecules within cells.

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Excited-State Dynamics of the Thiopurine Prodrug 6-Thioguanine: Can N9-Glycosylation Affect Its Phototoxic Activity?

6-Thioguanine, an immunosuppressant and anticancer prodrug, has been shown to induce DNA damage and cell death following exposure to UVA radiation. Its metabolite, 6-thioguanosine, plays a major role in the prodrug's overall photoreactivity. However, 6-thioguanine itself has proven to be cytotoxic following UVA irradiation, warranting further investigation into its excited-state dynamics. In this contribution, the excited-state dynamics and photochemical properties of 6-thioguanine are studied in aqueous solution following UVA excitation at 345 nm in order to provide mechanistic insight regarding its photochemical reactivity and to scrutinize whether N9-glycosylation modulates its phototoxicity in solution. The experimental results are complemented with time-dependent density functional calculations that include solvent dielectric effects by means of a reaction-field solvation model. UVA excitation results in the initial population of the S₂(ππ*) state, which is followed by ultrafast internal conversion to the S₁(nπ*) state and then intersystem crossing to the triplet manifold within 560 ± 60 fs. A small fraction (ca. 25%) of the population that reaches the S₁(nπ*) state repopulates the ground state. The T₁(ππ*) state decays to the ground state in 1.4 ± 0.2 μs under N₂-purged conditions, using a 0.2 mM concentration of 6-thioguanine, or it can sensitize singlet oxygen in 0.21 ± 0.02 and 0.23 ± 0.02 yields in air- and O₂-saturated solution, respectively. This demonstrates the efficacy of 6-thioguanine to act as a Type II photosensitizer. N9-glycosylation increases the rate of intersystem crossing from the singlet to triplet manifold, as well as from the T₁(ππ*) state to the ground state, which lead to a ca. 40% decrease in the singlet oxygen yield under air-saturated conditions. Enhanced vibronic coupling between the singlet and triplet manifolds due to a higher density of vibrational states is proposed to be responsible for the observed increase in the rates of intersystem crossing in 6-thioguanine upon N9-glycosylation.

On the decay of the triplet state of thionucleobases

The double-well triplet state of thionucleobases allows for a two-step mechanistic control of their triplet decay lifetime.

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.

Ab initio molecular dynamics of thiophene: the interplay of internal conversion and intersystem crossing

Ab initio on-the-fly molecular dynamics reveals that excited thiophene decays via low lying conical intersections and via intersystem crossing. Open-ring structures are responsible for the observed long life times.

Ab initio molecular dynamics relaxation and intersystem crossing mechanisms of 5-azacytosine

Nonadiabatic SHARC dynamics simulations reveal the molecular deformations involved in the photodeactivation pathways of 5-azacytosine.

Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution

The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.

Electronic relaxation pathways of the biologically relevant pterin chromophore

Femtosecond-to-microsecond transient absorption spectroscopy is used to report the ultrafast relaxation mechanism of 2-amino-1H-pteridin-4-one (pterin) for the first time.

Covalent-reaction-induced interfacial assembly to transform doxorubicin into nanophotomedicine with highly enhanced anticancer efficiency

By one-pot covalent-reaction-induced interfacial assembly, doxorubicin is facilely transformed into nanophotomedicine with remarkable ability of singlet oxygen generation and greatly improved anticancer efficiency.

Challenges in Simulating Light-Induced Processes in DNA

In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.