When Tautomers Matter: UV-Vis Absorption Spectra of Hypoxanthine in Aqueous Solution from Fully Atomistic Simulations

The UV-Vis spectrum of the solvated purine derivative Hypoxanthine (HYX) is investigated using the Quantum Mechanics/Fluctuating Charges (QM/FQ) multiscale approach combined with a sampling of configurations through atomistic Molecular Dynamics (MD) simulations. Keto 1H7H and 1H9H tautomeric forms of HYX are the most stable in aqueous solution and form different stable complexes with the surrounding water molecules, ultimately affecting the electronic absorption spectra. The final simulated spectrum resulting from the combination of the individual spectra of tautomers agrees very well with most of the characteristics in the measured spectrum. The importance of considering the effect of the solute tautomers and, in parallel, the contribution of the different solvent arrangements around the solute when modeling spectral properties, is highlighted. In addition, the high quality of the computed spectra leads to suggesting an alternative way for acquiring tautomeric populations from combined computational/experimental spectra.

The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations

2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.

UV-VUV absorption spectra of azido-based energetic plasticizer bis(1,3-diazido prop-2-yl)malonate in gas phase

Ultraviolet and vacuum ultraviolet photo-absorption spectra of azido (-N3)-based energetic plasticizer, bis(1,3-diazido-prop-2-yl)-malonate (abbreviated as BDAzPM), in the gas phase is recorded at room temperature and in the photon energy range of 5.5-9.9 eV using a synchrotron radiation source. Complementary computational results obtained using the time-dependent density functional theory document the vertical transition energies and oscillator strengths. Comparison of the simulated spectra with the experimental absorption spectrum of BDAzPM reveals that the early part of the absorption spectrum of BDAzPM is of pure valence excitation character, whereas the later intense part of the absorption spectrum is dominated by mixed Rydberg and valence electronic excitations.

On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2)

Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.

Photophysical Characterization of Isoguanine in a Prebiotic-Like Environment

It is intriguing how a mixture of organic molecules survived the prebiotic UV fluxes and evolved into the actual genetic building blocks. Scientists are trying to shed light on this issue by synthesizing nucleic acid monomers and their analogues under prebiotic Era-like conditions and by exploring their excited state dynamics. To further add to this important body of knowledge, this study discloses new insights into the photophysical properties of protonated isoguanine, an isomorph of guanine, using steady-state and femtosecond broadband transient absorption spectroscopies, and quantum mechanical calculations. Protonated isoguanine decays in ultrafast time scales following 292 nm excitation, consistently with the barrierless paths connecting the bright S₁ (ππ*) state with different internal conversion funnels. Complementary calculations for neutral isoguanine predict similar photophysical properties. These results demonstrate that protonated isoguanine can be considered photostable in contrast to protonated guanine, which exhibits 40-fold longer excited state lifetimes.

Rationalizing the Unexpected Sensitivity in Excited State Lifetimes of Adenine to Tautomerization by Nonadiabatic Molecular Dynamics

The remarkable photostability of canonical nucleobases makes them ideal building blocks for DNA and RNA. Even minor structural changes are expected to lead to drastic alteration of their subpicosecond excited state lifetimes. However, it is interesting to note that while the 9H- and 7H-amino tautomers of adenine possess drastically different lifetimes, 9H- and 7H-keto guanine possess similar excited state lifetimes. With an aim to explain this unexpected difference in sensitivity of lifetimes to tautomerization, we have investigated the excited state relaxation mechanism of UV-excited adenine and guanine tautomers using surface hopping based nonadiabatic molecular dynamics. We find that internal conversion in both guanine tautomers is almost barrierless while both adenine tautomers encounter significant barriers before they can deactivate. Moreover, the major deactivation channel (C2-puckering) in 9H-amino adenine is overall more efficient than the one (C6-puckering) in the 7H-amino form. We trace this difference to the frequent rotation of the amino group which disrupts its conjugation with the heterocyclic ring thereby reducing the strength of nonadiabatic coupling and, hence, delaying internal conversion.

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

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

Accurate Non-Adiabatic Couplings from Optimally-Tuned Range-Separated Hybrid Functionals

Precise theoretical calculations of non-adiabatic couplings, which describe the interaction between two Born-Oppenheimer surfaces, are important for the modeling of radiationless decay mechanisms in photochemical processes. Here, we demonstrate that accurate non-adiabatic couplings can be calculated in the framework of linear-response time-dependent density functional theory by using non-empirical, optimally-tuned range-separated hybrid (OT-RSH) functionals. We focus on molecular radicals, in which ultrafast non-radiative decay plays a crucial role, to find that the OT-RSH functional compares well to wave-function based reference data and competes with the accuracy of semi-empirical CAM-B3LYP calculations. Our findings show that the OT-RSH approach provides very accurate non-adiabatic couplings and, therefore, provides a computationally efficient alternative to wave-function based techniques.

Excited state dynamics of 2'-deoxyisoguanosine and isoguanosine in aqueous solution

Photostability is thought to be an inherent property of nucleobases required to survive the extreme ultraviolet radiation conditions of the prebiotic era. Previous studies have shown that absorption of ultraviolet radiation by the canonical nucleosides results in ultrafast internal conversion to the ground state, demonstrating that these nucleosides efficiently dissipate the excess electronic energy to the environment. In recent years, studies on the photophysical and photochemical properties of nucleobase derivatives have revealed that chemical substitution influences the electronic relaxation pathways of purine and pyrimidine nucleobases. It has been suggested that amino or carbonyl substitution at the C6 position could increase the photostability of the purine derivatives more than the substitution at the C2 position. This investigation aims to elucidate the excited state dynamics of 2'-deoxyisoguanosine (dIsoGuo) and isoguanosine (IsoGuo) in aqueous solution at pH 7.4 and 1.4, which contain an amino group at the C6 position and a carbonyl group at the C2 position of the purine chromophore. The study of these derivatives is performed using absorption and emission spectroscopies, broadband transient absorption spectroscopy, and density functional and time-dependent density functional levels of theory. It is shown that the primary relaxation mechanism of dIsoGuo and IsoGuo involves nonradiative decay pathways, where the population decays from the S₁(ππ*) state through internal conversion to the ground state via two relaxation pathways with lifetimes of hundreds of femtoseconds and less than 2 ps, making these purine nucleosides photostable in aqueous solution.

A molecular insight into the photophysics of barbituric acid, a candidate for canonical nucleobases' ancestor

This work investigates the photophysics of barbituric acid at different pH conditions using ab initio methods. Our calculations ascribe the most intense bands at ca. 260 nm at neutral pH and 210 nm at acidic pH conditions in the absorption spectra of this chromophore to the lowest lying ππ* transitions. Consistently with the ultrashort excited state lifetimes experimentally registered, the potential energy landscapes of both the neutral and deprotonated forms of barbituric acid combined with the interpretation of their transient absorption spectra suggest the deactivation of these systems along the singlet manifold. Compared to uracil, its closest natural nucleobase, barbituric acid presents a red shifted absorption spectrum, due to the lowering by more than 0.5 eV of the lowest-energy ππ* excited state, and a much more complex topography of the S₁ potential energy surface, with several energetically accessible local minima. This fact, however, does not affect the excited state lifetimes, which for barbituric acid were experimentally registered in the sub-ps time scale.

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

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

Ultrafast excited-state dynamics of promising nucleobase ancestor 2,4,6-triaminopyrimidine

The ultrafast excited-state dynamics of 2,4,6-triaminopyrimidine - thought to be a promising candidate for a proto-RNA nucleobase - have been investigated via static multireference quantum-chemical calculations and mixed-quantum-classical/trajectory surface-hopping dynamics with a focus on the lowest-lying electronic states of the singlet manifold and with a view towards understanding the UV(C)/UV(B) photostability of the molecule. Ultrafast internal conversion channels have been identified that connect the lowest-lying ππ* electronically-excited state of 2,4,6-triaminopyrimidine with the ground electronic state, and non-radiative decay has been observed to take place on the picosecond timescale via a ππ* out-of-plane NH2 ("oop-NH2") minimum-energy crossing point. The short excited-state lifetime is competitive with the excited-state lifetimes of the canonical pyrimidine nucleobases, affirming the promise of 2,4,6-triaminopyrimidine as an ancestor. Evidence for energy-dependent excited-state dynamics is presented, and the open question of intersystem crossing is discussed speculatively.

Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study

In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.

Vacuum-Ultraviolet Absorption Spectrum of 3-Methoxyacrylonitrile

The high-resolution absorption spectrum of 3-methoxyacrylonitrile (3MAN) was measured between 5.27 and 12.59 eV using a synchrotron-based Fourier-transform spectrometer. It was related to an absolute absorption cross-section scale. Complementary calculations at the DFT-MRCI/aug-cc-pVTZ level of theory document the vertical transition energies and oscillator strengths toward the first 19 states of both the E and Z geometrical isomers of 3MAN. Comparisons with the experimental absorption spectrum reveal the similarities and differences between 3MAN, a bifunctional molecule, with acrylonitrile and methylvinylether, where only one functional group is present. As in acrylonitrile, several broad valence transitions were observed up to the ionization limit. They are likely associated with the extended π-system induced by the nitrile group but might also involve σσ* transitions close to the ionization limit. As in methylvinylether, Rydberg series converging to the ionization limit are absent. This is attributed to a difference in neutral and cationic geometry due to a 60° rotation of the methyl group.

High-resolution vacuum ultraviolet absorption spectra of 2,3- and 2,5-dihydrofuran

Using a synchrotron-based Fourier-transform spectrometer, the high-resolution absorption spectra of the C₁-symmetric 2,3-dihydrofuran (23DHF) and C_2v-symmetric 2,5-dihydrofuran (25DHF) have been measured from 5.5 eV to 9.4 eV with an absolute absorption cross section scale. Oscillator strengths and vertical excitation energies of the lowest 18 states have been computed using the average of the second- and third-order algebraic diagrammatic construction polarization propagator method and the equation-of-motion coupled-cluster method at the level of singles and doubles model. These show that the bright valence transitions of ππ^*-character are embedded into Rydberg transitions, whose oscillator strengths are at least one order of magnitude lower. To account for intensity borrowing, the first broad valence transition between 5.5 eV and 6.8 eV was simulated using a nuclear ensemble, and the agreement between experiment and theory is excellent. Whereas 23DHF only exhibits one broad valence transition followed by d/f Rydberg series converging to the ionization energy, the absorption spectrum of 25DHF has four bands, attributed to a valence nπσ → π^*-transition, nπσ → 3p_x,z/3d_xz transitions, a second valence nπ → π^*-transition followed by d/f Rydberg series converging to the ionization energy, respectively. All Rydberg series converging to the ionization energy have been characterized in terms of their quantum defects.

Exploration of the theobromine-water dimer: comparison with DNA microhydration

Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.