Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method

Recently, much interest has been devoted to finding effective G-quadruplex ligands, both of synthetic or natural origins, which may be of potential use in the field of cancer therapy. Among compounds of natural origin, a common flavonol quercetin has attracted notable attention. Yet, only a modest number of papers have been concerned with a comparison of quercetin conjugates binding to G-quadruplexes. In this study, we applied the survival yield (SY) method in order to compare the stability of G-tetrad complexes with quercetin and its conjugates, namely, 3-O-glycosides and O-methylated conjugates. According to the determined values of Ecomδ50, flavonol glycosides bind most effectively with G-tetrads, whereas, among flavonols, 3-O-methylquercetin makes the most effective bonds. Because the aglycone structure is of crucial importance for biological processes, 3-O-methylquercetin seems to be a suitable candidate for anticancer therapeutics, and the extracts from the plants, which contain high amounts of 3-O-methylquercetin or its glycosides, should be considered as interesting materials for preparation of pharmaceuticals or dietary supplements.

A Perspective on Femtosecond Pump-Probe Spectroscopy in the Development of Future Sunscreens

Given the negative impacts of overexposure to ultraviolet radiation (UVR) on humans, sunscreens have become a widely used product. Certain ingredients within sunscreens are responsible for photoprotection and these are known, collectively herein, as ultraviolet (UV) filters. Generally speaking, organic UV filters work by absorbing the potentially harmful UVR and dissipating this energy as harmless heat. This process happens on picosecond time scales and so femtosecond pump–probe spectroscopy (FPPS) is an ideal technique for tracking this energy conversion in real time. Coupling FPPS with complementary techniques, including steady-state spectroscopy and computational methods, can provide a detailed mechanistic picture of how UV filters provide photoprotection. As such, FPPS is crucial in aiding the future design of UV filters. This Perspective sheds light on the advancements made over the past two years on both approved and nature-inspired UV filters. Moreover, we suggest where FPPS can be further utilized within sunscreen applications for future considerations.

Elucidating the photoprotective properties of natural UV screening agents: ZEKE-PFI spectroscopy of methyl sinapate

As a prominent derivative of a natural sunscreen, methyl sinapate is an ideal candidate to provide fundamental insight into strategies on how to come to a rational design of artificial sunscreen filters with improved photoprotective properties. Here, static and time-resolved Zero Kinetic Energy-Pulsed Field Ionization (ZEKE-PFI) photoelectron spectroscopy has been used to study the spectroscopy and decay pathways of its electronically excited states. We find that different conformers are subject to distinct structural changes upon electronic excitation, and trace the structural changes that occur upon excitation back to the character of the LUMO. Ionization efficiency spectra in combination with pump-probe ZEKE-PFI spectra are consistent with the conclusion that the long-lived electronically excited state observed in the decay of the lowest excited singlet state is the lowest excited triplet state. Concurrently with providing information on the electronically excited states, the studies allow for a detailed characterization of the spectroscopic properties of the ground state of the radical ion, which is important in the context of the use of cinnamates in nature as antioxidants. Our studies determine the adiabatic ionization energies of the syn/cis, anti/cis and anti/trans conformers as 60 291.1 ± 0.5, 60 366.9 ± 0.5 and 60 503.9 ± 1.0 cm^-1, respectively, and provide accurate vibrational fequencies of low-frequency modes of the molecular ion in its electronic ground state. Finally, the studies emphasize the important role of vibrational and electronic autoionization processes that start to dominate the ionization dynamics in non-rigid molecules of the present size.

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

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

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

Approaching black-box calculations of pump-probe fragmentation dynamics of polyatomic molecules

A general framework for the simulation of ultrafast pump-probe time resolved experiments based on Born-Oppenheimer molecular dynamics (BOMD) is presented. Interaction of the molecular species with a laser is treated by a simple maximum entropy distribution of the excited state occupancies. The latter decay of the electronic excitation into the vibrations is based on an on-the-fly estimation of the rate of the internal conversion, while the energy is distributed in a thermostat-like fashion. The approach was tested by reproducing the results of previous femtosecond studies on ethylene, naphthalene and new results for phenanthrene.

Unravelling photoprotection in microbial natural products

Mycosporine-like amino acids have long been known as a natural form of photoprotection for fungi and cyanobacteria. This review will highlight the key time-resolved experimental and theoretical techniques unravelling their photochemistry and photophysics, and directly link this to their use in commercial skin-care products, namely as sunscreen filters. Three case studies have been selected, each having aided advancement in this burgeoning field of research. We discuss these studies in the context of photoprotection and conclude by evaluating the necessary future steps towards translating the photochemistry and photophysics insight of these nature derived sunscreen filters to commercial application.

UV absorption spectra of DNA bases in the 350-190 nm range: assignment and state specific analysis of solvation effects

The theoretical assignment of electronic spectra of polyatomic molecules is a challenging problem that requires the specification of the character of a large number of electronic states. We propose a procedure for automatically determining the character of electronic transitions and apply it to the study of UV spectra of DNA bases in the gas phase and in the aqueous environment. The procedure is based on the computation of electronic wave function overlaps and accounts for an extensive sampling of nuclear geometries. Novelties of this work are the theoretical assignment of the electronic spectra of DNA bases up to 190 nm and a state specific analysis of solvation effects. By accounting for different effects contributing to the total solvent shift we obtained a good agreement between the computed and experimental spectra. Effects of vibrational averaging, temperature and solvent-induced structural changes shift excitation energies to lower values. Solvent-solute electrostatic interactions are state specific and strongly destabilize nRyd states, and to lesser extent nπ* and πRyd states. Altogether, this results in the stabilization of ππ* states and destabilization of nπ*, πRyd and nRyd states in solution.

Exotic Bonding Regimes Uncovered in Excited States

Real-space tools were employed to show that the chemical bonding scenario used routinely to understand ground states lacks the necessary flexibility in excited states. It is shown that, even for two-center, two-electron bonds, the real-space bond orders have exotic values that have never been reported. The nature of these situations was uncovered by using electron-counting techniques that provide an appealing statistical interpretation of bonding descriptors, together with simple physical models. Bond orders greater than one as well as negative bond orders for a single bonding electron pair emerge in situations in which the electrons in the pair show a gregarious (bosonic) instead of the usual lonely (fermionic) behavior. In the first case the gregarious pair is intra-atomic, whereas the coupling is interatomic in the second. A number of examples are used to substantiate these claims.

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.

A Perspective on the Ultrafast Photochemistry of Solution-Phase Sunscreen Molecules

Sunscreens are one of the most common ways of providing on-demand additional photoprotection to the skin. Ultrafast transient absorption spectroscopy has recently proven to be an invaluable tool in understanding how the components of commercial sunscreen products display efficient photoprotection. Important examples of how this technique has unravelled the photodynamics of common components are given in this Perspective, and some of the remaining unanswered questions are discussed.

Photophysics of sunscreen molecules in the gas phase: a stepwise approach towards understanding and developing next-generation sunscreens

The relationship between exposure to ultraviolet (UV) radiation and skin cancer urges the need for extra photoprotection, which is presently provided by widespread commercially available sunscreen lotions. Apart from having a large absorption cross section in the UVA and UVB regions of the electromagnetic spectrum, the chemical absorbers in these photoprotective products should also be able to dissipate the excess energy in a safe way, i.e. without releasing photoproducts or inducing any further, harmful, photochemistry. While sunscreens are tested for both their photoprotective capability and dermatological compatibility, phenomena occurring at the molecular level upon absorption of UV radiation are largely overlooked. To date, there is only a limited amount of information regarding the photochemistry and photophysics of these sunscreen molecules. However, a thorough understanding of the intrinsic mechanisms by which popular sunscreen molecular constituents dissipate excess energy has the potential to aid in the design of more efficient, safer sunscreens. In this review, we explore the potential of using gas-phase frequency- and time-resolved spectroscopies in an effort to better understand the photoinduced excited-state dynamics, or photodynamics, of sunscreen molecules. Complementary computational studies are also briefly discussed. Finally, the future outlook of expanding these gas-phase studies into the solution phase is considered.

Gas-Phase Femtosecond Particle Spectroscopy: A Bottom-Up Approach to Nucleotide Dynamics

We summarize how gas-phase ultrafast charged-particle spectroscopy has been used to provide an understanding of the photophysics of DNA building blocks. We focus on adenine and discuss how, following UV excitation, specific interactions determine the fates of its excited states. The dynamics can be probed using a systematic bottom-up approach that provides control over these interactions and that allows ever-larger complexes to be studied. Starting from a chromophore in adenine, the excited state decay mechanisms of adenine and chemically substituted or clustered adenine are considered and then extended to adenosine mono-, di-, and trinucleotides. We show that the gas-phase approach can offer exquisite insight into the dynamics observed in aqueous solution, but we also highlight stark differences. An outlook is provided that discusses some of the most promising developments in this bottom-up approach.

Bottom-up excited state dynamics of two cinnamate-based sunscreen filter molecules

We have used time-resolved pump–probe spectroscopy to explore E-MMC's and E-EHMC's excited state dynamics upon UV-B photoexcitation.

Vacuum ultraviolet photoionization of carbohydrates and nucleotides

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

Solvent induced conformer specific photochemistry of guaiacol

Using a combination of ultrafast solution- and gas-phase spectroscopies, together with high-level theory calculations, we demonstrate that we are able to track conformer-specific photodissociation dynamics in solution through solvent choice. We reveal this phenomenon in guaiacol (2-methoxyphenol), a key subunit of the natural biopolymer lignin. In cyclohexane, the first electronically excited (1)ππ* (S1) state in guaiacol relaxes with a time-constant of τ = 4.5 ± 0.2 ns, mediated through intersystem crossing to lower lying triplet (Tn) states and internal conversion and fluorescence back to the ground state (S0). In contrast, in methanol, a further relaxation channel is also present; the S1 state relaxes with a time-constant of τ = 2.9 ± 0.1 ns, which is now additionally mediated through coupling onto a dissociative (1)πσ* (S2) state and subsequent O-H bond fission, evidenced through the appearance of a spectral signature for the guaiacoxyl radical after ∼250 ps. With the aid of complementary calculations, we attribute this to the now absent intramolecular H-bond between OH and OMe moieties, which now favours intermolecular H-bonding to methanol, lowering the barrier to O-H dissociation and facilitating H-atom loss via tunnelling.

Time-resolved photoelectron imaging of the isolated deprotonated nucleotides

Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.