Energy-Dependent UV Photodissociation of Gas-Phase Adenosine Monophosphate Nucleotide Ions: The Role of a Single Solvent Molecule

Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment

Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.

Water is a radiation protection agent for ionised pyrrole

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we experimentally observed a hydrogen-bonded water molecule acting as a radiation protection agent for ionised pyrrole, a prototypical aromatic biomolecule. Pure samples of pyrrole and pyrrole(H2O) were outer-valence ionised and the subsequent damage and relaxation processes were studied. Bare pyrrole ions fragmented through the breaking of C-C or N-C covalent bonds. However, for pyrrole(H2O)+, we observed a strong protection of the pyrrole ring through the dissociative release of neutral water or by transferring an electron or proton across the hydrogen bond. Overall, a single water molecule strongly reduces the fragmentation probability and thus the persistent radiation damage of singly-ionised pyrrole.

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.

UV Photolysis of Mono- and Dichloramine Using UV-LEDs as Radiation Sources: Photodecay Rates and Radical Concentrations

UV-LEDs with four characteristic wavelengths (255, 265, 285, and 300 nm) were used to investigate the wavelength-dependence of the photolysis of two inorganic chloramines (NH₂Cl and NHCl₂) and their subsequent radical formation. The fluence-based photodecay rates of NH₂Cl decreased with increasing wavelength from 255 to 300 nm, while NHCl₂ photodecay rates exhibited the opposite wavelength-dependence. The fluence-based photodecay rate of NH₂Cl was comparable to that of NHCl₂ at 255 nm, but was lower than NHCl₂ at other tested wavelengths. The wavelength-dependence was more influenced by the molar absorption coefficient than the apparent/innate quantum yield and the lower photosensitivity was mainly attributed to the higher bond (N-Cl) dissociation energy (BDE) of NH₂Cl than NHCl₂. The steady-state concentrations of HO^• and reactive chlorine species (e.g., Cl₂^•-, ClO^•, and Cl^•) that were generated from the photolysis of NH₂Cl and NHCl₂ at different wavelengths were determined experimentally and compared with the simulated results by a kinetic model. UV photolysis of NHCl₂ at 265, 285, and 300 nm generated higher concentrations of radicals (e.g., HO^•, ClO^•, Cl^•, and Cl₂^-•) than NH₂Cl, while UV photolysis of NH₂Cl at 255 nm generated higher concentrations of HO^•, ClO^•, and Cl^• but not Cl₂^-• than NHCl₂. The findings of this study provide fundamental information to be used in selecting specific wavelengths of UV radiation for enhancing/optimizing NH₂Cl/NHCl₂ photodecay in swimming pools and radical generation for micropollutant abatement in drinking water treatment or potable water reuse.

Photoexcitation of Adenosine 5'-Triphosphate Anions in Vacuo: Probing the Influence of Charge State on the UV Photophysics of Adenine

We report the first UV laser photodissociation spectra (4.0-5.8 eV) of gas-phase deprotonated adenosine 5'-triphosphate, diphosphate and monophosphate anions. The photodepletion spectra of these anions display strong absorption bands across the region of 4.6-5.2 eV, consistent with excitation of a primarily adenine-centered π-π* transition. The spectra appear insensitive to the charge of the species (i.e., the spectrum of [ATP-2H]^2- closely resembles that of [ATP-H]^-), while the spectral profile is affected to a greater extent by the variation of the molecular structure, i.e. the [AMP-H]^- and [ADP-H]^- photodepletion spectra display similar profiles while the [ATP-H]^- spectrum is distinctive. The photodepletion cross-section also decreases for the ATP anions compared to both the AMP and ADP anions, reflecting a high intrinsic photostability of ATP versus both AMP and ADP. A range of photofragments are produced across the 4.0-5.8 eV spectral range for all of the ATP analogues studied. These fragments are primarily associated with fragmentation on the ground-state electronic surface, indicative of a statistical decay process where ultrafast decay is followed by ergodic dissociation. However, while the photofragments observed following photoexcitation of the monoanionic species, [AMP-H]^- to [ADP-H]^- to [ATP-H]^- are entirely consistent with statistical decay, an additional group of photofragments are observed for the dianionic species, [ADP-2H]^2- and [ATP-2H]^2-, that we associate with electron detachment, and subsequent fragmentation of the resulting electron-detached photofragment. TDDFT calculations are presented to support the interpretation of the experimental data, and confirm that the electronic structure of the adenine moiety is relatively unperturbed by varying the overall charge.

Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase

Radical creation after single-photon ionisation of collagen peptides induces the loss of molecules from amino-acid residue side-chains.

Triplet Mediated C-N Dissociation versus Internal Conversion in Electronically Excited N-Methylpyrrole

The photochemical and photophysical pathways operative in N-methylpyrrole, after excitation in the near part of its ultraviolet absorption spectrum, have been investigated by the combination of time-resolved total ion yield and photoelectron spectroscopies with high-level ab initio calculations. The results collected are remarkably different from the observations made for pyrrole and other aromatic systems, whose dynamics is dictated by the presence of πσ* excitations on X-H (X: N, O, S, ...) bonds. The presence of a barrier along the C-N dissociation coordinate that can not be tunneled triggers two alternative decay mechanisms for the S1 A″ πσ* state. While at low vibrational content the C-N dissociation occurs on the surface of a lower (3)ππ* state reached after efficient intersystem crossing, at higher excitation energies, the A″ πσ* directly internally converts to the ground state through a ring-twisted S1/S0 conical intersection. The findings explain previous observations on the molecule and may be relevant for more complex systems containing similar C-N bonds, such as the DNA nucleotides.

Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage

We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.

On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in 'top-down' strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)(n+) and (M-nH)(n-) ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into C: and Y: ions from phosphodiester bond cleavage.