Microhydration Prevents Fragmentation of Uracil and Thymine by Low-Energy Electrons

What does it take to stabilize a naphthalene anion?

We investigate attachment of slow electrons (0-10 eV) to naphthalene (Np) clusters in a crossed beam experiment. Supersonic expansions under different conditions using different buffer gases generate the clusters: in He, Ne, and low pressure Ar, neat (Np)N clusters are formed, while we also observe mixed clusters of naphthalene with rare-gas atoms in co-expansion with Ar above 0.5 bar and with Kr. Negatively charged (Np)n- and Rgm(Np)n- (Rg = Ar, Kr) clusters are analyzed by mass spectrometry, and electron energy dependent ion yields are measured. We show that the smallest stable naphthalene complex with an excess electron, the dimer (Np)2- anion, cannot be formed in a binary collision of a free electron with (Np)2 dimer, nor with (Np)3 trimer. Evaporation of a weakly bound Ar atom(s) from a mixed ArM(Np)2 cluster following electron attachment leads to the dimer (Np)2- anion. Larger (Np)n-, n > 3, transient cluster anions decay via evaporation of an Np unit on a timescale of tens of microseconds. The self-scavenging process opens around 6 eV, where a naphthalene unit is electronically excited by the incoming electron, which is slowed down and trapped. However, the transient negative ion is efficiently stabilized only in the mixed clusters, from which Ar atom(s) can be evaporated.

Toward a numerically efficient description of bulk-solvated anionic states

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.

Dynamics of Anions: From Bound to Unbound States and Everything In Between

Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.

Hydrated Formic Acid Clusters and their Interaction with Electrons

We investigate ion formation in hydrated formic acid (FA) clusters upon collision with electrons of variable energy, focusing on electron ionization at 70 eV (EI) and low-energy (1.5-15 eV) electron attachment (EA). To uncover details about the composition of neutral clusters, we aim to elucidate the ion formation processes in FAM ⋅ WN clusters initiated by interaction with electrons and determine the extent of cluster fragmentation. EI predominantly produces protonated [FAm+H]+ ions, and in FA-rich clusters, the stable ring structures surrounding H3O+ ions are formed. In contrast, EA leads to a competition between the formation of intact [FAm ⋅ Wn]- and dissociated [FAm ⋅ Wn-H]- fragment ions, influenced by the cluster size, level of hydration, and electron energy. Our findings reveal a predisposition of low-energy EA towards forming [FAm ⋅ Wn]-, while higher electron energies tend to favor the formation of [FAm ⋅ Wn-H]- due to intracluster ion-molecule reactions. The comparison of positive and negative ion spectra suggests that the mass spectra of FA-rich clusters may indicate their actual size and composition. On the other hand, the more weakly bound water evaporation from the clusters depends strongly on the ionization. Thus, for the hydrated clusters, the neutral cluster size can hardly be estimated from the mass spectra.

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.

Interaction of low-energy electrons with radiosensitizers

We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.

Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer

Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized.

Electron-triggered processes in halogenated carboxylates: dissociation pathways in CF3COCl and its clusters

Trifluoroacetyl chloride, CF3COCl, is produced in the Earth's atmosphere by photooxidative degradation of hydrochlorofluorocarbons, and represents a potential source of highly reactive halogen radicals. Despite considerable insight into photochemistry of CF3COCl, its reactivity towards electrons has not been addressed so far. We investigate the electron ionization and attachment in isolated CF3COCl molecules and (CF3COCl)N, max. N ≥ 10, clusters using a molecular beam experiment in combination with quantum chemical calculations. The ionization of the molecule at 70 eV electron energy leads to strong fragmentation: weakening of the C-C bond yields the CF3+ and COCl+ ions, while the fission of the C-Cl bond produces the major CF3CO+ fragment ion. The cluster spectra are dominated by Mn·COCl+ and Mn·CF3CO+ ions (M = CF3COCl). The electron attachment at energies between 1.5 and 11 eV also leads to the dissociation of the molecule breaking either the C-Cl bond at low energies below 3 eV yielding mainly Cl- ions, or dissociating the C-C bond at higher energies above 4 eV leading mainly to CF3- ions. In the clusters, the intact Mn- ions are stabilized after electron attachment at low energies with contribution of Mn·Cl- fragment ions. At higher energies, the Mn·Cl- fragments dominate the spectra, and C-C bond dissociation occurs as well yielding Mn·CF3-. Interestingly, Mn·Cl2- ions appear in the spectra at higher energies. We briefly discuss possible atmospheric implications.

Shape resonance induced electron attachment to cytosine: The effect of aqueous media

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.

Prebiotic chemical origin of biomolecular complementarity

The early Earth, devoid of the protective stratospheric ozone layer, must have sustained an ambient prebiotic physicochemical medium intensified by the co-existence of shortwave UV photons and very low energy electrons (vLEEs). Consequently, only intrinsically stable molecules against these two co-existing molecular destructors must have proliferated and thereby chemically evolved into the advanced molecules of life. Based on this view, we examined the stability inherent in nucleobases and their complementary pairs as resistance to the molecular damaging effects of shortwave UV photons and vLEEs. This leads to the conclusion that nucleobases could only proliferated as their complementary pairs under the unfavorable prebiotic conditions on early Earth. The complementary base pairing not only enhances but consolidates the intrinsic stability of nucleobases against short-range UV photons, vLEEs, and possibly many as-yet-unknown deleterious agents co-existed in the prebiotic conditions of the early Earth. In short, complementary base pairing is a manifestation of chemical evolution in the unfavorable prebiotic medium created by the absence of the stratospheric ozone layer.

Dissociative Electron Attachment to 5-Iodo-4-thio-2'-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells

In the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2'-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry. The experimental results were supported by calculations on the threshold energies of formed anions and transition state calculations. We show that low-energy electrons with kinetic energies near 0 eV may effectively decompose the molecule upon DEA. The by far most abundant anion observed corresponds to the iodine anion (I-). Due to the associated bond cleavage, a radical site is formed at the C5 position, which may initiate strand break formation if the molecule is incorporated into a DNA strand. Our results reflect the conclusion from previous radiolysis studies with the title compound, suggesting its potential as a radiosensitizer.

Secondary ionization of pyrimidine nucleobases and their microhydrated derivatives in helium nanodroplets

Radiation damage in biological systems by ionizing radiation is predominantly caused by secondary processes such as charge and energy transfer leading to the breaking of bonds in DNA. Here, we study the fragmentation of cytosine (Cyt) and thymine (Thy) molecules, clusters and microhydrated derivatives induced by direct and indirect ionization initiated by extreme-ultraviolet (XUV) irradiation. Photofragmentation mass spectra and photoelectron spectra of free Cyt and Thy molecules are compared with mass and electron spectra of Cyt/Thy clusters and microhydrated Cyt/Thy molecules formed by aggregation in superfluid helium (He) nanodroplets. Penning ionization after resonant excitation of the He droplets is generally found to cause less fragmentation compared to direct photoionization and charge-transfer ionization after photoionization of the He droplets. When Cyt/Thy molecules and oligomers are complexed with water molecules, their fragmentation is efficiently suppressed. However, a similar suppression of fragmentation is observed when homogeneous Cyt/Thy clusters are formed in He nanodroplets, indicating a general trend. Penning ionization electron spectra (PIES) of Cyt/Thy are broad and nearly featureless but PIES of their microhydrated derivatives point at a sequential ionization process ending in unfragmented microsolvated Cyt/Thy cations.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters

The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.

Electron Attachment to DNA: The Protective Role of Amino Acids

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Low-Energy Shape Resonances of a Nucleobase in Water

When high-energy radiation passes through aqueous material, low-energy electrons are produced which cause DNA damage. Electronic states of anionic nucleobases have been suggested as an entrance channel to capture the electron. However, identifying these electronic resonances have been restricted to gas-phase electron-nucleobase studies and offer limited insight into the resonances available within the aqueous environment of DNA. Here, resonance and detachment energies of the micro-hydrated uracil pyrimidine nucleobase anion are determined by two-dimensional photoelectron spectroscopy and are shown to extrapolate linearly with cluster size. This extrapolation allows the corresponding resonance and detachment energies to be determined for uracil in aqueous solution as well as the reorganization energy associated with electron capture. Two shape resonances are clearly identified that can capture low-energy electrons and subsequently form the radical anion by solvent stabilization and internal conversion to the ground electronic state. The resonances and their dynamics probed here are the nucleobase-centered doorway states for low-energy electron capture and damage in DNA.

Distant Symmetry Control in Electron-Induced Bond Cleavage

We experimentally show that N-H bond cleavage in the pyrrole molecule following resonant electron attachment is allowed and controlled by the motion of the atoms which are not dissociating, namely, of the carbon-attached hydrogen atoms. We use this fact to steer the efficiency of this bond cleavage. In order to interpret the experimental findings, we have developed a method for locating all resonant and virtual states of an electron-molecule system in the complex plane, based on all-electron R-matrix scattering calculations. Mapping these as a function of molecular geometry allows us to separate two contributing dissociation mechanisms: a π* resonance formation inducing strong bending deformations and a nonresonant σ* mechanism originating in a virtual state. The coupling between the two mechanisms is enabled by the out-of-plane motion of the C-H bonds, and we show that it must happen on an ultrafast (few fs) time scale.

Stabilization of benzene radical anion in ammonia clusters

We investigate electron attachment to large ammonia clusters doped with a single benzene (Bz) molecule (NH3)N·Bz, N̄ ≈ 320. Negatively charged clusters are probed by mass spectrometry, and the energy-dependent ion yields are derived from mass spectra measured at different electron energies. The ion efficiency curves of pure ammonia clusters exhibit two maxima. At around 6 eV, (NH3)n-1NH2- ions are produced via dissociative electron attachment (DEA) to NH3 molecules. (NH3)n- ions produced at this energy are formed by DEA followed by fragment caging. At low energies around 1.3 eV, only (NH3)n- ions are formed for cluster sizes n ≥ 35 that correspond to solvated electrons in ammonia clusters. The doped (NH3)n·Bz- cluster ions exhibit essentially the same energy dependence. The (NH3)n·Bz- ions are metastable and evaporate NH3 molecule(s), while pure (NH3)n- ions are stable. The lifetime for NH3 molecule evaporation from the Bz-doped clusters was estimated as τ ≈ 18 μs. We interpret the metastability of the doped clusters by the charge localization on a Bz- ion solvated in the ammonia, which is accompanied by an energy release leading to the evaporation of NH3 molecule(s).

Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity

The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.

Low-Energy Electron Induced Reactions in Metronidazole at Different Solvation Conditions

Metronidazole belongs to the class of nitroimidazole molecules and has been considered as a potential radiosensitizer for radiation therapy. During the irradiation of biological tissue, secondary electrons are released that may interact with molecules of the surrounding environment. Here, we present a study of electron attachment to metronidazole that aims to investigate possible reactions in the molecule upon anion formation. Another purpose is to elucidate the effect of microhydration on electron-induced reactions in metronidazole. We use two crossed electron/molecular beam devices with the mass-spectrometric analysis of formed anions. The experiments are supported by quantum chemical calculations on thermodynamic properties such as electron affinities and thresholds of anion formation. For the single molecule, as well as the microhydrated condition, we observe the parent radical anion as the most abundant product anion upon electron attachment. A variety of fragment anions are observed for the isolated molecule, with NO2- as the most abundant fragment species. NO2- and all other fragment anions except weakly abundant OH- are quenched upon microhydration. The relative abundances suggest the parent radical anion of metronidazole as a biologically relevant species after the physicochemical stage of radiation damage. We also conclude from the present results that metronidazole is highly susceptible to low-energy electrons.

Effect of Microhydration on the Temporary Anion States of Pyrene

The influence of incremental hydration (≤4) on the electronic resonances of the pyrene anion is studied using two-dimensional photoelectron spectroscopy. The photoexcitation energies of the resonances do not change; therefore, from the anion's perspective, the resonances remain the same, but from the neutral's perspective of the electron-molecule reaction, the resonances decrease in energy by the binding energy of the water molecules. The autodetachment of the resonances shows that hydration has very little effect, showing that even the dynamics of most of the resonances are not impacted by hydration. Two specific resonances do show changes that are explained by the closing of specific autodetachment channels. The lowest-energy resonance leads to efficient electron capture as observed through thermionic emission and evaporation of water molecules (dissociative electron attachment). The implications of low-energy electron capture in dense molecular interstellar clouds are discussed.

Damage Induced to DNA and Its Constituents by 0-3 eV UV Photoelectrons†

The complex physical and chemical interactions between DNA and 0-3 eV electrons released by UV photoionization can lead to the formation of various lesions such as base modifications and cleavage, crosslinks and single strand breaks. Furthermore, in the presence of platinum chemotherapeutic agents, these electrons can cause clustered lesions, including double strand breaks. We explain the mechanisms responsible for these damages via the production 0-3 eV electrons by UVC radiation, and by UV photons of any wavelengths, when they are produced by photoemission from nanoparticles lying within about 10 nm from DNA. We review experimental evidence showing that a single 0-3 eV electron can produce these damages. The foreseen benefits UV-irradiation of nanoparticles targeted to the cell nucleus are mentioned in the context of cancer therapy, as well as the potential hazards to human health when they are present in cells.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

Quasi-Free Electron-Mediated Radiation Sensitization by C5-Halopyrimidines

Substitution of the thymidine moiety in DNA by C5-substituted halogenated thymidine analogues causes significant augmentation of radiation damage in living cells. However, the molecular pathway involved in such radiosensitization process has not been clearly elucidated to date in solution at room temperature. So far, low-energy electrons (LEEs; 0-20 eV) under vacuum condition and solvated electrons (esol-) in solution are shown to produce the σ-type C5-centered pyrimidine base radical through dissociative electron attachment involving carbon-halogen bond breakage. Formation of this σ-type radical and its subsequent reactions are proposed to cause cellular radiosensitization. Here, we report time-resolved measurements at room temperature, showing that a radiation-produced quasi-free electron (eqf-) in solution promptly breaks the C5-halogen bond in halopyrimidines forming the σ-type C5 radical via an excited transient anion radical. These results demonstrate the importance of ultrafast reactions of eqf-, which are extremely important in chemistry, physics, and biology, including tumor radiochemotherapy.

Electron attachment to microhydrated 4-nitro- and 4-bromo-thiophenol

We investigate the effect of microhydration on electron attachment to thiophenols with halogen (Br) and nitro (NO₂) functional groups in the para position. We focus on the formation of anions upon the attachment of low-energy electrons with energies below 8 eV to heterogeneous clusters of the thiophenols with water. For nitro-thiophenol (NTP), the primary reaction channel observed is the associative electron attachment, irrespective of the microhydration. On the other hand, bromothiophenol (BTP) fragments significantly upon the electron attachment, producing Br^- and (BTP-H)^- anions. Microhydration suppresses fragmentation of both molecules, however in bromothiophenol, the Br^- channel remains intense and Br(H₂O)_n^- hydrated fragment clusters are observed. The results are supported by the reaction energetics obtained from ab initio calculations. Different dissociation dynamics of NTP and BTP can be related to different products of their plasmon induced reactions on Au nanoparticles. Computational modeling of the simplified BTP(H₂O) system indicates that the electron attachment products reflect the structure of neutral precursor clusters - the anion dissociation dynamics is controlled by the hydration site.

Electron attachment to isolated and microhydrated favipiravir

Electron attachment and its equivalent in complex environments, single-electron reduction, are important in many biological processes. Here, we experimentally study the electron attachment to favipiravir, a well-known antiviral agent. Electron attachment spectroscopy is used to explore the energetics of associative (AEA) and dissociative (DEA) electron attachment to isolated favipiravir. AEA dominates the interaction and the yields of the fragment anions after DEA are an order of magnitude lower than that of the parent anion. DEA primary proceeds via decomposition of the CONH2 functional group, which is supported by reaction threshold calculations using ab initio methods. Mass spectrometry of small favipiravir-water clusters demonstrates that a lot of energy is transferred to the solvent upon electron attachment. The energy gained upon electron attachment, and the high stability of the parent anion were previously suggested as important properties for the action of several electron-affinic radiosensitizers. If any of these mechanisms cause synergism in chemo-radiation therapy, favipiravir could be repurposed as a radiosensitizer.

Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, e_pre^-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence e_pre^- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.

The effect of solvation on electron capture revealed using anion two-dimensional photoelectron spectroscopy

The reaction of low-energy electrons with neutral molecules to form anions plays an important role in chemistry, being involved in, for example, various biological and astrochemical processes. However, key aspects of electron-molecule interactions, such as the effect of incremental solvation on the initially excited electronic resonances, remain poorly understood. Here two-dimensional photoelectron spectroscopy of anionic anthracene and nitrogen-substituted derivatives-solvated by up to five water molecules-reveals that for an incoming electron, resonances red-shift with increasing hydration; but for the anion, the excitation energies of the resonances remain essentially the same. These complementary points of view show that the observed onset of enhanced anion formation for a specific cluster size is mediated by a bound excited state of the anion. Our findings suggest that polycyclic aromatic hydrocarbons may be more efficient at electron capture than previously predicted with important consequences for the ionization fraction in dense molecular clouds.

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

Water-biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation?

The properties of mixed water-uracil nanoaggregates have been probed by core electron-photoemission measurements to investigate supramolecular assembly in the gas phase driven by weak interactions. The interpretation of the measurements has been assisted by multilevel atomistic simulations, based on semi-empirical tight-binding and DFT-based methods. Our protocol established a positive-feedback loop between experimental and computational techniques, which has enabled a sound and detailed atomistic description of such complex heterogeneous molecular aggregates. Among biomolecules, uracil offers interesting and generalized skeletal features; its structure encompasses an alternation of hydrophilic H-bond donor and acceptor sites and hydrophobic moieties, typical in biomolecular systems, that induces a supramolecular core-shell-like organization of the mixed clusters with a water core and an uracil shell. This structure is far from typical models of both solid-state hydration, with water molecules in defined positions, or liquid solvation, where disconnected uracil molecules are completely surrounded by water.

Electron Attachment to Cytosine: The Role of Water

We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.

Water-Assisted Electron-Induced Chemistry of the Nanofabrication Precursor Iron Pentacarbonyl

Focused electron beam deposition often requires the use of purification techniques to increase the metal content of the respective deposit. One of the promising methods is adding H₂O vapor as a reactive agent during the electron irradiation. However, various contrary effects of such addition have been reported depending on the experimental condition. We probe the elementary electron-induced processes that are operative in a heterogeneous system consisting of iron pentacarbonyl as an organometallic precursor and water. We use an electron beam of controlled energy that interacts with free mixed Fe(CO)₅/H₂O clusters. These mimic the heterogeneous system and, at the same time, allow direct mass spectrometric analysis of the reaction products. The anionic decomposition pathways are initiated by dissociative electron attachment (DEA), either to Fe(CO)₅ or to H₂O. The former one proceeds mainly at low electron energies (<3 eV). Comparison of nonhydrated and hydrated conditions reveals that the presence of water actually stabilizes the ligands against dissociation. The latter one proceeds at higher electron energies (>6 eV), where the DEA to H₂O forms OH^- in the first reaction step. This intermediate reacts with Fe(CO)₅, leading to enhanced decomposition, with the desorption of up to three CO ligands. The present results demonstrate that the water action on Fe(CO)₅ decomposition is sensitive to the involved electron energy range and depends on the hydration degree.

Stability of pyruvic acid clusters upon slow electron attachment

Pyruvic acid represents a key molecule in prebiotic chemistry and it has recently been proposed to be synthesized on interstellar ices. In order to probe the stability of pyruvic acid in the interstellar medium with respect to decomposition by slow electrons, we investigate the electron attachment to its homomolecular and heteromolecular clusters. Using mass spectrometry, we follow the changes in the fragmentation pattern and its dependence on the electron energy for various cluster sizes of pure and microhydrated pyruvic acid. The assignment of fragmentation reaction pathways is supported by ab initio calculations. The fragmentation degree dramatically decreases upon clustering. This decrease is even stronger in the heteromolecular clusters of pyruvic acid with water, where the non-dissociative attachment is by far the strongest channel. In the homomolecular clusters, the dissociative channel leading to dehydrogenation is active over a larger electron energy range than in the isolated molecules. To probe the role of the self-scavenging effects, we explore the excited states of pyruvic acid. This has been done both experimentally, by using electron energy loss spectroscopy, and theoretically, by photochemical calculations. Data on both optically-allowed and forbidden states allow for the explanation of processes emerging upon clustering.

Pickup and reactions of molecules on clusters relevant for atmospheric and interstellar processes

In this perspective, we review experiments with molecules picked up on large clusters in molecular beams with the focus on the processes in atmospheric and interstellar chemistry. First, we concentrate on the pickup itself, and we discuss the pickup cross sections. We measure the uptake of different atmospheric molecules on mixed nitric acid-water clusters and determine the accommodation coefficients relevant for aerosol formation in the Earth's atmosphere. Then the coagulation of the adsorbed molecules on the clusters is investigated. In the second part of this perspective, we review examples of different processes triggered by UV-photons or electrons in the clusters with embedded molecules. We start with the photodissociation of hydrogen halides and Freon CF₂Cl₂ on ice nanoparticles in connection with the polar stratospheric ozone depletion. Next, we mention reactions following the excitation and ionization of the molecules adsorbed on clusters. The first ionization-triggered reaction observed between two different molecules picked up on the cluster was the proton transfer between methanol and formic acid deposited on large argon clusters. Finally, negative ion reactions after slow electron attachment are illustrated by two examples: mixed nitric acid-water clusters, and hydrogen peroxide deposited on large Ar_N and (H₂O)_N clusters. The selected examples are discussed from the perspective of the atmospheric and interstellar chemistry, and several future directions are proposed.

5-Nitro-2,4-Dichloropyrimidine as an Universal Model for Low-Energy Electron Processes Relevant for Radiosensitization

We report experimental results of low-energy electron interactions with.

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.

Ion and radical chemistry in (H2O2)N clusters

We investigate the ionization induced chemistry of hydrogen peroxide in (H₂O₂)_N clusters generated after the pickup of individual H₂O₂ molecules on large free Ar_M, M[combining macron]≈ 160, nanoparticles in molecular beams. Positive and negative ion mass spectra are recorded after an electron ionization of the clusters at energies 5-70 eV and after a slow electron attachment (below 4 eV), respectively. The spectra demonstrate that (H₂O₂)_N clusters with N≥ 20 are formed on argon nanoparticles. This is the first experimental report on hydrogen peroxide clusters in molecular beams. The major negative cluster ion series (H₂O₂)_nO₂^- indicates O₂^- ion formation. The dissociative electron attachment to H₂O₂ molecules in the gas phase yielded only OH^- and O^- (Nandi et al., Chem. Phys. Lett., 2003, 373, 454). These ions and the series containing them are much less abundant in the clusters. We propose a sequence of ion-molecule and radical reactions to explain the formation of O₂^-, HO₂^- and other ions observed in the negatively charged cluster ion series. Since hydrogen peroxide plays an important role in many areas of chemistry from the Earth's atmosphere to biological tissues, our study opens new horizons for experimental investigations of hydrogen peroxide chemistry in complex environments.

Dissociative electron attachment to benzoic acid (C7H6O2)

The dissociative electron attachment (DEA) to benzoic acid (C₆H₅COOH) has been studied using an experimental crossed beam setup of a quadrupole mass spectrometer and a trochoidal electron monochromator. Relative partial cross sections for the DEA to produce negative ion fragments show the main channels for dissociation. The comparison of the present results with the ultraviolet photoelectron spectrum of benzoic acid [J. Meeks, A. Wahlborg, and S. P. McGlynn, J. Electron Spectrosc. Relat. Phenom. 22, 43 (1981)] implies that most DEA bands in the high energy range are due to Feshbach resonances with double occupation of diffuse Rydberg-like orbitals. The measurements are supported by density functional theory calculations of the threshold energies.

Water acting as a catalyst for electron-driven molecular break-up of tetrahydrofuran

Low-energy electron-induced reactions in hydrated molecular complexes are important in various fields ranging from the Earth’s environment to radiobiological processes including radiation therapy. Nevertheless, our understanding of the reaction mechanisms in particular in the condensed phase and the role of water in aqueous environments is incomplete. Here we use small hydrogen-bonded pure and mixed dimers of the heterocyclic molecule tetrahydrofuran (THF) and water as models for biochemically relevant systems. For electron-impact-induced ionization of these dimers, a molecular ring-break mechanism is observed, which is absent for the THF monomer. Employing coincident fragment ion mass and electron momentum spectroscopy, and theoretical calculations, we find that ionization of the outermost THF orbital initiates significant rearrangement of the dimer structure increasing the internal energy and leading to THF ring-break. These results demonstrate that the local environment in form of hydrogen-bonded molecules can considerably affect the stability of molecular covalent bonds.

Reactions induced by low-energy electrons in hydrated systems are central to radiation therapy, but a full understanding of their mechanism is lacking. Here the authors investigate the electron-impact induced ionization and subsequent dissociation of tetrahydrofuran, model for biochemically relevant systems, in a micro-solvated environment.

Low energy (1-19 eV) electron scattering from condensed thymidine (dT) II: comparison of vibrational excitation cross sections with those of tetrahydrofuran and the recalibrated values of thymine

Recent measurements of absolute vibrational cross sections (CSs) for low-energy electron (LEE) scattering from condensed thymidine (dT) allows comparison with CSs of its constituents; thymine and tetrahydrofuran (THF). To facilitate this comparison, the vibrational CSs of condensed thymine were remeasured at six electron incident energies and a correction was applied to the earlier thymine CS values measured by Lévesque et al. [Nucl. Instrum. Methods Phys. Res., Sect. B, 2003, 208, 225]. The incident energy dependence of the CS of each vibrational mode of dT is compared with the corresponding modes in thymine and/or THF. It is found that the magnitude of the CSs of the thymine breathing mode and the C-C stretch mode of THF are greatly attenuated in dT. Finally, the magnitudes of the total vibrational CSs of each molecule are compared. Below 4 eV, the total vibrational CSs of dT is greater than each of its two constituents. Interestingly, at higher energy (>6 eV), the magnitude of the total vibrational CS of dT is roughly equal to that of THF and is greater than thymine by only 15% at 10 eV, showing that the CSs of dT cannot be approximated by the addition of the CSs of its constituents over the entire energy range. These comparisons are discussed in terms of the basic principles involved in the formation and decay of shape resonances, which are known to be responsible for major enhancements of LEE-induced vibrational excitation at low electron energies.

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations

Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.

Fragmentation dynamics of nitrogen trifluoride induced by electron collision

The fragmentation dynamics of nitrogen trifluoride (NF₃) in collisions with a 500 eV electron is studied by using a momentum imaging spectrometer. The kinetic energy releases of two-body, three-body, and four-body fragmentation channels of NF₃ ^q+ (q = 2, 3) are investigated. The fragmentation dynamics of three-body, as well as four-body, dissociation channels is analyzed by the Dalitz plot and the Newton diagram. It is found that for all of the dissociation channels, the fragment including N atom (ion) always shares significant momenta, regardless of whether it is charged. For F atom, however, it is always emitted with negligible momenta.

Ring Formation and Hydration Effects in Electron Attachment to Misonidazole

We study the reactivity of misonidazole with low-energy electrons in a water environment combining experiment and theoretical modelling. The environment is modelled by sequential hydration of misonidazole clusters in vacuum. The well-defined experimental conditions enable computational modeling of the observed reactions. While the NO 2 - dissociative electron attachment channel is suppressed, as also observed previously for other molecules, the OH - channel remains open. Such behavior is enabled by the high hydration energy of OH - and ring formation in the neutral radical co-fragment. These observations help to understand the mechanism of bio-reductive drug action. Electron-induced formation of covalent bonds is then important not only for biological processes but may find applications also in technology.

Low-energy electrons transform the nimorazole molecule into a radiosensitiser

While matter is irradiated with highly-energetic particles, it may become chemically modified. Thereby, the reactions of free low-energy electrons (LEEs) formed as secondary particles play an important role. It is unknown to what degree and by which mechanism LEEs contribute to the action of electron-affinic radiosensitisers applied in radiotherapy of hypoxic tumours. Here we show that LEEs effectively cause the reduction of the radiosensitiser nimorazole via associative electron attachment with the cross-section exceeding most of known molecules. This supports the hypothesis that nimorazole is selectively cytotoxic to tumour cells due to reduction of the molecule as prerequisite for accumulation in the cell. In contrast, dissociative electron attachment, commonly believed to be the source of chemical activity of LEEs, represents only a minor reaction channel which is further suppressed upon hydration. Our results show that LEEs may strongly contribute to the radiosensitising effect of nimorazole via associative electron attachment.