Quantifying hydroxyl radicals generated by a low-temperature plasma using coumarin: methodology and precautions.

The detection and quantification of hydroxyl radicals (HO˙) generated by low-temperature plasmas (LTPs) are crucial for understanding their role in diverse applications of plasma radiation. In this study, the formation of HO˙ in the irradiated aqueous phase is investigated at various plasma parameters, by probing them indirectly using the coumarin molecule. We propose a quantification methodology for these radicals, combining spectrophotometry to study the coumarin reaction with hydroxyl radicals and fluorimetry to evaluate the formation yield of the hydroxylated product, 7-hydroxycoumarin. Additionally, we thoroughly examine and discuss the impact of pH on this quantification process. This approach enhances our comprehension of HO˙ formation during LTP irradiation, adding valuable insights to plasma's biological applications.

Direct Probing of Water Adsorption on Liquid-Phase Exfoliated WS2 Films Formed by the Langmuir-Schaefer Technique.

Tungsten disulfide, a transition metal dichalcogenide, has numerous applications as active components in gas- and chemical-sensing devices, photovoltaic sources, photocatalyst substrates, etc. In such devices, the presence of water in the sensing environment is a factor whose role has not been well-understood. To address this problem, the in situ probing of H2O molecule adsorption on WS2 films supported on solid substrates has been performed in a near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) setup. Instead, on the individual nanoflakes or spray-coated samples, the measurements were performed on highly transparent, homogeneous, thin films of WS2 nanosheets self-assembled at the interface of two immiscible liquids, water and toluene, transferred onto a solid substrate by the Langmuir-Schaefer technique. This experiment shows that edge defects in nanoflakes, tungsten dangling bond ensuing the exfoliation in the liquid phase, represent active sites for the WO3, WO3-x, and WO3·nH2O formation under ambient conditions. These oxides interact with water molecules when the WS2 films are exposed to water vapor in the NAP-XPS reaction cell. However, water molecules do not influence the W-S chemical bond, thus indicating the physisorption of H2O molecules at the WS2 film surface.

Dissociative electron attachment to amide bond containing molecules: N-ethylformamide and N-ethylacetamide.

To advance our quest to understand the role of low energy electrons in biomolecular systems, we performed investigations on dissociative electron attachment (DEA) to gas-phase N-ethylformamide (NEF) and N-ethylacetamide (NEA) molecules. Both molecules contain the amide bond, which is the linkage between two consecutive amino acid residues in proteins. Thus, their electron-induced dissociation can imitate the resonant behavior of the DEA process in more complex biostructures. Our experimental results indicate that in these two molecules, the dissociation of the amide bond results in a double resonant structure with peaks at ∼5 eV and 9 eV. We also determined the energy position of resonant states for several negative ions, i.e., the other dissociation products from NEF and NEA. Our predictions of dissociation channels were supported by density functional theory calculations of the corresponding threshold energies. Our results and those previously reported for small amides and peptides imply the fundamental nature for breakage of the amide bond through the DEA process.

Irradiation-induced reactions at the CeO2/SiO2/Si interface.

The influence of high-energy (1.6 MeV) Ar2+ irradiation on the interfacial interaction between cerium oxide thin films (∼15 nm) with a SiO2/Si substrate is investigated using transmission electron microscopy, ultrahigh vacuum x-ray photoelectron spectroscopy (XPS), and a carbon monoxide (CO) oxidation catalytic reaction using ambient pressure XPS. The combination of these methods allows probing the dynamics of vacancy generation and its relation to chemical interactions at the CeO2/SiO2/Si interface. The results suggest that irradiation causes amorphization of some portion of CeO2 at the CeO2/SiO2/Si interface and creates oxygen vacancies due to the formation of Ce2O3 at room temperature. The subsequent ultra-high-vacuum annealing of irradiated films increases the concentration of Ce2O3 with the simultaneous growth of the SiO2 layer. Interactions with CO molecules result in an additional reduction of cerium and promote the transition of Ce2O3 to a silicate compound. Thermal annealing of thin films exposed to oxygen or carbon monoxide shows that the silicate phase is highly stabile even at 450 °C.

Large-Scale Image Analysis for Investigating Spatio-Temporal Changes in Nuclear DNA Damage Caused by Nitrogen Atmospheric Pressure Plasma Jets.

The effective clinical application of atmospheric pressure plasma jet (APPJ) treatments requires a well-founded methodology that can describe the interactions between the plasma jet and a treated sample and the temporal and spatial changes that result from the treatment. In this study, we developed a large-scale image analysis method to identify the cell-cycle stage and quantify damage to nuclear DNA in single cells. The method was then tested and used to examine spatio-temporal distributions of nuclear DNA damage in two cell lines from the same anatomic location, namely the oral cavity, after treatment with a nitrogen APPJ. One cell line was malignant, and the other, nonmalignant. The results showed that DNA damage in cancer cells was maximized at the plasma jet treatment region, where the APPJ directly contacted the sample, and declined radially outward. As incubation continued, DNA damage in cancer cells decreased slightly over the first 4 h before rapidly decreasing by approximately 60% at 8 h post-treatment. In nonmalignant cells, no damage was observed within 1 h after treatment, but damage was detected 2 h after treatment. Notably, the damage was 5-fold less than that detected in irradiated cancer cells. Moreover, examining damage with respect to the cell cycle showed that S phase cells were more susceptible to DNA damage than either G1 or G2 phase cells. The proposed methodology for large-scale image analysis is not limited to APPJ post-treatment applications and can be utilized to evaluate biological samples affected by any type of radiation, and, more so, the cell-cycle classification can be used on any cell type with any nuclear DNA staining.

Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage.

Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8 eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.

Total yield of reactive species originating from an atmospheric pressure plasma jet in real time.

It is now well established that plasma-induced reactive species are key agents involved in many biochemical reactions. This work reports on the formation of plasma reactive species in an acidified ferrous sulfate (Fricke) solution interacting with an atmospheric pressure plasma jet (APPJ). A yield of ferric (Fe3+) ions measured using in situ absorption spectroscopy was attributed to the formation of plasma reactive species provided and/or originated in the solution. The results indicated that the number of reactive species formed was proportional to plasma frequency and voltage. However, the Fe3+ yield per pulse decreased with increased frequency. To obtain a better understanding of the processes and species involved in the chemical reactions due to plasma exposure, Fe3+ yields were calculated and compared to the experimental data. At higher frequencies, there was insufficient time to complete all the reactions before the next pulse reached the solution; at lower frequencies, the Fe3+ yield was higher because of the relatively longer time available for reactions to occur. In addition, the comparison between DNA damage levels and Fe3+ yields was investigated under different experimental conditions in order to verify the usefulness of both the Fricke solution and the DNA molecule as a probe to characterize APPJs.

Dissociative electron attachment induced ring opening in five-membered heterocyclic compounds.

Five-membered heterocyclic structures, which exist widely in biological systems and play an active role in various biochemical processes, have been studied extensively from a fundamental perspective. Here, the fragmentation patterns of isoxazole, a representative five-membered heterocycle, upon dissociative electron attachment (DEA) were examined carefully by comparing isoxazole's products with those of its methylated derivatives. It was found that the most dominant DEA pathway occurs through the loss of hydrogen at C(3), which leads to ring opening by O-N bond cleavage at an energy of ∼1.5 eV. The ring opening was investigated further for DEA to other related five-membered ring compounds, i.e., oxazole and thiazole. The DEA-induced hydrogen loss was much less pronounced or quenched completely in these two compounds and simultaneous ring-opening behavior was not detected. This observation is of special interest to applied fields, for example, the pharmaceutical industry, because several drugs that contain isoxazole substructures exhibit extensive ring opening during biotransformation.

Characterization of Neutral Radicals from a Dissociative Electron Attachment Process.

Despite decades of gas-phase studies on dissociative electron attachment (DEA) to various molecules, as yet there has been no direct detection and characterization of the neutral radical species produced by this process. In this study, we performed stepwise electron spectroscopy to directly measure and characterize the neutrals produced upon zero-electron-energy DEA to the model molecule, carbon tetrachloride (CCl_{4}). We observed the direct yield of the trichloromethyl radical (CCl_{3}^{·}) formed by DEA to CCl_{4} and measured the appearance energies of all the other neutral species. By combining these experimental findings with high-level quantum chemical calculations, we performed a complete analysis of both the DEA to CCl_{4} and the subsequent electron-impact ionization of CCl_{3}^{·}. This work paves the way toward a complete experimental characterization of DEA processes, which will lead to a better understanding of the low-energy electron-induced formation of radical species.

Low-energy electron-induced dissociation in gas-phase nicotine, pyridine, and methyl-pyrrolidine.

Dissociative electron attachment to nicotine, pyridine, and N-methyl-pyrrolidine was studied in the gas phase in order to assess their stability with respect to low-energy electron interactions. Anion yield curves for different products at electron energies ranging from zero to 15 eV were measured, and the molecular fragmentation pathways were proposed. Nicotine does not form a stable parent anion or a dehydrogenated anion, contrary to other biological systems. However, we have observed complex dissociation pathways involving fragmentation at the pyrrolidine side accompanied by isomerization mechanisms. Combining structure optimization and enthalpy calculations, performed with the Gaussian09 package, with the comparison with a deuterium-labeled N-methyl-d3-pyrrolidine allowed for the determination of the fragmentation pathways. In contrast to nicotine and N-methylpyrrolidine, the dominant pathway in dissociative electron attachment to pyridine is the loss of hydrogen, leading to the formation of an [M-H]- anion. The presented results provide important new information about the stability of nicotine and its constituent parts and contribute to a better understanding of the fragmentation mechanisms and their effects on the biological environment.

Low-Energy Electron-Induced Transformations in Organolead Halide Perovskite.

Methylammonium lead iodide perovskite (MAPbI3 ), a prototype material for potentially high-efficient and low-cost organic-inorganic hybrid perovskite solar cells, has been investigated intensively in recent years. A study of low-energy electron-induced transformations in MAPbI3 is presented, performed by combining controlled electron-impact irradiation with X-ray photoelectron spectroscopy and scanning electron microscopy. Changes were observed in both the elemental composition and the morphology of irradiated MAPbI3 thin films as a function of the electron fluence for incident energies from 4.5 to 60 eV. The results show that low-energy electrons can affect structural and chemical properties of MAPbI3 . It is proposed that the transformations are triggered by the interactions with the organic part of the material (methylammonium), resulting in the MAPbI3 decomposition and aggregation of the hydrocarbon layer.

Distinct and dramatic water dissociation on GaP(111) tracked by near-ambient pressure X-ray photoelectron spectroscopy.

Water adsorption and dissociation on a GaP(111) crystal surface are investigated using near-ambient pressure X-ray photoelectron spectroscopy (NAP XPS) in a wide range of pressures (∼10(-10)-5 mbar) and temperatures (∼300-773 K). Dynamic changes in chemical evolution at the H2O/GaP(111) interface are reflected in Ga 2p3/2, O 1s, and P 2p spectra. In the pressure-dependent study performed at room temperature, an enhancement of surface Ga hydroxylation and oxidation with an increase in H2O pressure is observed. In the temperature-dependent study performed at elevated pressures, two distinct regions can be defined in which drastic changes occur in the surface chemistry. Below 673 K, the surface Ga hydroxylation and oxidation progress continuously. However, above 673 K, a large-scale conversion of surface O-Ga-OH species into non-stoichiometric Ga hydroxide along with oxidation of surface P atoms occurs through an intermediate state. The NAP XPS technique enabled us to experimentally track the chemistry at the H2O/GaP interface under near-realistic conditions, thereby providing evidence to compare with recent theoretical efforts to improve the understanding of water-splitting mechanisms and photo-corrosion on semiconductor surfaces.

Functionalisation and immobilisation of an Au(110) surface via uracil and 2-thiouracil anchored layer.

We study surface functionalisation by uracil and 2-thiouracil, and immobilisation of several DNA moieties on functionalised gold surfaces. The combination of X-ray photoelectron and near-edge X-ray absorption spectroscopy allowed us to obtain a complete understanding of complex interfacial processes, starting from adsorption of biomolecules onto the metallic surface and progressing towards a specific surface functionality for interactions with other biologically related adsorbates. Au(110) surfaces were functionalised by deposition of uracil and 2-thiouracil molecules under vacuum conditions, and then tested for their selectivity by immobilisation of different DNA moieties deposited from aqueous solutions. We observed that adenine, adenosine, and RNA polymer (polyadenylic acid) from saturated solutions were immobilized successfully on the 2-thiouracil, but those from dilute (1%) solutions were not. However, cytosine failed to adsorb even from saturated solution. The chemical states of the biologically related adsorbates were investigated and the geometrical orientation of uracil and 2-thiouracil on the Au(110) surface was determined using both spectroscopic techniques.

Dissociative electron attachment to the gas-phase nucleobase hypoxanthine.

We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C5H4N4O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp - H) anion (C5H3N4O(-)) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp - NH)(-), C4H3N4 (-)/C4HN3O(-), C4H2N3 (-), C3NO(-)/HC(HCN)CN(-), OCN(-), CN(-), and O(-). Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

Effects of atmospheric pressure plasmas on isolated and cellular DNA-a review.

Atmospheric Pressure Plasma (APP) is being used widely in a variety of biomedical applications. Extensive research in the field of plasma medicine has shown the induction of DNA damage by APP in a dose-dependent manner in both prokaryotic and eukaryotic systems. Recent evidence suggests that APP-induced DNA damage shows potential benefits in many applications, such as sterilization and cancer therapy. However, in several other applications, such as wound healing and dentistry, DNA damage can be detrimental. This review reports on the extensive investigations devoted to APP interactions with DNA, with an emphasis on the critical role of reactive species in plasma-induced damage to DNA. The review consists of three main sections dedicated to fundamental knowledge of the interactions of reactive oxygen species (ROS)/reactive nitrogen species (RNS) with DNA and its components, as well as the effects of APP on isolated and cellular DNA in prokaryotes and eukaryotes.

Cyclic dipeptide immobilization on Au(111) and Cu(110) surfaces.

Soft X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to probe the electronic and adsorption properties of two cyclic dipeptides, i.e. cyclo(glycyl-histidyl) and cyclo(phenylalanyl-prolyl), on Au(111) and Cu(110) surfaces. The core level spectra show chemical shifts which indicate weak chemisorption on Au(111), and stronger chemisorption on the Cu(110) surface, mainly via one of the nitrogen atoms in the central rings of both molecules, and nitrogen in the imidazole ring of cyclo(glycyl-histidyl). From the angular dependence of the NEXAFS spectra at the O and N K-edges, we conclude that both dipeptides have a preferred orientation on the two surfaces.

Electron ionization of the nucleobases adenine and hypoxanthine near the threshold: a combined experimental and theoretical study.

Electron ionization of the DNA nucleobase, adenine, and the tRNA nucleobase, hypoxanthine, was investigated near the threshold region (∼5-20 eV) using a high-resolution hemispherical electron monochromator and a quadrupole mass spectrometer. Ion efficiency curves of the threshold regions and the corresponding appearance energies (AEs) are presented for the parent cations and the five most abundant fragment cations of each molecule. The experimental ionization energies (IEs) of adenine and hypoxanthine were determined to be 8.70 ± 0.3 eV and 8.88 ± 0.5 eV, respectively. Quantum chemical calculations (B3LYP/6-311+G(2d,p)) yielded a vertical IE of 8.08 eV and an adiabatic IE of 8.07 eV for adenine and a vertical IE of 8.51 eV and an adiabatic IE of 8.36 eV for hypoxanthine, and the lowest energy optimized structures of the fragment cations and their respective neutral species were calculated. The enthalpies of the possible reactions from the adenine and hypoxanthine cations were also obtained computationally, which assisted in determining the most likely electron ionization pathways leading to the major fragment cations. Our results suggest that the imidazole ring is more stable than the pyrimidine ring in several of the fragmentation reactions from both adenine and hypoxanthine. This electron ionization study contributes to the understanding of the biological effects of electrons on nucleobases and to the database of the electronic properties of biomolecules, which is necessary for modeling the damage of DNA in living cells that is induced by ionizing radiation.

Monocarbon cationic cluster yields from N2/CH4 mixtures embedded in He nanodroplets and their calculated binding energies.

The formation of monocarbon cluster ions has been investigated by electron ionization mass spectrometry of cold helium nanodroplets doped with nitrogen/methane mixtures. Ion yields for two groups of clusters, CHmN2(+) or CHmN4(+), were determined for mixtures with different molecular ratios of CH4. The possible geometrical structures of these clusters were analyzed using electronic structure computations. Little correlation between the ion yields and the associated binding energies has been observed indicating that in most cases kinetic control is more important than thermodynamic control for forming the clusters.

From Light to Dark: Dancing with Electrons in Colloidal 2D MoS2 Nanosheets.

Extending the lifetime of photogenerated electrons in semiconductor systems is an important criterion for the conversion of light into storable energy. We have now succeeded in storing electrons in a photoirradiated colloidal molybdenum disulfide (MoS2) suspension, showcasing its unique reversible photoresponsive behavior. The dampened A and B excitonic peaks indicate the accumulation of photogenerated electrons and the minimization of interactions between MoS2 interlayers. The stored electrons were quantitatively extracted by titrating with a ferrocenium ion in the dark, giving ca. 0.2 electrons per MoS2 formula unit. The emergence of the photoinduced A1g* Raman mode and the decrease in zeta potential after irradiation suggest intercalation of counterions to maintain overall charge balance upon electron storage. These results provide insights into the mechanism of photogenerated electron storage in 2D materials and pave the way for the potential application of colloidal 2D materials in electron storage.

DNA Strand Breaks and Denaturation as Probes of Chemical Reactivity versus Thermal Effects of Atmospheric Pressure Plasma Jets.

An atmospheric pressure plasma jet (APPJ) is being advanced as an alternative radiation type that offers excellent efficacy in an array of medical applications against specific biological targets such as DNA. This work explores the possibility of implementing DNA and its damage as a probe for specific plasma diagnostics such as reactive plasma species formation and transient local heating. We analyzed both APPJ characteristics based on the detection of plasma-induced strand breaks and DNA denaturation. Further, we implemented a machine learning model based on artificial neural networks to predict the type and extent of DNA damage for a given combination of APPJ parameter values. This methodology is an important step toward deciphering and explaining the potential adverse effects of APPJ on biological samples of any prospective interest in medicine.