Absolute electron total ionization cross-sections: molecular analogues of DNA and RNA nucleobase and sugar constituents

Electron stimulated desorption from condensed benzene

The electron induced dissociation of condensed benzene (C6H6) in thin films deposited on a Pt substrate is investigated by electron stimulated desorption (ESD) of anions and cations. The desorbed yields are recorded as a function of incident electron energy in the range of 10 to 950 eV for a fixed film thickness of 2 monolayers (ML) and for a fixed energy of 950 eV, as well as a function of film thickness from 0.5 to 8 monolayers (ML) for anions, and from 0.5 to 12ML for cations. Both energy and thickness dependencies are discussed in terms of the three main mechanisms yielding positively and/or negatively charged fragments: dissociative electron attachment (DEA), dipolar dissociation (DD) and dissociative ionization (DI) processes. At the probed energies, DD is the major mechanism, while DEA is predominantly induced by secondary electrons from the Pt substrate. Desorption of the parent positive ion is strongly suppressed. Similar qualitative behaviours are observed for the energy dependence of both anion and cation ESD yields, while some discrepancies exist in the thickness dependence, including a very significant systematic magnitude difference found between such ions formation. An estimation of the effective DD cross-section including the desorption probability is obtained. Feasible mechanisms behind the observed energy and thickness dependences for anion and cation yields are proposed. These results highlight the need for further investigations to better understand the underlying processes of electron induced dissociation in condensed matter.

Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment

Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.

Evaluated electron scattering cross section dataset for gaseous benzene in the energy range 0.1-1000 eV

In this study, a complete and self-consistent cross section dataset for electron transport simulations through gaseous benzene in the energy range 0.1-1000 eV has been critically compiled. Its reliability has been evaluated through a joint experimental and computational procedure. To accomplish this, the compiled dataset has been used as input for event-by-event Monte Carlo simulations of the magnetically confined electron transport through gaseous benzene, and the simulated transmitted intensity has been compared with the experimental one for different incident energies and benzene gas pressures.

Electron Impact Ionization of Adenine: Partial Cross Sections

Electron ionization of a genetically important nucleobase, adenine, was investigated from threshold to 500 eV using crossed electron beam–effusive molecular beam geometry and time-of-flight mass spectrometry. We measured the complete set of absolute partial cross sections for adenine using the relative flow technique (RFT) up to an electron energy of 500 eV. Normalization to absolute values was performed using electron ionization cross sections for argon and the vapor pressure data of adenine. The total cross sections obtained by summing the partial cross sections were compared with the existing theoretical and experimental data. The appearance energies of various fragment ions were also measured and compared with the reported data. The prominence of ions with mass (HCN)n+ (n = 1 to 5) indicated a possible pathway to form adenine in the interstellar medium through aggregation of HCN units. Analysis of the partial cross sections for various groups of fragment ions as a function of electron energy was found to give insights into their composition.

Perspectives of Gas Phase Ion Chemistry: Spectroscopy and Modeling

The study of ions in the gas phase has a long history and has involved both chemists and physicists. The interplay of their competences with the use of very sophisticated commercial and/or homemade instrumentations and theoretical models has improved the knowledge of thermodynamics and kinetics of many chemical reactions, even if still many stages of these processes need to be fully understood. The new technologies and the novel free-electron laser facilities based on plasma acceleration open new opportunities to investigate the chemical reactions in some unrevealed fundamental aspects. The synchrotron light source can be put beside the FELs, and by mass spectrometric techniques and spectroscopies coupled with versatile ion sources it is possible to really change the state of the art of the ion chemistry in different areas such as atmospheric and astro chemistry, plasma chemistry, biophysics, and interstellar medium (ISM). In this manuscript we review the works performed by a joint combination of the experimental studies of ion–molecule reactions with synchrotron radiation and theoretical models adapted and developed to the experimental evidence. The review concludes with the perspectives of ion–molecule reactions by using FEL instrumentations as well as pump probe measurements and the initial attempt in the development of more realistic theoretical models for the prospective improvement of our predictive capability.

Energy Deposition around Swift Carbon-Ion Tracks in Liquid Water

Energetic carbon ions are promising projectiles used for cancer radiotherapy. A thorough knowledge of how the energy of these ions is deposited in biological media (mainly composed of liquid water) is required. This can be attained by means of detailed computer simulations, both macroscopically (relevant for appropriately delivering the dose) and at the nanoscale (important for determining the inflicted radiobiological damage). The energy lost per unit path length (i.e., the so-called stopping power) of carbon ions is here theoretically calculated within the dielectric formalism from the excitation spectrum of liquid water obtained from two complementary approaches (one relying on an optical-data model and the other exclusively on ab initio calculations). In addition, the energy carried at the nanometre scale by the generated secondary electrons around the ion's path is simulated by means of a detailed Monte Carlo code. For this purpose, we use the ion and electron cross sections calculated by means of state-of-the art approaches suited to take into account the condensed-phase nature of the liquid water target. As a result of these simulations, the radial dose around the ion's path is obtained, as well as the distributions of clustered events in nanometric volumes similar to the dimensions of DNA convolutions, contributing to the biological damage for carbon ions in a wide energy range, covering from the plateau to the maximum of the Bragg peak.

Total Electron Detachment and Induced Cationic Fragmentation Cross Sections for Superoxide Anion (O2-) Collisions with Benzene (C6H6) Molecules

In this study, novel experimental total electron detachment cross sections for O2- collisions with benzene molecules are reported for the impact energy range (10-1000 eV), as measured with a transmission beam apparatus. By analysing the positively charged species produced during the collision events, relative total ionisation cross sections were derived in the incident energy range of 160-900 eV. Relative partial ionisation cross sections for fragments with m/z ≤ 78 u were also given in this energy range. We also confirmed that heavier compounds (m/z > 78 u) formed for impact energies between 550 and 800 eV. In order to further our knowledge about the collision dynamics governing the fragmentation of such heavier molecular compounds, we performed molecular dynamics calculations within the framework of the Density Functional Theory (DFT). These results demonstrated that the fragmentation of these heavier compounds strongly supports the experimental evidence of m/z = 39-42, 50, 60 (u) cations formation, which contributed to the broad local maximum in the total ionisation observed from 550 to 800 eV. This work reveals the reactivity induced by molecular anions colliding with hydrocarbons at high energies, processes that can take place in the interstellar medium under various local conditions.

Thermionic Electron Beam Current and Accelerating Voltage Controller for Gas Ion Sources

Thermionic emission sources are key components of electron impact gas ion sources used in measuring instruments, such as mass spectrometers, ionization gauges, and apparatus for ionization cross-section measurements. The repeatability of the measurements taken with such instruments depends on the stability of the ion current, which is a function, among other things, of the electron beam current and electron accelerating voltage. In this paper, a laboratory thermionic electron beam current and accelerating voltage controller is presented, based on digital algorithm implementation. The average value of the percentage standard deviation of the emission current is 0.021%, and the maximum electron accelerating voltage change versus the emission current is smaller than 0.011% in the full operating range of the emission current. Its application as a trap current or emission current-regulated ion source power supply could be useful in many measuring instruments, such as in microelectromechanical system (MEMS) mass spectrometers as universal gas sensors, where a stable emission current and electron energy are needed.

An improved set of electron-THFA cross sections refined through a neural network-based analysis of swarm data

We review experimental and theoretical cross sections for electron transport in α-tetrahydrofurfuryl alcohol (THFA) and, in doing so, propose a plausible complete set. To assess the accuracy and self-consistency of our proposed set, we use the pulsed-Townsend technique to measure drift velocities, longitudinal diffusion coefficients, and effective Townsend first ionization coefficients for electron swarms in admixtures of THFA in argon, across a range of density-reduced electric fields from 1 to 450 Td. These measurements are then compared to simulated values derived from our proposed set using a multi-term solution of Boltzmann's equation. We observe discrepancies between the simulation and experiment, which we attempt to address by employing a neural network model that is trained to solve the inverse swarm problem of unfolding the cross sections underpinning our experimental swarm measurements. What results from our neural network-based analysis is a refined set of electron-THFA cross sections, which we confirm is of higher consistency with our swarm measurements than that which we initially proposed. We also use our database to calculate electron transport coefficients in pure THFA across a range of reduced electric fields from 0.001 to 10 000 Td.

Relative Role of Physical Mechanisms on Complex Biodamage Induced by Carbon Irradiation

The effective use of swift ion beams in cancer treatment (known as hadrontherapy) as well as appropriate protection in manned space missions rely on the accurate understanding of the energy delivery to cells that damages their genetic information. The key ingredient characterizing the response of a medium to the perturbation induced by charged particles is its electronic excitation spectrum. By using linear-response time-dependent density functional theory, we obtained the energy and momentum transfer excitation spectrum (the energy-loss function, ELF) of liquid water (the main constituent of biological tissues), which was in excellent agreement with experimental data. The inelastic scattering cross sections obtained from this ELF, together with the elastic scattering cross sections derived by considering the condensed phase nature of the medium, were used to perform accurate Monte Carlo simulations of the energy deposited by swift carbon ions in liquid water and carried away by the generated secondary electrons, producing inelastic events such as ionization, excitation, and dissociative electron attachment (DEA). The latter are strongly correlated with cellular death, which is scored in sensitive volumes with the size of two DNA convolutions. The sizes of the clusters of damaging events for a wide range of carbon-ion energies, from those relevant to hadrontherapy up to those for cosmic radiation, predict with unprecedented statistical accuracy the nature and relative magnitude of the main inelastic processes contributing to radiation biodamage, confirming that ionization accounts for the vast majority of complex damage. DEA, typically regarded as a very relevant biodamage mechanism, surprisingly plays a minor role in carbon-ion induced clusters of harmful events.

Improved insights in time-resolved photoelectron imaging

We review new light source developments and data analysis considerations relevant to the time-resolved photoelectron imaging technique. Case studies illustrate how these themes may enhance understanding in studies of excited state molecular dynamics.

Excitation and ionisation cross-sections in condensed-phase biomaterials by electrons down to very low energy: application to liquid water and genetic building blocks

A model is presented for computing electron-impact electronic excitation and ionisation cross-sections for arbitrary condensed-phase biomaterials in a wide energy range, showing a general good agreement with the available experimental data.

Predicting Total Electron-Ionization Cross Sections and GC-MS Calibration Factors Using Machine Learning

Concentrations in GC-MS using electron-ionization mass spectrometry can be determined without pure calibration standards through prediction of relative total-ionization cross sections. An atom- and group-based artificial neural network (FF-NN-AG) model is created to generate EI cross sections and calibrations for organic compounds. This model is easy to implement and is more accurate than the widely used atom-additivity-based correlation of Fitch and Sauter (Anal. Chem. 1983). Ninety-two new measurements of experimental EI cross sections (70-75 eV) are joined with different interlaboratory datasets, creating a 396-compound cross-section database, the largest to date. The FF-NN-AG model uses 16 atom-type descriptors, 79 structural-group descriptors, and one hidden layer of 10 nodes, trained 500 times. In each cycle, 96% of the compounds in this database are freshly chosen at random, and then the model is tested with the remaining 4%. The resulting r² is 0.992 versus 0.904 for the Fitch and Sauter correlation, root mean square deviation is 2.8 versus 9.2, and maximum relative error is 0.30 versus 0.73. As an example of the model's use, a list of cross sections is generated for various sugars and anhydrosugars.

A Complete Cross Section Data Set for Electron Scattering by Pyridine: Modelling Electron Transport in the Energy Range 0-100 eV

Electron scattering cross sections for pyridine in the energy range 0–100 eV, which we previously measured or calculated, have been critically compiled and complemented here with new measurements of electron energy loss spectra and double differential ionization cross sections. Experimental techniques employed in this study include a linear transmission apparatus and a reaction microscope system. To fulfill the transport model requirements, theoretical data have been recalculated within our independent atom model with screening corrected additivity rule and interference effects (IAM-SCAR) method for energies above 10 eV. In addition, results from the R-matrix and Schwinger multichannel with pseudopotential methods, for energies below 15 eV and 20 eV, respectively, are presented here. The reliability of this complete data set has been evaluated by comparing the simulated energy distribution of electrons transmitted through pyridine, with that observed in an electron-gas transmission experiment under magnetic confinement conditions. In addition, our representation of the angular distribution of the inelastically scattered electrons is discussed on the basis of the present double differential cross section experimental results.

Total ionization cross section of cyclic organic molecules

Two independent methods, namely, Binary-encounter Bethe (BEB) and complex scattering potential-ionization contribution (CSP-ic) methods, are employed to calculate the total ionization cross section (Q_ion) for cyclic organic molecules from ionization threshold to 5 keV for which there is a paucity of data in the literature. The Q_ion calculated with the (BEB/ωB97X) combination is found to give good agreement with the experimental results, the CSP-ic method, and the Q_ion calculated from Irikura orbital energies. The Q_ion for most of the targets are calculated for the first time over such a wide energy range. Hence, to check the consistency and reliability of the present data, we have also computed the static polarizability for all the targets and the variation of maximum ionization cross section (Q_ion,max) with polarizability is studied. A linear relationship is observed between these quantities indicating the consistency and reliability of the present Q_ion data. The targets studied are important for industrial applications, radiation biology, and astrophysics.

C–I and C–F bond-breaking dynamics in the dissociative electron ionization of CF3I

We present a comprehensive experimental study into the dissociative electron ionization dynamics of CF₃I at energies ranging from 20 to 100 eV.

Simple and universal model for electron-impact ionization of complex biomolecules

We present a simple and universal approach to calculate the total ionization cross section (TICS) for electron impact ionization in DNA bases and other biomaterials in the condensed phase. Evaluating the electron impact TICS plays a vital role in ion-beam radiobiology simulation at the cellular level, as secondary electrons are the main cause of DNA damage in particle cancer therapy. Our method is based on extending the dielectric formalism. The calculated results agree well with experimental data and show a good comparison with other theoretical calculations. This method only requires information of the chemical composition and density and an estimate of the mean binding energy to produce reasonably accurate TICS of complex biomolecules. Because of its simplicity and great predictive effectiveness, this method could be helpful in situations where the experimental TICS data are absent or scarce, such as in particle cancer therapy.

Communication: Electron ionization of DNA bases

No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.

Ultraviolet relaxation dynamics of aniline,N,N-dimethylaniline and 3,5-dimethylaniline at 250 nm

Time-resolved photoelectron imaging was used to investigate the electronic relaxation dynamics of gas-phase aniline, N, N-dimethylaniline, and 3,5-dimethylaniline following ultraviolet excitation at 250 nm. Our analysis was supported by ab initio coupled-cluster calculations evaluating excited state energies and (in aniline) the evolution of a range of excited state physical properties as a function of N-H bond extension. Due to a lack of consistency between several earlier studies undertaken in aniline, the specific aim of this present work was to gain new insight into the previously proposed non-adiabatic coupling interaction between the two lowest lying singlet excited states S1(ππ(∗)) and S2(3s/πσ(∗)). The methyl-substituted systems N, N-dimethylaniline and 3,5-dimethylaniline were included in order to obtain more detailed dynamical information about the key internal molecular coordinates that drive the S1(ππ(∗))/S2(3s/πσ(∗)) coupling mechanism. Our findings suggest that in all three systems, both electronic states are directly populated during the initial excitation, with the S2(3s/πσ(∗)) state then potentially decaying via either direct dissociation along the N-X stretching coordinate (X = H or CH3) or internal conversion to the S1(ππ(∗)) state. In aniline and N, N-dimethylaniline, both pathways most likely compete in the depletion of S2(3s/πσ(∗)) state population. However, in 3,5-dimethylaniline, only the direct dissociation mechanism appears to be active. This is rationalized in terms of changes in the relative rates of the two decay pathways upon methylation of the aromatic ring system.

Time-resolved photoionization spectroscopy of mixed Rydberg-valence states: indole case study

Time-resolved photoelectron imaging reveals subtle new mechanistic insight into the ultraviolet relaxation dynamics of gas-phase indole.

Differential cross sections for intermediate-energy electron scattering from α-tetrahydrofurfuryl alcohol: excitation of electronic-states

We report on measurements of differential cross sections (DCSs) for electron impact excitation of a series of Rydberg electronic-states in α-tetrahydrofurfuryl alcohol (THFA). The energy range of these experiments was 20-50 eV, while the scattered electron was detected in the 10°-90° angular range. There are currently no other experimental data or theoretical computations against which we can directly compare the present measured results. Nonetheless, we are able to compare our THFA DCSs with earlier cross section measurements for Rydberg-state electronic excitation for tetrahydrofuran, a similar cyclic ether, from Do et al. [J. Chem. Phys. 134, 144302 (2011)]. In addition, "rotationally averaged" elastic DCSs, calculated using our independent atom model with screened additivity rule correction approach are also reported. Those latter results give integral cross sections consistent with the optical theorem, and supercede those from the only previous study of Milosavljević et al. [Eur. Phys. J. D 40, 107 (2006)].