Ion Patterns Research Articles

Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs.

The front cover artwork is provided by Prof. Papadantonakis' group. The image shows a Watson-Crick Guanine-Cytosine pair, and the difference between vertical and adiabatic ionization potentials. Read the full text of the Research Article at 10.1002/cphc.202300946.

Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs.

Gas-phase and aqueous vertical ionization potentials, vIPgas and vIPaq respectively and measurements of the molecular electrostatic and local ionization maps calculated at the DFT/B3LYP-D3/ 6-311+G** level of theory and the C-PCM reaction field model for single- and double-stranded CpG and 5MeCpG pairs show that the vIPaq for single- and double-stranded pairs of C-G and 5MeC-G are practically the same, in the range of 5.79 to 5.81 eV. The aqueous adiabatic ionization potentials for single-stranded CpG and 5MeCpG are 5.52 eV and 5.51 eV respectively and they reflect the nuclear reorganization that takes place after the abstraction of the electron. The aqueous adiabatic ionization energy values that correspond to the CpG+. radical cation and the hydrated electron, e-,, being at infinite distance, adIPaq+Vo, are 3.92 eV and 3.91 eV respectively with (Vo=-1.6 eV) Analysis of data suggest that the HOMO-LUMO energy gap in the hard/soft-acid/base (HSAB) concept cannot be used a priori to determine the effect of cytosine methylation on the guanine enhanced oxidative damage in DNA.

Theoretical Study of the Electronic Structure and Ionization Spectrum of γ-Pyrone

The electronic structure and ionization spectrum of γ-pyrone (4H-pyran-4-one) were calculated using the third-order algebraic diagrammatic construction method for the single-particle Green function [IP-ADC(3)] and some other high-level quantum chemical methods. The results of calculations were used to interpret its recently recorded photoelectron spectra. New assignments have been proposed for the nature of a series of photoelectron maxima of γ-pyrone located above 12 eV, where, according to calculations, the one-electron ionization pattern is disturbed due to electron correlation effects. The obtained results significantly change the interpretation of the spectrum available in the literature.

Analysis of Volatile Esters and Alkanoic Acids by an Atmospheric Pressure Corona Discharge Ionization Collision-Induced Dissociation Mass Spectrometry in Positive-Ion Mode: Ionization, Fragmentation Patterns, and Discrimination between Isomeric Compounds.

The ionization and fragmentation patterns of 24 compounds with elemental composition of CmH2mO2, including isomeric esters and alkanoic acids, were investigated by atmospheric pressure corona discharge ionization collision-induced dissociation (CID) mass spectrometry in the positive-ion mode. All compounds were ionized as protonated molecules and NH4+ adducts. In addition, fragment ions were observed in mass spectra of esters other than methyl esters, which are owing to the dissociation of the alkyl group in the alcohol side from the protonated molecules. In CID spectra, protonated alkanoic acids/methyl esters split off H2O/CH3OH and CO or the alkyl group in the acid side, depending on the carbon chain length. Protonated esters (other than methyl esters) mainly fragmented the alkyl group in the alcohol side. These general rules on ionization and fragmentation patterns can provide relevant information on the discrimination of isomers.

Seismo Ionospheric Anomalies around and over the Epicenters of Pakistan Earthquakes

Global Navigation Satellite System (GNSS)-based ionospheric anomalies are nowadays used to identify a possible earthquake (EQ) precursor and hence a new research topic in seismic studies. The current study also aims to provide an investigation of ionospheric anomalies associated to EQs. In order to study possible pre-and post-seismic perturbations during the preparation phase of large-magnitude EQs, statistical and machine learning algorithms are applied to Total Electron Content (TEC) from the Global Positioning System (GPS) and Global Ionosphere Maps (GIMs). We observed TEC perturbation from the Sukkur (27.8° N, 68.9° E) GNSS station near the epicenter of Mw 5.4 Mirpur EQ within 5–10 days before the main shock day by implementing machine learning and statistical analysis. However, no TEC anomaly occurred in GIM-TEC over the Mirpur EQ epicenter. Furthermore, machine learning and statistical techniques are also implemented on GIM TEC data before and after the Mw 7.7 Awaran, where TEC anomalies can be clearly seen within 5–10 days before the seismic day and the subsequent rise in TEC during the 2 days after the main shock. These variations are also evident in GIM maps over the Awaran EQ epicenter. The findings point towards a large emission of EQ energy before and after the main shock during quiet storm days, which aid in the development of lithosphere ionosphere coupling. However, the entire analysis can be expanded to more satellite and ground-based measurements in Pakistan and other countries to reveal the pattern of air ionization from the epicenter through the atmosphere to the ionosphere.

Panchromatic HST/WFC3 Imaging Studies of Young, Rapidly Evolving Planetary Nebulae. II. NGC 7027

The iconic planetary nebula (PN) NGC 7027 is bright, nearby (D ∼ 1 kpc), highly ionized, intricately structured, and well observed. This nebula is hence an ideal case study for understanding PN shaping and evolution processes. Accordingly, we have conducted a comprehensive imaging survey of NGC 7027 comprised of 12 HST Wide Field Camera 3 images in narrow-band and continuum filters spanning the wavelength range 0.243–1.67 μm. The resulting panchromatic image suite reveals the spatial distributions of emission lines covering low-ionization species such as singly ionized Fe, N, and Si, through H recombination lines, to more highly ionized O and Ne. These images, combined with available X-ray and radio data, provide the most extensive view of the structure of NGC 7027 obtained to date. Among other findings, we have traced the ionization structure and dust extinction within the nebula in subarcsecond detail; uncovered multipolar structures actively driven by collimated winds that protrude through and beyond the PN’s bright inner core; compared the ionization patterns in the WFC3 images to X-ray and radio images of its interior hot gas and to its molecular outflows; pinpointed the loci of thin, shocked interfaces deep inside the nebula; and more precisely characterized the central star. We use these results to describe the recent history of this young and rapidly evolving PN in terms of a series of shaping events. This evolutionary sequence involves both thermal and ram pressures, and is far more complex than predicted by extant models of UV photoionization or winds from a single central progenitor star, thereby highlighting the likely influence of an unseen binary companion.

Qualitative Determination of Polysulfide Species in a Lithium-Sulfur Battery by HR-LC-APCI-MSn with One-Step Derivatization.

Lithium-Sulfur (Li-S) batteries are one of the most promising next-generation batteries due to their ultrahigh energy density up to 500 W h kg-1. However, despite the steady progress during the last several decades, there have been significant challenges for practical applications and commercialization. One of the major issues is controlling the lithium polysulfide (LiPS) shuttling process, which causes premature cell failure. To better understand the mechanism of the LiPS shuttling chemistry, a qualitative and quantitative analysis on polysulfide species in Li-S cell has profound significance for realizing highly efficient sulfur electrochemistry. Here we report a qualitative determination of the derivatized polysulfides in the electrolyte of a custom-made Li-S pouch cell with a high-resolution liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry method for the first time. The ionization efficiency of the methylated polysulfides was affected by the tune parameters such as the corona discharge current, the vaporizer temperature, and the source capillary temperature. It was found that the source capillary temperature was the dominant parameter to increase the peak intensity of CH3S7- ion, which was the smallest peak in the spectrum. An unusual and unique ionization pattern for methylated polysulfides detected in atmospheric pressure chemical ionization negative mode was elucidated by using first-principles calculations.

Excitation and Excavation of the Claws of the Southern Crab

We show that the Southern Crab (aka Hen2–104) presents an auspicious opportunity to study the form and speed of the invisible winds that excavate and shock the lobes of various types of bipolar nebulae associated with close and highly evolved binary stars. A deep three-color image overlay of Hen2–104 reveals that the ionization state of its lobe edges, or “claws,” increases steadily from singly to doubly ionized values with increasing wall latitude. This “reverse” ionization pattern is unique among planetary nebulae (and similar objects) and incompatible with UV photoionization from a central source. We show that the most self-consistent explanation for the ionization pattern is shock ionization by a fast (∼600 km s−1) “tapered” stellar wind in which the speed and momentum flux of the wind increase with equatorial latitude. We present a hydrodynamic simulation that places the latitude-dependent form, the knotty walls, and the reverse ionization of the outer lobes of Hen2–104 into a unified context.

The role of neutral gas in validated global edge turbulence simulations

To make predictions for and design fusion reactors, a multitude of physical processes must be considered. In the edge and scrape-off layer (SOL), turbulent fluctuations intertwine with the plasma background, which is largely determined by neutral gas, and magnetic geometry plays an important role. A diffusive neutrals model has now been implemented in the global Braginskii edge turbulence code GRILLIX. The code is based on the flux-coordinate independent (FCI) approach, which allows efficient turbulence simulations in diverted equilibria. We validate simulations across the ASDEX Upgrade edge and SOL against measurements in discharge #36190, and find much better agreement thanks to the neutrals. Disentangling the effects of the neutral gas, we find that it affects the plasma in several ways. Firstly, the ionization of neutrals modifies the radial profiles of plasma density and temperature, leading to a transition of the turbulence drive from the general ballooning type to the ion temperature gradient type. Secondly, strong poloidal asymmetries can be induced due to divertor recycling, depending on the ionization pattern. As ballooned perpendicular plasma transport is stronger at the low-field side, neutrals penetrate deeper into the plasma at the high-field side, leading to significant ionization and radiation there. With increasing divertor neutrals density, the targets cool down while plasma density increases, more strongly at the high-field side. Much of the dynamics take place directly around the X-point and along the separatrix, which can be resolved by the FCI approach. Potential remains in extending the model and the code, but our results build confidence that predictive capability is within reach for major design questions for fusion reactors, such as the near SOL fall-off length.

Photoionized Herbig–Haro Objects in the Orion Nebula through Deep High Spectral Resolution Spectroscopy. II. HH 204

Abstract We analyze the physical conditions, chemical composition, and other properties of the photoionized Herbig–Haro (HH) object HH 204 through Very Large Telescope echelle spectroscopy and Hubble Space Telescope imaging. We kinematically isolate the high-velocity emission of HH 204 from the emission of the background nebula and study the subarcsecond distribution of physical conditions and ionic abundances across the HH object. We find that low- and intermediate-ionization emission arises exclusively from gas at photoionization equilibrium temperatures, whereas the weak high-ionization emission from HH 204 shows a significant contribution from higher-temperature shock-excited gas. We separately derive the ionic abundances of HH 204, the emission of the Orion Nebula, and the fainter diffuse blue layer. In HH 204, the O+ abundance determined from collisional excited lines matches the one based on recombination lines, while the O2+ abundance is very low, so that the oxygen abundance discrepancy is zero. The ionic abundances of Ni and Fe in HH 204 have similar ionization and depletion patterns, with total abundances that are a factor of 3.5 higher than in the rest of the Orion Nebula due to dust destruction in the bow shock. We show that a failure to resolve the kinematic components in our spectra would lead to significant error in the determination of chemical abundances (for instance, a 40% underestimate of O), mainly due to incorrect estimation of the electron density.

Boosting background suppression in the NEXT experiment through Richardson-Lucy deconvolution

Next-generation neutrinoless double beta decay experiments aim for half-life sensitivities of ∼ 1027 yr, requiring suppressing backgrounds to < 1 count/tonne/yr. For this, any extra background rejection handle, beyond excellent energy resolution and the use of extremely radiopure materials, is of utmost importance. The NEXT experiment exploits differences in the spatial ionization patterns of double beta decay and single-electron events to discriminate signal from background. While the former display two Bragg peak dense ionization regions at the opposite ends of the track, the latter typically have only one such feature. Thus, comparing the energies at the track extremes provides an additional rejection tool. The unique combination of the topology-based background discrimination and excellent energy resolution (1% FWHM at the Q-value of the decay) is the distinguishing feature of NEXT. Previous studies demonstrated a topological background rejection factor of ∼ 5 when reconstructing electron-positron pairs in the 208Tl 1.6 MeV double escape peak (with Compton events as background), recorded in the NEXT-White demonstrator at the Laboratorio Subterráneo de Canfranc, with 72% signal efficiency. This was recently improved through the use of a deep convolutional neural network to yield a background rejection factor of ∼ 10 with 65% signal efficiency. Here, we present a new reconstruction method, based on the Richardson-Lucy deconvolution algorithm, which allows reversing the blurring induced by electron diffusion and electroluminescence light production in the NEXT TPC. The new method yields highly refined 3D images of reconstructed events, and, as a result, significantly improves the topological background discrimination. When applied to real-data 1.6 MeV e−e+ pairs, it leads to a background rejection factor of 27 at 57% signal efficiency.

Accurate and ultrasensitive determination of 72 parent and halogenated polycyclic aromatic hydrocarbons in a variety of environmental samples via gas chromatography–triple quadrupole mass spectrometry

Polycyclic aromatic hydrocarbons (PAHs) and their halogenated derivatives (XPAHs) are ubiquitous in various environmental media. Analytical problems, however, make it difficult to accurately determine their concentrations. To develop a satisfactory analytical method suitable for a diversity of PAHs and XPAHs in multiple environmental samples, we evaluated three commercial analytical columns (DB-5MS, Select PAH, and Rxi-PAH) for better chromatographic separation and optimized the analytical conditions for gas chromatography–triple quadrupole mass spectrometry (GC-MS/MS). Comparison of the abilities of the columns to separate peaks revealed that the Rxi-PAH was the best column for both PAH and XPAH analyses. Optimization of analytical conditions for GC-MS/MS resulted in sensitivities for PAHs and XPAHs that were 4.2-fold–2600-fold higher than the sensitivities of GC-high-resolution MS (GC-HRMS) (an example of a traditional analytical method). Although there were no statistically significant differences between the instrumental detection limits (IDLs) of PAHs and XPAHs measured by GC-HRMS, the IDLs of XPAHs were significantly lower than those of PAHs when measured by GC-MS/MS. This difference could be attributed to the unique ionization patterns of XPAHs in the GC-MS/MS analysis, which suppressed background noise and increased the analytical sensitivity. Analyses of PAHs and XPAHs in grilled chicken, vehicle exhaust, sea sediment, ambient air, and indoor dust via the analytical method optimized in this study revealed that the proposed method was sufficiently sensitive, comprehensive, and versatile for risk assessment purposes, and could eliminate interferences associated with the co-elution of target PAHs and XPAHs.

An Experimental and Theoretical Study of Laser Postionization of Femtosecond-Laser-Desorbed Drug Molecules.

Femtosecond laser desorption postionization mass spectrometry using 7.9 eV single-photon ionization (7.9 eV fs-LDPI-MS) detected three of four drug compounds previously found to have very low ionization efficiencies by secondary ion mass spectrometry. Electronic structure calculations of the ionization energies and other properties of these four drug compounds predicted that all display ionization energies below the 7.9 eV photon energy, as required for single-photon ionization. The 7.9 eV fs-LDPI-MS of carbamazepine, imipramine, and verapamil all showed significant precursor (M+) ion signal, but no representative signal was observed for ciprofloxacin. Furthermore, 7.9 eV fs-LDPI-MS displayed higher M+ signals and mostly similar fragment ions compared with 70 eV electron impact mass spectrometry. Ionization and fragmentation patterns are discussed in terms of calculated wave functions for the highest occupied molecular orbitals. The implications for improving lateral resolution and sensitivity of MS imaging of drug compounds are also considered.

Rings and arcs around evolved stars – II. The Carbon Star AFGL 3068 and the Planetary Nebulae NGC 6543, NGC 7009, and NGC 7027

ABSTRACT We present a detailed comparative study of the arcs and fragmented ring-like features in the haloes of the planetary nebulae (PNe) NGC 6543, NGC 7009, and NGC 7027 and the spiral pattern around the carbon star AFGL 3068 using high-quality multi-epoch HST images. This comparison allows us to investigate the connection and possible evolution between the regular patterns surrounding AGB stars and the irregular concentric patterns around PNe. The radial proper motion of these features, ≃15 km s−1, are found to be consistent with the AGB wind and their linear sizes and interlapse times (500–1900 yr) also agree with those found around AGB stars, suggesting a common origin. We find evidence using radiative-hydrodynamic simulations that regular patterns produced at the end of the AGB phase become highly distorted by their interactions with the expanding PN and the anisotropic illumination and ionization patterns caused by shadow instabilities. These processes will disrupt the regular (mostly spiral) patterns around AGB stars, plausibly becoming the arcs and fragmented rings observed in the haloes of PNe.

Determination of anabolic androgenic steroids as imidazole carbamate derivatives in human urine using liquid chromatography-tandem mass spectrometry.

Anabolic androgenic steroids are widely abused substances in sports doping. Their detection present limitations regarding the use of soft ion sources such as electrospray or atmospheric pressure chemical ionization by liquid chromatography-tandem mass spectrometry. In the current study, a novel derivatization method was developed for the ionization enhancement of selected anabolic androgenic steroids. The proposed method aims at the introduction of an easily ionizable moiety into the steroid molecule by converting the hydroxyl groups into imidazole carbamates using 1,1'-carbonyldiimidazole as derivatization reagent. The proposed method was applied to water and urine samples spiked with exogenous anabolic androgenic steroids in various concentration levels. Steroid imidazole carbamate derivatives have shown intensive [M+H]+ signals under electrospray ionization and common fragmentation patterns in tandem mass spectrometry mode with [M-CO2 +H]+ and [M-ΙmCO2 +H]+ as major ions with low collision energy. The obtained results showed that the majority of steroids were detectable at concentrations equal or lower to their minimum required performance level according to the World Anti-Doping Agency technical document. The proposed method is sensitive with a preparation procedure that could be easily applied to the analysis of doping control samples.

Unimolecular decomposition of methyl ketene and its dimer in the gas phase: theory and experiment.

We present a combined theoretical and experimental investigation on the single photoionization and dissociative photoionization of gas-phase methyl ketene (MKE) and its neutral dimer (MKE2). The performed experiments entail the recording of photoelectron photoion coincidence (PEPICO) spectra and slow photoelectron spectra (SPES) in the energy regime 8.7-15.5 eV using linearly polarized synchrotron radiation. We observe both dimerization and trimerization of the monomer which brings about significantly complex and abstruse dissociative ionization patterns. These require the implementation of theoretical calculations to explore the potential energy surfaces of the monomer and dimer's neutral and ionized geometries. To this end, explicitly correlated quantum chemical methodologies involving the coupled cluster with single, double and perturbative triple excitations (R)CCSD(T)-F12 method, are utilized. An improvement in the adiabatic ionization energy of MKE is presented (AIE = 8.937 ± 0.020 eV) as well as appearance energies for multiple fragments formed through dissociative ionization of either the MKE monomer or dimer. In this regard, the synergy of experiment and theory is crucial to interpreting the obtained results. We discuss the potential astrochemical implications of this work in the context of recent advances in the field of astrochemistry and speculate on the potential presence and eventual fate of interstellar MKE molecules.

Nanodosimetric quantities and RBE of a clinically relevant carbon-ion beam.

Although carbon-ion therapy is becoming increasingly attractive to the treatment of tumors, details about the ionization pattern formed by therapeutic carbon-ion beam in tissue have not been fully investigated. In this work, systematic calculations for the nanodosimetric quantities and relative biological effectiveness (RBE) of a clinically relevant carbon-ion beam were studied for the first time. The method combining both track structure and condensed history Monte Carlo (MC) simulations was adopted to calculate the nanodosimetric quantities. Fragments and energy spectra at different positions of the radiation field of a clinically relevant carbon-ion pencil beam were generated by means of MC simulations in water. Nanodosimetric quantities such as mean ionization cluster size ( ), the first moment of conditional cluster size ( ), cumulative probability ( ), and conditional cumulative probability ( ) at these positions were then acquired based on the spectra and the pre-calculated nanodosimetric database created by track structure MC simulations. What's more, a novel approach to calculate RBE based on the said nanodosimetric quantities was introduced. The RBE calculations were then conducted for the carbon-ion beam at different water-equivalent depths. Lateral distributions at various water-equivalent depths of both the nanodosimetric quantities and RBE values were obtained. The values of , , , and were 1.49, 2.67, 0.30, and 0.38 at the plateau at the beam central axis and maximized at 2.79, 5.69, 0.47, and 0.68 at the depths around the Bragg peak, respectively. At a given depth, and decreased laterally with increasing the distance to the beam central axis while and remained nearly unchanged at first and then decreased except for at the rising edge of the Bragg peak. The calculated RBE values were 1.07 at the plateau and 3.13 around the Bragg peak. Good agreement between the calculated RBE values and experimental data was obtained. Different nanodosimetric quantities feature the track structure of therapeutic carbon-ion beam in different manners. Detailed ionization patterns generated by carbon-ion beam could be characterized by nanodosimetric quantities. Moreover the combined method adopted in this work to calculate nanodosimetric quantities is not only valid but also convenient. Nanodosimetric quantities are significantly helpful for the RBE calculations in carbon-ion therapy.

EDGE2D-EIRENE simulations of the influence of isotope effects and anomalous transport coefficients on near scrape-off layer radial electric field

EDGE2D-EIRENE (the ‘code’) simulations show that radial electric field, Er, in the near scrape-off layer (SOL) of tokamaks can have large variations leading to a strong local E × B shear greatly exceeding that in the core region. This was pointed out in simulations of JET plasmas with varying divertor geometry, where the magnetic configuration with larger predicted near SOL Er was found to have lower H-mode power threshold, suggesting that turbulence suppression in the SOL by local E × B shear can be a player in the L–H transition physics (Delabie et al 2015 42nd EPS Conf. on Plasma Physics (Lisbon, Portugal, 22–26 June 2015) paper O3.113 (http://ocs.ciemat.es/EPS2015PAP/pdf/O3.113.pdf), Chankin et al 2017 Nucl. Mater. Energy 12 273). Further code modeling of JET plasmas by changing hydrogen isotopes (H–D–T) showed that the magnitude of the near SOL Er is lower in H cases in which the H-mode threshold power is higher (Chankin et al 2017 Plasma Phys. Control. Fusion 59 045012). From the experiment it is also known that hydrogen plasmas have poorer particle and energy confinement than deuterium plasmas, consistent with the code simulation results showing larger particle diffusion coefficients at the plasma edge, including SOL, in hydrogen plasmas (Maggi et al 2018 Plasma Phys. Control. Fusion 60 014045). All these experimental observations and code results support the hypothesis that the near SOL E × B shear can have an impact on the plasma confinement. The present work analyzes neutral ionization patterns of JET plasmas with different hydrogen isotopes in L-mode cases with fixed input power and gas puffing rate, and its impact on target electron temperature, Te, and SOL Er. The possibility of a self-feeding mechanism for the increase in the SOL Er via the interplay between poloidal E × B drift and target Te is discussed. It is also shown that reducing anomalous turbulent transport coefficients, particle diffusion and electron and ion heat conductivities, leads to higher peak target Te and larger Er, suggesting the possibility of a positive feedback loop, under an implicitly made assumption that the E × B shear in the SOL is capable of suppressing turbulence.

Precessing winds from the nucleus of the prototype Red Geyser?

Super-massive black holes (SMBH) are present at the center of most galaxies, with the related mass accretion processes giving origin to outflows in Active Galactic Nuclei (AGN). It has been presumed that only intense winds from luminous AGN were able to suppress star formation until the discovery of a new class of galaxies with no recent star formation and with the nucleus in a quiescent state showing kpc scale outflows. We used SDSS MaNGA and Gemini Integral Field Spectroscopy of the prototype Red Geyser Akira and found that the orientation of the outflow changes by about 50$^\circ$ from its nucleus to kpc scales. A possible interpretation is that the outflow is produced by a precessing accretion disk due to a misalignment between the orientation of the disk and the spin of the SMBH. The precession of the central source is also supported by a similar change in the orientation of the ionization pattern. Although similar behavior has commonly being reported for collimated relativistic jets, the precession of an AGN wide wind is reported here for the first time, implying on a larger work surface of the wind, which in turn increases the star formation suppression efficiency of the outflow.

Biochemical analysis of protein arginylation.

Protein arginylation-enzymatic addition of the amino acid arginine (Arg) to proteins, mediated by arginyltransferase ATE1, has been discovered in 1963, but is still relatively poorly understood. Studies of arginylation present many technical challenges, which arise from the fact that Arg is a regular amino acid that also incorporates into proteins during translation. Thus, in vitro arginylation needs to be conducted in a strictly ribosome-free system, in highly controlled conditions. Identification of arginylated proteins is currently only possible by high precision mass spectrometry, which relies on very high mass accuracy of the instruments, specific ionization patterns during mass fragmentation, as well as multiple stringent steps of automated and manual validation. Below we describe the methods of in vitro arginylation and mass spectrometry analysis of arginylated proteins, developed by our groups during the last 15 years.